Amber Archive Mar 2003: by subject

(no subject)
- Steve Seibold (Sat Mar 08 2003 - 11:51:35 PST)
[Fwd: MPI problem in modi4.ncsa.uiuc.edu]
- David A. Case (Fri Mar 14 2003 - 08:30:48 PST)
- Eddy (Thu Mar 13 2003 - 21:57:23 PST)
a perl question for Hbond occupancies analysis
- Vlad Cojocaru (Wed Mar 19 2003 - 05:43:30 PST)
a question about simulation at high temperature
- Xiaoqin Huang (Thu Mar 20 2003 - 09:24:18 PST)
- Carlos Simmerling (Thu Mar 20 2003 - 11:25:19 PST)
- Xiaoqin Huang (Thu Mar 20 2003 - 05:38:24 PST)
about maxium number of residues read by xleap (fwd)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:03 PST)
abt. Plastocyanin tutorial
- S.Swaminathan (Tue Mar 25 2003 - 10:51:50 PST)
Algorithm for the motion equations?
- Andreas Svrcek-Seiler (Fri Mar 14 2003 - 05:11:07 PST)
- Marco Aurelio Correia Preto (Fri Mar 14 2003 - 04:20:41 PST)
amber installation problems (fwd)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:12:44 PST)
Amber web page
- caldwell.heimdal.compchem.ucsf.edu (Wed Mar 12 2003 - 14:28:20 PST)
- caldwell.heimdal.compchem.ucsf.edu (Wed Mar 12 2003 - 13:48:04 PST)
AMBER/FEP: RESP charges
- caldwell.heimdal.compchem.ucsf.edu (Fri Mar 14 2003 - 07:32:48 PST)
- Ghislain Deslongchamps (Fri Mar 14 2003 - 05:37:13 PST)
AMBER6 in Solaris 8
- Sanjeev B.S. (Fri Mar 21 2003 - 01:44:37 PST)
- S.Swaminathan (Fri Mar 21 2003 - 10:37:45 PST)
- S.Swaminathan (Thu Mar 20 2003 - 16:28:11 PST)
amber7 & mpich on sgi (fwd)
- David A. Case (Fri Mar 07 2003 - 11:24:00 PST)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:22 PST)
amber7 on sgi
- Wiktor Jurkowski (Fri Mar 21 2003 - 06:26:54 PST)
ambpdb
- David A. Case (Fri Mar 28 2003 - 10:42:34 PST)
- GUILLERMINA L ESTIU (Fri Mar 28 2003 - 09:05:09 PST)
Analysis of Curves program output
- Andrei Leitão (Tue Mar 11 2003 - 11:34:13 PST)
antechamber -rn keyword
- David A. Case (Fri Mar 28 2003 - 11:54:46 PST)
- Giulio Rastelli (Tue Mar 25 2003 - 15:06:48 PST)
Antechamber atom types
- Simon Lenzen (Tue Mar 25 2003 - 02:41:30 PST)
Antechamber Manual
- Nicholson, James D Mr ARO (Fri Mar 28 2003 - 12:17:12 PST)
Antechamber questions
- Scott Shandler (Mon Mar 31 2003 - 15:42:35 PST)
- David A. Case (Fri Mar 28 2003 - 11:58:00 PST)
- Scott Shandler (Thu Mar 27 2003 - 17:35:32 PST)
atom type
- Emmanuel Giudice (Wed Mar 12 2003 - 09:21:18 PST)
Barium
- Holger Gohlke (Mon Mar 10 2003 - 08:21:20 PST)
- Patrizia Rossi (Sun Mar 09 2003 - 23:38:13 PST)
Carnal processing of binary mdcrd files (IOUTFM=1) Sander 7
- Chris Switzer (Wed Mar 19 2003 - 19:14:01 PST)
charge neutralization in DNA
- sychen (Thu Mar 20 2003 - 08:52:38 PST)
CHARMm force field for AMBER
- kbyun.wesleyan.edu (Thu Mar 27 2003 - 09:18:17 PST)
CMC/MD
- David A. Case (Fri Mar 14 2003 - 13:01:57 PST)
- Andrew Petersen (Fri Mar 14 2003 - 11:31:29 PST)
Compiling Amber7 for linux
- caldwell.heimdal.compchem.ucsf.edu (Fri Mar 14 2003 - 08:59:07 PST)
- Miguel de Federico (Fri Mar 14 2003 - 08:49:06 PST)
DelphiLinux V. 4 Segmentation Fault
- Thomas Steinbrecher (Wed Mar 19 2003 - 05:10:16 PST)
Diferences in gibbs
- David A. Case (Tue Mar 18 2003 - 07:43:10 PST)
- Miguel de Federico (Tue Mar 18 2003 - 01:37:21 PST)
Disulphide bridges
- caldwell.heimdal.compchem.ucsf.edu (Thu Mar 27 2003 - 10:05:06 PST)
- Vlad Cojocaru (Thu Mar 27 2003 - 09:10:24 PST)
doubts
- David A. Case (Sat Mar 22 2003 - 08:56:11 PST)
- Yong Duan (Fri Mar 21 2003 - 06:30:59 PST)
- thenmalar rathinavelan (Thu Mar 20 2003 - 20:26:50 PST)
EWALD
- Yuguang Mu (Sun Mar 09 2003 - 23:13:31 PST)
- caldwell.heimdal.compchem.ucsf.edu (Sun Mar 09 2003 - 19:11:51 PST)
- caldwell.heimdal.compchem.ucsf.edu (Sun Mar 09 2003 - 15:41:02 PST)
- David A. Case (Sun Mar 09 2003 - 14:10:40 PST)
- Yuguang Mu (Sun Mar 09 2003 - 08:46:16 PST)
Extracting structures
- Jose Ramon Blas (Thu Mar 27 2003 - 08:18:31 PST)
format of 'mask' in ptraj
- Jose Ramon Blas (Mon Mar 24 2003 - 08:14:33 PST)
- Jiyoung Heo (Sun Mar 23 2003 - 22:46:18 PST)
Forwarded mail....
- Natasja Brooijmans (Wed Mar 05 2003 - 11:02:42 PST)
- amber.heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 10:05:51 PST)
Forwarded mail.... (fwd)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:12:49 PST)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:12:19 PST)
Fourth European Workshop in Drug Design
- Andrea Tafi (Mon Mar 10 2003 - 06:12:40 PST)
GB simulation on protein (fwd)
- David A. Case (Fri Mar 07 2003 - 10:02:13 PST)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:34 PST)
GB vs. explicit solvent calculations
- David A. Case (Thu Mar 20 2003 - 07:46:53 PST)
- Yong Duan (Thu Mar 20 2003 - 06:48:30 PST)
- Carlos Simmerling (Thu Mar 20 2003 - 06:25:12 PST)
- Thomas Steinbrecher (Thu Mar 20 2003 - 05:53:44 PST)
GIBBS - Non periodic simulations.
- Miguel de Federico (Mon Mar 03 2003 - 10:08:03 PST)
GRASP (fwd)
- Peter Gannett (Fri Mar 07 2003 - 10:50:01 PST)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:49 PST)
Hbond analysis with Carnal
- Vlad Cojocaru (Fri Mar 21 2003 - 06:50:36 PST)
Helical Drift
- Gemma Kinsella (Fri Mar 21 2003 - 08:55:17 PST)
how to convert the amber force field files to any proper format that can be used by gaussian98
- Yong Duan (Sun Mar 09 2003 - 20:17:33 PST)
- Ye Mei (Sat Mar 08 2003 - 19:06:10 PST)
how to generate FF of DNA complex?
- tang kwa (Thu Mar 27 2003 - 07:43:47 PST)
hydrogen bonding
- seraphimo.gmx.de (Tue Mar 18 2003 - 07:51:48 PST)
improper torsion for X -CB-CB-X
- sychen (Mon Mar 24 2003 - 21:16:17 PST)
- Scott Brozell (Mon Mar 24 2003 - 20:16:13 PST)
- yuann (Mon Mar 24 2003 - 19:23:33 PST)
Install Amber 7
- Wen Li (Thu Mar 27 2003 - 08:05:53 PST)
- Wen Li (Thu Mar 27 2003 - 08:01:10 PST)
install amber7 on Linux (fwd)
- David A. Case (Fri Mar 07 2003 - 09:51:55 PST)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:40 PST)
installing AMBER 7
- Chuck Schneider (Mon Mar 10 2003 - 12:05:37 PST)
- Scott Brozell (Mon Mar 10 2003 - 11:42:23 PST)
- Mauro Carlos Costa Ribeiro (Mon Mar 10 2003 - 11:11:46 PST)
intel ifc amber5 and mpich-1.2.5
- Scott Brozell (Wed Mar 12 2003 - 14:09:21 PST)
- Karl N. Kirschner (Wed Mar 12 2003 - 13:25:46 PST)
intra-perturbed group (fwd)
- David A. Case (Fri Mar 07 2003 - 09:55:29 PST)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:57 PST)
lanes when solvating in LEAP (fwd)
- David A. Case (Fri Mar 07 2003 - 09:56:39 PST)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:14:24 PST)
leap remove command
- Yong Duan (Mon Mar 17 2003 - 04:32:21 PST)
- CUI, Guanglei (Sun Mar 16 2003 - 21:30:44 PST)
- Yong Duan (Sun Mar 16 2003 - 19:31:12 PST)
- darden (Sun Mar 16 2003 - 13:26:02 PST)
- CUI, Guanglei (Fri Mar 14 2003 - 14:19:12 PST)
Leap to prep
- caldwell.heimdal.compchem.ucsf.edu (Mon Mar 03 2003 - 15:03:25 PST)
- Dominico J Vigil (Mon Mar 03 2003 - 14:26:45 PST)
Lipids
- Arvid Soederhaell (Tue Mar 18 2003 - 02:33:15 PST)
- Gemma Kinsella (Tue Mar 18 2003 - 00:43:16 PST)
Machine for IBM Horizon
- Carlos P. Sosa (Mon Mar 10 2003 - 15:13:49 PST)
- David A. Case (Mon Mar 10 2003 - 15:04:09 PST)
- Sichun Yang (Mon Mar 10 2003 - 14:23:35 PST)
Max residues (fwd)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:12:54 PST)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:12:29 PST)
- amber.heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 10:05:20 PST)
Maximum molecular size for Amber?
- Wen Li (Tue Mar 18 2003 - 11:21:16 PST)
Mg2+ ion parameters
- Arpita Mitra (Mon Mar 17 2003 - 16:09:52 PST)
MM-PBSA results
- Thomas Steinbrecher (Fri Mar 21 2003 - 05:15:25 PST)
MM_PBSA (Amber7) and delphi
- CUI, Guanglei (Fri Mar 21 2003 - 07:04:04 PST)
- Sue Heavner (Fri Mar 21 2003 - 06:27:00 PST)
Move the atom with specific velosity
- Alexei Valiaev (Thu Mar 20 2003 - 12:28:19 PST)
mpirun problem!
- William Wei (Thu Mar 20 2003 - 08:21:17 PST)
namelist read: variable not in namelist
- Majid moghaddam (Tue Mar 18 2003 - 02:18:46 PST)
nasty npt md problem (fwd)
- David A. Case (Sun Mar 09 2003 - 21:58:58 PST)
- amber.heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 10:05:58 PST)
Notes: Compiling Amber 7 on Mac OS X (fwd)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:10 PST)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:28 PST)
NTX / INIT inconsistency
- caldwell.heimdal.compchem.ucsf.edu (Wed Mar 19 2003 - 15:13:15 PST)
- Sichun Yang (Wed Mar 19 2003 - 14:31:36 PST)
Parameters for Cy3 and Fluorescein
- Vlad Cojocaru (Fri Mar 28 2003 - 04:27:14 PST)
Parameters for Hyddantoin derivatives?
- William Wei (Mon Mar 10 2003 - 10:13:48 PST)
parameters GB/SA
- Franck Chevalier (Mon Mar 03 2003 - 07:41:52 PST)
Parameters: additive, lone pair
- David A. Case (Mon Mar 10 2003 - 08:11:35 PST)
- William Wei (Mon Mar 10 2003 - 06:57:35 PST)
PBC without solvent
- caldwell.heimdal.compchem.ucsf.edu (Tue Mar 18 2003 - 08:21:40 PST)
- David A. Case (Tue Mar 18 2003 - 07:38:04 PST)
- CUI, Guanglei (Tue Mar 18 2003 - 06:58:41 PST)
- Franck Chevalier (Tue Mar 18 2003 - 02:37:55 PST)
Polarization simulation
- Lepsa (Thu Mar 20 2003 - 01:55:33 PST)
Preparation of RESP input from GAUSSIAN output
- Lepsa (Mon Mar 17 2003 - 05:11:41 PST)
- Martin Klvana (Mon Mar 17 2003 - 04:55:24 PST)
pressure variation control
- Vlad Cojocaru (Fri Mar 07 2003 - 10:20:38 PST)
pressure variation control (fwd)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:16 PST)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:12:35 PST)
- amber.heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 10:05:29 PST)
problem of mass center
- David A. Case (Wed Mar 12 2003 - 21:02:10 PST)
- yuan bo (Wed Mar 12 2003 - 19:06:32 PST)
problem with "Example 3" tutorials
- S.Swaminathan (Fri Mar 28 2003 - 11:41:20 PST)
- S.Swaminathan (Tue Mar 25 2003 - 14:39:23 PST)
profec
- Michael Trieb (Mon Mar 10 2003 - 06:46:40 PST)
Protein Reorientation
- Carlos Simmerling (Mon Mar 03 2003 - 07:39:19 PST)
- samantha hughes (Mon Mar 03 2003 - 06:02:11 PST)
- Gemma Kinsella (Mon Mar 03 2003 - 05:54:48 PST)
Protein Reorientation (fwd)
- amber.heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 10:05:11 PST)
Protein-Inhibitor binding afinity
- William Wei (Mon Mar 24 2003 - 10:02:04 PST)
ptraj html documentation still available?
- Vlad Cojocaru (Fri Mar 21 2003 - 06:39:08 PST)
question about dummy atoms? (fwd)
- amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:14:06 PST)
question about mm_pbsa
- Joachim Reichelt (Mon Mar 10 2003 - 04:43:58 PST)
- Holger Gohlke (Sun Mar 09 2003 - 19:31:10 PST)
- Lishan Yao (Sun Mar 09 2003 - 18:26:47 PST)
question about mm_pbsa?
- Holger Gohlke (Tue Mar 18 2003 - 13:05:29 PST)
- Lishan Yao (Tue Mar 18 2003 - 12:00:46 PST)
- Holger Gohlke (Tue Mar 18 2003 - 09:06:20 PST)
- Lishan Yao (Tue Mar 18 2003 - 08:43:51 PST)
- Lishan Yao (Mon Mar 10 2003 - 08:04:17 PST)
reg. problem with SM and ICE libraries
- S.Swaminathan (Fri Mar 21 2003 - 12:56:59 PST)
Regarding the quotation for AMBER 7 Programme
- Prof.S.B.Rai (Wed Mar 12 2003 - 08:53:00 PST)
Resp Charges for large ligand.
- John Bushnell (Mon Mar 17 2003 - 16:47:33 PST)
- Bengt Svensson (Mon Mar 17 2003 - 16:11:42 PST)
RMS in carnal
- Shunzhou Wan (Mon Mar 24 2003 - 03:12:53 PST)
sander outputs
- Holger Gohlke (Fri Mar 28 2003 - 16:26:10 PST)
- S.Swaminathan (Fri Mar 28 2003 - 11:47:18 PST)
SANDER vs GIBBS equilibration
- Carlos Simmerling (Thu Mar 27 2003 - 12:58:58 PST)
- David A. Case (Thu Mar 27 2003 - 12:44:08 PST)
Script and MPICH
- FyD (Fri Mar 21 2003 - 06:01:40 PST)
sequence
- CUI, Guanglei (Tue Mar 11 2003 - 20:50:59 PST)
- Ioana Cozmuta (Tue Mar 11 2003 - 17:23:02 PST)
Solaris Benchmark for Amber7
- Jeffrey Dyason (Tue Mar 11 2003 - 17:04:53 PST)
subscribe
- Xiaodong ZHANG (Mon Mar 10 2003 - 14:46:24 PST)
Summary: Protein-Inhibitor binding affinity
- William Wei (Fri Mar 28 2003 - 06:51:30 PST)
surface accesible area
- David A. Case (Fri Mar 07 2003 - 16:11:02 PST)
- Yongmei Wang (Fri Mar 07 2003 - 15:22:22 PST)
tautp in gibbs
- David A. Case (Mon Mar 03 2003 - 13:59:35 PST)
- Sophia Kondratova (Mon Mar 03 2003 - 12:57:03 PST)
teleap
- Carlos Simmerling (Wed Mar 05 2003 - 10:38:42 PST)
The gblambda parameter
- David A. Case (Thu Mar 13 2003 - 08:34:08 PST)
- Thomas Steinbrecher (Thu Mar 13 2003 - 06:29:03 PST)
three digits in the charges of extPDB
- David A. Case (Fri Mar 07 2003 - 13:21:39 PST)
- Giulio Rastelli (Fri Mar 07 2003 - 16:27:48 PST)
tip5p water model
- David A. Case (Thu Mar 13 2003 - 11:53:26 PST)
- Marvin Rich (Thu Mar 13 2003 - 10:35:22 PST)
- Carlos Simmerling (Thu Mar 13 2003 - 09:58:31 PST)
- Marvin Rich (Thu Mar 13 2003 - 09:44:04 PST)
tleap in large systems
- GUILLERMINA L ESTIU (Thu Mar 27 2003 - 12:57:21 PST)
- David A. Case (Thu Mar 27 2003 - 12:43:01 PST)
unit of energy
- Holger Gohlke (Fri Mar 28 2003 - 16:36:02 PST)
- Monica (Thu Mar 27 2003 - 00:01:56 PST)
using antechamber
- David A. Case (Tue Mar 18 2003 - 08:54:49 PST)
- Pascal Bonnet (Tue Mar 18 2003 - 08:36:23 PST)
- Mauro Carlos Costa Ribeiro (Tue Mar 18 2003 - 08:39:44 PST)
using xleap
- Mauro Carlos Costa Ribeiro (Wed Mar 12 2003 - 09:29:23 PST)
- caldwell.heimdal.compchem.ucsf.edu (Tue Mar 11 2003 - 11:31:47 PST)
- David A. Case (Tue Mar 11 2003 - 11:05:56 PST)
- Mauro Carlos Costa Ribeiro (Tue Mar 11 2003 - 10:33:47 PST)
velocities
- Bill Ross (Mon Mar 10 2003 - 13:14:57 PST)
- David A. Case (Mon Mar 10 2003 - 08:04:58 PST)
- sara nunez (Mon Mar 10 2003 - 02:30:09 PST)
Water density and force output questions
- David A. Case (Fri Mar 07 2003 - 16:15:38 PST)
- dianah.unm.edu (Fri Mar 07 2003 - 15:36:41 PST)
waterbox
- caldwell.heimdal.compchem.ucsf.edu (Fri Mar 21 2003 - 15:33:31 PST)
- caldwell.heimdal.compchem.ucsf.edu (Fri Mar 21 2003 - 14:31:07 PST)
- GUILLERMINA L ESTIU (Fri Mar 21 2003 - 14:22:41 PST)
Why the NMA discrepancies?
- Jones de Andrade (Mon Mar 17 2003 - 06:35:05 PST)
- Yong Duan (Sun Mar 16 2003 - 19:46:57 PST)
- Jones de Andrade (Sun Mar 16 2003 - 17:09:16 PST)
writing mol2 files using antechamber
- David A. Case (Sat Mar 22 2003 - 10:08:29 PST)
- Giulio Rastelli (Sat Mar 22 2003 - 15:41:41 PST)

Amber Archive Mar 2003 by subject