Amber Archive Feb 2003: by author

A. Hungie
- Velocity (Mon Feb 17 2003 - 08:01:04 PST)
Alexei Valiaev
- File in the tutorial (Tue Feb 18 2003 - 15:18:05 PST)
Andreas Svrcek-Seiler
- Re: compatibility of amber with NAMD (Fri Feb 14 2003 - 06:27:27 PST)
Andrei Leitão
- Minimization after dynamic? (Wed Feb 19 2003 - 16:13:31 PST)
Andrei Leit�o
- Final energy minimization step (Tue Feb 18 2003 - 12:30:08 PST)
- Carnal problem... (Thu Feb 06 2003 - 14:17:49 PST)
Artem Mamonov
- Re: EXTRA_PTS: frtype 2 Should not be here (Tue Feb 25 2003 - 15:49:42 PST)
- EXTRA_PTS: frtype 2 Should not be here (Tue Feb 25 2003 - 14:09:56 PST)
Bayly, Christopher
- force field problem (Mon Feb 10 2003 - 12:01:37 PST)
Bill Ross
- Re: Backbone torsional angles' format? (Fri Feb 07 2003 - 20:01:26 PST)
Bimo Ario Tejo
- Re: MM-PBSA error (Tue Feb 04 2003 - 19:05:30 PST)
- MM-PBSA error (Mon Feb 03 2003 - 21:56:34 PST)
caldwell.heimdal.compchem.ucsf.edu
- Web site problems. (Wed Feb 19 2003 - 13:47:11 PST)
caldwell_at_heimdal.compchem.ucsf.edu
- Re: Velocity (Mon Feb 17 2003 - 08:10:06 PST)
- web page update (Thu Feb 13 2003 - 15:34:45 PST)
- UCSF moving day. (Mon Feb 10 2003 - 17:29:07 PST)
- Re: Gibbs stops after a finite number of window runs (Sat Feb 01 2003 - 14:42:54 PST)
Carlos P. Sosa
- Re: Info request: Amber on 64-bit CPUs (Tue Feb 25 2003 - 09:43:23 PST)
Carlos Simmerling
- Re: Velocity (Mon Feb 17 2003 - 10:02:34 PST)
- Re: energy calculation (Sun Feb 09 2003 - 05:27:03 PST)
- Re: question about temperature (Mon Feb 03 2003 - 09:31:28 PST)
case
- RE: TAUP and density problem (Sun Feb 16 2003 - 17:36:48 PST)
chernhoe
- protein dna simulation (Thu Feb 27 2003 - 20:13:58 PST)
- problem patch files (Tue Feb 25 2003 - 00:15:44 PST)
- Re: new-style prmtop file (Sun Feb 23 2003 - 22:48:47 PST)
- new-style prmtop file (Sun Feb 23 2003 - 19:45:46 PST)
Chuck Schneider
- Re: Info request: Amber on 64-bit CPUs (Tue Feb 25 2003 - 07:02:49 PST)
Craig A Bayse
- Re: bond command (Wed Feb 12 2003 - 13:36:29 PST)
- Re: bond command (Wed Feb 05 2003 - 13:30:36 PST)
- bond command (Tue Feb 04 2003 - 21:46:20 PST)
CUI, Guanglei
- RE: adding hydrogens (Wed Feb 19 2003 - 06:06:27 PST)
- adding hydrogens (Tue Feb 18 2003 - 10:44:13 PST)
- Re: Question about quasih (Sun Feb 09 2003 - 18:59:11 PST)
Daniel Svozil
- Info request: Amber on 64-bit CPUs (Tue Feb 25 2003 - 05:34:57 PST)
David A. Case
- Re: GB/SA (Fri Feb 28 2003 - 18:29:29 PST)
- Re: new-style prmtop file (Sun Feb 23 2003 - 21:38:29 PST)
- Re: minimization with fixed UC dimensions (Fri Feb 21 2003 - 12:00:09 PST)
- Re: AMBER6 problem in Solaris 8 (Thu Feb 20 2003 - 23:56:21 PST)
- Re: probelms with antechamber (Thu Feb 20 2003 - 17:19:24 PST)
- Re: How do NTC=2 recognize hydrogen atom? (Thu Feb 20 2003 - 08:19:27 PST)
- Re: antechamber and its prepin files (Wed Feb 19 2003 - 13:08:55 PST)
- Re: restrained atoms NTR (Tue Feb 18 2003 - 20:16:50 PST)
- Re: charge neutralization in DNA (Tue Feb 18 2003 - 14:27:20 PST)
- Re: Final energy minimization step (Tue Feb 18 2003 - 14:25:05 PST)
- Re: File in the tutorial (Tue Feb 18 2003 - 14:19:24 PST)
- Re: (no subject) (Tue Feb 18 2003 - 14:16:34 PST)
- Re: question on EWALD (Mon Feb 17 2003 - 10:08:53 PST)
- Re: RE: TAUP and density problem (Mon Feb 17 2003 - 10:06:03 PST)
- Re: bond command (Thu Feb 13 2003 - 22:38:09 PST)
- Re: inter & intra-molecular interaction energies (Thu Feb 13 2003 - 15:21:15 PST)
- Re: xleap crash under Irix (Thu Feb 13 2003 - 12:57:35 PST)
- Re: Error Massage in Sander amber7 in Linux (Wed Feb 12 2003 - 05:22:55 PST)
- Re: decrease a force const. for angle (Mon Feb 10 2003 - 17:04:55 PST)
- Re: Internal dielectric in MM-GBSA (Mon Feb 10 2003 - 12:29:44 PST)
- Re: Gibbs: DynamicWin and NSTMEQ? (Fri Feb 07 2003 - 16:12:07 PST)
- Re: essential dynamics (Fri Feb 07 2003 - 13:19:04 PST)
- Re: bond command (Wed Feb 05 2003 - 22:13:22 PST)
- Re: noninteger charge (Wed Feb 05 2003 - 10:59:32 PST)
- Re: bond command (Tue Feb 04 2003 - 22:30:26 PST)
- Re: Ptraj problem with small molecules (Tue Feb 04 2003 - 07:20:54 PST)
- Re: some questions in gibbs calculation (Tue Feb 04 2003 - 07:16:40 PST)
- Re: Gibbs stops after a finite number of window runs (Sat Feb 01 2003 - 13:11:43 PST)
David Smith
- ifc, gibbs and ewald (Tue Feb 04 2003 - 08:49:53 PST)
Dvira Segal
- Ptraj problem with small molecules (Tue Feb 04 2003 - 06:18:11 PST)
E.S.
- nmode on Linux : another memory question (Thu Feb 27 2003 - 14:42:15 PST)
eric hu
- seperate one trajectory file into two (Thu Feb 27 2003 - 19:02:58 PST)
- no statistics.out in mm_pbsa binding energy calculations (Wed Feb 19 2003 - 10:27:10 PST)
- mm_pbsa energy unit (Mon Feb 10 2003 - 11:22:38 PST)
- noninteger charge (Wed Feb 05 2003 - 10:03:08 PST)
- Re: desolvation energy in mm_pbsa (Tue Feb 04 2003 - 12:38:18 PST)
- desolvation energy in mm_pbsa (Mon Feb 03 2003 - 18:36:44 PST)
- trajectory file in mm_pbsa (Mon Feb 03 2003 - 18:11:21 PST)
Fabian Boes
- boron parameters (Mon Feb 03 2003 - 09:51:20 PST)
Fabrice Yerly
- Compilation error of Amber 7 using pgi and mpich on Linux Cluster (Tue Feb 25 2003 - 05:02:00 PST)
Florian Barth
- Re: Amber7 & mpich (Tue Feb 04 2003 - 15:39:51 PST)
Franck Chevalier
- GB/SA (Mon Feb 24 2003 - 01:04:22 PST)
frankikpendu_at_hknetmail.com
- URGENT UPDATE . (Mon Feb 17 2003 - 13:02:33 PST)
FyD
- xleap crash under Irix (Thu Feb 13 2003 - 11:46:07 PST)
- Re: Amber7 & mpich (Wed Feb 05 2003 - 06:58:25 PST)
- Amber7 & mpich (Tue Feb 04 2003 - 06:27:23 PST)
Giulio Rastelli
- Re: ptraj residue number out of range (Tue Feb 25 2003 - 15:35:24 PST)
- ptraj residue number out of range (Tue Feb 25 2003 - 09:20:30 PST)
Guoxi Zhang
- questions about AMBER (Sun Feb 02 2003 - 18:57:21 PST)
Holger Gohlke
- Re: seperate one trajectory file into two (Thu Feb 27 2003 - 19:45:50 PST)
- Re: ptraj residue number out of range (Tue Feb 25 2003 - 09:31:14 PST)
- Re: ptraj residue number out of range (Tue Feb 25 2003 - 08:24:00 PST)
- Re: Nmode (Thu Feb 20 2003 - 10:35:57 PST)
- Re: Energy calculation (Wed Feb 19 2003 - 14:54:30 PST)
- Re: no statistics.out in mm_pbsa binding energy calculations (Wed Feb 19 2003 - 10:48:59 PST)
- Re: mm_pbsa (Tue Feb 18 2003 - 16:13:51 PST)
- Re: delphi and charge file (Wed Feb 12 2003 - 14:43:39 PST)
- Re: mm_pbsa energy unit (Mon Feb 10 2003 - 11:48:51 PST)
- [Fwd: Re: Backbone torsional angles' format?] (Fri Feb 07 2003 - 16:23:15 PST)
- Re: Carnal DECLARE of TORSION problem (Fri Feb 07 2003 - 10:34:07 PST)
- Re: Misaligned Coords from Alanine Scanning (Fri Feb 07 2003 - 08:00:31 PST)
- Re: desolvation energy in mm_pbsa (Tue Feb 04 2003 - 12:59:21 PST)
- [Fwd: Re: trajectory file in mm_pbsa] (Tue Feb 04 2003 - 09:47:08 PST)
Ioana Cozmuta
- adjust virial (Tue Feb 25 2003 - 00:15:45 PST)
- RE: failure of minimization (Mon Feb 24 2003 - 15:11:23 PST)
- RE: failure of minimization (Mon Feb 24 2003 - 11:33:58 PST)
- Re: minimization with fixed UC dimensions (Fri Feb 21 2003 - 17:24:32 PST)
- failure of minimization (Fri Feb 21 2003 - 17:10:37 PST)
- minimization with fixed UC dimensions (Fri Feb 21 2003 - 11:38:01 PST)
- one time evaluation (Mon Feb 17 2003 - 16:14:32 PST)
- compatibility of amber with NAMD (Thu Feb 13 2003 - 10:42:41 PST)
- references (Mon Feb 10 2003 - 18:22:51 PST)
Jarrod Smith
- AMBER mail reflector archive (Mon Feb 10 2003 - 12:37:09 PST)
Jiyoung Heo
- how to validate ff parameters obtained from antechamber (Thu Feb 27 2003 - 21:27:54 PST)
John Bushnell
- Re: Error Massage in Sander amber7 in Linux (Wed Feb 12 2003 - 13:49:56 PST)
John D. Chodera
- Binary output switch (IOUTFM=1) broken in sander? (AMBER7) (Sun Feb 23 2003 - 20:49:56 PST)
John Finke
- Periodic Box (Fri Feb 07 2003 - 16:25:10 PST)
Jose Ramon Blas
- Itanium II (Tue Feb 11 2003 - 10:50:58 PST)
- Re: acetonitrile parameters (Tue Feb 04 2003 - 11:21:39 PST)
- Re: How to calculate new force field? (Mon Feb 03 2003 - 11:06:24 PST)
k.watanabe
- About antechamber (Wed Feb 12 2003 - 21:32:18 PST)
- How to calculate new force field? (Sun Feb 02 2003 - 23:22:31 PST)
kalyan_at_mbu.iisc.ernet.in
- Number of water too large (Mon Feb 17 2003 - 08:10:52 PST)
Layi Adekoya
- mm_pbsa (Wed Feb 26 2003 - 02:05:35 PST)
Lepsa
- Re: mm_pbsa (Wed Feb 26 2003 - 04:41:47 PST)
- Fw: adding hydrogens (Wed Feb 19 2003 - 06:23:54 PST)
- Re: adding hydrogens (Wed Feb 19 2003 - 00:26:36 PST)
- Re: interaction between ligand & protein (Tue Feb 18 2003 - 09:28:35 PST)
- Re: question about partial charge (Mon Feb 17 2003 - 23:56:59 PST)
- Re: charge determination for polariable ff02 force fields (Mon Feb 17 2003 - 00:16:07 PST)
- Fw: charge determination for polariable ff02 force fields (Sat Feb 15 2003 - 08:12:02 PST)
- charges, opt and iops (Sat Feb 15 2003 - 07:59:44 PST)
- Fw: RESP charge derivation (Wed Feb 05 2003 - 00:33:53 PST)
- RESP charge derivation (Tue Feb 04 2003 - 09:34:57 PST)
Ling Zhang
- The image command of ptraj of Amber 6 is not working. (Wed Feb 12 2003 - 12:36:58 PST)
- How to put the outside atoms back to the truncated octahedron box? (Wed Feb 12 2003 - 11:49:12 PST)
Lishan Yao
- interaction between ligand & protein (Tue Feb 18 2003 - 08:59:56 PST)
- question about antechamber (Thu Feb 13 2003 - 14:55:39 PST)
- question about antechamber (Wed Feb 12 2003 - 12:06:23 PST)
- Question about quasih (Sun Feb 09 2003 - 15:18:38 PST)
- essential dynamics (Fri Feb 07 2003 - 08:31:05 PST)
- about Mg++ (Wed Feb 05 2003 - 09:17:12 PST)
- question about temperature (Mon Feb 03 2003 - 09:02:13 PST)
- Re: question about ligand (Sat Feb 01 2003 - 18:24:57 PST)
Luis Gracia
- Re: compatibility of amber with NAMD (Fri Feb 14 2003 - 10:16:12 PST)
- SASA calculation (Mon Feb 03 2003 - 14:58:25 PST)
Mahadevan Seetharaman
- charge neutralization in DNA (Tue Feb 18 2003 - 11:08:55 PST)
Majid moghaddam
- (no subject) (Sun Feb 16 2003 - 05:57:21 PST)
Marc Dobler
- metallic ions (Tue Feb 18 2003 - 01:10:29 PST)
Markus Drumm
- Analysis of close waters (Wed Feb 26 2003 - 04:23:25 PST)
Mengjuei Hsieh
- Re: amber web site (Wed Feb 12 2003 - 12:59:11 PST)
Michael Crowley
- Re: mpi/sander help (Fri Feb 07 2003 - 14:05:10 PST)
- Re: Amber7 & mpich (Tue Feb 04 2003 - 09:56:22 PST)
Michael Ford
- Re: desolvation energy in mm_pbsa (Tue Feb 04 2003 - 06:21:15 PST)
- Re: SASA calculation (Mon Feb 03 2003 - 15:22:26 PST)
Michal Otyepka
- decrease a force const. for angle (Mon Feb 10 2003 - 04:47:35 PST)
N. Jiten Singh
- Isotropic Solvent Box (Thu Feb 13 2003 - 03:28:55 PST)
- Including the Peroidiic Box info ?? (Wed Feb 12 2003 - 19:21:41 PST)
- Re: Re: Error Massage in Sander amber7 in Linux (Wed Feb 12 2003 - 06:13:17 PST)
- Error Massage in Sander amber7 in Linux (Wed Feb 12 2003 - 05:07:26 PST)
- Acetonitrile parameters (Mon Feb 03 2003 - 21:52:16 PST)
Natasja Brooijmans
- Re: How to put the outside atoms back to the truncated octahedron box? (Wed Feb 12 2003 - 12:00:50 PST)
Nicolas Le Novere
- Postdoctoral position available in Molecular Modeling (Fri Feb 14 2003 - 02:27:56 PST)
Nicole A Rutkowski
- Amber Documents (Mon Feb 17 2003 - 11:42:26 PST)
Nikolai Smolin
- about urea and glycerol (Fri Feb 21 2003 - 03:04:33 PST)
Oliver Hucke
- Re: adding hydrogens (Wed Feb 19 2003 - 00:02:30 PST)
Osmar Norberto de Souza
- Neutral ARG (Mon Feb 03 2003 - 09:19:02 PST)
Pascal Bonnet
- Re: MM_PBSA Errors (Wed Feb 12 2003 - 01:50:23 PST)
- Re: Acetonitrile parameters (Tue Feb 04 2003 - 07:22:04 PST)
Patricia Burgess
- gibbs input file (Sun Feb 02 2003 - 16:01:59 PST)
Paula Petrone
- Gibbs: Electrostatic Decoupling (Tue Feb 18 2003 - 09:31:41 PST)
- Gibbs: DynamicWin and NSTMEQ? (Thu Feb 06 2003 - 10:48:02 PST)
Peter Gannett
- Re: compatibility of amber with NAMD (Thu Feb 13 2003 - 14:05:54 PST)
pu xuemei
- hexane parameters (Wed Feb 19 2003 - 04:06:50 PST)
- hexane parameters (Wed Feb 12 2003 - 02:00:19 PST)
Ram�n Gardu�o-Ju�rez
- MM_PBSA Errors (Tue Feb 11 2003 - 16:16:00 PST)
Robert Cave
- (no subject) (Tue Feb 25 2003 - 11:55:51 PST)
Robert J. Woods
- Internal dielectric in MM-GBSA (Mon Feb 10 2003 - 11:29:36 PST)
- Misaligned Coords from Alanine Scanning (Fri Feb 07 2003 - 07:54:07 PST)
Ross Walker
- RE: Itanium II (Wed Feb 12 2003 - 15:46:27 PST)
- RE: amber web site (Wed Feb 12 2003 - 13:13:07 PST)
S.Swaminathan
- Re: AMBER6 problem in Solaris 8 (Wed Feb 26 2003 - 10:10:56 PST)
- AMBER6 problem in Solaris 8 (Fri Feb 21 2003 - 11:18:19 PST)
Sanjeev B.S.
- Re: AMBER6 problem in Solaris 8 (Tue Feb 25 2003 - 21:03:55 PST)
Scott Brozell
- Re: Amber under Linux (Tue Feb 25 2003 - 13:13:11 PST)
- RE: Itanium II (Wed Feb 12 2003 - 16:21:06 PST)
Seongeun Yang
- Re: Gibbs stops after a finite number of window runs (Sat Feb 01 2003 - 13:42:42 PST)
- Gibbs stops after a finite number of window runs (Sat Feb 01 2003 - 11:22:16 PST)
Sichun Yang
- Re: Energy calculation (Wed Feb 19 2003 - 18:51:11 PST)
- Energy calculation (Wed Feb 19 2003 - 14:25:45 PST)
- Re: restrained atoms NTR (Wed Feb 19 2003 - 09:27:18 PST)
- restrained atoms NTR (Tue Feb 18 2003 - 13:45:33 PST)
- RE: question on EWALD (Mon Feb 17 2003 - 15:28:00 PST)
- RE: question on EWALD (Mon Feb 17 2003 - 14:12:42 PST)
- Re: question on EWALD (Mon Feb 17 2003 - 11:37:04 PST)
- Re: question on EWALD (Mon Feb 17 2003 - 11:16:25 PST)
- question on EWALD (Sun Feb 16 2003 - 15:54:49 PST)
Steve Seibold
- antechamber and its prepin files (Wed Feb 19 2003 - 11:11:23 PST)
- amber web site (Wed Feb 12 2003 - 12:30:40 PST)
Subba.Raju
- Force field ? (Mon Feb 24 2003 - 02:17:54 PST)
Sue Heavner
- delphi and charge file (Wed Feb 12 2003 - 12:49:01 PST)
sychen
- Re: question about partial charge (Tue Feb 18 2003 - 19:52:32 PST)
thenmalar rathinavelan
- Nmode (Wed Feb 19 2003 - 22:21:03 PST)
- energy calculation (Sat Feb 08 2003 - 23:19:59 PST)
- stacking energy (Wed Feb 05 2003 - 02:19:06 PST)
Thomas Cheatham
- Re: The image command of ptraj of Amber 6 is not working. (Wed Feb 12 2003 - 13:40:28 PST)
Thomas Steinbrecher
- Re: Namelist READ error - solved (Wed Feb 26 2003 - 06:54:54 PST)
- Namelist READ error (Wed Feb 26 2003 - 04:54:46 PST)
Thu Zar Lwin
- mpi/sander help (Fri Feb 07 2003 - 14:01:05 PST)
Tian-Xiang Xiang
- inter & intra-molecular interaction energies (Thu Feb 13 2003 - 14:10:07 PST)
Tormod Skauge
- Re: Compilation error of Amber 7 using pgi and mpich on Linux Cluster (Tue Feb 25 2003 - 07:00:19 PST)
Vlad
- Beyond 1,000,000 atoms... (Thu Feb 27 2003 - 17:45:14 PST)
William Wei
- Backbone torsional angles' format? (Fri Feb 07 2003 - 15:35:56 PST)
- Carnal DECLARE of TORSION problem (Fri Feb 07 2003 - 10:20:37 PST)
Xiang, Tian-Xiang
- RE: charge determination for polariable ff02 force fields (Sun Feb 16 2003 - 10:19:39 PST)
- charge determination for polariable ff02 force fields (Fri Feb 14 2003 - 12:27:51 PST)
- RE: inter & intra-molecular interaction energies (Thu Feb 13 2003 - 15:47:54 PST)
- RE: Periodic Box (Sat Feb 08 2003 - 08:52:49 PST)
- some questions in gibbs calculation (Mon Feb 03 2003 - 05:46:39 PST)
Yong Duan
- RE: failure of minimization (Mon Feb 24 2003 - 17:42:14 PST)
- RE: failure of minimization (Fri Feb 21 2003 - 18:34:04 PST)
- RE: question on EWALD (Mon Feb 17 2003 - 14:54:14 PST)
- RE: question on EWALD (Mon Feb 17 2003 - 13:08:17 PST)
- RE: Velocity (Mon Feb 17 2003 - 13:00:01 PST)
- RE: energy calculation (Sun Feb 09 2003 - 08:36:28 PST)
Yongmei Wang
- probelms with antechamber (Thu Feb 20 2003 - 12:09:44 PST)
- mm_pbsa (Tue Feb 18 2003 - 15:14:01 PST)
Yongxing Liu
- Re: essential dynamics (Fri Feb 07 2003 - 10:13:09 PST)
yuan bo
- How do NTC=2 recognize hydrogen atom? (Wed Feb 19 2003 - 02:24:55 PST)
- RE:RE: TAUP and density problem (Mon Feb 17 2003 - 01:50:08 PST)
- TAUP and density problem (Sun Feb 16 2003 - 01:29:34 PST)
- MAXINT problem (Fri Feb 14 2003 - 21:51:13 PST)
- NTC=3 for organic solvent and NTC=2 for solute? (Wed Feb 12 2003 - 01:57:42 PST)
- NTC=3 for organic solvent and NTC=2 for soluter? (Wed Feb 12 2003 - 01:57:21 PST)
yuann
- question about partial charge (Mon Feb 17 2003 - 18:43:48 PST)
Yuhui Cheng
- How to do the image using ptraj? (Tue Feb 04 2003 - 18:35:53 PST)

Amber Archive Feb 2003 by author