Amber Archive Feb 2003: by subject

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

Amber Archive Feb 2003 by subject