Amber Archive Mar 2003: By Thread

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

Amber Archive Mar 2003 By Thread