AMBER Archive (2003) - Jun 2003 By Subject

185 messages sorted by: [ author ] [ date ] [ thread ]
About this archive

Starting: Sun Jun 01 2003 - 19:14:04 CDT
Ending: Mon Jun 30 2003 - 17:44:18 CDT

1-4 vdw term in Glycam2000
- yuann (Sun Jun 22 2003 - 23:24:16 CDT)
A question of time
- David A. Case (Tue Jun 10 2003 - 11:34:19 CDT)
- Darren Davies (Tue Jun 10 2003 - 10:52:31 CDT)
Amber Installation on Octane
- Joseph Maxwell (Sun Jun 08 2003 - 16:55:55 CDT)
AMBER parameters
- David A. Case (Tue Jun 24 2003 - 10:25:35 CDT)
- D Fernandez (Tue Jun 24 2003 - 00:26:09 CDT)
AMBER question
- David A. Case (Fri Jun 20 2003 - 19:59:04 CDT)
- David (Fri Jun 20 2003 - 11:31:55 CDT)
Amber6 on RH 9
- David A. Case (Thu Jun 26 2003 - 12:31:56 CDT)
- Yichen Cao (Thu Jun 26 2003 - 10:37:09 CDT)
AMBER7 on linux cluster
- Yong Duan (Fri Jun 20 2003 - 20:35:04 CDT)
- Carlos Simmerling (Fri Jun 20 2003 - 09:55:10 CDT)
- Venkata S Koppuravuri (Fri Jun 20 2003 - 09:53:17 CDT)
- Carlos Simmerling (Tue Jun 17 2003 - 11:54:28 CDT)
- Venkata S Koppuravuri (Tue Jun 17 2003 - 11:49:06 CDT)
angle violation in SANDER simulation
- David A. Case (Wed Jun 04 2003 - 10:17:32 CDT)
- XU Xingfu (Wed Jun 04 2003 - 04:11:24 CDT)
Another mm_pbsa problem
- Holger Gohlke (Tue Jun 24 2003 - 12:08:25 CDT)
- Peter Anderson (Tue Jun 24 2003 - 11:47:58 CDT)
Antechamber
- Shweta Sikri (Wed Jun 25 2003 - 14:26:31 CDT)
- David A. Case (Wed Jun 25 2003 - 12:31:31 CDT)
- Shweta Sikri (Wed Jun 25 2003 - 11:47:52 CDT)
antechamber read gaussian file
- David A. Case (Sun Jun 01 2003 - 19:18:54 CDT)
any tool to know what functions are being called while sander is being run??
- Guanglei Cui (Wed Jun 11 2003 - 08:53:45 CDT)
- Satish Mummadi (Wed Jun 11 2003 - 08:42:58 CDT)
- Satish Mummadi (Wed Jun 11 2003 - 00:32:11 CDT)
belly vs. position restraints
- David A. Case (Wed Jun 04 2003 - 10:57:02 CDT)
- Peter Anderson (Wed Jun 04 2003 - 09:17:05 CDT)
bugfix ptraj-6.4 (need to confirm)
- Bimo Ario Tejo (Thu Jun 12 2003 - 07:51:27 CDT)
calculated b-factor higher than x-ray
- Bimo Ario Tejo (Wed Jun 11 2003 - 13:23:03 CDT)
can you give me more advice about: vlimit exceeded when sander calculate free energies using TI
- sxzheng (Sun Jun 29 2003 - 20:05:55 CDT)
- David A. Case (Mon Jun 16 2003 - 10:12:05 CDT)
- sxzheng (Mon Jun 16 2003 - 07:47:53 CDT)
CCL: Amber free energy equation
- Daquan Gao (Tue Jun 17 2003 - 11:33:39 CDT)
constant volume
- David A. Case (Fri Jun 06 2003 - 17:48:16 CDT)
- Shuang Ding (Thu Jun 05 2003 - 17:26:39 CDT)
constraint + restraint
- David A. Case (Thu Jun 19 2003 - 10:39:44 CDT)
- Jose Ramon Blas (Thu Jun 19 2003 - 18:58:41 CDT)
debug sander
- Yong Duan (Thu Jun 19 2003 - 04:21:27 CDT)
- Satish Mummadi (Thu Jun 19 2003 - 03:32:02 CDT)
- Andrew Petersen (Thu Jun 19 2003 - 01:40:04 CDT)
delphi on linux
- chernhoe (Wed Jun 11 2003 - 04:03:13 CDT)
EGB problem in MMPBSA
- Obdulia Rabal (Mon Jun 02 2003 - 06:11:45 CDT)
electrostatic interaction energ. /delphi
- Natasja Brooijmans (Tue Jun 24 2003 - 14:45:22 CDT)
- Tommi Kajander (Tue Jun 24 2003 - 14:39:51 CDT)
Error in minimization using sander_classic of AMBER6
- David A. Case (Tue Jun 17 2003 - 15:53:49 CDT)
- dicksmit_at_umich.edu (Tue Jun 17 2003 - 15:20:03 CDT)
Flag for antechamber
- Nick Polfer (Wed Jun 18 2003 - 03:59:01 CDT)
GAFF in GUI MD apps
- FyD (Wed Jun 25 2003 - 00:50:58 CDT)
- Thomas (Tue Jun 24 2003 - 14:07:54 CDT)
GB model
- MF Yang (Tue Jun 10 2003 - 14:54:33 CDT)
glycam force field with amber
- David A. Case (Fri Jun 13 2003 - 11:42:31 CDT)
- PSR04996_at_mailstudenti.unimi.it (Fri Jun 13 2003 - 06:28:07 CDT)
helix axis for A-RNA
- M. L. Dodson (Tue Jun 10 2003 - 08:36:44 CDT)
- Vlad Cojocaru (Tue Jun 10 2003 - 07:25:09 CDT)
helix movement
- Yuguang Mu (Wed Jun 11 2003 - 07:47:34 CDT)
- Bimo Ario Tejo (Tue Jun 10 2003 - 07:18:14 CDT)
- Andreas Svrcek-Seiler (Tue Jun 10 2003 - 07:07:49 CDT)
- Bimo Ario Tejo (Tue Jun 10 2003 - 06:19:05 CDT)
- Yuguang Mu (Tue Jun 10 2003 - 05:47:42 CDT)
- Bimo Ario Tejo (Tue Jun 10 2003 - 05:10:29 CDT)
help on solvatecap
- Mao Xiang (Wed Jun 18 2003 - 20:47:36 CDT)
How do I perform an Nmode calculation on a big protein-ligand complex?
- Thomas Steinbrecher (Mon Jun 30 2003 - 04:31:38 CDT)
how to restrain water
- Alfonso Garcia Sosa (Mon Jun 23 2003 - 10:42:42 CDT)
- Alfonso Garcia Sosa (Mon Jun 23 2003 - 10:14:02 CDT)
- Mao Xiang (Mon Jun 23 2003 - 09:59:23 CDT)
how to use profec???
- sxzheng (Sun Jun 08 2003 - 03:04:09 CDT)
information
- David A. Case (Sun Jun 01 2003 - 19:14:29 CDT)
Install Amber7 in linux cluster
- Viktor Hornak (Mon Jun 02 2003 - 10:11:10 CDT)
- Wen Li (Mon Jun 02 2003 - 09:20:51 CDT)
install problem
- Dave S Walker (Thu Jun 12 2003 - 19:03:21 CDT)
- David A. Case (Thu Jun 12 2003 - 17:26:56 CDT)
- Dave S Walker (Thu Jun 12 2003 - 16:18:02 CDT)
IR6 and makeDIST-RST
- David A. Case (Sun Jun 01 2003 - 19:14:04 CDT)
jarrod
- Matheus Froeyen (Fri Jun 13 2003 - 02:36:14 CDT)
- Holger Gohlke (Thu Jun 12 2003 - 10:18:43 CDT)
- Jarrod Wesley Barnes (Thu Jun 12 2003 - 09:51:33 CDT)
keeping pdb residues numbers ?
- David A. Case (Wed Jun 04 2003 - 12:40:08 CDT)
- GUILBAUD Philippe 153683 (Wed Jun 04 2003 - 07:48:50 CDT)
LEAP compiling problem
- yuann (Tue Jun 17 2003 - 20:17:56 CDT)
- David A. Case (Tue Jun 17 2003 - 11:09:26 CDT)
- David A. Case (Tue Jun 17 2003 - 10:51:21 CDT)
- yuann (Tue Jun 17 2003 - 05:14:23 CDT)
May I get you help from new user of amber?
- Satish Mummadi (Mon Jun 09 2003 - 10:28:54 CDT)
- Yong Duan (Mon Jun 09 2003 - 10:12:41 CDT)
- Guanglei Cui (Mon Jun 09 2003 - 09:41:07 CDT)
- Wu Yingliang (Mon Jun 09 2003 - 09:21:49 CDT)
May I get you help from new user of amber?(xmkmf)
- Satish Kumar (Mon Jun 09 2003 - 10:46:53 CDT)
Memory problem
- Frederico.Miranda_at_ibmb.uib.no (Tue Jun 24 2003 - 19:17:40 CDT)
Mg++ polarizability
- Robert Duke (Tue Jun 03 2003 - 06:39:25 CDT)
MGB RADII PARAMETRIZATION
- Obdulia Rabal (Tue Jun 03 2003 - 06:08:15 CDT)
Minimization does not converge.
- David A. Case (Wed Jun 11 2003 - 00:52:29 CDT)
- Javier Cuervo (Tue Jun 10 2003 - 22:14:43 CDT)
mm_pbsa error message
- Holger Gohlke (Sun Jun 08 2003 - 11:19:24 CDT)
- chernhoe (Sun Jun 08 2003 - 04:48:02 CDT)
mm_pbsa problem
- Holger Gohlke (Fri Jun 20 2003 - 20:47:21 CDT)
- Peter Anderson (Fri Jun 20 2003 - 17:31:17 CDT)
mpirun problem: no rsh
- Michael Crowley (Wed Jun 18 2003 - 14:04:52 CDT)
- Carlos Simmerling (Wed Jun 18 2003 - 12:56:48 CDT)
- Peter Anderson (Wed Jun 18 2003 - 12:50:26 CDT)
Nancy's leaving
- caldwell_at_heimdal.compchem.ucsf.edu (Tue Jun 03 2003 - 21:42:00 CDT)
Need help recompiling
- caldwell_at_heimdal.compchem.ucsf.edu (Mon Jun 02 2003 - 10:14:06 CDT)
- Peter Anderson (Mon Jun 02 2003 - 09:23:11 CDT)
New location for the Amber web site
- David A. Case (Wed Jun 11 2003 - 01:04:54 CDT)
new tutorial available: introduction to ptraj
- David A. Case (Tue Jun 17 2003 - 13:03:54 CDT)
NOESY restraints
- Steph (Sat Jun 21 2003 - 05:27:35 CDT)
- David A. Case (Fri Jun 20 2003 - 19:49:00 CDT)
- Teletchéa Stéphane (Fri Jun 20 2003 - 06:28:03 CDT)
parallel sander jobs die with error: "MPI_COMM_RANK : Null communicator"
- chris switzer (Sat Jun 14 2003 - 21:00:51 CDT)
perl question
- Ioana Cozmuta (Fri Jun 20 2003 - 17:28:57 CDT)
PME
- darden (Wed Jun 11 2003 - 10:21:25 CDT)
- darden (Wed Jun 11 2003 - 09:33:12 CDT)
- Yuguang Mu (Wed Jun 11 2003 - 03:33:29 CDT)
- Yuguang Mu (Tue Jun 10 2003 - 07:04:08 CDT)
pol_h
- David A. Case (Tue Jun 03 2003 - 11:26:41 CDT)
- Giulio Rastelli (Tue Jun 03 2003 - 11:34:23 CDT)
Problem in separating LES copies into different trajectory
- Viktor Hornak (Tue Jun 10 2003 - 10:50:36 CDT)
- Sameer P. Kawatkar (Tue Jun 10 2003 - 10:15:18 CDT)
Problem with a library
- David A. Case (Fri Jun 13 2003 - 16:07:37 CDT)
- Frederico.Miranda_at_ibmb.uib.no (Fri Jun 13 2003 - 15:27:36 CDT)
Problem with LES topology file
- Carlos Simmerling (Tue Jun 17 2003 - 17:42:07 CDT)
- Courtney Stanton (Tue Jun 17 2003 - 17:28:10 CDT)
PROBLEM WITH LIBRARY
- Frederico.Miranda_at_ibmb.uib.no (Thu Jun 05 2003 - 15:06:27 CDT)
Problem with Snader
- Guanglei Cui (Sat Jun 28 2003 - 09:53:59 CDT)
- Frederico.Miranda_at_ibmb.uib.no (Sat Jun 28 2003 - 08:17:12 CDT)
Problem with XLEaP in Mandrake 9.1
- John Bushnell (Sun Jun 22 2003 - 20:04:43 CDT)
- CUI, Guanglei (Sun Jun 22 2003 - 12:44:51 CDT)
- Ross Walker (Sun Jun 22 2003 - 12:31:02 CDT)
- Karthikeyan Pasupathy (Sun Jun 22 2003 - 12:08:23 CDT)
protonate
- David A. Case (Mon Jun 30 2003 - 17:44:18 CDT)
- Giulio Rastelli (Sun Jun 29 2003 - 16:31:20 CDT)
ptraj question
- Thomas Cheatham (Tue Jun 24 2003 - 15:56:51 CDT)
- Ioana Cozmuta (Tue Jun 24 2003 - 02:59:48 CDT)
pyroglutamic acid (PCA)
- David A. Case (Thu Jun 26 2003 - 12:34:25 CDT)
- Javier Cuervo (Wed Jun 25 2003 - 20:16:44 CDT)
Q) vdw radii & GBSA error
- Sukjoon Yoon (Fri Jun 06 2003 - 11:58:03 CDT)
quasih problem
- David A. Case (Wed Jun 11 2003 - 10:12:54 CDT)
- Yang, Mingfeng (Wed Jun 11 2003 - 09:10:30 CDT)
Question about defining force field
- FUNG WAI KEUNG (Fri Jun 20 2003 - 22:12:59 CDT)
Question about defining force field (followup)
- FUNG WAI KEUNG (Tue Jun 24 2003 - 23:14:10 CDT)
Questions about output archive and micromolecules
- Andrei Leitão (Mon Jun 30 2003 - 15:17:46 CDT)
RDPARM problems (ptraj)
- Sophia Kondratova (Thu Jun 05 2003 - 12:13:35 CDT)
restart MD
- Shuang Ding (Tue Jun 10 2003 - 13:12:08 CDT)
run sander?
- Michael Crowley (Tue Jun 03 2003 - 07:42:53 CDT)
- quch quch (Mon Jun 02 2003 - 13:52:22 CDT)
- David A. Case (Mon Jun 02 2003 - 12:52:00 CDT)
- quch quch (Mon Jun 02 2003 - 11:22:35 CDT)
Running MD
- Carlos Simmerling (Mon Jun 23 2003 - 07:40:24 CDT)
- Balvinder Singh (Mon Jun 23 2003 - 13:02:33 CDT)
- Carlos Simmerling (Mon Jun 23 2003 - 07:10:23 CDT)
- Balvinder Singh (Mon Jun 23 2003 - 12:33:56 CDT)
Sander error
- Natasja Brooijmans (Tue Jun 17 2003 - 13:44:53 CDT)
- Yuhui Cheng (Tue Jun 17 2003 - 13:37:21 CDT)
Sander problem
- David A. Case (Wed Jun 25 2003 - 17:30:21 CDT)
- Yuhui Cheng (Tue Jun 24 2003 - 21:31:28 CDT)
saving trajectory of solute only
- David A. Case (Mon Jun 09 2003 - 11:24:03 CDT)
- Carlos Simmerling (Mon Jun 09 2003 - 11:06:01 CDT)
- Peter Anderson (Mon Jun 09 2003 - 11:01:53 CDT)
shake problem?
- Shuang Ding (Mon Jun 09 2003 - 13:33:50 CDT)
Software Sales
- Pete Koladich (Tue Jun 24 2003 - 15:41:53 CDT)
solventbox at constant pressure
- David A. Case (Wed Jun 04 2003 - 10:13:37 CDT)
- Petrodler_at_aol.com (Wed Jun 04 2003 - 02:19:05 CDT)
Superimposed trajectory
- David A. Case (Tue Jun 10 2003 - 09:53:42 CDT)
- Filip Razga (Tue Jun 10 2003 - 08:59:06 CDT)
T in MD vs. T in wet experiments
- Jianhui Wu (Tue Jun 24 2003 - 20:34:31 CDT)
unifying trajectory files
- Ioana Cozmuta (Wed Jun 25 2003 - 14:58:39 CDT)
- Natasja Brooijmans (Wed Jun 25 2003 - 11:25:41 CDT)
- Carlos Simmerling (Wed Jun 25 2003 - 11:05:57 CDT)
- Peter Anderson (Wed Jun 25 2003 - 10:57:42 CDT)
unit of output velocity
- Andreas Svrcek-Seiler (Fri Jun 06 2003 - 11:49:32 CDT)
- Satish Mummadi (Fri Jun 06 2003 - 11:39:45 CDT)
- Satish Kumar (Fri Jun 06 2003 - 11:25:58 CDT)
- Holger Gohlke (Fri Jun 06 2003 - 10:46:38 CDT)
- Yuguang Mu (Fri Jun 06 2003 - 10:33:01 CDT)
VdW in FEP
- ENikitina (Wed Jun 18 2003 - 09:02:14 CDT)
- ENikitina (Tue Jun 10 2003 - 06:56:23 CDT)
- David A. Case (Mon Jun 09 2003 - 10:05:58 CDT)
- ENikitina (Mon Jun 09 2003 - 02:06:49 CDT)
viewing movie with VMD
- Ross Walker (Mon Jun 23 2003 - 17:36:30 CDT)
- Lepsa (Mon Jun 23 2003 - 03:09:29 CDT)
- Layi Adekoya (Mon Jun 23 2003 - 03:00:51 CDT)
vlimit exceeded when sander calculate free energies using TI
- David A. Case (Wed Jun 11 2003 - 10:21:31 CDT)
- zsx (Wed Jun 11 2003 - 06:51:09 CDT)
web link for PLEP is not available.
- Margaret Shun Cheung (Tue Jun 17 2003 - 15:28:40 CDT)
which AMBER program to use to get the e-density output?
- salinthip thipayang (Wed Jun 11 2003 - 14:24:40 CDT)

Last message date: Fri Feb 06 2004 - 10:15:04 CST
Archived on: Thu May 05 2005 - 14:17:44 CDT

185 messages sorted by: [ author ] [ date ] [ thread ]
About this archive