Amber Archive Nov 2004: By Thread

Re: AMBER: ptraj questions Oliver Hucke (Mon Nov 01 2004 - 09:59:06 PST)
- AMBER: Building the parallel version in AMBER 8 and GIBBS Ilyas Yildirim (Tue Nov 09 2004 - 19:03:54 PST)
  - Re: AMBER: Building the parallel version in AMBER 8 and GIBBS David A. Case (Tue Nov 09 2004 - 21:07:05 PST)
AMBER: Amber7 installation error on Solaris 9 Joe Nolan (Mon Nov 01 2004 - 12:03:25 PST)
- Re: AMBER: Amber7 installation error on Solaris 9 David A. Case (Mon Nov 01 2004 - 13:11:24 PST)
AMBER: MD & folding bybaker.itsa.ucsf.edu (Mon Nov 01 2004 - 23:03:42 PST)
- Re: AMBER: MD & folding Bimo Ario Tejo (Mon Nov 01 2004 - 23:26:09 PST)
AMBER: about FEP Xiao He (Tue Nov 02 2004 - 00:29:43 PST)
- Re: AMBER: about FEP Annette Ho (Tue Nov 02 2004 - 02:44:03 PST)
  - Re: AMBER: about FEP david.evans.ulsop.ac.uk (Tue Nov 02 2004 - 03:28:44 PST)
    - Re: AMBER: about FEP Annette Höglund (Tue Nov 02 2004 - 03:58:27 PST)
    - Re: AMBER: about FEP david.evans.ulsop.ac.uk (Tue Nov 02 2004 - 04:42:25 PST)
    - Re: AMBER: about FEP Ray Luo (Tue Nov 02 2004 - 06:05:41 PST)
    - Re: Re: AMBER: about FEP Xiao He (Tue Nov 02 2004 - 19:18:22 PST)
    - Re: Re: AMBER: about FEP Thomas Steinbrecher (Wed Nov 03 2004 - 00:07:51 PST)
    - AMBER: FEP and charges Annette Höglund (Wed Nov 03 2004 - 03:59:16 PST)
    - Re: AMBER: FEP and charges Chunhu Tan (Thu Nov 04 2004 - 14:23:16 PST)
    - AMBER: Solvation free energy of a charged molecule. Chunhu Tan (Thu Nov 11 2004 - 17:53:58 PST)
    - Re: AMBER: Solvation free energy of a charged molecule. David A. Case (Fri Nov 12 2004 - 08:11:15 PST)
    - Re: AMBER: Solvation free energy of a charged molecule. Chunhu Tan (Fri Nov 12 2004 - 10:43:32 PST)
    - AMBER: a quick question about carnal Haijun Yang (Fri Nov 12 2004 - 12:51:17 PST)
  - Re: AMBER: about FEP David A. Case (Tue Nov 02 2004 - 08:19:27 PST)
AMBER: ESP fitting from Gaussian03 cube files Ye Mei (Tue Nov 02 2004 - 01:01:40 PST)
AMBER: MD & folding bybaker.itsa.ucsf.edu (Tue Nov 02 2004 - 13:31:31 PST)
- Re: AMBER: MD & folding Carlos Simmerling (Tue Nov 02 2004 - 15:03:41 PST)
AMBER: MD & folding bybaker.itsa.ucsf.edu (Tue Nov 02 2004 - 16:05:00 PST)
AMBER: Clustering in PTRAJ Stephen.Titmuss.csiro.au (Tue Nov 02 2004 - 17:38:31 PST)
AMBER: SANDER BOMB in subroutine nonbond_list Marc Perea (Tue Nov 02 2004 - 04:45:34 PST)
- Re: AMBER: SANDER BOMB in subroutine nonbond_list David A. Case (Wed Nov 03 2004 - 10:05:15 PST)
AMBER: basis set Yanze Zhang (Tue Nov 02 2004 - 21:57:19 PST)
- Re: AMBER: basis set FyD (Fri Nov 05 2004 - 11:55:06 PST)
: AMBER: basis set ying xiong (Tue Nov 02 2004 - 22:43:52 PST)
AMBER: ESPGEN problems to read G03 output files Hernán Alonso (Tue Nov 02 2004 - 23:03:12 PST)
- Re: AMBER: ESPGEN problems to read G03 output files Jiten (Wed Nov 03 2004 - 00:33:04 PST)
- Re: AMBER: ESPGEN problems to read G03 output files FyD (Fri Nov 05 2004 - 11:56:52 PST)
AMBER: Extracting torsional angles for specific conformation Darian, Eva (Wed Nov 03 2004 - 10:12:33 PST)
AMBER: gaff parameter ambiguities Anthony Fejes (Wed Nov 03 2004 - 15:16:07 PST)
AMBER: MD simulation at pH=1 Kijeong Kwac (Wed Nov 03 2004 - 20:20:01 PST)
AMBER: Fluctuation in temperature anshul.imtech.res.in (Thu Nov 04 2004 - 14:09:58 PST)
- Re: AMBER: Fluctuation in temperature Oliver Hucke (Thu Nov 04 2004 - 10:14:36 PST)
- RE: AMBER: Fluctuation in temperature Ross Walker (Thu Nov 04 2004 - 12:05:57 PST)
AMBER: H-bonded waters selection pl (Thu Nov 04 2004 - 04:41:32 PST)
- Re: AMBER: H-bonded waters selection Thomas E. Cheatham, III (Thu Nov 04 2004 - 21:05:24 PST)
  - Re: AMBER: H-bonded waters selection pl (Fri Nov 05 2004 - 02:42:01 PST)
AMBER: gaussian command line Yanze Zhang (Thu Nov 04 2004 - 11:40:27 PST)
- Re: AMBER: gaussian command line FyD (Fri Nov 05 2004 - 12:02:45 PST)
AMBER: Kara Wald (Thu Nov 04 2004 - 13:05:42 PST)
AMBER: Re: Antechamber Kara Wald (Thu Nov 04 2004 - 13:13:28 PST)
- RE: AMBER: Re: Antechamber Ross Walker (Thu Nov 04 2004 - 13:31:48 PST)
  - Re: AMBER: Re: Antechamber Kara Wald (Mon Nov 08 2004 - 13:49:13 PST)
AMBER: ptraj problem Abd Ghani Abd Aziz (Thu Nov 04 2004 - 17:53:39 PST)
- Re: AMBER: ptraj problem Thomas E. Cheatham, III (Thu Nov 04 2004 - 18:13:51 PST)
  - Re: AMBER: ptraj problem Abd Ghani Abd Aziz (Thu Nov 04 2004 - 18:39:37 PST)
AMBER: constructing a small colecule mathew k varghese (Thu Nov 04 2004 - 20:41:58 PST)
- Re: AMBER: constructing a small colecule david.evans.ulsop.ac.uk (Fri Nov 05 2004 - 01:53:07 PST)
AMBER: translational and rotational entropy hj zou (Thu Nov 04 2004 - 22:48:22 PST)
- Re: AMBER: translational and rotational entropy Andreas Svrcek-Seiler (Thu Nov 04 2004 - 23:43:00 PST)
AMBER: end point contribution in MCTI Cai, Yufeng (Fri Nov 05 2004 - 06:12:11 PST)
- Re: AMBER: end point contribution in MCTI David A. Case (Fri Nov 05 2004 - 08:36:31 PST)
AMBER: Amber7 compilation error Joe Nolan (Fri Nov 05 2004 - 07:17:39 PST)
- Re: AMBER: Amber7 compilation error David A. Case (Fri Nov 05 2004 - 08:50:01 PST)
AMBER: Problems using mm_pbsa.perl Daniel Wetzler (Fri Nov 05 2004 - 08:28:15 PST)
- Re: AMBER: Problems using mm_pbsa.perl Holger Gohlke (Fri Nov 05 2004 - 08:41:39 PST)
AMBER: ptraj radial Sandro Fornili (Fri Nov 05 2004 - 08:28:57 PST)
AMBER: Minimization failure: 1cbn Harianto (Fri Nov 05 2004 - 09:16:30 PST)
- Re: AMBER: Minimization failure: 1cbn Bimo Ario Tejo (Fri Nov 05 2004 - 14:12:03 PST)
- Re: AMBER: Minimization failure: 1cbn Bill Ross (Fri Nov 05 2004 - 14:32:41 PST)
AMBER: where is the VDW radius? Cai, Yufeng (Sat Nov 06 2004 - 07:42:29 PST)
- Re: AMBER: where is the VDW radius? Oliver Hucke (Sat Nov 06 2004 - 11:16:00 PST)
AMBER: positive VDWAALS John (Sun Nov 07 2004 - 10:11:13 PST)
- Re: AMBER: positive VDWAALS Michael Crowley (Sun Nov 07 2004 - 13:51:26 PST)
AMBER: mm_PBSA: problems calculating molecular surface for some snapshots Magne Olufsen (Mon Nov 08 2004 - 01:50:39 PST)
AMBER: time-averaged restraints John (Mon Nov 08 2004 - 12:21:51 PST)
AMBER: amber 7 nmode on osx Knut Langsetmo (Mon Nov 08 2004 - 15:26:26 PST)
AMBER: salt bridge detection Ye Mei (Mon Nov 08 2004 - 18:33:21 PST)
AMBER: error message about the input file of sander Ru-Zhen Li (Mon Nov 08 2004 - 18:23:23 PST)
- Re: AMBER: error message about the input file of sander Michael Crowley (Mon Nov 08 2004 - 22:48:03 PST)
  - Re: AMBER: error message about the input file of sander Ru-Zhen Li (Tue Nov 09 2004 - 04:20:40 PST)
  - Re: AMBER: error message about the input file of sander Ru-Zhen Li (Tue Nov 09 2004 - 04:49:26 PST)
    - RE: AMBER: error message about the input file of sander Ross Walker (Tue Nov 09 2004 - 09:44:31 PST)
    - Re: AMBER: error message about the input file of sander Ru-Zhen Li (Tue Nov 09 2004 - 12:33:57 PST)
AMBER: Problem with Water solute during MD Daniel Wetzler (Tue Nov 09 2004 - 05:20:13 PST)
- Re: AMBER: Problem with Water solute during MD David A. Case (Tue Nov 09 2004 - 08:06:31 PST)
  - Re: AMBER: Problem with Water solute during MD Daniel Wetzler (Wed Nov 10 2004 - 02:19:11 PST)
    - Re: AMBER: Problem with Water solute during MD David A. Case (Wed Nov 10 2004 - 07:42:50 PST)
- Re: AMBER: Problem with Water solute during MD Bill Ross (Wed Nov 10 2004 - 07:20:23 PST)
AMBER: Leap Greg Kellogg (Tue Nov 09 2004 - 08:24:43 PST)
- Re: AMBER: Leap David A. Case (Tue Nov 09 2004 - 09:00:38 PST)
Re: AMBER: Problem with Water solute during MD Bill Ross (Tue Nov 09 2004 - 09:36:22 PST)
AMBER: IBELLY Harianto (Tue Nov 09 2004 - 12:40:58 PST)
AMBER: Solaris f77 Machine file for Amber7? Joe Nolan (Tue Nov 09 2004 - 14:13:58 PST)
- Re: AMBER: Solaris f77 Machine file for Amber7? David A. Case (Tue Nov 09 2004 - 16:57:24 PST)
- Re: AMBER: Solaris f77 Machine file for Amber7? Joe Nolan (Wed Nov 10 2004 - 08:45:50 PST)
  - Re: AMBER: Solaris f77 Machine file for Amber7? David A. Case (Wed Nov 10 2004 - 09:07:13 PST)
- Re: AMBER: Solaris f77 Machine file for Amber7? Joe Nolan (Wed Nov 10 2004 - 13:11:44 PST)
  - Re: AMBER: Solaris f77 Machine file for Amber7? David A. Case (Wed Nov 10 2004 - 13:49:47 PST)
- Re: AMBER: Solaris f77 Machine file for Amber7? Joe Nolan (Wed Nov 10 2004 - 14:43:54 PST)
  - Re: AMBER: Solaris f77 Machine file for Amber7? David A. Case (Wed Nov 10 2004 - 16:15:32 PST)
- Re: AMBER: Solaris f77 Machine file for Amber7? Joe Nolan (Thu Nov 11 2004 - 10:50:06 PST)
- Re: AMBER: Solaris f77 Machine file for Amber7? Joe Nolan (Thu Nov 11 2004 - 14:00:33 PST)
AMBER: single strand simulation ding (Tue Nov 09 2004 - 16:12:17 PST)
- Re: AMBER: single strand simulation Thomas E. Cheatham, III (Tue Nov 09 2004 - 16:32:58 PST)
AMBER: AMBER Parameter Database Yanze Zhang (Wed Nov 10 2004 - 07:35:32 PST)
AMBER: parameter set Yanze Zhang (Wed Nov 10 2004 - 11:56:54 PST)
- Re: AMBER: parameter set David A. Case (Wed Nov 10 2004 - 12:10:40 PST)
Re: AMBER: parameter set Bill Ross (Wed Nov 10 2004 - 12:17:25 PST)
- AMBER: About the parameter names Ilyas Yildirim (Wed Nov 10 2004 - 13:20:31 PST)
  - Re: AMBER: About the parameter names David A. Case (Wed Nov 10 2004 - 13:50:58 PST)
RE: AMBER: Can parallel simulation have a nonperiodic boundary condition? Ross Walker (Wed Nov 10 2004 - 16:26:27 PST)
AMBER: ptraj MURAT CETINKAYA (Thu Nov 11 2004 - 13:19:45 PST)
AMBER: glibc version Ye Mei (Thu Nov 11 2004 - 22:04:00 PST)
- Re: AMBER: glibc version David A. Case (Fri Nov 12 2004 - 14:17:53 PST)
AMBER: AMBER 4 Manual? Ru-Zhen Li (Fri Nov 12 2004 - 09:02:16 PST)
- Re: AMBER: AMBER 4 Manual? David A. Case (Fri Nov 12 2004 - 14:10:42 PST)
AMBER: Energy change for isomerization reaction of cyclic peptide nlxc (Fri Nov 12 2004 - 10:03:00 PST)
- Re: AMBER: Energy change for isomerization reaction of cyclic peptide David A. Case (Fri Nov 12 2004 - 14:02:10 PST)
Re: AMBER: a quick question about carnal Bill Ross (Fri Nov 12 2004 - 13:53:41 PST)
- Re: AMBER: a quick question about carnal Haijun Yang (Mon Nov 15 2004 - 09:31:53 PST)
AMBER: the energy difference between sander and nmode xiaowei li (Fri Nov 12 2004 - 13:52:57 PST)
- Re: AMBER: the energy difference between sander and nmode David A. Case (Fri Nov 12 2004 - 14:43:28 PST)
AMBER: xleap problems Kepa Koldo Burusco Goñi (Fri Nov 12 2004 - 11:33:42 PST)
- Re: AMBER: xleap problems Mark Williamson (Fri Nov 12 2004 - 15:58:05 PST)
- Re: AMBER: xleap problems Ilyas Yildirim (Fri Nov 12 2004 - 15:58:21 PST)
AMBER: Parameters for new residue? Satpal Virdee (Sat Nov 13 2004 - 11:34:27 PST)
- Re: AMBER: Parameters for new residue? David A. Case (Sat Nov 13 2004 - 17:30:39 PST)
AMBER: convert .pdb to .mol2 bybaker.itsa.ucsf.edu (Sat Nov 13 2004 - 20:35:45 PST)
- Re: AMBER: convert .pdb to .mol2 Ye Mei (Sat Nov 13 2004 - 20:57:32 PST)
AMBER: Babel bybaker.itsa.ucsf.edu (Sat Nov 13 2004 - 23:29:40 PST)
- Re: AMBER: Babel Carlos Simmerling (Sun Nov 14 2004 - 06:02:17 PST)
- Re: AMBER: Babel FyD (Mon Nov 15 2004 - 15:07:11 PST)
AMBER: nmode:Number of atoms in -p and -c files do not agree! myang.vitamin.uni.cc (Sun Nov 14 2004 - 18:20:25 PST)
- Re: AMBER: nmode:Number of atoms in -p and -c files do not agree! David A. Case (Mon Nov 15 2004 - 08:10:43 PST)
  - Re: AMBER: nmode:Number of atoms in -p and -c files do not agree! myang.vitamin.uni.cc (Mon Nov 15 2004 - 11:58:58 PST)
    - Re: AMBER: nmode:Number of atoms in -p and -c files do not agree! David A. Case (Mon Nov 15 2004 - 13:43:15 PST)
    - AMBER: ifort 8.0 Ilyas Yildirim (Mon Nov 15 2004 - 14:41:28 PST)
    - Re: AMBER: ifort 8.0 Jack Lei (Mon Nov 15 2004 - 14:46:01 PST)
    - RE: AMBER: ifort 8.0 Ross Walker (Wed Nov 17 2004 - 10:39:49 PST)
    - Re: AMBER: nmode:Number of atoms in -p and -c files do not agree! myang.vitamin.uni.cc (Mon Nov 15 2004 - 17:26:17 PST)
AMBER: restraintmask problem in ptraj Takanori TANAKA (Mon Nov 15 2004 - 03:06:23 PST)
- Re: AMBER: restraintmask problem in ptraj Viktor Hornak (Mon Nov 15 2004 - 05:37:24 PST)
AMBER: gibbs compilation error Nelson Fonseca (Mon Nov 15 2004 - 09:41:27 PST)
- Re: AMBER: gibbs compilation error David A. Case (Mon Nov 15 2004 - 10:18:12 PST)
AMBER: AMBER8 parallel job Emmanuel Giudice (Sun Nov 14 2004 - 23:39:50 PST)
AMBER: Re: Amber Re: Antechamber problems Kara Wald (Mon Nov 15 2004 - 13:05:19 PST)
AMBER: Can xleap to handle homology model altogether X-ray structure? Jack Lei (Mon Nov 15 2004 - 14:39:55 PST)
- AMBER: Can xleap handle homology model altogether with X-ray structure? Jack Lei (Mon Nov 15 2004 - 15:08:44 PST)
- Re: AMBER: Can xleap to handle homology model altogether X-ray structure? David A. Case (Tue Nov 16 2004 - 08:13:11 PST)
  - Re: AMBER: Can xleap to handle homology model altogether X-ray structure? Joachim Reichelt (Tue Nov 16 2004 - 09:42:02 PST)
    - AMBER: Problem with a single aminoacid as inhibitor Daniel Wetzler (Wed Nov 17 2004 - 03:54:04 PST)
    - Re: AMBER: Problem with a single aminoacid as inhibitor Carlos Simmerling (Wed Nov 17 2004 - 04:43:08 PST)
AMBER: AMBER8 compiling error under Itanium 2. qlu.notes.cc.sunysb.edu (Mon Nov 15 2004 - 16:39:36 PST)
- Re: AMBER: AMBER8 compiling error under Itanium 2. Ye Mei (Mon Nov 15 2004 - 17:46:52 PST)
  - Re: AMBER: AMBER8 compiling error under Itanium 2. Jack Lei (Tue Nov 16 2004 - 09:32:23 PST)
AMBER: constant pH simulations reference Sergio E. Wong (Mon Nov 15 2004 - 17:50:16 PST)
- Re: AMBER: constant pH simulations reference David A. Case (Mon Nov 15 2004 - 18:23:42 PST)
AMBER: ambpdb segmentation fault justin litchfield (Mon Nov 15 2004 - 18:57:14 PST)
- RE: AMBER: ambpdb segmentation fault Ross Walker (Wed Nov 17 2004 - 13:35:40 PST)
  - Re: AMBER: ambpdb segmentation fault justin litchfield (Wed Nov 17 2004 - 14:46:01 PST)
    - Re: AMBER: ambpdb segmentation fault justin litchfield (Sun Nov 21 2004 - 21:09:25 PST)
- Re: AMBER: ambpdb segmentation fault Bill Ross (Sun Nov 21 2004 - 21:34:13 PST)
FWD: RE: AMBER: xleap problems Kepa Koldo Burusco Goñi (Tue Nov 16 2004 - 02:56:40 PST)
- AMBER: SUSE 9.1 and AMBER 8 Ilyas Yildirim (Tue Nov 16 2004 - 03:12:16 PST)
  - Re: AMBER: SUSE 9.1 and AMBER 8 Andreas Svrcek-Seiler (Tue Nov 16 2004 - 05:10:44 PST)
  - INSTALLATION GUIDE FOR IFORT AND AMBER8 IN LINUX SUSE 9.1 ....Re: AMBER: SUSE 9.1 and AMBER 8 Cenk Andac (Tue Nov 16 2004 - 06:19:03 PST)
AMBER: How to compile the downloadable RESP in UNIX Yanze Zhang (Tue Nov 16 2004 - 07:33:03 PST)
- Re: AMBER: How to compile the downloadable RESP in UNIX Satpal Virdee (Tue Nov 16 2004 - 07:58:41 PST)
  - Re: AMBER: How to compile the downloadable RESP in UNIX Yanze Zhang (Wed Nov 17 2004 - 15:04:57 PST)
    - Re: AMBER: How to compile the downloadable RESP in UNIX Satpal Virdee (Thu Nov 18 2004 - 04:36:07 PST)
    - Re: AMBER: How to compile the downloadable RESP in UNIX Yanze Zhang (Thu Nov 18 2004 - 12:10:13 PST)
AMBER: restrained options Toshifumi Yui (Tue Nov 16 2004 - 08:42:22 PST)
AMBER: <dV/dL> fluctuations in TI Nelson Fonseca (Wed Nov 17 2004 - 03:39:01 PST)
- Re: AMBER: <dV/dL> fluctuations in TI Thomas Steinbrecher (Wed Nov 17 2004 - 05:06:40 PST)
- Re: AMBER: <dV/dL> fluctuations in TI Chunhu Tan (Thu Nov 18 2004 - 14:57:05 PST)
- Re: AMBER: <dV/dL> fluctuations in TI Chunhu Tan (Fri Nov 19 2004 - 11:07:03 PST)
AMBER: Problem with a single aminoacid as inhibitor Daniel Wetzler (Wed Nov 17 2004 - 03:59:12 PST)
- Re: AMBER: Problem with a single aminoacid as inhibitor david.evans.ulsop.ac.uk (Wed Nov 17 2004 - 04:55:58 PST)
  - Re: AMBER: Problem with a single aminoacid as inhibitor M. L. Dodson (Wed Nov 17 2004 - 07:29:26 PST)
    - Re: AMBER: Problem with a single aminoacid as inhibitor Daniel Wetzler (Wed Nov 17 2004 - 08:13:50 PST)
AMBER: Problem to update antechamber package. Guillaume Bollot (Wed Nov 17 2004 - 05:50:49 PST)
AMBER: RMS of energy in Minimization using SANDER Jack Lei (Wed Nov 17 2004 - 10:15:31 PST)
- RE: AMBER: RMS of energy in Minimization using SANDER Ross Walker (Wed Nov 17 2004 - 10:36:25 PST)
AMBER: Fifth European Workshop in Drug Design Andrea Tafi (Thu Nov 18 2004 - 04:35:02 PST)
AMBER: Diastereoisomers of ATP William Boxford (Thu Nov 18 2004 - 07:18:42 PST)
AMBER: calcium van der Waals parameters cailliez (Thu Nov 18 2004 - 08:53:23 PST)
- Re: AMBER: calcium van der Waals parameters Bill Ross (Mon Nov 22 2004 - 10:57:09 PST)
- Re: AMBER: calcium van der Waals parameters Piotr Cieplak (Mon Nov 22 2004 - 11:03:57 PST)
Re: AMBER: calcium van der Waals parameters Bill Ross (Thu Nov 18 2004 - 10:25:49 PST)
- Re: AMBER: calcium van der Waals parameters cailliez (Mon Nov 22 2004 - 09:10:30 PST)
AMBER: Problem with carnal on linux Sébastien Fiorucci (Fri Nov 19 2004 - 06:13:26 PST)
- RE: AMBER: Problem with carnal on linux Ross Walker (Fri Nov 19 2004 - 09:36:08 PST)
AMBER: SHAKE probelm Huang, Hai (Fri Nov 19 2004 - 08:25:24 PST)
- RE: AMBER: SHAKE probelm Ross Walker (Fri Nov 19 2004 - 09:35:18 PST)
- RE: AMBER: SHAKE probelm Huang, Hai (Fri Nov 19 2004 - 14:56:54 PST)
  - RE: AMBER: SHAKE probelm Ross Walker (Fri Nov 19 2004 - 15:09:05 PST)
- RE: AMBER: SHAKE probelm Huang, Hai (Tue Nov 23 2004 - 14:01:25 PST)
AMBER: amber8 compilation lucian livadaru (Fri Nov 19 2004 - 10:51:00 PST)
- RE: AMBER: amber8 compilation Ross Walker (Fri Nov 19 2004 - 11:20:00 PST)
  - RE: AMBER: amber8 compilation lucian livadaru (Mon Nov 22 2004 - 14:22:43 PST)
    - RE: AMBER: amber8 compilation Ross Walker (Mon Nov 22 2004 - 14:48:03 PST)
AMBER: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Fri Nov 19 2004 - 11:13:22 PST)
- RE: AMBER: leap compiling problem on a 64-bit machine Ross Walker (Fri Nov 19 2004 - 11:32:01 PST)
  - Re: RE: AMBER: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Fri Nov 19 2004 - 15:51:58 PST)
    - Re: RE: AMBER: leap compiling problem on a 64-bit machine Tomas Linhart (Fri Nov 19 2004 - 17:14:51 PST)
  - Re: RE: AMBER: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Sat Nov 20 2004 - 12:19:27 PST)
    - Re: RE: AMBER: leap compiling problem on a 64-bit machine Tomas Linhart (Sat Nov 20 2004 - 14:15:44 PST)
  - Re: RE: AMBER: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Sun Nov 21 2004 - 14:52:02 PST)
    - Re: RE: AMBER: leap compiling problem on a 64-bit machine Tomas Linhart (Sun Nov 21 2004 - 15:22:25 PST)
  - Re: RE: AMBER: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Sun Nov 21 2004 - 19:31:53 PST)
AMBER: Electrolyte concentrations in MD arubin.unmc.edu (Fri Nov 19 2004 - 12:56:09 PST)
Re: AMBER: leap compiling problem on a 64-bit machine Bill Ross (Fri Nov 19 2004 - 13:14:07 PST)
AMBER: calculation of pKa values Peter Trodler (Mon Nov 22 2004 - 00:32:25 PST)
AMBER: sander, MD problems Kepa Koldo Burusco Goñi (Mon Nov 22 2004 - 04:00:37 PST)
- Re: AMBER: sander, MD problems Carlos Simmerling (Mon Nov 22 2004 - 04:53:29 PST)
AMBER: problem solved: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Mon Nov 22 2004 - 12:51:28 PST)
AMBER: New problem on our 64bit box: xleap Segmentation fault xhu1.memphis.edu (Mon Nov 22 2004 - 13:03:48 PST)
- RE: AMBER: New problem on our 64bit box: xleap Segmentation fault Ross Walker (Mon Nov 22 2004 - 13:29:13 PST)
  - Re: RE: AMBER: New problem on our 64bit box: xleap Segmentation fault xhu1.memphis.edu (Mon Nov 22 2004 - 14:37:03 PST)
AMBER: LEaP compilation error on Solaris 9 Joe Nolan (Mon Nov 22 2004 - 13:21:41 PST)
- Re: AMBER: LEaP compilation error on Solaris 9 David A. Case (Mon Nov 22 2004 - 14:02:35 PST)
- Re: AMBER: LEaP compilation error on Solaris 9 Bill Ross (Mon Nov 22 2004 - 14:16:10 PST)
Re: AMBER: New problem on our 64bit box: xleap Segmentation fault Bill Ross (Mon Nov 22 2004 - 13:27:21 PST)
- Re: AMBER: New problem on our 64bit box: xleap Segmentation fault xhu1.memphis.edu (Mon Nov 22 2004 - 14:38:37 PST)
AMBER: generating parmfile containing topology and parameter information Nitin Bhardwaj (Mon Nov 22 2004 - 13:29:00 PST)
- RE: AMBER: generating parmfile containing topology and parameter information Ross Walker (Mon Nov 22 2004 - 13:46:30 PST)
  - RE: AMBER: generating parmfile containing topology and parameter information Nitin Bhardwaj (Mon Nov 22 2004 - 15:53:07 PST)
    - Re: AMBER: generating parmfile containing topology and parameter information David A. Case (Mon Nov 22 2004 - 16:12:20 PST)
AMBER: questions on dummy atom types in FEP setup Eric Hu (Mon Nov 22 2004 - 13:37:54 PST)
- Re: AMBER: questions on dummy atom types in FEP setup Chunhu Tan (Mon Nov 22 2004 - 15:37:57 PST)
  - Re: AMBER: questions on dummy atom types in FEP setup Eric Hu (Mon Nov 22 2004 - 18:22:45 PST)
AMBER: mm_pbsa +fillratio Carsten Detering (Mon Nov 22 2004 - 15:14:55 PST)
- Re: AMBER: mm_pbsa +fillratio David A. Case (Mon Nov 22 2004 - 15:20:03 PST)
  - Re: AMBER: mm_pbsa +fillratio Carsten Detering (Mon Nov 22 2004 - 16:38:13 PST)
Re: AMBER: problem solved: leap compiling problem on a 64-bit machine Bill Ross (Mon Nov 22 2004 - 14:37:58 PST)
- Re: AMBER: problem solved: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Mon Nov 22 2004 - 15:48:43 PST)
AMBER: Problem with converting AMBER PREP to MOL2 Cenk Andac (Mon Nov 22 2004 - 16:13:39 PST)
- Re: AMBER: Problem with converting AMBER PREP to MOL2 David A. Case (Tue Nov 23 2004 - 08:12:06 PST)
  - Re: AMBER: Problem with converting AMBER PREP to MOL2 david.evans.ulsop.ac.uk (Tue Nov 23 2004 - 09:06:22 PST)
- Re: AMBER: Problem with converting AMBER PREP to MOL2 Bill Ross (Tue Nov 23 2004 - 10:00:31 PST)
AMBER: mm_pbsa + vertex atom mismatch Carsten Detering (Mon Nov 22 2004 - 19:01:28 PST)
AMBER: Resend: Problem with converting AMBER8 PREP to MOL2 Cenk Andac (Tue Nov 23 2004 - 00:57:55 PST)
AMBER: langevin dynamic in sander Stefano.Pieraccini.unimi.it (Tue Nov 23 2004 - 01:33:08 PST)
- Re: AMBER: langevin dynamic in sander David A. Case (Tue Nov 23 2004 - 08:21:30 PST)
AMBER: TI with electrostatic decoupling Nelson Fonseca (Tue Nov 23 2004 - 01:56:44 PST)
- AMBER: Problem with minimisation of an protein-inhibitor complex Daniel Wetzler (Tue Nov 23 2004 - 02:31:33 PST)
- Re: AMBER: TI with electrostatic decoupling David A. Case (Tue Nov 23 2004 - 08:42:16 PST)
- Re: AMBER: TI with electrostatic decoupling Chunhu Tan (Tue Nov 23 2004 - 11:01:48 PST)
AMBER: restart calculation tang kwa (Tue Nov 23 2004 - 02:31:22 PST)
- Re: AMBER: restart calculation Tomas Linhart (Tue Nov 23 2004 - 02:53:29 PST)
  - Re: AMBER: restart calculation tang kwa (Tue Nov 23 2004 - 03:44:45 PST)
    - Re: AMBER: restart calculation David A. Case (Tue Nov 23 2004 - 08:39:37 PST)
- Re: AMBER: restart calculation Carlos Simmerling (Tue Nov 23 2004 - 04:45:28 PST)
- RE: AMBER: restart calculation Ross Walker (Tue Nov 23 2004 - 10:02:12 PST)
AMBER: Problem with minimisation of an protein-inhibitor complex Daniel Wetzler (Tue Nov 23 2004 - 04:31:38 PST)
- RE: AMBER: Problem with minimisation of an protein-inhibitor complex Ross Walker (Tue Nov 23 2004 - 10:16:04 PST)
AMBER: add dummy atoms tang kwa (Tue Nov 23 2004 - 06:27:05 PST)
- Re: AMBER: add dummy atoms David A. Case (Tue Nov 23 2004 - 08:27:48 PST)
AMBER: Antechamber problems Kara Wald (Tue Nov 23 2004 - 10:49:43 PST)
AMBER: md.out & plot bybaker.itsa.ucsf.edu (Tue Nov 23 2004 - 14:23:41 PST)
- Re: AMBER: md.out & plot Luis Gracia (Tue Nov 23 2004 - 14:43:33 PST)
- RE: AMBER: md.out & plot Ross Walker (Tue Nov 23 2004 - 14:59:58 PST)
AMBER: cannot load frcmod file properly Eric Hu (Tue Nov 23 2004 - 15:10:17 PST)
- Re: AMBER: cannot load frcmod file properly Chunhu Tan (Tue Nov 23 2004 - 18:12:42 PST)
  - Re: AMBER: cannot load frcmod file properly Eric Hu (Wed Nov 24 2004 - 10:28:02 PST)
    - Re: AMBER: cannot load frcmod file properly Chunhu Tan (Wed Nov 24 2004 - 12:37:46 PST)
AMBER: Re: md.out & plot bybaker.itsa.ucsf.edu (Tue Nov 23 2004 - 17:26:36 PST)
- Re: AMBER: Re: md.out & plot Furse, Kristina Elisabet (Tue Nov 23 2004 - 20:29:37 PST)
- Re: AMBER: Re: md.out & plot Furse, Kristina Elisabet (Tue Nov 23 2004 - 20:37:21 PST)
AMBER: build a cyclic peptide Eric Hu (Tue Nov 23 2004 - 17:34:13 PST)
- Re: AMBER: build a cyclic peptide Carlos Simmerling (Tue Nov 23 2004 - 18:43:13 PST)
  - Re: AMBER: build a cyclic peptide Eric Hu (Wed Nov 24 2004 - 10:26:44 PST)
    - Re: AMBER: build a cyclic peptide Carlos Simmerling (Wed Nov 24 2004 - 10:56:57 PST)
    - Re: AMBER: build a cyclic peptide Eric Hu (Wed Nov 24 2004 - 12:11:18 PST)
    - Re: AMBER: build a cyclic peptide Carlos Simmerling (Wed Nov 24 2004 - 12:33:10 PST)
- Re: AMBER: build a cyclic peptide Bill Ross (Wed Nov 24 2004 - 10:39:15 PST)
- Re: AMBER: build a cyclic peptide Bill Ross (Wed Nov 24 2004 - 13:56:44 PST)
Re: AMBER: build a cyclic peptide Bill Ross (Tue Nov 23 2004 - 18:33:04 PST)
AMBER: Installation of AMBER8 on AMD cluster using pgf90 Hwankyu Lee (Tue Nov 23 2004 - 18:41:13 PST)
- Re: AMBER: Installation of AMBER8 on AMD cluster using pgf90 David A. Case (Tue Nov 23 2004 - 23:03:55 PST)
  - Re: AMBER: Installation of AMBER8 on AMD cluster using pgf90 Hwankyu Lee (Wed Nov 24 2004 - 06:03:28 PST)
AMBER: Re: md.out & plot bybaker.itsa.ucsf.edu (Tue Nov 23 2004 - 22:21:10 PST)
AMBER: missing XaLeap_wcl file Nitin Bhardwaj (Wed Nov 24 2004 - 10:22:04 PST)
AMBER: extracting energy from trajector? MURAT CETINKAYA (Wed Nov 24 2004 - 10:33:04 PST)
- Re: AMBER: extracting energy from trajector? Carlos Simmerling (Wed Nov 24 2004 - 10:55:49 PST)
- Re: AMBER: extracting energy from trajector? Bill Ross (Wed Nov 24 2004 - 11:33:29 PST)
- Re: AMBER: extracting energy from trajector? David Smith (Wed Nov 24 2004 - 11:29:34 PST)
- Re: AMBER: extracting energy from trajector? MURAT CETINKAYA (Sun Nov 28 2004 - 16:59:27 PST)
  - Re: AMBER: extracting energy from trajector? David Smith (Mon Nov 29 2004 - 04:37:41 PST)
  - Re: AMBER: extracting energy from trajector? David Smith (Mon Nov 29 2004 - 05:04:52 PST)
- Re: AMBER: extracting energy from trajector? MURAT CETINKAYA (Mon Nov 29 2004 - 07:31:14 PST)
  - Re: AMBER: extracting energy from trajector? David Smith (Mon Nov 29 2004 - 08:54:53 PST)
- Re: AMBER: extracting energy from trajector? MURAT CETINKAYA (Mon Nov 29 2004 - 09:20:12 PST)
  - Re: AMBER: extracting energy from trajector? David Smith (Mon Nov 29 2004 - 09:39:30 PST)
Re: AMBER: extracting energy from trajector? Bill Ross (Wed Nov 24 2004 - 10:50:30 PST)
- Re: AMBER: extracting energy from trajector? Carlos Simmerling (Wed Nov 24 2004 - 11:07:12 PST)
AMBER: nucgen problem opitz.che.udel.edu (Wed Nov 24 2004 - 14:08:52 PST)
- Re: AMBER: nucgen problem david.evans.ulsop.ac.uk (Thu Nov 25 2004 - 01:04:28 PST)
- Re: AMBER: nucgen problem Bill Ross (Thu Nov 25 2004 - 09:08:14 PST)
AMBER: Regarding Dielectric Constant in AMBER8 pande.vineet.fc.up.pt (Thu Nov 25 2004 - 07:22:41 PST)
- Re: AMBER: Regarding Dielectric Constant in AMBER8 Carlos Simmerling (Thu Nov 25 2004 - 07:50:12 PST)
  - Re: AMBER: Regarding Dielectric Constant in AMBER8 pande.vineet.fc.up.pt (Thu Nov 25 2004 - 08:03:27 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 Carlos Simmerling (Thu Nov 25 2004 - 08:45:34 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 pande.vineet.fc.up.pt (Fri Nov 26 2004 - 00:45:50 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 Carlos Simmerling (Fri Nov 26 2004 - 06:02:56 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 pande.vineet.fc.up.pt (Fri Nov 26 2004 - 08:35:43 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 pande.vineet.fc.up.pt (Fri Nov 26 2004 - 08:45:47 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 Carlos Simmerling (Fri Nov 26 2004 - 08:55:48 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 pande.vineet.fc.up.pt (Fri Nov 26 2004 - 10:59:19 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 Carlos Simmerling (Fri Nov 26 2004 - 11:24:59 PST)
Re: AMBER: question about molsurf Chris Page (Thu Nov 25 2004 - 10:45:28 PST)
AMBER: combine crd files bybaker.itsa.ucsf.edu (Fri Nov 26 2004 - 14:54:43 PST)
- Re: AMBER: combine crd files Furse, Kristina Elisabet (Fri Nov 26 2004 - 15:42:09 PST)
- Re: AMBER: combine crd files Carlos Simmerling (Fri Nov 26 2004 - 16:03:28 PST)
AMBER: sander.QMMM on Mac justin litchfield (Fri Nov 26 2004 - 15:17:35 PST)
- RE: AMBER: sander.QMMM on Mac Ross Walker (Fri Nov 26 2004 - 17:56:56 PST)
  - Re: AMBER: sander.QMMM on Mac justin litchfield (Sat Nov 27 2004 - 00:29:26 PST)
AMBER: Protein with maximum hydrogen bonds anshul.imtech.res.in (Sat Nov 27 2004 - 09:23:43 PST)
- RE: AMBER: Protein with maximum hydrogen bonds Ross Walker (Fri Nov 26 2004 - 23:15:34 PST)
- Re: AMBER: Protein with maximum hydrogen bonds pande.vineet.fc.up.pt (Sat Nov 27 2004 - 06:13:58 PST)
- Re: AMBER: Protein with maximum hydrogen bonds Sanjeev B.S. (Sat Nov 27 2004 - 07:14:01 PST)
AMBER: About Disulfer bond Xiao He (Sat Nov 27 2004 - 00:11:00 PST)
- Re: AMBER: About Disulfer bond David A. Case (Sat Nov 27 2004 - 10:05:28 PST)
Fwd: Re: AMBER: Protein with maximum hydrogen bonds pande.vineet.fc.up.pt (Sat Nov 27 2004 - 06:19:31 PST)
AMBER: xfl90 and xlc "C" compiler Dr. Noah Allen (Sat Nov 27 2004 - 12:05:28 PST)
- Re: AMBER: xfl90 and xlc "C" compiler justin litchfield (Sat Nov 27 2004 - 12:42:22 PST)
AMBER: GO lie Amber simulation Alena Shmygelska (Sat Nov 27 2004 - 13:48:53 PST)
- Re: AMBER: GO lie Amber simulation David A. Case (Sat Nov 27 2004 - 15:37:45 PST)
AMBER: saving trajectory parameters Ed Pate (Sat Nov 27 2004 - 16:17:40 PST)
- RE: AMBER: saving trajectory parameters Ross Walker (Sat Nov 27 2004 - 16:52:03 PST)
AMBER: MD run: frozen bybaker.itsa.ucsf.edu (Sat Nov 27 2004 - 22:17:36 PST)
- RE: AMBER: MD run: frozen Ross Walker (Sat Nov 27 2004 - 23:00:37 PST)
- Re: AMBER: MD run: frozen Carlos Simmerling (Sun Nov 28 2004 - 07:32:25 PST)
- Re: AMBER: MD run: frozen bybaker.itsa.ucsf.edu (Sun Nov 28 2004 - 16:39:30 PST)
AMBER: FEP - GIBBS of charged sidechains using IELPER Annette Höglund (Sun Nov 28 2004 - 09:26:06 PST)
- Re: AMBER: FEP - GIBBS of charged sidechains using IELPER David A. Case (Sun Nov 28 2004 - 15:28:43 PST)
AMBER: question! Marsita M (Sun Nov 28 2004 - 19:01:41 PST)
AMBER: problem in quasih.f diagonalising matrix Phineus Markwick (Mon Nov 29 2004 - 05:14:35 PST)
- Re: AMBER: problem in quasih.f diagonalising matrix David A. Case (Mon Nov 29 2004 - 08:38:46 PST)
AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem) Hannes Barsch (Mon Nov 29 2004 - 09:02:15 PST)
AMBER: Restrained minimization problem opitz.che.udel.edu (Mon Nov 29 2004 - 14:11:56 PST)
- Re: AMBER: Restrained minimization problem Bill Ross (Mon Nov 29 2004 - 14:31:54 PST)
- Re: AMBER: Restrained minimization problem opitz.che.udel.edu (Mon Nov 29 2004 - 14:50:14 PST)
- Re: AMBER: Restrained minimization problem opitz.che.udel.edu (Mon Nov 29 2004 - 14:56:47 PST)
  - Re: AMBER: Restrained minimization problem David A. Case (Mon Nov 29 2004 - 15:27:41 PST)
    - AMBER: increasing the maximum value of NPHB parameter Alena Shmygelska (Mon Nov 29 2004 - 21:05:08 PST)
    - Re: AMBER: increasing the maximum value of NPHB parameter David A. Case (Tue Nov 30 2004 - 17:58:59 PST)
- Re: AMBER: Restrained minimization problem Thomas E. Cheatham, III (Mon Nov 29 2004 - 15:02:44 PST)
- Re: AMBER: Restrained minimization problem Bill Ross (Mon Nov 29 2004 - 15:25:58 PST)
- Re: AMBER: Restrained minimization problem Furse, Kristina Elisabet (Mon Nov 29 2004 - 15:32:28 PST)
AMBER: Slowly releasing restraints Marcin Krol (Tue Nov 30 2004 - 03:12:37 PST)
- Re: AMBER: Slowly releasing restraints David A. Case (Tue Nov 30 2004 - 11:55:40 PST)
AMBER: amber8 parallel installation with mpich cailliez (Tue Nov 30 2004 - 04:24:41 PST)
- Re: AMBER: amber8 parallel installation with mpich Marc Baaden (Tue Nov 30 2004 - 04:00:26 PST)
  - Re: AMBER: amber8 parallel installation with mpich Marc Baaden (Tue Nov 30 2004 - 04:27:18 PST)
AMBER: problem loading mdcrd to VMD Ru-Zhen Li (Tue Nov 30 2004 - 04:59:40 PST)
- Re: AMBER: problem loading mdcrd to VMD Stefano.Pieraccini.unimi.it (Tue Nov 30 2004 - 06:04:07 PST)
- Re: AMBER: problem loading mdcrd to VMD David Smith (Tue Nov 30 2004 - 06:19:24 PST)
  - Re: AMBER: problem loading mdcrd to VMD Ru-Zhen Li (Tue Nov 30 2004 - 09:05:57 PST)
    - Re: AMBER: problem loading mdcrd to VMD David Smith (Tue Nov 30 2004 - 09:44:16 PST)
    - Re: AMBER: problem loading mdcrd to VMD myang.vitamin.uni.cc (Tue Nov 30 2004 - 10:48:43 PST)
    - Re: AMBER: problem loading mdcrd to VMD Ru-Zhen Li (Tue Nov 30 2004 - 15:17:08 PST)
  - AMBER: memory prolem of the nmode calculation Xiao Jian Tan (Tue Nov 30 2004 - 15:24:18 PST)
    - Re: AMBER: memory prolem of the nmode calculation David A. Case (Tue Nov 30 2004 - 17:40:29 PST)
- Re: AMBER: problem loading mdcrd to VMD David E. Konerding (Tue Nov 30 2004 - 07:45:59 PST)
- Re: AMBER: problem loading mdcrd to VMD John Bushnell (Tue Nov 30 2004 - 14:41:14 PST)
AMBER: Implicit 4r md yen li (Tue Nov 30 2004 - 08:58:34 PST)
AMBER: Re: AMBER: problem loading mdcrd to VMD Dawsonzhu.aol.com (Tue Nov 30 2004 - 15:03:46 PST)

Amber Archive Nov 2004 By Thread