Amber Archive Mar 2003: by author

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

Amber Archive Mar 2003 by author