Amber Archive Jan 2003: by author

A.Madhumalar
- Re: structure image (Mon Jan 27 2003 - 17:51:35 PST)
- High temperature MD (Sun Jan 19 2003 - 08:02:41 PST)
Ahammadunny Pathiaseril
- mm_pbsa and ALA scan (Wed Jan 29 2003 - 08:24:06 PST)
Alfonso Garcia Sosa
- posphinic acid parameters (Sun Jan 26 2003 - 08:28:11 PST)
amkumar_at_post.its.mcw.edu
- (no subject) (Fri Jan 10 2003 - 09:35:12 PST)
Andreas Svrcek-Seiler
- Re: average structure generated by carnal (Wed Jan 22 2003 - 07:16:53 PST)
- Re: shake and H-O-H angle (Tue Jan 21 2003 - 11:29:22 PST)
- Re: electrostatic potential calculations (Sat Jan 11 2003 - 08:43:33 PST)
Anke Eisenmann
- (no subject) (Tue Jan 21 2003 - 06:07:25 PST)
Artur Galstyan
- RESP-group constraint (Fri Jan 24 2003 - 06:38:53 PST)
arubin_at_unmc.edu
- xleap in Amber7 (Mon Jan 27 2003 - 16:56:16 PST)
- xleap in Amber7 (Mon Jan 27 2003 - 16:54:46 PST)
Arvid Soederhaell
- antechamber and gamess (Wed Jan 29 2003 - 07:08:00 PST)
- chloroform, dichlormethane f.f. (Tue Jan 14 2003 - 02:24:33 PST)
Bayly, Christopher
- RE: script for H-bonds extracting (Tue Jan 28 2003 - 10:40:53 PST)
- RE: Intramolecular H-bonds in charge fitting (Tue Jan 28 2003 - 07:35:14 PST)
Bimo Ario Tejo
- script for H-bonds extracting (Tue Jan 28 2003 - 02:00:52 PST)
- SASA and H-bond over trajectories (Mon Jan 20 2003 - 20:59:12 PST)
caldwell_at_heimdal.compchem.ucsf.edu
- Amber Web page. (Fri Jan 24 2003 - 08:45:00 PST)
- UCSF Network changes to affect Amber Web site. (Fri Jan 17 2003 - 11:41:19 PST)
- mail reflector (Thu Jan 16 2003 - 13:07:10 PST)
Carlos Simmerling
- Re: conformational sampling (Thu Jan 23 2003 - 15:45:58 PST)
- JACS 125th and PAK (Fri Jan 03 2003 - 09:02:12 PST)
Chris Switzer
- Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap (Fri Jan 03 2003 - 19:18:11 PST)
Chuck Schneider
- Re: LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi (Thu Jan 23 2003 - 04:52:41 PST)
Colin Connelly
- Force Fields (Fri Jan 10 2003 - 21:44:35 PST)
Craig A Bayse
- problem with antechamber (Sun Jan 12 2003 - 10:54:05 PST)
CUI, Guanglei
- Re: Moil-view (Tue Jan 14 2003 - 09:48:49 PST)
- Re: looking for 'pdb_to_mass' (Tue Jan 07 2003 - 06:06:05 PST)
darden
- Re: polarization + ewald (Mon Jan 27 2003 - 16:58:10 PST)
David A. Case
- Re: question about ligand (Fri Jan 31 2003 - 15:14:41 PST)
- Re: Gibbs, ewald and ifc (Fri Jan 31 2003 - 13:56:25 PST)
- Re: Quasi-harmonic analysis (Thu Jan 30 2003 - 17:58:32 PST)
- Re: new amino acid residues (Thu Jan 30 2003 - 09:46:35 PST)
- antechamber and gamess (Wed Jan 29 2003 - 08:16:03 PST)
- Re: gibbs calculation (Tue Jan 28 2003 - 12:03:37 PST)
- Re: Question: about restarting Energy (Mon Jan 27 2003 - 18:33:14 PST)
- Re: crystal structure of DNA/RNA homopolymers (Mon Jan 27 2003 - 11:48:35 PST)
- Re: gibbs run (Mon Jan 27 2003 - 10:38:13 PST)
- Re: lastrst (Mon Jan 27 2003 - 10:33:12 PST)
- terminal phosphate group in RNA (Fri Jan 24 2003 - 16:03:06 PST)
- Re: problems in equilibrating NaCl solution (Fri Jan 24 2003 - 14:20:12 PST)
- Re: Shake problem in organic solvent (Fri Jan 24 2003 - 13:43:20 PST)
- Re: Gibbs tutorial question (Wed Jan 22 2003 - 13:54:10 PST)
- Re: shake and belly (Wed Jan 22 2003 - 10:17:22 PST)
- Re: How to control box size (Wed Jan 22 2003 - 08:53:02 PST)
- Re: equilibrated solvent box (Wed Jan 22 2003 - 08:48:12 PST)
- Re: SCSL (Wed Jan 22 2003 - 08:37:33 PST)
- Re: octahedral volume (Tue Jan 21 2003 - 09:03:23 PST)
- Re: Polarization charges -geometry (Tue Jan 21 2003 - 08:56:07 PST)
- Re: Amber tutorial crown-ether (Tue Jan 21 2003 - 08:48:47 PST)
- Re: 'hot-solvent' and 'cold solute' problem (Tue Jan 21 2003 - 08:38:14 PST)
- Re: your mail (Tue Jan 21 2003 - 08:35:52 PST)
- Re: Ewald error (Mon Jan 20 2003 - 09:31:49 PST)
- Re: morse potential (Mon Jan 20 2003 - 09:29:59 PST)
- Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold (Sun Jan 19 2003 - 23:26:16 PST)
- Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold (Sat Jan 18 2003 - 10:53:54 PST)
- Re: UCSF Network changes to affect Amber Web site. (Fri Jan 17 2003 - 12:14:59 PST)
- Re: solvent free energy, GB (Thu Jan 16 2003 - 16:25:16 PST)
- Re: nscm (Tue Jan 14 2003 - 16:55:14 PST)
- Re: solvatecap (Tue Jan 14 2003 - 14:29:43 PST)
- Re: how to stop mapping of N- and C-terminal residues in xleap (Tue Jan 14 2003 - 11:59:52 PST)
- Re: chloroform, dichlormethane f.f. (Tue Jan 14 2003 - 08:19:24 PST)
- Re: xleap crashes (Mon Jan 13 2003 - 09:08:15 PST)
- Re: Dummy atoms in free energy calculation (Sun Jan 12 2003 - 23:37:35 PST)
- Re: problem with antechamber (Sun Jan 12 2003 - 14:01:06 PST)
- Re: MM_pbsa prmtop file (Thu Jan 09 2003 - 15:53:53 PST)
- Re: nmanal & quasih question (Thu Jan 09 2003 - 09:16:11 PST)
- Re: building molecules by script files for leap (Wed Jan 08 2003 - 09:27:13 PST)
- Re: the unit of velocity (Wed Jan 08 2003 - 08:09:43 PST)
- Re: virtual box (Tue Jan 07 2003 - 15:56:29 PST)
- Re: reducing restrains (Tue Jan 07 2003 - 09:08:24 PST)
- Re: Small organic molecules (Tue Jan 07 2003 - 08:16:48 PST)
- Re: water reordering in sander (Tue Jan 07 2003 - 08:03:58 PST)
- Re: JACS 125th and PAK (Fri Jan 03 2003 - 10:36:47 PST)
- Re: Sander box error and thanks on previous mdin error (Fri Jan 03 2003 - 07:40:07 PST)
David Case
- Re: xleap crashes (Fri Jan 10 2003 - 22:05:45 PST)
- Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap (Fri Jan 03 2003 - 21:46:00 PST)
David Smith
- Gibbs, ewald and ifc (Fri Jan 31 2003 - 14:16:14 PST)
Dr Chris L. Brown
- LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi (Wed Jan 22 2003 - 19:10:34 PST)
Dvira Segal
- ptraj on Methane in water box (Fri Jan 31 2003 - 02:45:03 PST)
- Amber tutorial crown-ether (Tue Jan 21 2003 - 06:06:55 PST)
- building molecules by script files for leap (Wed Jan 08 2003 - 08:07:57 PST)
- Small organic molecules (Tue Jan 07 2003 - 07:55:31 PST)
eric hu
- Re: average structure generated by carnal (Tue Jan 21 2003 - 13:02:34 PST)
- average structure generated by carnal (Tue Jan 21 2003 - 10:53:49 PST)
- reduce the disk space (Tue Jan 21 2003 - 10:48:14 PST)
- scripts for compiling UHBD/MEAD with amber 7.0 (Mon Jan 20 2003 - 09:54:37 PST)
- Re: virtual box (Tue Jan 07 2003 - 23:35:21 PST)
- Re: virtual box (Tue Jan 07 2003 - 23:35:09 PST)
- virtual box (Tue Jan 07 2003 - 15:26:15 PST)
Fan Gao
- one question (Tue Jan 28 2003 - 08:14:56 PST)
Florian Barth
- Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap (Fri Jan 03 2003 - 22:36:27 PST)
FyD
- AMBER7 & mpich (Fri Jan 31 2003 - 06:05:41 PST)
GUILBAUD Philippe 153683
- polarization + ewald (Mon Jan 27 2003 - 03:21:44 PST)
GUILLERMINA L ESTIU
- Re: shake and belly (Wed Jan 22 2003 - 10:47:30 PST)
- shake and belly (Tue Jan 21 2003 - 13:38:59 PST)
- solvatecap (Wed Jan 15 2003 - 06:48:05 PST)
- solvatecap (Tue Jan 14 2003 - 12:33:16 PST)
hagop demirdjian
- roar-cp : input for QM part ; output for CM2 charges (Fri Jan 31 2003 - 07:38:29 PST)
- morse potential (Mon Jan 20 2003 - 08:22:03 PST)
Heike Meiselbach
- Proper torsion parameters missing? (Thu Jan 23 2003 - 11:05:05 PST)
Holger Gohlke
- Re: mm-pbsa problem & possible solution (Thu Jan 30 2003 - 09:22:39 PST)
- Re: MM_PBSA (Wed Jan 29 2003 - 07:24:58 PST)
- Re: one question (Tue Jan 28 2003 - 08:17:02 PST)
- Re: script for Potential/kinectic energy (Mon Jan 20 2003 - 08:44:13 PST)
- Re: mm_pbsa -- COMPT must be specified (correctly) (Mon Jan 13 2003 - 09:01:10 PST)
- Re: mm_gbsa error message (Wed Jan 08 2003 - 13:52:31 PST)
- Re: mm_pbsa question (Tue Jan 07 2003 - 16:41:30 PST)
Ioana Cozmuta
- Re: crystal structure of DNA/RNA homopolymers (Mon Jan 27 2003 - 11:54:18 PST)
- crystal structure of DNA/RNA homopolymers (Mon Jan 27 2003 - 11:34:13 PST)
- question on ptraj (Wed Jan 22 2003 - 13:01:26 PST)
- nucleic acid structures (Fri Jan 17 2003 - 17:12:35 PST)
Jake Isaacs
- coordinates for quasih (Mon Jan 13 2003 - 06:43:54 PST)
- pdb_to_mass (Fri Jan 10 2003 - 12:42:35 PST)
Jash, Panchatapa
- Probelm with the generation of topology file (Tue Jan 21 2003 - 10:01:45 PST)
Jian Zhang
- Re: the unit of velocity (Wed Jan 08 2003 - 18:12:15 PST)
- the unit of velocity (Tue Jan 07 2003 - 20:36:58 PST)
Jianhui Wu
- Domain/Helix movement/MD (Fri Jan 31 2003 - 08:35:18 PST)
Jim Newhouse
- Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap (Tue Jan 07 2003 - 11:07:32 PST)
Joffre Heredia
- SCSL (Wed Jan 22 2003 - 12:23:12 PST)
John D. Chodera
- Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold (Sat Jan 18 2003 - 01:26:12 PST)
johneluwa_at_eircom.net
- Request (Wed Jan 29 2003 - 18:42:28 PST)
Jose Ramon Blas
- Re: chloroform, dichlormethane f.f. (Tue Jan 14 2003 - 16:05:34 PST)
- Predefined Water_cap with xleap (Wed Jan 08 2003 - 10:42:16 PST)
kinsellg
- Nmode query (Fri Jan 24 2003 - 07:00:40 PST)
Kristina Furse
- RE: average structure generated by carnal (Tue Jan 21 2003 - 17:55:46 PST)
- RE: nscm (Wed Jan 15 2003 - 11:13:00 PST)
- nscm (Tue Jan 14 2003 - 16:21:52 PST)
kxg2248_at_njit.edu
- Re: Sander box error and thanks on previous mdin error (Fri Jan 03 2003 - 09:37:05 PST)
- Sander box error and thanks on previous mdin error (Thu Jan 02 2003 - 19:41:49 PST)
Layi Adekoya
- script for Potential/kinectic energy (Mon Jan 20 2003 - 08:30:09 PST)
- xleap crashes (Tue Jan 14 2003 - 00:46:49 PST)
- xleap crashes (Sun Jan 12 2003 - 23:54:20 PST)
- xleap crashes (Fri Jan 10 2003 - 04:16:26 PST)
Lepsa
- Re: Domain/Helix movement/MD (Fri Jan 31 2003 - 08:52:59 PST)
- Re: ptraj distanse question (Fri Jan 31 2003 - 04:16:25 PST)
- Re: High temperature MD (Wed Jan 29 2003 - 23:27:19 PST)
- Re: mm_pbsa and ALA scan (Wed Jan 29 2003 - 08:31:41 PST)
- MM_PBSA (Wed Jan 29 2003 - 05:12:34 PST)
- Re: one question (Tue Jan 28 2003 - 08:16:05 PST)
- Intramolecular H-bonds in charge fitting (Tue Jan 28 2003 - 01:05:58 PST)
- Re: CARNAL (Tue Jan 21 2003 - 10:07:18 PST)
- pi-pi in AMBER (Tue Jan 21 2003 - 09:53:27 PST)
- Re: CARNAL (Tue Jan 21 2003 - 01:33:37 PST)
- CARNAL (Mon Jan 20 2003 - 07:22:22 PST)
- Polarization charges -geometry (Fri Jan 17 2003 - 00:21:30 PST)
- Re: mm_pbsa -- COMPT must be specified (correctly) (Tue Jan 14 2003 - 00:49:55 PST)
- Dummy atoms in free energy calculation (Sat Jan 11 2003 - 10:18:44 PST)
- IDSX0 in free energy calculations (Fri Jan 10 2003 - 05:29:04 PST)
- Re: free energy perturbation (Gibbs/Amber 5)? (Fri Jan 10 2003 - 01:56:50 PST)
Ling Zhang
- Moil-view (Tue Jan 14 2003 - 09:47:14 PST)
Lishan Yao
- question about ligand (Fri Jan 31 2003 - 14:43:39 PST)
Luis Gracia
- shake and H-O-H angle (Tue Jan 21 2003 - 08:57:16 PST)
- Re: script for Potential/kinectic energy (Mon Jan 20 2003 - 10:16:52 PST)
- reducing restrains (Tue Jan 07 2003 - 08:14:43 PST)
Mahadevan Seetharaman
- terminal phosphate group in RNA (Thu Jan 16 2003 - 14:10:13 PST)
- mm_gbsa error message (Wed Jan 08 2003 - 10:17:23 PST)
Manuel Rueda
- Amber parameters for Netropsin (Wed Jan 08 2003 - 15:48:12 PST)
meiselba
- Dummy-parameters in Amber? (Thu Jan 23 2003 - 02:39:17 PST)
- free energy perturbation (Gibbs/Amber 5)? (Thu Jan 09 2003 - 08:49:09 PST)
Michael Ford
- Re: how to stop mapping of N- and C-terminal residues in xleap (The RTFM solution) (Wed Jan 15 2003 - 10:02:52 PST)
- Re: mm_gbsa: Unit 5 Error on OPEN: sander_com.in (Wed Jan 15 2003 - 10:00:34 PST)
- how to stop mapping of N- and C-terminal residues in xleap (Tue Jan 14 2003 - 11:37:27 PST)
- Re: mm_gbsa: Unit 5 Error on OPEN: sander_com.in (Tue Jan 14 2003 - 09:34:33 PST)
Michael Trieb
- water reordering in sander (Tue Jan 07 2003 - 05:43:38 PST)
Miguel de Federico
- Re: Proper torsion parameters missing? (Fri Jan 24 2003 - 01:27:21 PST)
- Re: Dummy-parameters in Amber? (Thu Jan 23 2003 - 03:07:14 PST)
- Ewald error (Mon Jan 20 2003 - 07:32:21 PST)
- GIBBS - Routine TORCON failed. Required change is too large. (Thu Jan 09 2003 - 02:11:41 PST)
Miyashita, Osamu
- Re: Quasi-harmonic analysis (Fri Jan 31 2003 - 10:25:23 PST)
N. Jiten Singh
- Chloroform Parameters (Thu Jan 23 2003 - 21:27:24 PST)
Nathan A. Baker
- Re: CCL:electrostatic potential calculations (Mon Jan 13 2003 - 14:27:00 PST)
Ndubuisi Emmanuel Okoro
- Polymers (Wed Jan 29 2003 - 13:40:53 PST)
- Polymers (Thu Jan 23 2003 - 19:12:10 PST)
Nick Polfer
- new amino acid residues (Thu Jan 30 2003 - 04:58:41 PST)
Patricia Burgess
- Gibbs tutorial question (Wed Jan 22 2003 - 12:27:34 PST)
Paula Petrone
- Gibbs dummy atom (Fri Jan 31 2003 - 15:49:52 PST)
Peter Gannett
- Re: average structure generated by carnal (Tue Jan 21 2003 - 12:14:38 PST)
- Re: electrostatic potential calculations (Mon Jan 13 2003 - 09:32:19 PST)
Peter Varnai
- octahedral volume (Fri Jan 17 2003 - 02:26:58 PST)
Pratul Agarwal
- Re: Domain/Helix movement/MD (Fri Jan 31 2003 - 13:00:54 PST)
- Quasi-harmonic analysis (Thu Jan 30 2003 - 15:48:22 PST)
- Re: coordinates for quasih (Mon Jan 13 2003 - 07:48:17 PST)
pu xuemei
- How much is minimum distance (Thu Jan 23 2003 - 23:11:29 PST)
- How to control box size (Wed Jan 22 2003 - 04:58:53 PST)
- equilibrated solvent box (Mon Jan 20 2003 - 00:55:26 PST)
- equilibrated solvent box (Mon Jan 20 2003 - 00:54:33 PST)
Ram�n Gardu�o-Ju�rez
- MM_PBSA for Linux (Wed Jan 22 2003 - 16:53:55 PST)
Robert G. Endres
- Re: Zn2+ parameters (Sat Jan 25 2003 - 12:25:36 PST)
- conformational sampling (Thu Jan 23 2003 - 06:17:57 PST)
- solvent free energy, GB (Thu Jan 16 2003 - 13:33:36 PST)
Roberto Gomperts
- Re: SCSL (Thu Jan 23 2003 - 07:52:06 PST)
Ross Walker
- RE: UCSF Network changes to affect Amber Web site. (Fri Jan 17 2003 - 12:07:29 PST)
Scott E. Boesch
- compiling amber on myrinet (Mon Jan 27 2003 - 12:12:31 PST)
Seongeun Yang
- Re: problems in equilibrating NaCl solution (Fri Jan 24 2003 - 16:13:41 PST)
- problems in equilibrating NaCl solution (Tue Jan 21 2003 - 14:48:04 PST)
Sichun Yang
- ptraj distanse question (Thu Jan 30 2003 - 20:16:06 PST)
- single point mutations to investigate the conformational change (Mon Jan 27 2003 - 19:43:29 PST)
Stefan Jungblut
- 'hot-solvent' and 'cold solute' problem (Tue Jan 21 2003 - 07:36:37 PST)
Steve Seibold
- lastrst (Mon Jan 27 2003 - 09:46:57 PST)
sychen
- Re: pdb_to_mass (Fri Jan 10 2003 - 17:53:37 PST)
Szilveszter Juhos
- Re: CCL:MEAD on SuSE 8.1 (Tue Jan 14 2003 - 08:22:08 PST)
Thomas Steinbrecher
- mm-pbsa problem & possible solution (Thu Jan 30 2003 - 07:51:57 PST)
- mm-pbsa error message (Tue Jan 28 2003 - 07:02:04 PST)
vannajan_at_chiangmai.ac.th
- Question: about restarting Energy (Mon Jan 27 2003 - 17:53:30 PST)
Vlad Cojocaru
- 2drms command in ptraj (Tue Jan 28 2003 - 04:52:17 PST)
- freeware to visualize RMSD matrices creatde with Carnal (Mon Jan 27 2003 - 14:41:00 PST)
- Has anyone ever used MEAD? (Mon Jan 20 2003 - 05:58:30 PST)
- MEAD on SuSE 8.1 (Tue Jan 14 2003 - 07:10:18 PST)
- electrostatic potential calculations (Sat Jan 11 2003 - 08:05:07 PST)
- errors in MD trajectories (Fri Jan 10 2003 - 10:13:03 PST)
wentaofu
- MM_pbsa prmtop file (Thu Jan 09 2003 - 15:29:38 PST)
- mm_pbsa question (Tue Jan 07 2003 - 16:17:08 PST)
William Wei
- mm_pbsa Stop at statistics (Fri Jan 17 2003 - 10:52:48 PST)
- mm_gbsa: Unit 5 Error on OPEN: sander_com.in (Tue Jan 14 2003 - 09:19:36 PST)
- Summary: mm_pbsa -- COMPT must be specified (correctly) (Tue Jan 14 2003 - 07:31:07 PST)
- mm_pbsa -- COMPT must be specified (correctly) (Mon Jan 13 2003 - 10:00:10 PST)
- RE: mm_pbsa -- COMPT must be specified (correctly) (Mon Jan 13 2003 - 09:32:36 PST)
Xiang, Tian-Xiang
- gibbs calculation (Tue Jan 28 2003 - 11:03:44 PST)
- gibbs run (Mon Jan 27 2003 - 09:05:06 PST)
- RE: structure image (Mon Jan 27 2003 - 08:25:34 PST)
- structure image (Mon Jan 27 2003 - 07:31:46 PST)
- Zn2+ parameters (Fri Jan 24 2003 - 13:42:07 PST)
Ying-Chieh Sun
- compiling amber: Machine file for new 64 bit HP-Itanium II CPU (Tue Jan 14 2003 - 17:40:40 PST)
yuan bo
- Shake problem in organic solvent (Fri Jan 24 2003 - 04:03:48 PST)
yuann
- naphthalene, anthracene force field (Wed Jan 29 2003 - 06:58:47 PST)
- Re: nmanal & quasih question (Thu Jan 09 2003 - 08:13:30 PST)
- nmanal & quasih question (Tue Jan 07 2003 - 23:16:56 PST)
- looking for 'pdb_to_mass' (Mon Jan 06 2003 - 22:54:32 PST)

Amber Archive Jan 2003 by author