Amber Archive Dec 2002: by author

A.Madhumalar
- err in specifying disulphide bridge using xleap! (Mon Dec 02 2002 - 08:25:30 PST)
Ambarish Nag
- Question on 2 stage RESP fit (Wed Dec 11 2002 - 22:39:08 PST)
amber_at_heimdal.compchem.ucsf.edu
- Reflector problems (Tue Dec 03 2002 - 15:05:02 PST)
- Energy decomposition with ANAL (fwd) (Tue Dec 03 2002 - 14:58:05 PST)
- Amber Trajectories + VMD (fwd) (Tue Dec 03 2002 - 14:58:00 PST)
- gB vs. explicit (fwd) (Tue Dec 03 2002 - 14:57:53 PST)
- Constraints in Amber (fwd) (Tue Dec 03 2002 - 14:57:30 PST)
- Re: CCL:freeware for RNA modeling on Linux (fwd) (Tue Dec 03 2002 - 14:57:21 PST)
- freeware for RNA modeling on Linux (fwd) (Tue Dec 03 2002 - 14:57:10 PST)
- Biphasic box (fwd) (Tue Dec 03 2002 - 14:13:10 PST)
Andreas Svrcek-Seiler
- Re: default GB radii (Sat Dec 07 2002 - 04:02:09 PST)
Andrei Leit�o
- Molecular dynamic protocol... (Fri Dec 27 2002 - 10:40:26 PST)
- About heating... (Wed Dec 18 2002 - 10:23:43 PST)
- About counterions (Thu Dec 05 2002 - 11:10:30 PST)
Anke Eisenmann
- off-to-mol2 (Wed Dec 18 2002 - 08:49:22 PST)
Arvid Soederhaell
- timings? (Fri Dec 06 2002 - 00:51:10 PST)
Asif Rahaman
- running sander_classic for amber6 using different version of mpi (Mon Dec 09 2002 - 15:01:35 PST)
Bill Ross
- Re: carnal (Fri Dec 06 2002 - 17:16:59 PST)
Carlos Simmerling
- Re: water box, (Wed Dec 18 2002 - 05:18:18 PST)
- Re: not compiled with -DHAS_10_12!! (Thu Dec 05 2002 - 09:03:08 PST)
- Re: combinig two trajectory files. (Mon Dec 02 2002 - 04:49:21 PST)
Carsten Detering
- antechamber (Wed Dec 18 2002 - 14:32:44 PST)
- antechamber (Wed Dec 18 2002 - 11:38:16 PST)
CUI, Guanglei
- Re: corrupted trajectory (Tue Dec 03 2002 - 18:04:13 PST)
darden
- Re: water box, (Wed Dec 18 2002 - 16:45:55 PST)
- Re: message during minimization (Wed Dec 18 2002 - 16:32:21 PST)
- Re: water box, (Wed Dec 18 2002 - 08:33:07 PST)
- Re: message during minimization (Wed Dec 18 2002 - 08:24:48 PST)
David A. Case
- new on the Amber web pages... (Tue Dec 31 2002 - 13:51:31 PST)
- Re: Molecular dynamic protocol... (Fri Dec 27 2002 - 11:25:51 PST)
- Re: atomicfluct in ptraj (Thu Dec 19 2002 - 09:28:43 PST)
- Re: ntwv saves v(t) or v(t+dt/2) ? (Thu Dec 19 2002 - 09:24:33 PST)
- Re: message during minimization (Thu Dec 19 2002 - 08:05:00 PST)
- Re: water box, (Wed Dec 18 2002 - 16:17:31 PST)
- Re: About heating... (Wed Dec 18 2002 - 11:42:51 PST)
- Re: off-to-mol2 (Wed Dec 18 2002 - 10:03:48 PST)
- Re: Chains, LEaP and ambpdb (Tue Dec 17 2002 - 19:28:21 PST)
- Re: Chains, LEaP and ambpdb (Tue Dec 17 2002 - 13:09:48 PST)
- Re: a question about force field in AMBER (Mon Dec 16 2002 - 17:56:29 PST)
- Re: Amber 7 MM-PBSA for Amber 6 trajectories (Sat Dec 14 2002 - 11:26:01 PST)
- Re: ambpdb (Fri Dec 13 2002 - 20:46:12 PST)
- Re: difference in energy in amber6 and amber7 (Wed Dec 11 2002 - 07:40:48 PST)
- Re: default GB radii (Fri Dec 06 2002 - 13:11:13 PST)
- Re: positional restraints (Fri Dec 06 2002 - 08:05:02 PST)
- Re: timings? (Fri Dec 06 2002 - 07:46:27 PST)
- Re: md failure: deep energetics problem (Thu Dec 05 2002 - 11:55:40 PST)
- Re: About counterions (Thu Dec 05 2002 - 11:47:04 PST)
- Re: bug fixes (Thu Dec 05 2002 - 08:41:02 PST)
- Re: Energy decomposition with ANAL (fwd) (Wed Dec 04 2002 - 08:31:52 PST)
- Re: gB vs. explicit (Wed Dec 04 2002 - 08:28:43 PST)
- Re: Constraints in Amber (Tue Dec 03 2002 - 15:16:02 PST)
- Re: freeware for RNA modeling on Linux (fwd) (Tue Dec 03 2002 - 15:11:48 PST)
- Re: Biphasic box (Tue Dec 03 2002 - 15:09:50 PST)
- Re: err in specifying disulphide bridge using xleap! (Mon Dec 02 2002 - 09:05:01 PST)
- Re: solvateOct (Mon Dec 02 2002 - 07:40:02 PST)
David Case
- Re: CCL:Amber7 and partial charges (Wed Dec 11 2002 - 10:07:10 PST)
dynamic group
- beginners question (Sun Dec 22 2002 - 21:17:52 PST)
eric hu
- targeted MD sample (Thu Dec 26 2002 - 12:25:36 PST)
- bad protein structure (Tue Dec 10 2002 - 17:30:52 PST)
- md failure: deep energetics problem (Thu Dec 05 2002 - 10:42:42 PST)
Filip Lankas
- bug fixes (Thu Dec 05 2002 - 06:48:00 PST)
Gemma Kinsella
- Re: Biphasic box (Wed Dec 04 2002 - 00:15:53 PST)
hagop demirdjian
- ntwv saves v(t) or v(t+dt/2) ? (Thu Dec 19 2002 - 08:04:55 PST)
Holger Gohlke
- Re: ambpdb (Thu Dec 12 2002 - 16:44:44 PST)
- Re: MM-PBSA: .crg file for Delphi (Wed Dec 11 2002 - 10:31:07 PST)
- Re: Amber 7 bugfix 27 !! urgent (Wed Dec 04 2002 - 13:18:48 PST)
Ioana Cozmuta
- cap option (Sun Dec 22 2002 - 17:21:01 PST)
- selection of residues (Fri Dec 20 2002 - 16:51:52 PST)
- Re: water/nonTIP3P (Wed Dec 18 2002 - 18:17:24 PST)
- Re: message during minimization (Wed Dec 18 2002 - 18:02:26 PST)
- water/nonTIP3P (Wed Dec 18 2002 - 17:33:23 PST)
- Re: SUMMARY: solvating a protein with large cavity (Wed Dec 18 2002 - 17:21:23 PST)
- Re: water box, (Wed Dec 18 2002 - 15:37:41 PST)
- Re: message during minimization (Wed Dec 18 2002 - 15:09:05 PST)
- message during minimization (Tue Dec 17 2002 - 21:31:52 PST)
- amber trajectory (Tue Dec 17 2002 - 21:16:14 PST)
- water box, (Tue Dec 17 2002 - 15:18:31 PST)
- Re: Chains, LEaP and ambpdb (Tue Dec 17 2002 - 13:07:24 PST)
- plotting electrostatic potential surface (Fri Dec 13 2002 - 15:18:17 PST)
- carnal (Fri Dec 06 2002 - 15:47:56 PST)
- increasing the number of processors (fwd) (Tue Dec 03 2002 - 16:19:24 PST)
- increasing the number of processors (Tue Dec 03 2002 - 16:17:58 PST)
James Caldwell
- Re: Sander rfree error (Mon Dec 30 2002 - 16:36:45 PST)
- Re: Nmode (Thu Dec 19 2002 - 13:17:31 PST)
James W. Caldwell
- Re: freeware for RNA modeling on Linux (fwd) (Tue Dec 17 2002 - 11:09:37 PST)
- Re: Cap-atom-pointer in GIBBS (Thu Dec 05 2002 - 11:23:45 PST)
- Re: Biphasic box (fwd) (Tue Dec 03 2002 - 15:15:50 PST)
- Re: LEAP - Introducing dummy atoms (Mon Dec 02 2002 - 11:11:27 PST)
- Re: err in specifying disulphide bridge using xleap! (Mon Dec 02 2002 - 11:07:07 PST)
Jennifer Hawkings
- (no subject) (Sat Dec 07 2002 - 14:48:46 PST)
Jim Caldwell
- test mail (Tue Dec 03 2002 - 14:48:07 PST)
Joerg-Gerald Siebers
- Re: freeware for RNA modeling on Linux (fwd) (Mon Dec 16 2002 - 18:43:05 PST)
Joffre Heredia
- Overwrite files (Thu Dec 05 2002 - 12:25:33 PST)
John Pritchard
- Studying in Australia (Tue Dec 17 2002 - 22:36:07 PST)
Jose Ramon Blas
- Cap-atom-pointer in GIBBS (Thu Dec 05 2002 - 11:50:45 PST)
jzhou
- a question about force field in AMBER (Sat Dec 14 2002 - 17:55:15 PST)
Karen Haskell
- RE: sander (CAP) chokes on efc (Itanium2/Linux) (Tue Dec 17 2002 - 14:05:31 PST)
Kristina Furse
- RE: atomicfluct in ptraj (Thu Dec 19 2002 - 11:28:16 PST)
- atomicfluct in ptraj (Wed Dec 18 2002 - 15:16:29 PST)
- RE: solvateOct (Sun Dec 01 2002 - 13:57:13 PST)
kxg2248_at_njit.edu
- Sander rfree error (Mon Dec 30 2002 - 14:58:19 PST)
Lepsa
- Fw: Valine to alanine Gibbs tutorial (Mon Dec 16 2002 - 05:20:26 PST)
- Fw: Fw: Charges derivation question! (Thu Dec 12 2002 - 01:55:17 PST)
- Fw: Charges derivation question! (Wed Dec 11 2002 - 08:21:23 PST)
- Re: FEP/Gibbs question (Tue Dec 10 2002 - 07:59:39 PST)
Long Hai
- Re: Overwrite files (Thu Dec 05 2002 - 13:33:53 PST)
Luis Gracia
- Re: solvatebox (Wed Dec 18 2002 - 07:58:47 PST)
- solvatebox (Tue Dec 17 2002 - 16:52:07 PST)
- Re: Chains, LEaP and ambpdb (Tue Dec 17 2002 - 13:23:55 PST)
- Chains, LEaP and ambpdb (Tue Dec 17 2002 - 11:47:59 PST)
M. L. Dodson
- roar-cp problems (Wed Dec 18 2002 - 13:00:37 PST)
- Re: solvating a protein with large cavity (Sat Dec 14 2002 - 08:23:15 PST)
- Re: Question on 2 stage RESP fit (Thu Dec 12 2002 - 05:05:15 PST)
Mahadevan Seetharaman
- CHARMm NPT input files (Sat Dec 07 2002 - 15:39:07 PST)
- penalty function in NMR refinement (Mon Dec 02 2002 - 09:09:05 PST)
Marcela Madrid
- NMR restrains (Mon Dec 09 2002 - 12:33:31 PST)
meiselba
- FEP/Gibbs question to valine alanine tutorial (Sat Dec 14 2002 - 08:58:12 PST)
- Question to perturbation charge (Tue Dec 10 2002 - 05:35:38 PST)
Michael Ford
- Re: chirality.c failure - diagnosis, but no cure... (Thu Dec 19 2002 - 15:25:21 PST)
- chirality.c failure - diagnosis, but no cure... (Thu Dec 19 2002 - 10:07:07 PST)
- Re: mm_pbsa error message! (Wed Dec 18 2002 - 09:37:57 PST)
- dual H-bonding of bridging waters - CARNAL (Tue Dec 10 2002 - 16:16:24 PST)
Miguel de Federico
- GIBBS - Routine TORCON (internal constraints) failed (Tue Dec 17 2002 - 07:29:04 PST)
- GIBBS - end-of-file during read (Fri Dec 13 2002 - 02:12:48 PST)
- LEAP - Introducing dummy atoms (Mon Dec 02 2002 - 08:42:49 PST)
Mr. Daniel Osondu
- Business Cooperation (Inheritance Claim) (Fri Dec 13 2002 - 01:50:38 PST)
- Business Cooperation (Inheritance Claim) (Thu Dec 12 2002 - 10:10:29 PST)
Natasja Brooijmans
- Re: RESTARTED DUE TO LINMIN FAILURE (Thu Dec 19 2002 - 13:16:44 PST)
- Re: disulfide bond link between two chains (Mon Dec 16 2002 - 05:49:46 PST)
- Re: Energy decomposition with ANAL (Fri Dec 06 2002 - 09:24:21 PST)
Nathan A. Baker
- Re: MPI_BCAST error (Wed Dec 18 2002 - 17:31:47 PST)
- MPI_BCAST error (Wed Dec 18 2002 - 07:51:02 PST)
Nicholson, James D Mr ARO
- RE: Amber Trajectories + VMD (fwd) (Tue Dec 03 2002 - 15:35:09 PST)
Numan Oezguen
- Re: Energy decomposition with ANAL (Mon Dec 16 2002 - 07:49:08 PST)
- Re: Energy decomposition with ANAL (Fri Dec 06 2002 - 09:08:20 PST)
Pascal Bonnet
- Re: Resp Multiconformational charge fitting! (Wed Dec 18 2002 - 02:21:46 PST)
- Re: combinig two trajectory files. (Mon Dec 02 2002 - 04:50:26 PST)
postmaster_at_bydnet.com.pl
- MDaemon Warning - Virus Found (Wed Dec 04 2002 - 19:49:28 PST)
Prabal Maiti
- difference in energy in amber6 and amber7 (Mon Dec 09 2002 - 18:07:15 PST)
Pratul Agarwal
- Nmode (Thu Dec 19 2002 - 13:07:47 PST)
pu xuemei
- disulfide bond link between two chains (Mon Dec 16 2002 - 04:50:35 PST)
Qing Zhang
- Amber 7 MM-PBSA for Amber 6 trajectories (Thu Dec 12 2002 - 11:52:23 PST)
Richard Henchman
- Re: SUMMARY: solvating a protein with large cavity (Wed Dec 18 2002 - 11:56:20 PST)
Robert G. Endres
- default GB radii (Fri Dec 06 2002 - 13:00:31 PST)
Sarah Tschampel
- Re: not compiled with -DHAS_10_12!! (Thu Dec 05 2002 - 08:43:40 PST)
Scott Brozell
- Re: MPI_BCAST error (Wed Dec 18 2002 - 13:24:55 PST)
- Re: Overwrite files (Thu Dec 05 2002 - 13:39:23 PST)
Shixiang Yan
- Re: corrupted trajectory (Tue Dec 03 2002 - 15:36:37 PST)
sychen
- Re: a question about force field in AMBER (Sat Dec 14 2002 - 21:17:59 PST)
Tadashi Takemori
- Re: sander (CAP) chokes on efc (Itanium2/Linux) (Wed Dec 18 2002 - 01:38:25 PST)
- sander (CAP) chokes on efc (Itanium2/Linux) (Mon Dec 16 2002 - 23:11:14 PST)
Thomas Steinbrecher
- MM-PBSA: .crg file for Delphi (Wed Dec 11 2002 - 10:08:40 PST)
- ptraj rmsd calculation (Thu Dec 05 2002 - 12:15:40 PST)
Tom Bishop
- SUMMARY: solvating a protein with large cavity (Wed Dec 18 2002 - 07:03:27 PST)
- solvating a protein with large cavity (Sat Dec 14 2002 - 07:42:38 PST)
vannajan_at_chiangmai.ac.th
- RST file for nonstandard residue (Tue Dec 17 2002 - 01:07:04 PST)
Vlad Cojocaru
- ambpdb (Thu Dec 12 2002 - 14:01:23 PST)
- positional restraints (Fri Dec 06 2002 - 04:55:05 PST)
- DIANA like files (Wed Dec 04 2002 - 12:24:12 PST)
- restrained MD (Wed Dec 04 2002 - 10:18:54 PST)
- carnal amber 7.0 (Mon Dec 02 2002 - 00:35:34 PST)
William Wei
- RESTARTED DUE TO LINMIN FAILURE (Thu Dec 19 2002 - 11:33:07 PST)
- mm_pbsa error message! (Wed Dec 18 2002 - 09:17:16 PST)
- not compiled with -DHAS_10_12!! (Thu Dec 05 2002 - 08:29:22 PST)
- Amber 7 bugfix 27 !! urgent (Wed Dec 04 2002 - 12:45:13 PST)
Yong Duan
- RE: Overwrite files (Thu Dec 05 2002 - 18:41:37 PST)
Yongjun Jiang
- Trajectory file converted in pdb file (Sun Dec 29 2002 - 17:13:38 PST)
- combinig two trajectory files. (Mon Dec 02 2002 - 04:18:29 PST)
yuann
- Re: cannot deal with large trajectory? (Mon Dec 30 2002 - 18:55:41 PST)
- cannot deal with large trajectory? (Sat Dec 28 2002 - 19:17:23 PST)

Amber Archive Dec 2002 by author