AMBER Archive (2003) - By Date

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Starting: Thu Jan 02 2003 - 04:37:41 CST
Ending: Fri Feb 06 2004 - 10:15:04 CST

TFE input Raja Swaminathan (Thu Jan 02 2003 - 04:37:41 CST)
Sander box error and thanks on previous mdin error kxg2248_at_njit.edu (Thu Jan 02 2003 - 21:41:49 CST)
Re: Sander box error and thanks on previous mdin error David A. Case (Fri Jan 03 2003 - 09:40:07 CST)
JACS 125th and PAK Carlos Simmerling (Fri Jan 03 2003 - 11:02:12 CST)
Re: Sander box error and thanks on previous mdin error kxg2248_at_njit.edu (Fri Jan 03 2003 - 11:37:05 CST)
Re: JACS 125th and PAK David A. Case (Fri Jan 03 2003 - 12:36:47 CST)
Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap Chris Switzer (Fri Jan 03 2003 - 21:18:11 CST)
Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap David Case (Fri Jan 03 2003 - 23:46:00 CST)
Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap Florian Barth (Sat Jan 04 2003 - 00:36:27 CST)
looking for 'pdb_to_mass' yuann (Tue Jan 07 2003 - 00:54:32 CST)
water reordering in sander Michael Trieb (Tue Jan 07 2003 - 07:43:38 CST)
Re: looking for 'pdb_to_mass' CUI, Guanglei (Tue Jan 07 2003 - 08:06:05 CST)
Small organic molecules Dvira Segal (Tue Jan 07 2003 - 09:55:31 CST)
Re: water reordering in sander David A. Case (Tue Jan 07 2003 - 10:03:58 CST)
reducing restrains Luis Gracia (Tue Jan 07 2003 - 10:14:43 CST)
Re: Small organic molecules David A. Case (Tue Jan 07 2003 - 10:16:48 CST)
Re: reducing restrains David A. Case (Tue Jan 07 2003 - 11:08:24 CST)
Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap Jim Newhouse (Tue Jan 07 2003 - 13:07:32 CST)
virtual box eric hu (Tue Jan 07 2003 - 17:26:15 CST)
Re: virtual box David A. Case (Tue Jan 07 2003 - 17:56:29 CST)
mm_pbsa question wentaofu (Tue Jan 07 2003 - 18:17:08 CST)
Re: mm_pbsa question Holger Gohlke (Tue Jan 07 2003 - 18:41:30 CST)
the unit of velocity Jian Zhang (Tue Jan 07 2003 - 22:36:58 CST)
nmanal & quasih question yuann (Wed Jan 08 2003 - 01:16:56 CST)
Re: virtual box eric hu (Wed Jan 08 2003 - 01:35:09 CST)
Re: virtual box eric hu (Wed Jan 08 2003 - 01:35:21 CST)
building molecules by script files for leap Dvira Segal (Wed Jan 08 2003 - 10:07:57 CST)
Re: the unit of velocity David A. Case (Wed Jan 08 2003 - 10:09:43 CST)
Re: building molecules by script files for leap David A. Case (Wed Jan 08 2003 - 11:27:13 CST)
mm_gbsa error message Mahadevan Seetharaman (Wed Jan 08 2003 - 12:17:23 CST)
Predefined Water_cap with xleap Jose Ramon Blas (Wed Jan 08 2003 - 12:42:16 CST)
Re: mm_gbsa error message Holger Gohlke (Wed Jan 08 2003 - 15:52:31 CST)
Amber parameters for Netropsin Manuel Rueda (Wed Jan 08 2003 - 17:48:12 CST)
Re: the unit of velocity Jian Zhang (Wed Jan 08 2003 - 20:12:15 CST)
GIBBS - Routine TORCON failed. Required change is too large. Miguel de Federico (Thu Jan 09 2003 - 04:11:41 CST)
Re: nmanal & quasih question yuann (Thu Jan 09 2003 - 10:13:30 CST)
free energy perturbation (Gibbs/Amber 5)? meiselba (Thu Jan 09 2003 - 10:49:09 CST)
Re: nmanal & quasih question David A. Case (Thu Jan 09 2003 - 11:16:11 CST)
MM_pbsa prmtop file wentaofu (Thu Jan 09 2003 - 17:29:38 CST)
Re: MM_pbsa prmtop file David A. Case (Thu Jan 09 2003 - 17:53:53 CST)
Re: free energy perturbation (Gibbs/Amber 5)? Lepsa (Fri Jan 10 2003 - 03:56:50 CST)
xleap crashes Layi Adekoya (Fri Jan 10 2003 - 06:16:26 CST)
IDSX0 in free energy calculations Lepsa (Fri Jan 10 2003 - 07:29:04 CST)
(no subject) amkumar_at_post.its.mcw.edu (Fri Jan 10 2003 - 11:35:12 CST)
errors in MD trajectories Vlad Cojocaru (Fri Jan 10 2003 - 12:13:03 CST)
pdb_to_mass Jake Isaacs (Fri Jan 10 2003 - 14:42:35 CST)
Re: pdb_to_mass sychen (Fri Jan 10 2003 - 19:53:37 CST)
Force Fields Colin Connelly (Fri Jan 10 2003 - 23:44:35 CST)
Re: xleap crashes David Case (Sat Jan 11 2003 - 00:05:45 CST)
electrostatic potential calculations Vlad Cojocaru (Sat Jan 11 2003 - 10:05:07 CST)
Re: electrostatic potential calculations Andreas Svrcek-Seiler (Sat Jan 11 2003 - 10:43:33 CST)
Dummy atoms in free energy calculation Lepsa (Sat Jan 11 2003 - 12:18:44 CST)
problem with antechamber Craig A Bayse (Sun Jan 12 2003 - 12:54:05 CST)
Re: problem with antechamber David A. Case (Sun Jan 12 2003 - 16:01:06 CST)
Re: Dummy atoms in free energy calculation David A. Case (Mon Jan 13 2003 - 01:37:35 CST)
xleap crashes Layi Adekoya (Mon Jan 13 2003 - 01:54:20 CST)
coordinates for quasih Jake Isaacs (Mon Jan 13 2003 - 08:43:54 CST)
Re: coordinates for quasih Pratul Agarwal (Mon Jan 13 2003 - 09:48:17 CST)
Re: mm_pbsa -- COMPT must be specified (correctly) Holger Gohlke (Mon Jan 13 2003 - 11:01:10 CST)
Re: xleap crashes David A. Case (Mon Jan 13 2003 - 11:08:15 CST)
Re: electrostatic potential calculations Peter Gannett (Mon Jan 13 2003 - 11:32:19 CST)
RE: mm_pbsa -- COMPT must be specified (correctly) William Wei (Mon Jan 13 2003 - 11:32:36 CST)
mm_pbsa -- COMPT must be specified (correctly) William Wei (Mon Jan 13 2003 - 12:00:10 CST)
Re: CCL:electrostatic potential calculations Nathan A. Baker (Mon Jan 13 2003 - 16:27:00 CST)
xleap crashes Layi Adekoya (Tue Jan 14 2003 - 02:46:49 CST)
Re: mm_pbsa -- COMPT must be specified (correctly) Lepsa (Tue Jan 14 2003 - 02:49:55 CST)
chloroform, dichlormethane f.f. Arvid Soederhaell (Tue Jan 14 2003 - 04:24:33 CST)
MEAD on SuSE 8.1 Vlad Cojocaru (Tue Jan 14 2003 - 09:10:18 CST)
Summary: mm_pbsa -- COMPT must be specified (correctly) William Wei (Tue Jan 14 2003 - 09:31:07 CST)
Re: chloroform, dichlormethane f.f. David A. Case (Tue Jan 14 2003 - 10:19:24 CST)
Re: CCL:MEAD on SuSE 8.1 Szilveszter Juhos (Tue Jan 14 2003 - 10:22:08 CST)
mm_gbsa: Unit 5 Error on OPEN: sander_com.in William Wei (Tue Jan 14 2003 - 11:19:36 CST)
Re: mm_gbsa: Unit 5 Error on OPEN: sander_com.in Michael Ford (Tue Jan 14 2003 - 11:34:33 CST)
Moil-view Ling Zhang (Tue Jan 14 2003 - 11:47:14 CST)
Re: Moil-view CUI, Guanglei (Tue Jan 14 2003 - 11:48:49 CST)
how to stop mapping of N- and C-terminal residues in xleap Michael Ford (Tue Jan 14 2003 - 13:37:27 CST)
Re: how to stop mapping of N- and C-terminal residues in xleap David A. Case (Tue Jan 14 2003 - 13:59:52 CST)
solvatecap GUILLERMINA L ESTIU (Tue Jan 14 2003 - 14:33:16 CST)
Re: solvatecap David A. Case (Tue Jan 14 2003 - 16:29:43 CST)
Re: chloroform, dichlormethane f.f. Jose Ramon Blas (Tue Jan 14 2003 - 18:05:34 CST)
nscm Kristina Furse (Tue Jan 14 2003 - 18:21:52 CST)
Re: nscm David A. Case (Tue Jan 14 2003 - 18:55:14 CST)
compiling amber: Machine file for new 64 bit HP-Itanium II CPU Ying-Chieh Sun (Tue Jan 14 2003 - 19:40:40 CST)
solvatecap GUILLERMINA L ESTIU (Wed Jan 15 2003 - 08:48:05 CST)
Re: mm_gbsa: Unit 5 Error on OPEN: sander_com.in Michael Ford (Wed Jan 15 2003 - 12:00:34 CST)
Re: how to stop mapping of N- and C-terminal residues in xleap (The RTFM solution) Michael Ford (Wed Jan 15 2003 - 12:02:52 CST)
RE: nscm Kristina Furse (Wed Jan 15 2003 - 13:13:00 CST)
mail reflector caldwell_at_heimdal.compchem.ucsf.edu (Thu Jan 16 2003 - 15:07:10 CST)
solvent free energy, GB Robert G. Endres (Thu Jan 16 2003 - 15:33:36 CST)
terminal phosphate group in RNA Mahadevan Seetharaman (Thu Jan 16 2003 - 16:10:13 CST)
Re: solvent free energy, GB David A. Case (Thu Jan 16 2003 - 18:25:16 CST)
Polarization charges -geometry Lepsa (Fri Jan 17 2003 - 02:21:30 CST)
octahedral volume Peter Varnai (Fri Jan 17 2003 - 04:26:58 CST)
mm_pbsa Stop at statistics William Wei (Fri Jan 17 2003 - 12:52:48 CST)
UCSF Network changes to affect Amber Web site. caldwell_at_heimdal.compchem.ucsf.edu (Fri Jan 17 2003 - 13:41:19 CST)
RE: UCSF Network changes to affect Amber Web site. Ross Walker (Fri Jan 17 2003 - 14:07:29 CST)
Re: UCSF Network changes to affect Amber Web site. David A. Case (Fri Jan 17 2003 - 14:14:59 CST)
nucleic acid structures Ioana Cozmuta (Fri Jan 17 2003 - 19:12:35 CST)
Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold John D. Chodera (Sat Jan 18 2003 - 03:26:12 CST)
Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold David A. Case (Sat Jan 18 2003 - 12:53:54 CST)
High temperature MD A.Madhumalar (Sun Jan 19 2003 - 10:02:41 CST)
Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold David A. Case (Mon Jan 20 2003 - 01:26:16 CST)
equilibrated solvent box pu xuemei (Mon Jan 20 2003 - 02:54:33 CST)
equilibrated solvent box pu xuemei (Mon Jan 20 2003 - 02:55:26 CST)
Has anyone ever used MEAD? Vlad Cojocaru (Mon Jan 20 2003 - 07:58:30 CST)
CARNAL Lepsa (Mon Jan 20 2003 - 09:22:22 CST)
Ewald error Miguel de Federico (Mon Jan 20 2003 - 09:32:21 CST)
morse potential hagop demirdjian (Mon Jan 20 2003 - 10:22:03 CST)
script for Potential/kinectic energy Layi Adekoya (Mon Jan 20 2003 - 10:30:09 CST)
Re: script for Potential/kinectic energy Holger Gohlke (Mon Jan 20 2003 - 10:44:13 CST)
Re: morse potential David A. Case (Mon Jan 20 2003 - 11:29:59 CST)
Re: Ewald error David A. Case (Mon Jan 20 2003 - 11:31:49 CST)
scripts for compiling UHBD/MEAD with amber 7.0 eric hu (Mon Jan 20 2003 - 11:54:37 CST)
Re: script for Potential/kinectic energy Luis Gracia (Mon Jan 20 2003 - 12:16:52 CST)
SASA and H-bond over trajectories Bimo Ario Tejo (Mon Jan 20 2003 - 22:59:12 CST)
Re: CARNAL Lepsa (Tue Jan 21 2003 - 03:33:37 CST)
Amber tutorial crown-ether Dvira Segal (Tue Jan 21 2003 - 08:06:55 CST)
(no subject) Anke Eisenmann (Tue Jan 21 2003 - 08:07:25 CST)
'hot-solvent' and 'cold solute' problem Stefan Jungblut (Tue Jan 21 2003 - 09:36:37 CST)
Re: your mail David A. Case (Tue Jan 21 2003 - 10:35:52 CST)
Re: 'hot-solvent' and 'cold solute' problem David A. Case (Tue Jan 21 2003 - 10:38:14 CST)
Re: Amber tutorial crown-ether David A. Case (Tue Jan 21 2003 - 10:48:47 CST)
Re: Polarization charges -geometry David A. Case (Tue Jan 21 2003 - 10:56:07 CST)
shake and H-O-H angle Luis Gracia (Tue Jan 21 2003 - 10:57:16 CST)
Re: octahedral volume David A. Case (Tue Jan 21 2003 - 11:03:23 CST)
pi-pi in AMBER Lepsa (Tue Jan 21 2003 - 11:53:27 CST)
Probelm with the generation of topology file Jash, Panchatapa (Tue Jan 21 2003 - 12:01:45 CST)
Re: CARNAL Lepsa (Tue Jan 21 2003 - 12:07:18 CST)
reduce the disk space eric hu (Tue Jan 21 2003 - 12:48:14 CST)
average structure generated by carnal eric hu (Tue Jan 21 2003 - 12:53:49 CST)
Re: shake and H-O-H angle Andreas Svrcek-Seiler (Tue Jan 21 2003 - 13:29:22 CST)
Re: average structure generated by carnal Peter Gannett (Tue Jan 21 2003 - 14:14:38 CST)
Re: average structure generated by carnal eric hu (Tue Jan 21 2003 - 15:02:34 CST)
shake and belly GUILLERMINA L ESTIU (Tue Jan 21 2003 - 15:38:59 CST)
problems in equilibrating NaCl solution Seongeun Yang (Tue Jan 21 2003 - 16:48:04 CST)
RE: average structure generated by carnal Kristina Furse (Tue Jan 21 2003 - 19:55:46 CST)
How to control box size pu xuemei (Wed Jan 22 2003 - 06:58:53 CST)
Re: average structure generated by carnal Andreas Svrcek-Seiler (Wed Jan 22 2003 - 09:16:53 CST)
Re: SCSL David A. Case (Wed Jan 22 2003 - 10:37:33 CST)
Re: equilibrated solvent box David A. Case (Wed Jan 22 2003 - 10:48:12 CST)
Re: How to control box size David A. Case (Wed Jan 22 2003 - 10:53:02 CST)
Re: shake and belly David A. Case (Wed Jan 22 2003 - 12:17:22 CST)
Re: shake and belly GUILLERMINA L ESTIU (Wed Jan 22 2003 - 12:47:30 CST)
SCSL Joffre Heredia (Wed Jan 22 2003 - 14:23:12 CST)
Gibbs tutorial question Patricia Burgess (Wed Jan 22 2003 - 14:27:34 CST)
question on ptraj Ioana Cozmuta (Wed Jan 22 2003 - 15:01:26 CST)
Re: Gibbs tutorial question David A. Case (Wed Jan 22 2003 - 15:54:10 CST)
MM_PBSA for Linux Ramón Garduño-Juárez (Wed Jan 22 2003 - 18:53:55 CST)
LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi Dr Chris L. Brown (Wed Jan 22 2003 - 21:10:34 CST)
Dummy-parameters in Amber? meiselba (Thu Jan 23 2003 - 04:39:17 CST)
Re: Dummy-parameters in Amber? Miguel de Federico (Thu Jan 23 2003 - 05:07:14 CST)
Re: LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi Chuck Schneider (Thu Jan 23 2003 - 06:52:41 CST)
conformational sampling Robert G. Endres (Thu Jan 23 2003 - 08:17:57 CST)
Re: SCSL Roberto Gomperts (Thu Jan 23 2003 - 09:52:06 CST)
Proper torsion parameters missing? Heike Meiselbach (Thu Jan 23 2003 - 13:05:05 CST)
Re: conformational sampling Carlos Simmerling (Thu Jan 23 2003 - 17:45:58 CST)
Polymers Ndubuisi Emmanuel Okoro (Thu Jan 23 2003 - 21:12:10 CST)
Chloroform Parameters N. Jiten Singh (Thu Jan 23 2003 - 23:27:24 CST)
How much is minimum distance pu xuemei (Fri Jan 24 2003 - 01:11:29 CST)
Re: Proper torsion parameters missing? Miguel de Federico (Fri Jan 24 2003 - 03:27:21 CST)
Shake problem in organic solvent yuan bo (Fri Jan 24 2003 - 06:03:48 CST)
RESP-group constraint Artur Galstyan (Fri Jan 24 2003 - 08:38:53 CST)
Nmode query kinsellg (Fri Jan 24 2003 - 09:00:40 CST)
Amber Web page. caldwell_at_heimdal.compchem.ucsf.edu (Fri Jan 24 2003 - 10:45:00 CST)
Zn2+ parameters Xiang, Tian-Xiang (Fri Jan 24 2003 - 15:42:07 CST)
Re: Shake problem in organic solvent David A. Case (Fri Jan 24 2003 - 15:43:20 CST)
Re: problems in equilibrating NaCl solution David A. Case (Fri Jan 24 2003 - 16:20:12 CST)
terminal phosphate group in RNA David A. Case (Fri Jan 24 2003 - 18:03:06 CST)
Re: problems in equilibrating NaCl solution Seongeun Yang (Fri Jan 24 2003 - 18:13:41 CST)
Re: Zn2+ parameters Robert G. Endres (Sat Jan 25 2003 - 14:25:36 CST)
posphinic acid parameters Alfonso Garcia Sosa (Sun Jan 26 2003 - 10:28:11 CST)
polarization + ewald GUILBAUD Philippe 153683 (Mon Jan 27 2003 - 05:21:44 CST)
structure image Xiang, Tian-Xiang (Mon Jan 27 2003 - 09:31:46 CST)
RE: structure image Xiang, Tian-Xiang (Mon Jan 27 2003 - 10:25:34 CST)
gibbs run Xiang, Tian-Xiang (Mon Jan 27 2003 - 11:05:06 CST)
lastrst Steve Seibold (Mon Jan 27 2003 - 11:46:57 CST)
Re: lastrst David A. Case (Mon Jan 27 2003 - 12:33:12 CST)
Re: gibbs run David A. Case (Mon Jan 27 2003 - 12:38:13 CST)
crystal structure of DNA/RNA homopolymers Ioana Cozmuta (Mon Jan 27 2003 - 13:34:13 CST)
Re: crystal structure of DNA/RNA homopolymers David A. Case (Mon Jan 27 2003 - 13:48:35 CST)
Re: crystal structure of DNA/RNA homopolymers Ioana Cozmuta (Mon Jan 27 2003 - 13:54:18 CST)
compiling amber on myrinet Scott E. Boesch (Mon Jan 27 2003 - 14:12:31 CST)
freeware to visualize RMSD matrices creatde with Carnal Vlad Cojocaru (Mon Jan 27 2003 - 16:41:00 CST)
xleap in Amber7 arubin_at_unmc.edu (Mon Jan 27 2003 - 18:54:46 CST)
xleap in Amber7 arubin_at_unmc.edu (Mon Jan 27 2003 - 18:56:16 CST)
Re: polarization + ewald darden (Mon Jan 27 2003 - 18:58:10 CST)
Re: structure image A.Madhumalar (Mon Jan 27 2003 - 19:51:35 CST)
Question: about restarting Energy vannajan_at_chiangmai.ac.th (Mon Jan 27 2003 - 19:53:30 CST)
Re: Question: about restarting Energy David A. Case (Mon Jan 27 2003 - 20:33:14 CST)
single point mutations to investigate the conformational change Sichun Yang (Mon Jan 27 2003 - 21:43:29 CST)
Intramolecular H-bonds in charge fitting Lepsa (Tue Jan 28 2003 - 03:05:58 CST)
script for H-bonds extracting Bimo Ario Tejo (Tue Jan 28 2003 - 04:00:52 CST)
2drms command in ptraj Vlad Cojocaru (Tue Jan 28 2003 - 06:52:17 CST)
mm-pbsa error message Thomas Steinbrecher (Tue Jan 28 2003 - 09:02:04 CST)
RE: Intramolecular H-bonds in charge fitting Bayly, Christopher (Tue Jan 28 2003 - 09:35:14 CST)
one question Fan Gao (Tue Jan 28 2003 - 10:14:56 CST)
Re: one question Lepsa (Tue Jan 28 2003 - 10:16:05 CST)
Re: one question Holger Gohlke (Tue Jan 28 2003 - 10:17:02 CST)
RE: script for H-bonds extracting Bayly, Christopher (Tue Jan 28 2003 - 12:40:53 CST)
gibbs calculation Xiang, Tian-Xiang (Tue Jan 28 2003 - 13:03:44 CST)
Re: gibbs calculation David A. Case (Tue Jan 28 2003 - 14:03:37 CST)
MM_PBSA Lepsa (Wed Jan 29 2003 - 07:12:34 CST)
naphthalene, anthracene force field yuann (Wed Jan 29 2003 - 08:58:47 CST)
antechamber and gamess Arvid Soederhaell (Wed Jan 29 2003 - 09:08:00 CST)
Re: MM_PBSA Holger Gohlke (Wed Jan 29 2003 - 09:24:58 CST)
antechamber and gamess David A. Case (Wed Jan 29 2003 - 10:16:03 CST)
mm_pbsa and ALA scan Ahammadunny Pathiaseril (Wed Jan 29 2003 - 10:24:06 CST)
Re: mm_pbsa and ALA scan Lepsa (Wed Jan 29 2003 - 10:31:41 CST)
Polymers Ndubuisi Emmanuel Okoro (Wed Jan 29 2003 - 15:40:53 CST)
Request johneluwa_at_eircom.net (Wed Jan 29 2003 - 20:42:28 CST)
Re: High temperature MD Lepsa (Thu Jan 30 2003 - 01:27:19 CST)
new amino acid residues Nick Polfer (Thu Jan 30 2003 - 06:58:41 CST)
mm-pbsa problem & possible solution Thomas Steinbrecher (Thu Jan 30 2003 - 09:51:57 CST)
Re: mm-pbsa problem & possible solution Holger Gohlke (Thu Jan 30 2003 - 11:22:39 CST)
Re: new amino acid residues David A. Case (Thu Jan 30 2003 - 11:46:35 CST)
Quasi-harmonic analysis Pratul Agarwal (Thu Jan 30 2003 - 17:48:22 CST)
Re: Quasi-harmonic analysis David A. Case (Thu Jan 30 2003 - 19:58:32 CST)
ptraj distanse question Sichun Yang (Thu Jan 30 2003 - 22:16:06 CST)
ptraj on Methane in water box Dvira Segal (Fri Jan 31 2003 - 04:45:03 CST)
Re: ptraj distanse question Lepsa (Fri Jan 31 2003 - 06:16:25 CST)
AMBER7 & mpich FyD (Fri Jan 31 2003 - 08:05:41 CST)
Re: AMBER7 & mpich Viktor Hornak (Fri Jan 31 2003 - 09:12:37 CST)
roar-cp : input for QM part ; output for CM2 charges hagop demirdjian (Fri Jan 31 2003 - 09:38:29 CST)
Domain/Helix movement/MD Jianhui Wu (Fri Jan 31 2003 - 10:35:18 CST)
Re: Domain/Helix movement/MD Lepsa (Fri Jan 31 2003 - 10:52:59 CST)
Re: Quasi-harmonic analysis Miyashita, Osamu (Fri Jan 31 2003 - 12:25:23 CST)
Re: Domain/Helix movement/MD Pratul Agarwal (Fri Jan 31 2003 - 15:00:54 CST)
Re: Gibbs, ewald and ifc David A. Case (Fri Jan 31 2003 - 15:56:25 CST)
Gibbs, ewald and ifc David Smith (Fri Jan 31 2003 - 16:16:14 CST)
question about ligand Lishan Yao (Fri Jan 31 2003 - 16:43:39 CST)
Re: question about ligand David A. Case (Fri Jan 31 2003 - 17:14:41 CST)
Gibbs dummy atom Paula Petrone (Fri Jan 31 2003 - 17:49:52 CST)
Gibbs stops after a finite number of window runs Seongeun Yang (Sat Feb 01 2003 - 13:22:16 CST)
Re: Gibbs stops after a finite number of window runs David A. Case (Sat Feb 01 2003 - 15:11:43 CST)
Re: Gibbs stops after a finite number of window runs Seongeun Yang (Sat Feb 01 2003 - 15:42:42 CST)
Re: Gibbs stops after a finite number of window runs caldwell_at_heimdal.compchem.ucsf.edu (Sat Feb 01 2003 - 16:42:54 CST)
Re: question about ligand Lishan Yao (Sat Feb 01 2003 - 20:24:57 CST)
gibbs input file Patricia Burgess (Sun Feb 02 2003 - 18:01:59 CST)
questions about AMBER Guoxi Zhang (Sun Feb 02 2003 - 20:57:21 CST)
How to calculate new force field? k.watanabe (Mon Feb 03 2003 - 01:22:31 CST)
some questions in gibbs calculation Xiang, Tian-Xiang (Mon Feb 03 2003 - 07:46:39 CST)
question about temperature Lishan Yao (Mon Feb 03 2003 - 11:02:13 CST)
Neutral ARG Osmar Norberto de Souza (Mon Feb 03 2003 - 11:19:02 CST)
Re: question about temperature Carlos Simmerling (Mon Feb 03 2003 - 11:31:28 CST)
boron parameters Fabian Boes (Mon Feb 03 2003 - 11:51:20 CST)
Re: How to calculate new force field? Jose Ramon Blas (Mon Feb 03 2003 - 13:06:24 CST)
SASA calculation Luis Gracia (Mon Feb 03 2003 - 16:58:25 CST)
Re: SASA calculation Michael Ford (Mon Feb 03 2003 - 17:22:26 CST)
trajectory file in mm_pbsa eric hu (Mon Feb 03 2003 - 20:11:21 CST)
desolvation energy in mm_pbsa eric hu (Mon Feb 03 2003 - 20:36:44 CST)
Acetonitrile parameters N. Jiten Singh (Mon Feb 03 2003 - 23:52:16 CST)
MM-PBSA error Bimo Ario Tejo (Mon Feb 03 2003 - 23:56:34 CST)
Ptraj problem with small molecules Dvira Segal (Tue Feb 04 2003 - 08:18:11 CST)
Re: desolvation energy in mm_pbsa Michael Ford (Tue Feb 04 2003 - 08:21:15 CST)
Amber7 & mpich FyD (Tue Feb 04 2003 - 08:27:23 CST)
Re: some questions in gibbs calculation David A. Case (Tue Feb 04 2003 - 09:16:40 CST)
Re: Ptraj problem with small molecules David A. Case (Tue Feb 04 2003 - 09:20:54 CST)
Re: Acetonitrile parameters Pascal Bonnet (Tue Feb 04 2003 - 09:22:04 CST)
ifc, gibbs and ewald David Smith (Tue Feb 04 2003 - 10:49:53 CST)
RESP charge derivation Lepsa (Tue Feb 04 2003 - 11:34:57 CST)
[Fwd: Re: trajectory file in mm_pbsa] Holger Gohlke (Tue Feb 04 2003 - 11:47:08 CST)
Re: Amber7 & mpich Michael Crowley (Tue Feb 04 2003 - 11:56:22 CST)
Re: Amber7 & mpich Viktor Hornak (Tue Feb 04 2003 - 12:07:47 CST)
Re: acetonitrile parameters Jose Ramon Blas (Tue Feb 04 2003 - 13:21:39 CST)
Re: desolvation energy in mm_pbsa eric hu (Tue Feb 04 2003 - 14:38:18 CST)
Re: desolvation energy in mm_pbsa Holger Gohlke (Tue Feb 04 2003 - 14:59:21 CST)
Re: Amber7 & mpich Florian Barth (Tue Feb 04 2003 - 17:39:51 CST)
How to do the image using ptraj? Yuhui Cheng (Tue Feb 04 2003 - 20:35:53 CST)
Re: MM-PBSA error Bimo Ario Tejo (Tue Feb 04 2003 - 21:05:30 CST)
bond command Craig A Bayse (Tue Feb 04 2003 - 23:46:20 CST)
Re: bond command David A. Case (Wed Feb 05 2003 - 00:30:26 CST)
Fw: RESP charge derivation Lepsa (Wed Feb 05 2003 - 02:33:53 CST)
stacking energy thenmalar rathinavelan (Wed Feb 05 2003 - 04:19:06 CST)
Re: Amber7 & mpich FyD (Wed Feb 05 2003 - 08:58:25 CST)
about Mg++ Lishan Yao (Wed Feb 05 2003 - 11:17:12 CST)
noninteger charge eric hu (Wed Feb 05 2003 - 12:03:08 CST)
Re: noninteger charge David A. Case (Wed Feb 05 2003 - 12:59:32 CST)
Re: bond command Craig A Bayse (Wed Feb 05 2003 - 15:30:36 CST)
Re: bond command David A. Case (Thu Feb 06 2003 - 00:13:22 CST)
Gibbs: DynamicWin and NSTMEQ? Paula Petrone (Thu Feb 06 2003 - 12:48:02 CST)
Carnal problem... Andrei Leitão (Thu Feb 06 2003 - 16:17:49 CST)
Misaligned Coords from Alanine Scanning Robert J. Woods (Fri Feb 07 2003 - 09:54:07 CST)
Re: Misaligned Coords from Alanine Scanning Holger Gohlke (Fri Feb 07 2003 - 10:00:31 CST)
essential dynamics Lishan Yao (Fri Feb 07 2003 - 10:31:05 CST)
Re: essential dynamics Yongxing Liu (Fri Feb 07 2003 - 12:13:09 CST)
Carnal DECLARE of TORSION problem William Wei (Fri Feb 07 2003 - 12:20:37 CST)
Re: Carnal DECLARE of TORSION problem Holger Gohlke (Fri Feb 07 2003 - 12:34:07 CST)
Re: essential dynamics David A. Case (Fri Feb 07 2003 - 15:19:04 CST)
mpi/sander help Thu Zar Lwin (Fri Feb 07 2003 - 16:01:05 CST)
Re: mpi/sander help Michael Crowley (Fri Feb 07 2003 - 16:05:10 CST)
Backbone torsional angles' format? William Wei (Fri Feb 07 2003 - 17:35:56 CST)
Re: Gibbs: DynamicWin and NSTMEQ? David A. Case (Fri Feb 07 2003 - 18:12:07 CST)
[Fwd: Re: Backbone torsional angles' format?] Holger Gohlke (Fri Feb 07 2003 - 18:23:15 CST)
Periodic Box John Finke (Fri Feb 07 2003 - 18:25:10 CST)
Re: Backbone torsional angles' format? Bill Ross (Fri Feb 07 2003 - 22:01:26 CST)
RE: Periodic Box Xiang, Tian-Xiang (Sat Feb 08 2003 - 10:52:49 CST)
energy calculation thenmalar rathinavelan (Sun Feb 09 2003 - 01:19:59 CST)
Re: energy calculation Carlos Simmerling (Sun Feb 09 2003 - 07:27:03 CST)
RE: energy calculation Yong Duan (Sun Feb 09 2003 - 10:36:28 CST)
Question about quasih Lishan Yao (Sun Feb 09 2003 - 17:18:38 CST)
Re: Question about quasih CUI, Guanglei (Sun Feb 09 2003 - 20:59:11 CST)
decrease a force const. for angle Michal Otyepka (Mon Feb 10 2003 - 06:47:35 CST)
mm_pbsa energy unit eric hu (Mon Feb 10 2003 - 13:22:38 CST)
Internal dielectric in MM-GBSA Robert J. Woods (Mon Feb 10 2003 - 13:29:36 CST)
Re: mm_pbsa energy unit Holger Gohlke (Mon Feb 10 2003 - 13:48:51 CST)
force field problem Bayly, Christopher (Mon Feb 10 2003 - 14:01:37 CST)
Re: Internal dielectric in MM-GBSA David A. Case (Mon Feb 10 2003 - 14:29:44 CST)
AMBER mail reflector archive Jarrod Smith (Mon Feb 10 2003 - 14:37:09 CST)
Re: decrease a force const. for angle David A. Case (Mon Feb 10 2003 - 19:04:55 CST)
UCSF moving day. caldwell_at_heimdal.compchem.ucsf.edu (Mon Feb 10 2003 - 19:29:07 CST)
references Ioana Cozmuta (Mon Feb 10 2003 - 20:22:51 CST)
Itanium II Jose Ramon Blas (Tue Feb 11 2003 - 12:50:58 CST)
MM_PBSA Errors Ramón Garduño-Juárez (Tue Feb 11 2003 - 18:16:00 CST)
NTC=3 for organic solvent and NTC=2 for soluter? yuan bo (Wed Feb 12 2003 - 03:57:21 CST)
NTC=3 for organic solvent and NTC=2 for solute? yuan bo (Wed Feb 12 2003 - 03:57:42 CST)
Re: MM_PBSA Errors Pascal Bonnet (Wed Feb 12 2003 - 03:50:23 CST)
hexane parameters pu xuemei (Wed Feb 12 2003 - 04:00:19 CST)
Error Massage in Sander amber7 in Linux N. Jiten Singh (Wed Feb 12 2003 - 07:07:26 CST)
Re: Error Massage in Sander amber7 in Linux David A. Case (Wed Feb 12 2003 - 07:22:55 CST)
Re: Re: Error Massage in Sander amber7 in Linux N. Jiten Singh (Wed Feb 12 2003 - 08:13:17 CST)
How to put the outside atoms back to the truncated octahedron box? Ling Zhang (Wed Feb 12 2003 - 13:49:12 CST)
Re: How to put the outside atoms back to the truncated octahedron box? Natasja Brooijmans (Wed Feb 12 2003 - 14:00:50 CST)
question about antechamber Lishan Yao (Wed Feb 12 2003 - 14:06:23 CST)
amber web site Steve Seibold (Wed Feb 12 2003 - 14:30:40 CST)
The image command of ptraj of Amber 6 is not working. Ling Zhang (Wed Feb 12 2003 - 14:36:58 CST)
delphi and charge file Sue Heavner (Wed Feb 12 2003 - 14:49:01 CST)
Re: amber web site Mengjuei Hsieh (Wed Feb 12 2003 - 14:59:11 CST)
RE: amber web site Ross Walker (Wed Feb 12 2003 - 15:13:07 CST)
Re: bond command Craig A Bayse (Wed Feb 12 2003 - 15:36:29 CST)
Re: The image command of ptraj of Amber 6 is not working. Thomas Cheatham (Wed Feb 12 2003 - 15:40:28 CST)
Re: Error Massage in Sander amber7 in Linux John Bushnell (Wed Feb 12 2003 - 15:49:56 CST)
Re: delphi and charge file Holger Gohlke (Wed Feb 12 2003 - 16:43:39 CST)
RE: Itanium II Ross Walker (Wed Feb 12 2003 - 17:46:27 CST)
RE: Itanium II Scott Brozell (Wed Feb 12 2003 - 18:21:06 CST)
Including the Peroidiic Box info ?? N. Jiten Singh (Wed Feb 12 2003 - 21:21:41 CST)
About antechamber k.watanabe (Wed Feb 12 2003 - 23:32:18 CST)
Isotropic Solvent Box N. Jiten Singh (Thu Feb 13 2003 - 05:28:55 CST)
compatibility of amber with NAMD Ioana Cozmuta (Thu Feb 13 2003 - 12:42:41 CST)
xleap crash under Irix FyD (Thu Feb 13 2003 - 13:46:07 CST)
Re: xleap crash under Irix David A. Case (Thu Feb 13 2003 - 14:57:35 CST)
Re: compatibility of amber with NAMD Peter Gannett (Thu Feb 13 2003 - 16:05:54 CST)
inter & intra-molecular interaction energies Tian-Xiang Xiang (Thu Feb 13 2003 - 16:10:07 CST)
question about antechamber Lishan Yao (Thu Feb 13 2003 - 16:55:39 CST)
Re: inter & intra-molecular interaction energies David A. Case (Thu Feb 13 2003 - 17:21:15 CST)
web page update caldwell_at_heimdal.compchem.ucsf.edu (Thu Feb 13 2003 - 17:34:45 CST)
RE: inter & intra-molecular interaction energies Xiang, Tian-Xiang (Thu Feb 13 2003 - 17:47:54 CST)
Re: bond command David A. Case (Fri Feb 14 2003 - 00:38:09 CST)
Postdoctoral position available in Molecular Modeling Nicolas Le Novere (Fri Feb 14 2003 - 04:27:56 CST)
Re: compatibility of amber with NAMD Andreas Svrcek-Seiler (Fri Feb 14 2003 - 08:27:27 CST)
Re: compatibility of amber with NAMD Luis Gracia (Fri Feb 14 2003 - 12:16:12 CST)
charge determination for polariable ff02 force fields Xiang, Tian-Xiang (Fri Feb 14 2003 - 14:27:51 CST)
MAXINT problem yuan bo (Fri Feb 14 2003 - 23:51:13 CST)
charges, opt and iops Lepsa (Sat Feb 15 2003 - 09:59:44 CST)
Fw: charge determination for polariable ff02 force fields Lepsa (Sat Feb 15 2003 - 10:12:02 CST)
TAUP and density problem yuan bo (Sun Feb 16 2003 - 03:29:34 CST)
(no subject) Majid moghaddam (Sun Feb 16 2003 - 07:57:21 CST)
RE: charge determination for polariable ff02 force fields Xiang, Tian-Xiang (Sun Feb 16 2003 - 12:19:39 CST)
question on EWALD Sichun Yang (Sun Feb 16 2003 - 17:54:49 CST)
RE: TAUP and density problem case (Sun Feb 16 2003 - 19:36:48 CST)
Re: charge determination for polariable ff02 force fields Lepsa (Mon Feb 17 2003 - 02:16:07 CST)
RE:RE: TAUP and density problem yuan bo (Mon Feb 17 2003 - 03:50:08 CST)
Number of water too large kalyan_at_mbu.iisc.ernet.in (Mon Feb 17 2003 - 10:10:52 CST)
Velocity A. Hungie (Mon Feb 17 2003 - 10:01:04 CST)
Re: Velocity caldwell_at_heimdal.compchem.ucsf.edu (Mon Feb 17 2003 - 10:10:06 CST)
Re: Velocity Carlos Simmerling (Mon Feb 17 2003 - 12:02:34 CST)
Re: RE: TAUP and density problem David A. Case (Mon Feb 17 2003 - 12:06:03 CST)
Re: question on EWALD David A. Case (Mon Feb 17 2003 - 12:08:53 CST)
Re: question on EWALD Sichun Yang (Mon Feb 17 2003 - 13:16:25 CST)
Re: question on EWALD Sichun Yang (Mon Feb 17 2003 - 13:37:04 CST)
Amber Documents Nicole A Rutkowski (Mon Feb 17 2003 - 13:42:26 CST)
RE: Velocity Yong Duan (Mon Feb 17 2003 - 15:00:01 CST)
RE: question on EWALD Yong Duan (Mon Feb 17 2003 - 15:08:17 CST)
RE: question on EWALD Sichun Yang (Mon Feb 17 2003 - 16:12:42 CST)
RE: question on EWALD Yong Duan (Mon Feb 17 2003 - 16:54:14 CST)
RE: question on EWALD Sichun Yang (Mon Feb 17 2003 - 17:28:00 CST)
one time evaluation Ioana Cozmuta (Mon Feb 17 2003 - 18:14:32 CST)
question about partial charge yuann (Mon Feb 17 2003 - 20:43:48 CST)
Re: question about partial charge Lepsa (Tue Feb 18 2003 - 01:56:59 CST)
metallic ions Marc Dobler (Tue Feb 18 2003 - 03:10:29 CST)
interaction between ligand & protein Lishan Yao (Tue Feb 18 2003 - 10:59:56 CST)
Re: interaction between ligand & protein Lepsa (Tue Feb 18 2003 - 11:28:35 CST)
Gibbs: Electrostatic Decoupling Paula Petrone (Tue Feb 18 2003 - 11:31:41 CST)
adding hydrogens CUI, Guanglei (Tue Feb 18 2003 - 12:44:13 CST)
charge neutralization in DNA Mahadevan Seetharaman (Tue Feb 18 2003 - 13:08:55 CST)
File in the tutorial Alexei Valiaev (Tue Feb 18 2003 - 17:18:05 CST)
Final energy minimization step Andrei Leitão (Tue Feb 18 2003 - 14:30:08 CST)
restrained atoms NTR Sichun Yang (Tue Feb 18 2003 - 15:45:33 CST)
Re: (no subject) David A. Case (Tue Feb 18 2003 - 16:16:34 CST)
Re: File in the tutorial David A. Case (Tue Feb 18 2003 - 16:19:24 CST)
Re: Final energy minimization step David A. Case (Tue Feb 18 2003 - 16:25:05 CST)
Re: charge neutralization in DNA David A. Case (Tue Feb 18 2003 - 16:27:20 CST)
mm_pbsa Yongmei Wang (Tue Feb 18 2003 - 17:14:01 CST)
Re: mm_pbsa Holger Gohlke (Tue Feb 18 2003 - 18:13:51 CST)
bugfix.33 not online chernhoe (Tue Feb 18 2003 - 19:45:12 CST)
Re: question about partial charge sychen (Tue Feb 18 2003 - 21:52:32 CST)
Re: restrained atoms NTR David A. Case (Tue Feb 18 2003 - 22:16:50 CST)
Re: adding hydrogens Oliver Hucke (Wed Feb 19 2003 - 02:02:30 CST)
Re: adding hydrogens Lepsa (Wed Feb 19 2003 - 02:26:36 CST)
How do NTC=2 recognize hydrogen atom? yuan bo (Wed Feb 19 2003 - 04:24:55 CST)
hexane parameters pu xuemei (Wed Feb 19 2003 - 06:06:50 CST)
RE: adding hydrogens CUI, Guanglei (Wed Feb 19 2003 - 08:06:27 CST)
Fw: adding hydrogens Lepsa (Wed Feb 19 2003 - 08:23:54 CST)
Re: restrained atoms NTR Sichun Yang (Wed Feb 19 2003 - 11:27:18 CST)
no statistics.out in mm_pbsa binding energy calculations eric hu (Wed Feb 19 2003 - 12:27:10 CST)
Re: no statistics.out in mm_pbsa binding energy calculations Holger Gohlke (Wed Feb 19 2003 - 12:48:59 CST)
antechamber and its prepin files Steve Seibold (Wed Feb 19 2003 - 13:11:23 CST)
Re: antechamber and its prepin files David A. Case (Wed Feb 19 2003 - 15:08:55 CST)
Web site problems. caldwell_at_heimdal.compchem.ucsf.edu (Wed Feb 19 2003 - 15:47:11 CST)
Energy calculation Sichun Yang (Wed Feb 19 2003 - 16:25:45 CST)
Re: Energy calculation Holger Gohlke (Wed Feb 19 2003 - 16:54:30 CST)
Minimization after dynamic? Andrei Leitão (Wed Feb 19 2003 - 18:13:31 CST)
Re: Energy calculation Sichun Yang (Wed Feb 19 2003 - 20:51:11 CST)
Nmode thenmalar rathinavelan (Thu Feb 20 2003 - 00:21:03 CST)
Re: How do NTC=2 recognize hydrogen atom? David A. Case (Thu Feb 20 2003 - 10:19:27 CST)
Re: Nmode Holger Gohlke (Thu Feb 20 2003 - 12:35:57 CST)
probelms with antechamber Yongmei Wang (Thu Feb 20 2003 - 14:09:44 CST)
Re: probelms with antechamber David A. Case (Thu Feb 20 2003 - 19:19:24 CST)
AMBER6 problem in Solaris 8 S.Swaminathan (Fri Feb 21 2003 - 13:18:19 CST)
Re: AMBER6 problem in Solaris 8 David A. Case (Fri Feb 21 2003 - 01:56:21 CST)
about urea and glycerol Nikolai Smolin (Fri Feb 21 2003 - 05:04:33 CST)
unsubscribe Xiang Mao (Fri Feb 21 2003 - 09:29:28 CST)
minimization with fixed UC dimensions Ioana Cozmuta (Fri Feb 21 2003 - 13:38:01 CST)
Re: minimization with fixed UC dimensions David A. Case (Fri Feb 21 2003 - 14:00:09 CST)
failure of minimization Ioana Cozmuta (Fri Feb 21 2003 - 19:10:37 CST)
Re: minimization with fixed UC dimensions Ioana Cozmuta (Fri Feb 21 2003 - 19:24:32 CST)
RE: failure of minimization Yong Duan (Fri Feb 21 2003 - 20:34:04 CST)
ÓÀ¼Îê±±±ÉÏÃ÷·§ÃÅ³§ by (Sat Feb 22 2003 - 23:49:08 CST)
new-style prmtop file chernhoe (Sun Feb 23 2003 - 21:45:46 CST)
Binary output switch (IOUTFM=1) broken in sander? (AMBER7) John D. Chodera (Sun Feb 23 2003 - 22:49:56 CST)
Re: new-style prmtop file David A. Case (Sun Feb 23 2003 - 23:38:29 CST)
Re: new-style prmtop file chernhoe (Mon Feb 24 2003 - 00:48:47 CST)
GB/SA Franck Chevalier (Mon Feb 24 2003 - 03:04:22 CST)
Force field ? Subba.Raju (Mon Feb 24 2003 - 04:17:54 CST)
a question~~ resister_at_pchome.com.tw (Mon Feb 24 2003 - 18:28:52 CST)
RE: failure of minimization Ioana Cozmuta (Mon Feb 24 2003 - 13:33:58 CST)
RE: failure of minimization Ioana Cozmuta (Mon Feb 24 2003 - 17:11:23 CST)
RE: failure of minimization Yong Duan (Mon Feb 24 2003 - 19:42:14 CST)
adjust virial Ioana Cozmuta (Tue Feb 25 2003 - 02:15:45 CST)
problem patch files chernhoe (Tue Feb 25 2003 - 02:15:44 CST)
ptraj residue number out of range Giulio Rastelli (Tue Feb 25 2003 - 11:20:30 CST)
Compilation error of Amber 7 using pgi and mpich on Linux Cluster Fabrice Yerly (Tue Feb 25 2003 - 07:02:00 CST)
Info request: Amber on 64-bit CPUs Daniel Svozil (Tue Feb 25 2003 - 07:34:57 CST)
Re: Compilation error of Amber 7 using pgi and mpich on Linux Cluster Tormod Skauge (Tue Feb 25 2003 - 09:00:19 CST)
Re: Info request: Amber on 64-bit CPUs Chuck Schneider (Tue Feb 25 2003 - 09:02:49 CST)
Re: ptraj residue number out of range Holger Gohlke (Tue Feb 25 2003 - 10:24:00 CST)
Re: ptraj residue number out of range Giulio Rastelli (Tue Feb 25 2003 - 17:35:24 CST)
Re: ptraj residue number out of range Holger Gohlke (Tue Feb 25 2003 - 11:31:14 CST)
Re: Info request: Amber on 64-bit CPUs Carlos P. Sosa (Tue Feb 25 2003 - 11:43:23 CST)
(no subject) Robert Cave (Tue Feb 25 2003 - 13:55:51 CST)
Re: Amber under Linux Scott Brozell (Tue Feb 25 2003 - 15:13:11 CST)
EXTRA_PTS: frtype 2 Should not be here Artem Mamonov (Tue Feb 25 2003 - 16:09:56 CST)
Re: EXTRA_PTS: frtype 2 Should not be here Artem Mamonov (Tue Feb 25 2003 - 17:49:42 CST)
Re: AMBER6 problem in Solaris 8 S.Swaminathan (Wed Feb 26 2003 - 12:10:56 CST)
Re: AMBER6 problem in Solaris 8 Sanjeev B.S. (Tue Feb 25 2003 - 23:03:55 CST)
mm_pbsa Layi Adekoya (Wed Feb 26 2003 - 04:05:35 CST)
Analysis of close waters Markus Drumm (Wed Feb 26 2003 - 06:23:25 CST)
Re: mm_pbsa Lepsa (Wed Feb 26 2003 - 06:41:47 CST)
Namelist READ error Thomas Steinbrecher (Wed Feb 26 2003 - 06:54:46 CST)
Re: Namelist READ error - solved Thomas Steinbrecher (Wed Feb 26 2003 - 08:54:54 CST)
Automated response taxquestions_at_nyit.edu (Wed Feb 26 2003 - 11:11:58 CST)
results of MD comparison Xiaoqin Huang (Wed Feb 26 2003 - 09:08:59 CST)
Re: results of MD comparison Carlos Simmerling (Wed Feb 26 2003 - 15:00:20 CST)
question about lysine? Lishan Yao (Wed Feb 26 2003 - 16:23:38 CST)
Re: question about lysine? Guanglei Cui (Wed Feb 26 2003 - 21:20:43 CST)
Re: Analysis of close waters Markus Drumm (Thu Feb 27 2003 - 06:24:13 CST)
extract coord and velocities sara nunez (Thu Feb 27 2003 - 06:55:18 CST)
stress - strain - pressure seraphimo_at_gmx.de (Thu Feb 27 2003 - 07:06:32 CST)
nmode on Linux : another memory question E.S. (Thu Feb 27 2003 - 16:42:15 CST)
Beyond 1,000,000 atoms... Vlad (Thu Feb 27 2003 - 19:45:14 CST)
seperate one trajectory file into two eric hu (Thu Feb 27 2003 - 21:02:58 CST)
Re: seperate one trajectory file into two Holger Gohlke (Thu Feb 27 2003 - 21:45:50 CST)
protein dna simulation chernhoe (Thu Feb 27 2003 - 22:13:58 CST)
how to validate ff parameters obtained from antechamber Jiyoung Heo (Thu Feb 27 2003 - 23:27:54 CST)
Re: GB/SA David A. Case (Fri Feb 28 2003 - 20:29:29 CST)
Protein Reorientation Gemma Kinsella (Mon Mar 03 2003 - 07:54:48 CST)
Re: Protein Reorientation samantha hughes (Mon Mar 03 2003 - 08:02:11 CST)
Re: Protein Reorientation Carlos Simmerling (Mon Mar 03 2003 - 09:39:19 CST)
parameters GB/SA Franck Chevalier (Mon Mar 03 2003 - 09:41:52 CST)
GIBBS - Non periodic simulations. Miguel de Federico (Mon Mar 03 2003 - 12:08:03 CST)
tautp in gibbs Sophia Kondratova (Mon Mar 03 2003 - 14:57:03 CST)
Re: tautp in gibbs David A. Case (Mon Mar 03 2003 - 15:59:35 CST)
Leap to prep Dominico J Vigil (Mon Mar 03 2003 - 16:26:45 CST)
Re: Leap to prep caldwell_at_heimdal.compchem.ucsf.edu (Mon Mar 03 2003 - 17:03:25 CST)
reflector text - please ignore caldwell_at_heimdal.compchem.ucsf.edu (Tue Mar 04 2003 - 15:46:48 CST)
Re: Protein Reorientation (fwd) amber_at_heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 12:05:11 CST)
Max residues (fwd) amber_at_heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 12:05:20 CST)
pressure variation control (fwd) amber_at_heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 12:05:29 CST)
Forwarded mail.... amber_at_heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 12:05:51 CST)
nasty npt md problem (fwd) amber_at_heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 12:05:58 CST)
teleap Carlos Simmerling (Wed Mar 05 2003 - 12:38:42 CST)
Re: Forwarded mail.... Natasja Brooijmans (Wed Mar 05 2003 - 13:02:42 CST)
Re: Forwarded mail.... (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:12:19 CST)
Re: Max residues (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:12:29 CST)
Re: pressure variation control (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:12:35 CST)
amber installation problems (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:12:44 CST)
Re: Forwarded mail.... (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:12:49 CST)
Re: Max residues (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:12:54 CST)
about maxium number of residues read by xleap (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:13:03 CST)
Notes: Compiling Amber 7 on Mac OS X (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:13:10 CST)
pressure variation control (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:13:16 CST)
amber7 & mpich on sgi (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:13:22 CST)
GB simulation on protein (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:13:34 CST)
install amber7 on Linux (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:13:40 CST)
GRASP (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:13:49 CST)
intra-perturbed group (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:13:57 CST)
question about dummy atoms? (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:14:06 CST)
lanes when solvating in LEAP (fwd) amber_at_heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 11:14:24 CST)
Re: install amber7 on Linux (fwd) David A. Case (Fri Mar 07 2003 - 11:51:55 CST)
three digits in the charges of extPDB Giulio Rastelli (Fri Mar 07 2003 - 18:27:48 CST)
Re: intra-perturbed group (fwd) David A. Case (Fri Mar 07 2003 - 11:55:29 CST)
Re: lanes when solvating in LEAP (fwd) David A. Case (Fri Mar 07 2003 - 11:56:39 CST)
Re: GB simulation on protein (fwd) David A. Case (Fri Mar 07 2003 - 12:02:13 CST)
Re: pressure variation control Vlad Cojocaru (Fri Mar 07 2003 - 12:20:38 CST)
Re: GRASP (fwd) Peter Gannett (Fri Mar 07 2003 - 12:50:01 CST)
Re: amber7 & mpich on sgi (fwd) David A. Case (Fri Mar 07 2003 - 13:24:00 CST)
Re: three digits in the charges of extPDB David A. Case (Fri Mar 07 2003 - 15:21:39 CST)
surface accesible area Yongmei Wang (Fri Mar 07 2003 - 17:22:22 CST)
Water density and force output questions dianah_at_unm.edu (Fri Mar 07 2003 - 17:36:41 CST)
Re: surface accesible area David A. Case (Fri Mar 07 2003 - 18:11:02 CST)
Re: Water density and force output questions David A. Case (Fri Mar 07 2003 - 18:15:38 CST)
(no subject) Steve Seibold (Sat Mar 08 2003 - 13:51:35 CST)
how to convert the amber force field files to any proper format that can be used by gaussian98 Ye Mei (Sat Mar 08 2003 - 21:06:10 CST)
EWALD Yuguang Mu (Sun Mar 09 2003 - 10:46:16 CST)
Re: EWALD David A. Case (Sun Mar 09 2003 - 16:10:40 CST)
Re: EWALD caldwell_at_heimdal.compchem.ucsf.edu (Sun Mar 09 2003 - 17:41:02 CST)
question about mm_pbsa Lishan Yao (Sun Mar 09 2003 - 20:26:47 CST)
Re: EWALD caldwell_at_heimdal.compchem.ucsf.edu (Sun Mar 09 2003 - 21:11:51 CST)
Re: question about mm_pbsa Holger Gohlke (Sun Mar 09 2003 - 21:31:10 CST)
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 - 22:17:33 CST)
Re: nasty npt md problem (fwd) David A. Case (Sun Mar 09 2003 - 23:58:58 CST)
Re: EWALD Yuguang Mu (Mon Mar 10 2003 - 01:13:31 CST)
barium Patrizia Rossi (Mon Mar 10 2003 - 01:38:13 CST)
velocities sara nunez (Mon Mar 10 2003 - 04:30:09 CST)
Re: question about mm_pbsa Joachim Reichelt (Mon Mar 10 2003 - 06:43:58 CST)
Fourth European Workshop in Drug Design Andrea Tafi (Mon Mar 10 2003 - 08:12:40 CST)
profec Michael Trieb (Mon Mar 10 2003 - 08:46:40 CST)
Parameters: additive, lone pair William Wei (Mon Mar 10 2003 - 08:57:35 CST)
Re: velocities David A. Case (Mon Mar 10 2003 - 10:04:58 CST)
question about mm_pbsa? Lishan Yao (Mon Mar 10 2003 - 10:04:17 CST)
Re: Parameters: additive, lone pair David A. Case (Mon Mar 10 2003 - 10:11:35 CST)
Barium Holger Gohlke (Mon Mar 10 2003 - 10:21:20 CST)
Parameters for Hyddantoin derivatives? William Wei (Mon Mar 10 2003 - 12:13:48 CST)
installing AMBER 7 Mauro Carlos Costa Ribeiro (Mon Mar 10 2003 - 13:11:46 CST)
Re: installing AMBER 7 Scott Brozell (Mon Mar 10 2003 - 13:42:23 CST)
Re: installing AMBER 7 Chuck Schneider (Mon Mar 10 2003 - 14:05:37 CST)
Re: velocities Bill Ross (Mon Mar 10 2003 - 15:14:57 CST)
Machine for IBM Horizon Sichun Yang (Mon Mar 10 2003 - 16:23:35 CST)
Re: Machine for IBM Horizon David A. Case (Mon Mar 10 2003 - 17:04:09 CST)
Re: Machine for IBM Horizon Carlos P. Sosa (Mon Mar 10 2003 - 17:13:49 CST)
using xleap Mauro Carlos Costa Ribeiro (Tue Mar 11 2003 - 12:33:47 CST)
Re: using xleap David A. Case (Tue Mar 11 2003 - 13:05:56 CST)
Re: using xleap caldwell_at_heimdal.compchem.ucsf.edu (Tue Mar 11 2003 - 13:31:47 CST)
Analysis of Curves program output Andrei Leitão (Tue Mar 11 2003 - 13:34:13 CST)
Solaris Benchmark for Amber7 Jeffrey Dyason (Tue Mar 11 2003 - 19:04:53 CST)
sequence Ioana Cozmuta (Tue Mar 11 2003 - 19:23:02 CST)
Re: sequence CUI, Guanglei (Tue Mar 11 2003 - 22:50:59 CST)
Regarding the quotation for AMBER 7 Programme Prof.S.B.Rai (Wed Mar 12 2003 - 01:56:46 CST)
atom type Emmanuel Giudice (Wed Mar 12 2003 - 11:21:18 CST)
Re: using xleap Mauro Carlos Costa Ribeiro (Wed Mar 12 2003 - 11:29:23 CST)
intel ifc amber5 and mpich-1.2.5 Karl N. Kirschner (Wed Mar 12 2003 - 15:25:46 CST)
Amber Web page caldwell_at_heimdal.compchem.ucsf.edu (Wed Mar 12 2003 - 15:48:04 CST)
Re: intel ifc amber5 and mpich-1.2.5 Scott Brozell (Wed Mar 12 2003 - 16:09:21 CST)
Amber web page caldwell_at_heimdal.compchem.ucsf.edu (Wed Mar 12 2003 - 16:28:20 CST)
problem of mass center yuan bo (Wed Mar 12 2003 - 21:06:32 CST)
Re: problem of mass center David A. Case (Wed Mar 12 2003 - 23:02:10 CST)
The gblambda parameter Thomas Steinbrecher (Thu Mar 13 2003 - 08:29:03 CST)
Re: The gblambda parameter David A. Case (Thu Mar 13 2003 - 10:34:08 CST)
tip5p water model Marvin Rich (Thu Mar 13 2003 - 11:44:04 CST)
Re: tip5p water model Carlos Simmerling (Thu Mar 13 2003 - 11:58:31 CST)
Re: tip5p water model Marvin Rich (Thu Mar 13 2003 - 12:35:22 CST)
Re: tip5p water model David A. Case (Thu Mar 13 2003 - 13:53:26 CST)
[Fwd: MPI problem in modi4.ncsa.uiuc.edu] Eddy (Thu Mar 13 2003 - 23:57:23 CST)
Algorithm for the motion equations? Marco Aurelio Correia Preto (Fri Mar 14 2003 - 06:20:41 CST)
Re: Algorithm for the motion equations? Andreas Svrcek-Seiler (Fri Mar 14 2003 - 07:11:07 CST)
AMBER/FEP: RESP charges Ghislain Deslongchamps (Fri Mar 14 2003 - 07:37:13 CST)
Re: AMBER/FEP: RESP charges caldwell_at_heimdal.compchem.ucsf.edu (Fri Mar 14 2003 - 09:32:48 CST)
Re: [Fwd: MPI problem in modi4.ncsa.uiuc.edu] David A. Case (Fri Mar 14 2003 - 10:30:48 CST)
Compiling Amber7 for linux Miguel de Federico (Fri Mar 14 2003 - 10:49:06 CST)
Re: Compiling Amber7 for linux caldwell_at_heimdal.compchem.ucsf.edu (Fri Mar 14 2003 - 10:59:07 CST)
CMC/MD Andrew Petersen (Fri Mar 14 2003 - 13:31:29 CST)
Re: CMC/MD David A. Case (Fri Mar 14 2003 - 15:01:57 CST)
leap remove command CUI, Guanglei (Fri Mar 14 2003 - 16:19:12 CST)
Re: leap remove command darden (Sun Mar 16 2003 - 15:26:02 CST)
Why the NMA discrepancies? Jones de Andrade (Sun Mar 16 2003 - 19:09:16 CST)
RE: leap remove command Yong Duan (Sun Mar 16 2003 - 21:31:12 CST)
RE: Why the NMA discrepancies? Yong Duan (Sun Mar 16 2003 - 21:46:57 CST)
RE: leap remove command CUI, Guanglei (Sun Mar 16 2003 - 23:30:44 CST)
RE: leap remove command Yong Duan (Mon Mar 17 2003 - 06:32:21 CST)
Preparation of RESP input from GAUSSIAN output Martin Klvana (Mon Mar 17 2003 - 06:55:24 CST)
Re: Preparation of RESP input from GAUSSIAN output Lepsa (Mon Mar 17 2003 - 07:11:41 CST)
RE: Why the NMA discrepancies? Jones de Andrade (Mon Mar 17 2003 - 08:35:05 CST)
Mg2+ ion parameters Arpita Mitra (Mon Mar 17 2003 - 18:09:52 CST)
Resp Charges for large ligand. Bengt Svensson (Mon Mar 17 2003 - 18:11:42 CST)
Re: Resp Charges for large ligand. John Bushnell (Mon Mar 17 2003 - 18:47:33 CST)
Lipids Gemma Kinsella (Tue Mar 18 2003 - 02:43:16 CST)
namelist read: variable not in namelist Majid moghaddam (Tue Mar 18 2003 - 04:18:46 CST)
Re: Lipids Arvid Soederhaell (Tue Mar 18 2003 - 04:33:15 CST)
Diferences in gibbs Miguel de Federico (Tue Mar 18 2003 - 03:37:21 CST)
PBC without solvent Franck Chevalier (Tue Mar 18 2003 - 04:37:55 CST)
Re: PBC without solvent CUI, Guanglei (Tue Mar 18 2003 - 08:58:41 CST)
Re: PBC without solvent David A. Case (Tue Mar 18 2003 - 09:38:04 CST)
Re: Diferences in gibbs David A. Case (Tue Mar 18 2003 - 09:43:10 CST)
hydrogen bonding seraphimo_at_gmx.de (Tue Mar 18 2003 - 09:51:48 CST)
Re: PBC without solvent caldwell_at_heimdal.compchem.ucsf.edu (Tue Mar 18 2003 - 10:21:40 CST)
using antechamber Mauro Carlos Costa Ribeiro (Tue Mar 18 2003 - 10:39:44 CST)
Question about mm_pbsa? Lishan Yao (Tue Mar 18 2003 - 10:43:51 CST)
Re: using antechamber Pascal Bonnet (Tue Mar 18 2003 - 10:36:23 CST)
Re: using antechamber David A. Case (Tue Mar 18 2003 - 10:54:49 CST)
Re: Question about mm_pbsa? Holger Gohlke (Tue Mar 18 2003 - 11:06:20 CST)
Maximum molecular size for Amber? Wen Li (Tue Mar 18 2003 - 13:21:16 CST)
question about mm_pbsa? Lishan Yao (Tue Mar 18 2003 - 14:00:46 CST)
Re: question about mm_pbsa? Holger Gohlke (Tue Mar 18 2003 - 15:05:29 CST)
DelphiLinux V. 4 Segmentation Fault Thomas Steinbrecher (Wed Mar 19 2003 - 07:10:16 CST)
a perl question for Hbond occupancies analysis Vlad Cojocaru (Wed Mar 19 2003 - 07:43:30 CST)
NTX / INIT inconsistency Sichun Yang (Wed Mar 19 2003 - 16:31:36 CST)
Re: NTX / INIT inconsistency caldwell_at_heimdal.compchem.ucsf.edu (Wed Mar 19 2003 - 17:13:15 CST)
Carnal processing of binary mdcrd files (IOUTFM=1) Sander 7 Chris Switzer (Wed Mar 19 2003 - 21:14:01 CST)
Polarization simulation Lepsa (Thu Mar 20 2003 - 03:55:33 CST)
AMBER6 in Solaris 8 S.Swaminathan (Thu Mar 20 2003 - 18:28:11 CST)
GB vs. explicit solvent calculations Thomas Steinbrecher (Thu Mar 20 2003 - 07:53:44 CST)
Re: GB vs. explicit solvent calculations Carlos Simmerling (Thu Mar 20 2003 - 08:25:12 CST)
RE: GB vs. explicit solvent calculations Yong Duan (Thu Mar 20 2003 - 08:48:30 CST)
Re: GB vs. explicit solvent calculations David A. Case (Thu Mar 20 2003 - 09:46:53 CST)
mpirun problem! William Wei (Thu Mar 20 2003 - 10:21:17 CST)
Re: charge neutralization in DNA sychen (Thu Mar 20 2003 - 10:52:38 CST)
Move the atom with specific velosity Alexei Valiaev (Thu Mar 20 2003 - 14:28:19 CST)
a question about simulation at high temperature Xiaoqin Huang (Thu Mar 20 2003 - 07:38:24 CST)
Re: a question about simulation at high temperature Carlos Simmerling (Thu Mar 20 2003 - 13:25:19 CST)
a question about simulation at high temperature Xiaoqin Huang (Thu Mar 20 2003 - 11:24:18 CST)
doubts thenmalar rathinavelan (Thu Mar 20 2003 - 22:26:50 CST)
Re: AMBER6 in Solaris 8 S.Swaminathan (Fri Mar 21 2003 - 12:37:45 CST)
reg. problem with SM and ICE libraries S.Swaminathan (Fri Mar 21 2003 - 14:56:59 CST)
Re: AMBER6 in Solaris 8 Sanjeev B.S. (Fri Mar 21 2003 - 03:44:37 CST)
MM-PBSA results Thomas Steinbrecher (Fri Mar 21 2003 - 07:15:25 CST)
Script and MPICH FyD (Fri Mar 21 2003 - 08:01:40 CST)
MM_PBSA (Amber7) and delphi Sue Heavner (Fri Mar 21 2003 - 08:27:00 CST)
amber7 on sgi Wiktor Jurkowski (Fri Mar 21 2003 - 08:26:54 CST)
RE: doubts Yong Duan (Fri Mar 21 2003 - 08:30:59 CST)
ptraj html documentation still available? Vlad Cojocaru (Fri Mar 21 2003 - 08:39:08 CST)
Hbond analysis with Carnal Vlad Cojocaru (Fri Mar 21 2003 - 08:50:36 CST)
Re: MM_PBSA (Amber7) and delphi CUI, Guanglei (Fri Mar 21 2003 - 09:04:04 CST)
Helical Drift Gemma Kinsella (Fri Mar 21 2003 - 10:55:17 CST)
waterbox GUILLERMINA L ESTIU (Fri Mar 21 2003 - 16:22:41 CST)
Re: waterbox caldwell_at_heimdal.compchem.ucsf.edu (Fri Mar 21 2003 - 16:31:07 CST)
Re: waterbox caldwell_at_heimdal.compchem.ucsf.edu (Fri Mar 21 2003 - 17:33:31 CST)
Re: doubts David A. Case (Sat Mar 22 2003 - 10:56:11 CST)
writing mol2 files using antechamber Giulio Rastelli (Sat Mar 22 2003 - 17:41:41 CST)
Re: writing mol2 files using antechamber David A. Case (Sat Mar 22 2003 - 12:08:29 CST)
format of 'mask' in ptraj Jiyoung Heo (Mon Mar 24 2003 - 00:46:18 CST)
Re: format of 'mask' in ptraj Jose Ramon Blas (Mon Mar 24 2003 - 10:14:33 CST)
RMS in carnal Shunzhou Wan (Mon Mar 24 2003 - 05:12:53 CST)
Protein-Inhibitor binding afinity William Wei (Mon Mar 24 2003 - 12:02:04 CST)
improper torsion for X -CB-CB-X yuann (Mon Mar 24 2003 - 21:23:33 CST)
Re: improper torsion for X -CB-CB-X Scott Brozell (Mon Mar 24 2003 - 22:16:13 CST)
Re: improper torsion for X -CB-CB-X sychen (Mon Mar 24 2003 - 23:16:17 CST)
abt. Plastocyanin tutorial S.Swaminathan (Tue Mar 25 2003 - 12:51:50 CST)
problem with "Example 3" tutorials S.Swaminathan (Tue Mar 25 2003 - 16:39:23 CST)
Antechamber atom types Simon Lenzen (Tue Mar 25 2003 - 04:41:30 CST)
antechamber -rn keyword Giulio Rastelli (Tue Mar 25 2003 - 17:06:48 CST)
PME cutoff box size kbyun_at_wesleyan.edu (Tue Mar 25 2003 - 11:24:07 CST)
Re: PME cutoff box size darden (Tue Mar 25 2003 - 13:49:57 CST)
hydration site yuan bo (Tue Mar 25 2003 - 20:33:31 CST)
SANDER vs GIBBS equilibration Sophia Kondratova (Wed Mar 26 2003 - 07:44:39 CST)
tleap in large systems GUILLERMINA L ESTIU (Wed Mar 26 2003 - 10:36:11 CST)
extracting structures Venkata S Koppuravuri (Wed Mar 26 2003 - 11:16:17 CST)
Extracting structures Venkata S Koppuravuri (Wed Mar 26 2003 - 11:20:51 CST)
Re: problem with "Example 3" tutorials Venkata S Koppuravuri (Wed Mar 26 2003 - 11:35:11 CST)
Neutral Arginine Joseph Nachman (Wed Mar 26 2003 - 15:00:54 CST)
Glycerol Parameters Gustavo A. Carri (Wed Mar 26 2003 - 18:20:55 CST)
How to do with two MG2+ ions? Yuhui Cheng (Wed Mar 26 2003 - 22:29:49 CST)
Re: Extracting structures Jose Ramon Blas (Thu Mar 27 2003 - 10:18:31 CST)
unit of energy Monica (Thu Mar 27 2003 - 02:01:56 CST)
how to generate FF of DNA complex? tang kwa (Thu Mar 27 2003 - 09:43:47 CST)
Install Amber 7 Wen Li (Thu Mar 27 2003 - 10:01:10 CST)
Install Amber 7 Wen Li (Thu Mar 27 2003 - 10:05:53 CST)
Disulphide bridges Vlad Cojocaru (Thu Mar 27 2003 - 11:10:24 CST)
CHARMm force field for AMBER kbyun_at_wesleyan.edu (Thu Mar 27 2003 - 11:18:17 CST)
Re: Disulphide bridges caldwell_at_heimdal.compchem.ucsf.edu (Thu Mar 27 2003 - 12:05:06 CST)
Re: tleap in large systems David A. Case (Thu Mar 27 2003 - 14:43:01 CST)
Re: SANDER vs GIBBS equilibration David A. Case (Thu Mar 27 2003 - 14:44:08 CST)
Re: SANDER vs GIBBS equilibration Carlos Simmerling (Thu Mar 27 2003 - 14:58:58 CST)
Re: tleap in large systems GUILLERMINA L ESTIU (Thu Mar 27 2003 - 14:57:21 CST)
Antechamber questions Scott Shandler (Thu Mar 27 2003 - 19:35:32 CST)
Re: problem with "Example 3" tutorials S.Swaminathan (Fri Mar 28 2003 - 13:41:20 CST)
sander outputs S.Swaminathan (Fri Mar 28 2003 - 13:47:18 CST)
Parameters for Cy3 and Fluorescein Vlad Cojocaru (Fri Mar 28 2003 - 06:27:14 CST)
Summary: Protein-Inhibitor binding affinity William Wei (Fri Mar 28 2003 - 08:51:30 CST)
ambpdb GUILLERMINA L ESTIU (Fri Mar 28 2003 - 11:05:09 CST)
Re: ambpdb David A. Case (Fri Mar 28 2003 - 12:42:34 CST)
Re: antechamber -rn keyword David A. Case (Fri Mar 28 2003 - 13:54:46 CST)
Re: Antechamber questions David A. Case (Fri Mar 28 2003 - 13:58:00 CST)
Antechamber Manual Nicholson, James D Mr ARO (Fri Mar 28 2003 - 14:17:12 CST)
Re: sander outputs Holger Gohlke (Fri Mar 28 2003 - 18:26:10 CST)
Re: unit of energy Holger Gohlke (Fri Mar 28 2003 - 18:36:02 CST)
amber BlackLoveliness_at_aol.com (Sun Mar 30 2003 - 22:47:47 CST)
Re: Antechamber questions Scott Shandler (Mon Mar 31 2003 - 17:42:35 CST)
Examples for Energy Minimisation methods S.Swaminathan (Tue Apr 01 2003 - 14:35:41 CST)
Polarizable simulation2 Lepsa (Tue Apr 01 2003 - 06:25:22 CST)
Problem of Hbond in CARNAL yuann (Tue Apr 01 2003 - 06:08:59 CST)
Re: Problem of Hbond in CARNAL sychen (Tue Apr 01 2003 - 08:23:11 CST)
size of a simulation system Wen Li (Tue Apr 01 2003 - 09:49:42 CST)
Re: Examples for Energy Minimisation methods Carlos P. Sosa (Tue Apr 01 2003 - 12:08:27 CST)
AMBER pdb help - lost atoms kxg2248_at_njit.edu (Tue Apr 01 2003 - 13:39:27 CST)
Re: AMBER pdb help - lost atoms David A. Case (Tue Apr 01 2003 - 14:19:35 CST)
Re: size of a simulation system David A. Case (Tue Apr 01 2003 - 15:44:14 CST)
Re: Polarizable simulation2 David A. Case (Tue Apr 01 2003 - 15:49:39 CST)
Re: AMBER pdb help - lost atoms Ioana Cozmuta (Tue Apr 01 2003 - 16:21:46 CST)
RE: size of a simulation system Kristina Furse (Tue Apr 01 2003 - 16:36:01 CST)
Re: AMBER pdb help - lost atoms David A. Case (Tue Apr 01 2003 - 20:17:41 CST)
A weird antechamber error Yuhui Cheng (Tue Apr 01 2003 - 22:21:46 CST)
About electrostatic force calculations Soonmin Jang (Tue Apr 01 2003 - 23:58:38 CST)
old prmtop format in AMBER 6 differs from what is presented in AMBER 7 manual Filip RyjXcek (Wed Apr 02 2003 - 06:29:07 CST)
Re: size of a simulation system Pratul Agarwal (Wed Apr 02 2003 - 08:32:44 CST)
Re: A weird antechamber error David A. Case (Wed Apr 02 2003 - 09:24:12 CST)
Re: size of a simulation system Ioana Cozmuta (Wed Apr 02 2003 - 12:37:40 CST)
Using MPI, PBS Venkata S Koppuravuri (Wed Apr 02 2003 - 12:58:23 CST)
Re: Using MPI, PBS Ioana Cozmuta (Wed Apr 02 2003 - 13:13:01 CST)
Re: Using MPI, PBS Carlos Simmerling (Wed Apr 02 2003 - 13:29:41 CST)
(no subject) dicksmit_at_umich.edu (Wed Apr 02 2003 - 13:32:37 CST)
Re: size of a simulation system Pratul Agarwal (Wed Apr 02 2003 - 14:02:29 CST)
Beyond 1,000,000 atoms Vlad (Wed Apr 02 2003 - 16:45:21 CST)
Side-chain/main-chain decomposition in MM-GBSA Lepsa (Thu Apr 03 2003 - 02:24:35 CST)
Hydrogen bond energy Dr.K.Veluraja (Thu Apr 03 2003 - 04:37:02 CST)
Unit of velocity A. Hungie (Thu Apr 03 2003 - 07:38:59 CST)
AMBER pdb help - lost atoms - Part 2 kxg2248_at_njit.edu (Thu Apr 03 2003 - 09:39:23 CST)
Re: Unit of velocity David A. Case (Thu Apr 03 2003 - 11:18:11 CST)
Re: AMBER pdb help - lost atoms - Part 2 David A. Case (Thu Apr 03 2003 - 11:23:41 CST)
Re: Hydrogen bond energy David A. Case (Thu Apr 03 2003 - 11:26:04 CST)
Re: Unit of velocity A. Hungie (Thu Apr 03 2003 - 11:46:18 CST)
Re: AMBER pdb help - lost atoms - Part 2 kxg2248_at_njit.edu (Thu Apr 03 2003 - 11:50:29 CST)
New Machine.sgi_mpi file Roberto Gomperts (Thu Apr 03 2003 - 12:33:35 CST)
frcmod file Wen Li (Thu Apr 03 2003 - 14:04:34 CST)
anal question Hai-Long Wang (Thu Apr 03 2003 - 15:48:11 CST)
Re: Side-chain/main-chain decomposition in MM-GBSA Holger Gohlke (Thu Apr 03 2003 - 16:46:52 CST)
general minimisation methods S.Swaminathan (Fri Apr 04 2003 - 18:26:48 CST)
ptraj problem Sophia Kondratova (Fri Apr 04 2003 - 08:00:46 CST)
frcmod file for Free energy perturbation tutorial of valine to alanine dicksmit_at_umich.edu (Fri Apr 04 2003 - 12:06:37 CST)
free energy calculations Joseph Fernandez (Fri Apr 04 2003 - 15:18:25 CST)
Re: sander & prmtop file generated from antechamber input ? sychen (Sun Apr 06 2003 - 11:12:44 CDT)
Re: sander & prmtop file generated from antechamber input ? David A. Case (Mon Apr 07 2003 - 00:28:58 CDT)
please kindly help S.Swaminathan (Mon Apr 07 2003 - 21:03:34 CDT)
(no subject) Carolina Salvador-Morales (Mon Apr 07 2003 - 08:22:27 CDT)
Re: please kindly help David A. Case (Mon Apr 07 2003 - 10:34:21 CDT)
growing side chains Robert G. Endres (Mon Apr 07 2003 - 13:37:30 CDT)
Nitro group introduction in tyrosine residue chandran karunakaran (Mon Apr 07 2003 - 14:23:33 CDT)
a-Helix direction? William Wei (Mon Apr 07 2003 - 15:26:40 CDT)
Trouble with AMBER 7 Shafinaz (Mon Apr 07 2003 - 15:59:52 CDT)
protonate S.Swaminathan (Tue Apr 08 2003 - 14:14:50 CDT)
problem with tleap S.Swaminathan (Tue Apr 08 2003 - 20:56:44 CDT)
addles Anonymous (Tue Apr 08 2003 - 11:56:44 CDT)
very important Shafinaz (Tue Apr 08 2003 - 09:19:18 CDT)
Re: very important CUI, Guanglei (Tue Apr 08 2003 - 09:47:55 CDT)
mm_pbsa & nmode FyD (Tue Apr 08 2003 - 10:04:38 CDT)
Re: protonate David A. Case (Tue Apr 08 2003 - 11:06:21 CDT)
mutating residues Craig A Bayse (Tue Apr 08 2003 - 11:09:38 CDT)
Re: problem with tleap David A. Case (Tue Apr 08 2003 - 11:12:34 CDT)
The error in the trajectory file Ling Zhang (Tue Apr 08 2003 - 11:37:58 CDT)
question about MM-PBSA? Lishan Yao (Tue Apr 08 2003 - 12:21:20 CDT)
characteristics of nucleic acids homopolymers Ioana Cozmuta (Tue Apr 08 2003 - 13:33:03 CDT)
Groups defenition Javier Cuervo (Tue Apr 08 2003 - 15:31:27 CDT)
Periodic Boundary Condition in AMBER7 (the sander module)! Dat H. Nguyen (Tue Apr 08 2003 - 16:44:37 CDT)
Re: Periodic Boundary Condition in AMBER7 (the sander module)! David A. Case (Tue Apr 08 2003 - 17:25:53 CDT)
Tleap chandran karunakaran (Tue Apr 08 2003 - 18:01:21 CDT)
nmode for S calculation wentaofu (Tue Apr 08 2003 - 18:22:47 CDT)
Trying to understand parm99.dat Sichun Yang (Tue Apr 08 2003 - 19:44:32 CDT)
Re: Tleap David A. Case (Tue Apr 08 2003 - 20:09:46 CDT)
RE: Trying to understand parm99.dat Yong Duan (Tue Apr 08 2003 - 20:48:48 CDT)
Re: Groups defenition David A. Case (Wed Apr 09 2003 - 10:59:11 CDT)
SANDER Source Code Documentation Jones, Garth A (Thu Apr 10 2003 - 02:07:13 CDT)
Amber7 and mpirun on Linux Wen Li (Thu Apr 10 2003 - 13:14:59 CDT)
Re: Amber7 and mpirun on Linux Scott Brozell (Thu Apr 10 2003 - 14:28:00 CDT)
free energy in sander Joseph Fernandez (Thu Apr 10 2003 - 16:32:52 CDT)
Re: free energy in sander David A. Case (Thu Apr 10 2003 - 17:45:05 CDT)
Re: Tleap-metalloprotein chandran karunakaran (Thu Apr 10 2003 - 20:20:40 CDT)
RE: Tleap-metalloprotein Yong Duan (Thu Apr 10 2003 - 21:42:53 CDT)
Re: free energy in sander Joseph Fernandez (Thu Apr 10 2003 - 21:58:30 CDT)
RE: Amber7 and mpirun on Linux Francesc Corcho (Fri Apr 11 2003 - 06:28:32 CDT)
Bugfixes Francesc Corcho (Fri Apr 11 2003 - 06:40:08 CDT)
Re: Bugfixes Natasja Brooijmans (Fri Apr 11 2003 - 11:49:59 CDT)
RE: Amber7 and mpirun on Linux Scott Brozell (Fri Apr 11 2003 - 14:40:38 CDT)
SSBonds and charge problems Steve Seibold (Fri Apr 11 2003 - 14:54:23 CDT)
Re: SSBonds and charge problems caldwell_at_heimdal.compchem.ucsf.edu (Fri Apr 11 2003 - 14:50:04 CDT)
Re: SSBonds and charge problems David A. Case (Sat Apr 12 2003 - 00:29:53 CDT)
Amber on Linux Wen Li (Sat Apr 12 2003 - 12:00:46 CDT)
Re: Amber on Linux Viktor Hornak (Sat Apr 12 2003 - 18:41:41 CDT)
Re: Amber on Linux Wen Li (Sun Apr 13 2003 - 10:06:52 CDT)
ALA-scan problem with mm_pbsa.pl Natasja Brooijmans (Sun Apr 13 2003 - 17:21:03 CDT)
diffusion coefficients yuan bo (Sun Apr 13 2003 - 21:34:25 CDT)
RE: diffusion coefficients Yong Duan (Sun Apr 13 2003 - 22:50:48 CDT)
Re: diffusion coefficients David A. Case (Mon Apr 14 2003 - 01:03:15 CDT)
A problem in Sander production dynamics yuann (Mon Apr 14 2003 - 03:37:50 CDT)
Re: A problem in Sander production dynamics Carlos Simmerling (Mon Apr 14 2003 - 06:21:04 CDT)
Re: addles Carlos Simmerling (Mon Apr 14 2003 - 11:22:29 CDT)
Re: A problem in Sander production dynamics Thomas Cheatham (Mon Apr 14 2003 - 16:24:31 CDT)
Re: diffusion coefficients Thomas Cheatham (Mon Apr 14 2003 - 16:34:39 CDT)
id_torus(): Could not find torus for atoms 1878 and 1894 Yunfeng Hu (Mon Apr 14 2003 - 17:26:18 CDT)
Metalloprotein chandran karunakaran (Mon Apr 14 2003 - 20:18:39 CDT)
A problem in opening the file Khanh.Dao_at_iac.uib.no (Tue Apr 15 2003 - 00:01:11 CDT)
Re: A problem in opening the file David A. Case (Tue Apr 15 2003 - 01:50:04 CDT)
Re: A problem in opening the file Khanh.Dao_at_iac.uib.no (Tue Apr 15 2003 - 02:19:58 CDT)
PME box information Khanh.Dao_at_iac.uib.no (Tue Apr 15 2003 - 04:56:38 CDT)
solvents aren't loading Mac Brown (Tue Apr 15 2003 - 15:20:15 CDT)
Proper Restraint usage Steve Seibold (Tue Apr 15 2003 - 15:42:59 CDT)
Re: Proper Restraint usage David A. Case (Tue Apr 15 2003 - 16:04:50 CDT)
Re: Proper Restraint usage CUI, Guanglei (Tue Apr 15 2003 - 16:30:22 CDT)
ibelly and ntr Youyi Peng (Tue Apr 15 2003 - 16:59:59 CDT)
Re: ibelly and ntr David A. Case (Tue Apr 15 2003 - 18:13:11 CDT)
AMBER chandran karunakaran (Tue Apr 15 2003 - 18:55:16 CDT)
Re: AMBER CUI, Guanglei (Tue Apr 15 2003 - 19:32:12 CDT)
Re: AMBER David A. Case (Tue Apr 15 2003 - 19:38:59 CDT)
ambpdb Youyi Peng (Tue Apr 15 2003 - 20:32:22 CDT)
Re: AMBER chandran karunakaran (Tue Apr 15 2003 - 20:25:08 CDT)
No statistical output for MM-PBSA? Lishan Yao (Tue Apr 15 2003 - 21:25:22 CDT)
Re: ibelly and ntr sychen (Tue Apr 15 2003 - 22:03:57 CDT)
Re: ambpdb Luis Gracia (Tue Apr 15 2003 - 23:40:57 CDT)
Re: ambpdb Florian Barth (Wed Apr 16 2003 - 06:59:42 CDT)
CYS and HIS Youyi Peng (Wed Apr 16 2003 - 09:20:40 CDT)
Re: CYS and HIS caldwell_at_heimdal.compchem.ucsf.edu (Wed Apr 16 2003 - 09:55:55 CDT)
MPI run problem William Wei (Wed Apr 16 2003 - 11:36:31 CDT)
velocity auto-correlation function A. Hungie (Wed Apr 16 2003 - 11:25:32 CDT)
Re: ALA-scan problem with mm_pbsa.pl Holger Gohlke (Wed Apr 16 2003 - 12:40:44 CDT)
Re: No statistical output for MM-PBSA? Holger Gohlke (Wed Apr 16 2003 - 13:05:38 CDT)
Re: ALA-scan problem with mm_pbsa.pl Natasja Brooijmans (Wed Apr 16 2003 - 13:14:55 CDT)
RE: ibelly and ntr Kristina Furse (Wed Apr 16 2003 - 14:51:43 CDT)
Adding ACE to chopped protein Karl N. Kirschner (Wed Apr 16 2003 - 15:08:45 CDT)
Re: CCL:MPI run problem Carlos Simmerling (Wed Apr 16 2003 - 15:26:42 CDT)
makeDIST_RST Youyi Peng (Wed Apr 16 2003 - 21:24:19 CDT)
ambpdb and protonate in AMBER7 Francisco Blanco (Thu Apr 17 2003 - 06:38:29 CDT)
Organic solvents Carlos P. Sosa (Thu Apr 17 2003 - 10:17:54 CDT)
Re: makeDIST_RST David A. Case (Thu Apr 17 2003 - 11:50:14 CDT)
quasih cailliez (Thu Apr 17 2003 - 10:35:26 CDT)
question about MM-PBSA? Lishan Yao (Thu Apr 17 2003 - 14:15:38 CDT)
topology file in large systems GUILLERMINA L ESTIU (Thu Apr 17 2003 - 16:58:35 CDT)
Re: topology file in large systems caldwell_at_heimdal.compchem.ucsf.edu (Thu Apr 17 2003 - 17:25:49 CDT)
Re: question about MM-PBSA? Holger Gohlke (Thu Apr 17 2003 - 20:31:31 CDT)
Re: question about MM-PBSA? Lishan Yao (Fri Apr 18 2003 - 09:10:24 CDT)
MD went crazy Youyi Peng (Fri Apr 18 2003 - 10:20:25 CDT)
Re: MD went crazy Carlos Simmerling (Fri Apr 18 2003 - 10:20:07 CDT)
Re: MD went crazy Youyi Peng (Fri Apr 18 2003 - 11:17:24 CDT)
Re: ambpdb Venkata S Koppuravuri (Fri Apr 18 2003 - 11:14:34 CDT)
Re: MD went crazy Carlos Simmerling (Fri Apr 18 2003 - 11:17:11 CDT)
Re: MD went crazy Youyi Peng (Fri Apr 18 2003 - 12:36:35 CDT)
Re: MD went crazy Michael Crowley (Fri Apr 18 2003 - 12:30:53 CDT)
Re: MD went crazy Carlos Simmerling (Fri Apr 18 2003 - 12:31:41 CDT)
Re: MD went crazy Youyi Peng (Fri Apr 18 2003 - 13:33:26 CDT)
Re: MD went crazy Youyi Peng (Fri Apr 18 2003 - 13:55:51 CDT)
Re: MD went crazy Carlos Simmerling (Fri Apr 18 2003 - 14:04:49 CDT)
Re: MD went crazy Youyi Peng (Fri Apr 18 2003 - 14:28:14 CDT)
MM-GBSA question Javier Cuervo (Fri Apr 18 2003 - 15:39:23 CDT)
debug leap vze6jslz_at_verizon.net (Sat Apr 19 2003 - 13:52:40 CDT)
Re: debug leap Scott Brozell (Sat Apr 19 2003 - 18:40:03 CDT)
AMBER chandran karunakaran (Sun Apr 20 2003 - 20:13:32 CDT)
(no subject) Khanh.Dao_at_iac.uib.no (Mon Apr 21 2003 - 11:35:02 CDT)
trouble with OFF files Mac Brown (Mon Apr 21 2003 - 14:07:32 CDT)
Re: trouble with OFF files M. L. Dodson (Mon Apr 21 2003 - 15:13:24 CDT)
Problem Finishing Tutorial Derek Smith (Mon Apr 21 2003 - 18:31:00 CDT)
Re: Problem Finishing Tutorial Ioana Cozmuta (Mon Apr 21 2003 - 18:41:13 CDT)
Re: question about MM-PBSA? Lepsa (Tue Apr 22 2003 - 01:50:42 CDT)
Re: Fwd: Re: Request for Amber7 (fwd) Rajendra P. OJHA (Tue Apr 22 2003 - 04:53:12 CDT)
Organic Solvents Petrodler_at_aol.com (Tue Apr 22 2003 - 05:57:11 CDT)
Re: Organic Solvents Jose Ramon Blas (Tue Apr 22 2003 - 17:00:58 CDT)
How to use GLYCAM force field in AMBER Peng Tao (Tue Apr 22 2003 - 10:08:06 CDT)
mm_pbsa_statistics.pm kbyun_at_wesleyan.edu (Tue Apr 22 2003 - 11:40:10 CDT)
Re: Request for Amber7 (xleap problem) John Bushnell (Tue Apr 22 2003 - 17:30:41 CDT)
converting amber to gromos format Jake Isaacs (Wed Apr 23 2003 - 08:59:19 CDT)
GB/SA Robert G. Endres (Wed Apr 23 2003 - 11:26:14 CDT)
mm_pbsa nmode calculation kbyun_at_wesleyan.edu (Wed Apr 23 2003 - 13:33:17 CDT)
anyone have AMBER benchmarks with gigabit ethernet? Carlos Simmerling (Wed Apr 23 2003 - 13:37:07 CDT)
Re: mm_pbsa nmode calculation Holger Gohlke (Wed Apr 23 2003 - 14:12:51 CDT)
Re: GB/SA David A. Case (Wed Apr 23 2003 - 14:36:56 CDT)
Re: mm_pbsa nmode calculation kbyun_at_wesleyan.edu (Wed Apr 23 2003 - 15:33:55 CDT)
Re: How to use GLYCAM force field in AMBER David A. Case (Wed Apr 23 2003 - 16:51:30 CDT)
leap problem yuan bo (Wed Apr 23 2003 - 22:49:36 CDT)
Problem_to_open_PROTON_INFO_file Khanh.Dao_at_iac.uib.no (Thu Apr 24 2003 - 03:46:10 CDT)
RE: anyone have AMBER benchmarks with gigabit ethernet? Ross Walker (Thu Apr 24 2003 - 04:42:57 CDT)
RE: anyone have AMBER benchmarks with gigabit ethernet? Ross Walker (Thu Apr 24 2003 - 08:20:07 CDT)
Re: Problem_to_open_PROTON_INFO_file David A. Case (Thu Apr 24 2003 - 10:30:32 CDT)
non bonded pair list Jean-François Taly (Thu Apr 24 2003 - 11:22:08 CDT)
Question: Nmode with counter ions. Masaki Tomimoto (Thu Apr 24 2003 - 12:09:02 CDT)
PSC Summer Workshop: Modeling from Protein Sequence to Structure Troy Wymore (Thu Apr 24 2003 - 12:33:39 CDT)
job stopped Youyi Peng (Thu Apr 24 2003 - 12:52:12 CDT)
Re: job stopped CUI, Guanglei (Thu Apr 24 2003 - 13:06:25 CDT)
Re: job stopped Youyi Peng (Thu Apr 24 2003 - 13:49:47 CDT)
Re: job stopped Natasja Brooijmans (Thu Apr 24 2003 - 13:55:06 CDT)
Future of structural biology conference David Cowburn (Thu Apr 24 2003 - 13:58:23 CDT)
Annealing blown up Nick Polfer (Thu Apr 24 2003 - 14:02:38 CDT)
Re: Problem_to_open_PROTON_INFO_file Venkata S Koppuravuri (Thu Apr 24 2003 - 14:43:59 CDT)
Re: job stopped Youyi Peng (Thu Apr 24 2003 - 15:33:37 CDT)
Re: job stopped CUI, Guanglei (Thu Apr 24 2003 - 15:32:29 CDT)
Re: Question: Nmode with counter ions. David A. Case (Thu Apr 24 2003 - 18:16:22 CDT)
Re: Annealing blown up David A. Case (Thu Apr 24 2003 - 18:21:53 CDT)
Re: non bonded pair list David A. Case (Thu Apr 24 2003 - 18:24:37 CDT)
question about H-bond in carnal? Lishan Yao (Fri Apr 25 2003 - 09:44:55 CDT)
Re: question about H-bond in carnal? Sanjeev B.S. (Fri Apr 25 2003 - 10:35:58 CDT)
Re: question about H-bond in carnal? Lishan Yao (Fri Apr 25 2003 - 10:24:56 CDT)
Re: question about H-bond in carnal? Sanjeev B.S. (Fri Apr 25 2003 - 10:53:35 CDT)
Re: question about H-bond in carnal? Bill Ross (Fri Apr 25 2003 - 13:57:20 CDT)
nmode and mm_pbsa questions? wentaofu (Fri Apr 25 2003 - 15:47:48 CDT)
Re: nmode and mm_pbsa questions? Holger Gohlke (Fri Apr 25 2003 - 17:21:05 CDT)
Re: question about H-bond in carnal? Lishan Yao (Sun Apr 27 2003 - 19:37:13 CDT)
troubles on RS6000 Wayne Dawson (Mon Apr 28 2003 - 04:37:50 CDT)
Re: GB/SA Robert G. Endres (Mon Apr 28 2003 - 13:10:56 CDT)
how to restrain base pair Shuang Ding (Mon Apr 28 2003 - 13:59:58 CDT)
Re: how to restrain base pair David A. Case (Mon Apr 28 2003 - 14:14:49 CDT)
Amber on Parallel Sun? Bengt Svensson (Mon Apr 28 2003 - 16:59:14 CDT)
Protein - DNA complex simulation - protocol Harikrishnan (Mon Apr 28 2003 - 23:40:39 CDT)
problem_namelist_reading Khanh.Dao_at_iac.uib.no (Tue Apr 29 2003 - 01:19:46 CDT)
Re: question about H-bond in carnal? Sanjeev B.S. (Tue Apr 29 2003 - 01:59:15 CDT)
Re: Protein - DNA complex simulation - protocol Andreas Svrcek-Seiler (Tue Apr 29 2003 - 03:50:22 CDT)
any one has references to parallelization aspects of AMBER Satish Kumar (Tue Apr 29 2003 - 04:59:05 CDT)
Re: any one has references to parallelization aspects of AMBER Harikrishnan (Tue Apr 29 2003 - 06:54:51 CDT)
atom position restraints Yuuki Komata (Tue Apr 29 2003 - 07:44:25 CDT)
Re: Protein - DNA complex simulation - protocol Harikrishnan (Tue Apr 29 2003 - 08:16:25 CDT)
force field parameters for phosphoserine Christoph Kluck (Tue Apr 29 2003 - 09:07:59 CDT)
Re: Protein - DNA complex simulation - protocol Pratul Agarwal (Tue Apr 29 2003 - 09:39:18 CDT)
Re: force field parameters for phosphoserine David A. Case (Tue Apr 29 2003 - 09:56:48 CDT)
Re: problem_namelist_reading David A. Case (Tue Apr 29 2003 - 10:12:01 CDT)
Description of ATOM type in GLYCAM Peng Tao (Tue Apr 29 2003 - 14:14:52 CDT)
Re: Description of ATOM type in GLYCAM FyD (Tue Apr 29 2003 - 16:07:35 CDT)
phi and psi angles analysis Xiao Jian Tan (Tue Apr 29 2003 - 18:27:17 CDT)
Re: phi and psi angles analysis Holger Gohlke (Tue Apr 29 2003 - 18:48:50 CDT)
about molecular dynamics ronnie (Tue Apr 29 2003 - 20:09:25 CDT)
Re: about molecular dynamics Carlos Simmerling (Tue Apr 29 2003 - 20:14:39 CDT)
atom position restraints Yuuki Komata (Tue Apr 29 2003 - 20:34:06 CDT)
Re: phi and psi angles analysis Guanglei Cui (Tue Apr 29 2003 - 22:31:11 CDT)
Re: about molecular dynamics Carlos Simmerling (Tue Apr 29 2003 - 22:30:06 CDT)
Re: problem_namelist_reading Khanh.Dao_at_iac.uib.no (Wed Apr 30 2003 - 00:26:58 CDT)
Residual dipolar couplings McAteer, Kathleen (Wed Apr 30 2003 - 12:56:34 CDT)
Re: GB/SA Robert G. Endres (Wed Apr 30 2003 - 14:57:31 CDT)
problem about virtual box? Youyi Peng (Thu May 01 2003 - 10:49:00 CDT)
Re: problem about virtual box? Carlos Simmerling (Thu May 01 2003 - 10:46:05 CDT)
Ewald: coeff, error estimate Paula Petrone (Thu May 01 2003 - 11:05:28 CDT)
Re: problem about virtual box? pengyo_at_rwja.umdnj.edu (Thu May 01 2003 - 11:20:10 CDT)
Re: problem about virtual box? Thomas Cheatham (Thu May 01 2003 - 12:07:52 CDT)
Re: problem about virtual box? Youyi Peng (Thu May 01 2003 - 12:42:47 CDT)
Re: problem about virtual box? Thomas E. Cheatham, III (Thu May 01 2003 - 12:33:49 CDT)
Simple math of memory calculation for nmode Masaki Tomimoto (Thu May 01 2003 - 13:26:08 CDT)
problem on MD simulation of damage DNA Shuang Ding (Thu May 01 2003 - 15:11:04 CDT)
Re: problem on MD simulation of damage DNA Carlos Simmerling (Thu May 01 2003 - 15:20:02 CDT)
Re: Ewald: coeff, error estimate darden (Thu May 01 2003 - 16:30:48 CDT)
carnal hbond Hai-Long Wang (Wed Apr 30 2003 - 13:03:39 CDT)
Re: Simple math of memory calculation for nmode David A. Case (Thu May 01 2003 - 19:23:06 CDT)
Questoin about temperature Maverick (Fri May 02 2003 - 00:27:29 CDT)
initial velocity Youyi Peng (Fri May 02 2003 - 09:22:52 CDT)
Re: initial velocity Natasja Brooijmans (Fri May 02 2003 - 09:18:26 CDT)
Re: initial velocity Carlos Simmerling (Fri May 02 2003 - 09:20:09 CDT)
Question about BELLY NMODE Masaki Tomimoto (Fri May 02 2003 - 10:30:36 CDT)
RE: Question about BELLY NMODE Masaki Tomimoto (Fri May 02 2003 - 10:46:36 CDT)
Re: Residual dipolar couplings David A. Case (Fri May 02 2003 - 12:21:53 CDT)
Help with Sander test output error Donald Keidel (Fri May 02 2003 - 12:38:11 CDT)
multiple timesteps Ioana Cozmuta (Fri May 02 2003 - 17:41:51 CDT)
upper limited of memory for nmode wentaofu (Fri May 02 2003 - 19:06:06 CDT)
(no subject) Narang Manpreet Kaur (Sat May 03 2003 - 00:02:20 CDT)
(no subject) smolnar_at_jadeinc.com (Sat May 03 2003 - 13:19:25 CDT)
Latest Leap Compile Errors smolnar_at_jadeinc.com (Sun May 04 2003 - 06:44:50 CDT)
Re: Latest Leap Compile Errors David A. Case (Sun May 04 2003 - 16:02:05 CDT)
SPC/E water model Ioana Cozmuta (Sun May 04 2003 - 16:38:06 CDT)
SPC/E model -LJ parameters Ioana Cozmuta (Sun May 04 2003 - 16:55:53 CDT)
Re: SPC/E water model Holger Gohlke (Sun May 04 2003 - 18:27:01 CDT)
can not minimize tang kwa (Mon May 05 2003 - 06:57:42 CDT)
Re: can not minimize Carlos Simmerling (Mon May 05 2003 - 07:00:04 CDT)
Re: Latest Leap Compile Errors Stephen P. Molnar, Ph.D. (Mon May 05 2003 - 08:18:35 CDT)
Re: can not minimize Guanglei Cui (Mon May 05 2003 - 08:42:37 CDT)
Re: can not minimize tang kwa (Mon May 05 2003 - 08:49:31 CDT)
Re: can not minimize tang kwa (Mon May 05 2003 - 08:57:40 CDT)
Re: can not minimize Guanglei Cui (Mon May 05 2003 - 09:07:39 CDT)
Re: can not minimize tang kwa (Mon May 05 2003 - 09:45:24 CDT)
minimizaiton in vacuum David A. Case (Mon May 05 2003 - 11:01:16 CDT)
how to set up a carbon nanotube pdb file zhaoxc_at_puccini.che.pitt.edu (Mon May 05 2003 - 16:24:10 CDT)
ANAL in AMBER A.Madhumalar (Tue May 06 2003 - 02:25:05 CDT)
saveAmberParm problems in xleap Wayne Dawson (Tue May 06 2003 - 03:14:58 CDT)
Re: minimizaiton in vacuum tang kwa (Tue May 06 2003 - 07:17:03 CDT)
minimization with restraints A. Hungie (Tue May 06 2003 - 07:57:22 CDT)
Re: minimization with restraints Carlos Simmerling (Tue May 20 2003 - 08:42:43 CDT)
Re: saveAmberParm problems in xleap caldwell_at_heimdal.compchem.ucsf.edu (Tue May 06 2003 - 07:45:36 CDT)
Re: saveAmberParm problems in xleap Guanglei Cui (Tue May 06 2003 - 08:42:13 CDT)
Re: saveAmberParm problems in xleap Wayne Dawson (Tue May 06 2003 - 12:04:19 CDT)
Pi-Pi stacking Fernando Martin (Tue May 06 2003 - 12:35:45 CDT)
Re: saveAmberParm problems in xleap Ioana Cozmuta (Tue May 06 2003 - 15:54:49 CDT)
non bonded pairlist? Arvid Soederhaell (Wed May 07 2003 - 02:34:27 CDT)
Re: SPC/E water model Ioana Cozmuta (Wed May 07 2003 - 03:53:43 CDT)
MD steps limit in sander (Amber 6) Marco Preto (Wed Oct 30 2002 - 20:09:14 CST)
Re: MD steps limit in sander (Amber 6) Carlos Simmerling (Wed May 07 2003 - 10:51:01 CDT)
Re: MD steps limit in sander (Amber 6) Marco Preto (Wed Oct 30 2002 - 21:41:01 CST)
help me switching from amber5 to amber6 Asif Rahaman (Wed May 07 2003 - 19:18:01 CDT)
Re: help me switching from amber5 to amber6 David A. Case (Wed May 07 2003 - 19:59:54 CDT)
Phosphotyrosine parametrization Obdulia Rabal (Thu May 08 2003 - 02:51:19 CDT)
Re: saveAmberParm problems in xleap Wayne Dawson (Thu May 08 2003 - 04:02:45 CDT)
current AMBER citation? Jake Isaacs (Thu May 08 2003 - 09:08:38 CDT)
RMSD fluctuation too much Youyi Peng (Thu May 08 2003 - 10:02:43 CDT)
Re: current AMBER citation? David A. Case (Thu May 08 2003 - 10:16:13 CDT)
Re: RMSD fluctuation too much Carlos Simmerling (Thu May 08 2003 - 10:26:41 CDT)
Use of Mg2+ in AMBER 7 Peter Anderson (Thu May 08 2003 - 13:55:06 CDT)
2 questions FyD (Fri May 09 2003 - 05:02:41 CDT)
Re: 2 questions Carlos Simmerling (Fri May 09 2003 - 06:08:51 CDT)
Etot is not constant in NVE ensemble A. Hungie (Fri May 09 2003 - 08:46:43 CDT)
Re: Etot is not constant in NVE ensemble darden (Fri May 09 2003 - 09:38:53 CDT)
RE: Etot is not constant in NVE ensemble Yong Duan (Fri May 09 2003 - 09:58:25 CDT)
Re: Etot is not constant in NVE ensemble Thomas Cheatham (Fri May 09 2003 - 10:49:18 CDT)
Re: 2 questions David A. Case (Fri May 09 2003 - 10:54:41 CDT)
Re: Etot is not constant in NVE ensemble A. Hungie (Fri May 09 2003 - 11:08:56 CDT)
Re: ANAL in AMBER David A. Case (Fri May 09 2003 - 11:11:33 CDT)
Re: Etot is not constant in NVE ensemble bishop (Fri May 09 2003 - 14:41:34 CDT)
What kind of interactions are ignored for end group interactions Huang Zunnan (Fri May 09 2003 - 15:41:10 CDT)
Re: What kind of interactions are ignored for end group interactions Carlos Simmerling (Fri May 09 2003 - 16:07:26 CDT)
10-12 H-bond terms Ioana Cozmuta (Fri May 09 2003 - 17:27:53 CDT)
Re: Etot is not constant in NVE ensemble darden (Fri May 09 2003 - 18:20:24 CDT)
RMSF problem yuan bo (Sat May 10 2003 - 04:31:27 CDT)
Re: 10-12 H-bond terms Andreas Svrcek-Seiler (Sat May 10 2003 - 18:13:08 CDT)
a question about scale factor Ye Mei (Sat May 10 2003 - 21:53:45 CDT)
Re: a question about scale factor Carlos Simmerling (Sat May 10 2003 - 23:00:24 CDT)
difference between iwrap and image? yuann (Sun May 11 2003 - 00:47:23 CDT)
Minimisation - peek_ewald_inpcrd: SHOULD NOT BE HERE Omar Wahab (Mon May 12 2003 - 04:49:52 CDT)
unit of vlimit? Fabian Boes (Mon May 12 2003 - 09:36:25 CDT)
Heat of Vaporization Karl N. Kirschner (Mon May 12 2003 - 09:46:17 CDT)
no MD output Youyi Peng (Mon May 12 2003 - 14:01:47 CDT)
Re: 10-12 H-bond terms Ioana Cozmuta (Mon May 12 2003 - 14:50:40 CDT)
Re: 10-12 H-bond terms David A. Case (Mon May 12 2003 - 16:58:52 CDT)
Re: 10-12 H-bond terms Ioana Cozmuta (Mon May 12 2003 - 18:32:19 CDT)
Re: no MD output Marco Preto (Wed Oct 30 2002 - 12:33:30 CST)
Simple question about sander parameter set Peng Tao (Tue May 13 2003 - 09:44:40 CDT)
Re: Simple question about sander parameter set David A. Case (Tue May 13 2003 - 10:00:22 CDT)
Re: Heat of Vaporization David A. Case (Tue May 13 2003 - 10:12:41 CDT)
Re: Simple question about sander parameter set Peng Tao (Tue May 13 2003 - 10:19:50 CDT)
re: parameters for nitro group Shixiang Yan (Tue May 13 2003 - 10:30:49 CDT)
Re: parameters for nitro group David A. Case (Tue May 13 2003 - 11:45:02 CDT)
water residence time analysis Mahadevan Seetharaman (Tue May 13 2003 - 12:18:14 CDT)
Increase lastist in the &cntrl namelist GUILLERMINA L ESTIU (Tue May 13 2003 - 13:16:09 CDT)
Re: Increase lastist in the &cntrl namelist GUILLERMINA L ESTIU (Tue May 13 2003 - 13:37:24 CDT)
Re: Increase lastist in the &cntrl namelist Ioana Cozmuta (Tue May 13 2003 - 13:58:09 CDT)
Re: Increase lastist in the &cntrl namelist Dodi Heryadi (Tue May 13 2003 - 15:14:25 CDT)
H-O-H angle Ioana Cozmuta (Tue May 13 2003 - 15:17:54 CDT)
Re: Increase lastist in the &cntrl namelist Ioana Cozmuta (Tue May 13 2003 - 15:26:48 CDT)
Re: H-O-H angle Luis Gracia (Tue May 13 2003 - 16:46:05 CDT)
Sander help tianxiao yang (Tue May 13 2003 - 18:47:17 CDT)
Re: Sander help David A. Case (Tue May 13 2003 - 19:51:12 CDT)
Re: H-O-H angle Ioana Cozmuta (Tue May 13 2003 - 23:32:17 CDT)
A question about AMBER, leaprc.ff02EP yuming chen (Wed May 14 2003 - 00:17:47 CDT)
Re: A question about AMBER, leaprc.ff02EP David A. Case (Wed May 14 2003 - 01:26:56 CDT)
Re: A question about AMBER, leaprc.ff02EP yuming chen (Wed May 14 2003 - 05:45:11 CDT)
mm_pbsa and B/Z DNA relative stabilities Peter Gannett (Wed May 14 2003 - 06:54:47 CDT)
serine/tyrosine in charged states Layi Adekoya (Wed May 14 2003 - 07:26:55 CDT)
Re: mm_pbsa and B/Z DNA relative stabilities Robert G. Endres (Wed May 14 2003 - 08:36:14 CDT)
protonate problem Venkata S Koppuravuri (Wed May 14 2003 - 12:17:39 CDT)
Re: protonate problem David A. Case (Wed May 14 2003 - 13:36:04 CDT)
Using GLYCAM in sander with a non-zero 10-12 coefficient Peng Tao (Wed May 14 2003 - 13:54:32 CDT)
Newton-Raphson minimization for large systems Qing Zhang (Wed May 14 2003 - 18:09:07 CDT)
Simulation under physiological conditions Michal Otyepka (Thu May 15 2003 - 10:02:34 CDT)
Re: Simulation under physiological conditions Michal Otyepka (Thu May 15 2003 - 10:50:44 CDT)
Re: Simulation under physiological conditions Andreas Svrcek-Seiler (Thu May 15 2003 - 11:11:13 CDT)
atomic positional fluctuation pengyo_at_rwja.umdnj.edu (Thu May 15 2003 - 13:22:25 CDT)
nucgen.dat Maria Zavodszky (Thu May 15 2003 - 13:37:14 CDT)
Re: nucgen.dat Ioana Cozmuta (Thu May 15 2003 - 15:08:50 CDT)
Re: atomic positional fluctuation Holger Gohlke (Thu May 15 2003 - 15:38:07 CDT)
using distance restraints in Sander (AIX 4.3 RS6000) Wayne Dawson (Fri May 16 2003 - 03:33:02 CDT)
ptraj generated PDB files Fabian Boes (Fri May 16 2003 - 09:01:38 CDT)
Re: ptraj generated PDB files caldwell_at_heimdal.compchem.ucsf.edu (Fri May 16 2003 - 08:07:57 CDT)
Re: ptraj generated PDB files David A. Case (Fri May 16 2003 - 10:43:34 CDT)
mm_pbsa with PBCAL = 0 wentaofu (Fri May 16 2003 - 14:14:42 CDT)
Re: using distance restraints in Sander (AIX 4.3 RS6000) David A. Case (Fri May 16 2003 - 15:42:18 CDT)
Re: mm_pbsa with PBCAL = 0 Holger Gohlke (Fri May 16 2003 - 16:34:41 CDT)
anal, amber7 and resnum 0 Sanjeev B.S. (Fri May 16 2003 - 17:15:19 CDT)
Re: anal, amber7 and resnum 0 Sanjeev B.S. (Fri May 16 2003 - 17:23:04 CDT)
Re: anal, amber7 and resnum 0 David A. Case (Fri May 16 2003 - 16:57:33 CDT)
DNA base-step distortion kbyun_at_wesleyan.edu (Sun May 18 2003 - 14:37:12 CDT)
Re: DNA base-step distortion kbyun_at_wesleyan.edu (Sun May 18 2003 - 18:43:59 CDT)
Re: DNA base-step distortion Jiri Sponer (Mon May 19 2003 - 04:56:00 CDT)
RESP, constraining Dipole Moment Artur Galstyan (Mon May 19 2003 - 05:06:51 CDT)
Mainchain.dat tang kwa (Mon May 19 2003 - 11:16:12 CDT)
force field parameters for torsions cailliez (Mon May 19 2003 - 10:19:36 CDT)
Re: force field parameters for torsions David A. Case (Mon May 19 2003 - 12:44:27 CDT)
Re: force field parameters for torsions (I am away) Charles Laughton (Mon May 19 2003 - 12:49:32 CDT)
Fluorine atom type in mm_pbsa? Lishan Yao (Mon May 19 2003 - 16:00:09 CDT)
Calcium in proteins Javier Cuervo (Mon May 19 2003 - 19:11:54 CDT)
off-diagonal VDW term Jiyoung Heo (Mon May 19 2003 - 20:01:13 CDT)
Re: off-diagonal VDW term Ioana Cozmuta (Mon May 19 2003 - 20:24:34 CDT)
RE: off-diagonal VDW term Yong Duan (Tue May 20 2003 - 02:24:25 CDT)
Re: Fluorine atom type in mm_pbsa? Lishan Yao (Tue May 20 2003 - 08:12:04 CDT)
Re: Mainchain.dat Lepsa (Tue May 20 2003 - 08:34:36 CDT)
parm99 cailliez (Tue May 20 2003 - 07:55:17 CDT)
Re: Fluorine atom type in mm_pbsa? David A. Case (Tue May 20 2003 - 09:30:53 CDT)
Re: Calcium in proteins David A. Case (Tue May 20 2003 - 09:40:06 CDT)
Re: off-diagonal VDW term David A. Case (Tue May 20 2003 - 09:43:33 CDT)
Xleap adding torsions Andrew Petersen (Tue May 20 2003 - 10:32:40 CDT)
Problem with CMC/MD Sameer P. Kawatkar (Tue May 20 2003 - 10:35:16 CDT)
a question about constructing a periodic box by PLEP. Margaret Shun Cheung (Tue May 20 2003 - 10:48:56 CDT)
Re: From Dr. Ekaterina Nikitina caldwell_at_heimdal.compchem.ucsf.edu (Tue May 20 2003 - 11:27:04 CDT)
Amber 7.xx installation on FreeBSD Joseph Maxwell (Tue May 20 2003 - 15:27:11 CDT)
Residual dipolar couplings McAteer, Kathleen (Tue May 20 2003 - 16:03:58 CDT)
Re: Amber 7.xx installation on FreeBSD M. L. Dodson (Tue May 20 2003 - 16:19:21 CDT)
Re: parm99 David A. Case (Tue May 20 2003 - 17:37:32 CDT)
Hybdrogen bonds and LJ 10-12 Michal Otyepka (Wed May 21 2003 - 04:49:47 CDT)
bad atom type f(fluorine) in MM-PBSA? Lishan Yao (Wed May 21 2003 - 08:29:01 CDT)
I still have problems with parm99.dat cailliez (Wed May 21 2003 - 08:37:19 CDT)
Re: bad atom type f(fluorine) in MM-PBSA? Holger Gohlke (Wed May 21 2003 - 10:49:20 CDT)
Re: bad atom type f(fluorine) in MM-PBSA? Lishan Yao (Wed May 21 2003 - 12:12:17 CDT)
RE: Residual dipolar couplings McAteer, Kathleen (Wed May 21 2003 - 12:49:18 CDT)
Re: parm99 Junmei Wang (Wed May 21 2003 - 13:30:18 CDT)
ptraj rdf help tianxiao yang (Wed May 21 2003 - 17:28:26 CDT)
non-periodic system Ioana Cozmuta (Wed May 21 2003 - 17:50:18 CDT)
Re: ptraj and rdf help tianxiao yang (Wed May 21 2003 - 17:54:59 CDT)
Re: non-periodic system Michael Crowley (Wed May 21 2003 - 18:27:03 CDT)
Re: non-periodic system Ioana Cozmuta (Wed May 21 2003 - 21:47:34 CDT)
RE: non-periodic system Yong Duan (Wed May 21 2003 - 22:17:03 CDT)
RE: non-periodic system Yong Duan (Wed May 21 2003 - 22:24:01 CDT)
Re: ptraj rdf help Thomas Cheatham (Wed May 21 2003 - 23:12:57 CDT)
Xleap: 'triangular' and 'square' bond Christian Gossens (Thu May 22 2003 - 05:58:51 CDT)
leap complains! Layi Adekoya (Thu May 22 2003 - 06:56:11 CDT)
rotational and translational motion Jean-François Taly (Thu May 22 2003 - 07:45:18 CDT)
Re: rotational and translational motion Carlos Simmerling (Thu May 22 2003 - 07:54:51 CDT)
Re: Xleap: 'triangular' and 'square' bond Andreas Svrcek-Seiler (Thu May 22 2003 - 08:00:58 CDT)
translational and rotational motion (more information) Jean-François Taly (Thu May 22 2003 - 08:25:49 CDT)
RE: parm99 Bayly, Christopher (Thu May 22 2003 - 08:36:18 CDT)
Re: leap complains! Jose Ramon Blas (Thu May 22 2003 - 17:03:02 CDT)
Minimization problem w/ counter-ion ! Marco Preto (Wed Oct 30 2002 - 20:54:27 CST)
Re: Minimization problem w/ counter-ion ! David A. Case (Thu May 22 2003 - 11:51:28 CDT)
Re: From Dr. Ekaterina Nikitina David A. Case (Thu May 22 2003 - 12:16:58 CDT)
Re: Hybdrogen bonds and LJ 10-12 David A. Case (Thu May 22 2003 - 12:21:18 CDT)
Questions about statistics output of mm_pbsa? Lishan Yao (Thu May 22 2003 - 16:04:04 CDT)
Re: Questions about statistics output of mm_pbsa? Holger Gohlke (Thu May 22 2003 - 16:41:32 CDT)
Please help on xleap: FATAL ERROR Margaret Shun Cheung (Thu May 22 2003 - 17:20:42 CDT)
RE: leap complains! Kristina Furse (Thu May 22 2003 - 18:17:16 CDT)
Re: Please help on xleap: FATAL ERROR David A. Case (Thu May 22 2003 - 19:25:07 CDT)
Re: Questions about statistics output of mm_pbsa? David A. Case (Thu May 22 2003 - 19:32:15 CDT)
Re: Please help on xleap: FATAL ERROR John Bushnell (Thu May 22 2003 - 21:04:15 CDT)
charge fitting for c-term homocysteine. X. Tan (Thu May 22 2003 - 21:25:19 CDT)
Re: Minimization problem w/ counter-ion ! Marco Preto (Wed Oct 30 2002 - 13:11:58 CST)
Re: Questions about statistics output of mm_pbsa? Lishan Yao (Fri May 23 2003 - 08:22:07 CDT)
Re: Questions about statistics output of mm_pbsa? Lishan Yao (Fri May 23 2003 - 08:31:44 CDT)
Re: Please help on xleap: FATAL ERROR Margaret Shun Cheung (Fri May 23 2003 - 09:06:10 CDT)
best force field for Protein+DNA Robert G. Endres (Fri May 23 2003 - 10:14:51 CDT)
A question of how to choose a appropriate box size for imposing periodic boundary conditions in the simulations. Margaret Shun Cheung (Fri May 23 2003 - 10:18:39 CDT)
distance-dependent dielectric function Robert G. Endres (Fri May 23 2003 - 10:44:27 CDT)
Re: distance-dependent dielectric function Shixiang Yan (Fri May 23 2003 - 11:39:04 CDT)
water box distortion GUILLERMINA L ESTIU (Fri May 23 2003 - 15:36:17 CDT)
Re: water box distortion caldwell_at_heimdal.compchem.ucsf.edu (Fri May 23 2003 - 16:21:33 CDT)
center command Ioana Cozmuta (Fri May 23 2003 - 16:40:50 CDT)
problems with anal in amber7 Liliana Wroblewska (Fri May 23 2003 - 16:53:28 CDT)
Re: water box distortion David A. Case (Fri May 23 2003 - 18:13:40 CDT)
MD input file for MM-PBSA calculations Thomas Steinbrecher (Sat May 24 2003 - 07:36:43 CDT)
Re: water box distortion GUILLERMINA L ESTIU (Sat May 24 2003 - 10:34:11 CDT)
Re: MD input file for MM-PBSA calculations Natasja Brooijmans (Sat May 24 2003 - 11:28:39 CDT)
IR6 and makeDIST-RST Francisco Blanco (Sat May 24 2003 - 14:15:29 CDT)
Re: water box distortion Holger Gohlke (Sat May 24 2003 - 20:26:21 CDT)
Re: From Dr. Ekaterina Nikitina Nikitina Ekaterina (Sun May 25 2003 - 05:26:09 CDT)
HBOND energies in sander Francisco Blanco (Sun May 25 2003 - 06:37:52 CDT)
Re: MD input file for MM-PBSA calculations Lepsa (Mon May 26 2003 - 04:03:02 CDT)
EWALD BOMB tang kwa (Mon May 26 2003 - 09:27:07 CDT)
Re: translational and rotational motion (more information) Carlos Simmerling (Thu May 22 2003 - 08:35:13 CDT)
Re: HBOND energies in sander Holger Gohlke (Mon May 26 2003 - 12:24:01 CDT)
Re: EWALD BOMB Holger Gohlke (Mon May 26 2003 - 14:58:00 CDT)
RE: EWALD BOMB Yong Duan (Mon May 26 2003 - 18:51:22 CDT)
Order parameters cailliez (Tue May 27 2003 - 03:25:30 CDT)
Amber on SGI with Itanium compilers for linux (fwd) Sanjeev B.S. (Tue May 27 2003 - 07:21:20 CDT)
Re: Amber on SGI with Itanium compilers for linux Sanjeev B.S. (Tue May 27 2003 - 08:58:17 CDT)
Re: EWALD BOMB tang kwa (Tue May 27 2003 - 10:38:31 CDT)
Re: EWALD BOMB Michael Crowley (Tue May 27 2003 - 10:45:22 CDT)
AMD opteron Hai-Long Wang (Tue May 27 2003 - 10:57:39 CDT)
Re: Order parameters Holger Gohlke (Tue May 27 2003 - 14:15:15 CDT)
mm_gbsa question Javier Cuervo (Tue May 27 2003 - 19:49:18 CDT)
Re: mm_gbsa question Holger Gohlke (Tue May 27 2003 - 20:40:36 CDT)
Does Leap has a problem with Isoleucines? Frederico.Miranda_at_ibmb.uib.no (Wed May 28 2003 - 01:28:21 CDT)
about the dielectric Ye Mei (Wed May 28 2003 - 02:42:22 CDT)
about the dielectric Ye Mei (Wed May 28 2003 - 02:57:49 CDT)
RE: about the dielectric Yong Duan (Wed May 28 2003 - 04:24:58 CDT)
Re: AMD opteron Tru Huynh (Wed May 28 2003 - 08:08:51 CDT)
NVT system implosion!!! Marco Preto (Wed Oct 30 2002 - 18:29:24 CST)
CFP: Informatics Approaches in Structural Genomics at PSB 2004 Sean Mooney (Wed May 28 2003 - 10:46:17 CDT)
Re: Does Leap has a problem with Isoleucines? Holger Gohlke (Wed May 28 2003 - 11:14:47 CDT)
Re: AMD opteron Tru Huynh (Wed May 28 2003 - 11:52:18 CDT)
Does Anyone Have a Working MACHINE File for Solaris/SPARC? Chen, Ya (Wed May 28 2003 - 12:30:53 CDT)
LES analysis tool other than Moil-view Sameer P. Kawatkar (Wed May 28 2003 - 13:21:38 CDT)
clustering trajectories chernhoe (Wed May 28 2003 - 22:19:41 CDT)
Re: NVT system implosion!!! Marco Preto (Wed Oct 30 2002 - 12:46:07 CST)
coordinate files from carnal jaw3_at_cec.wustl.edu (Thu May 29 2003 - 09:13:25 CDT)
antechamber read gaussian file quch quch (Thu May 29 2003 - 15:32:14 CDT)
antechamber read gaussian file quch quch (Thu May 29 2003 - 15:32:10 CDT)
MD problem Shuang Ding (Thu May 29 2003 - 15:47:20 CDT)
Re: MD problem Carlos Simmerling (Thu May 29 2003 - 15:56:27 CDT)
Re: MD problem Shuang Ding (Thu May 29 2003 - 16:04:22 CDT)
Re: MD problem Guanglei Cui (Thu May 29 2003 - 16:14:14 CDT)
Re: MD problem Shuang Ding (Thu May 29 2003 - 16:30:54 CDT)
Re: MD problem Guanglei Cui (Thu May 29 2003 - 16:28:07 CDT)
RE: MD problem Yong Duan (Thu May 29 2003 - 19:58:21 CDT)
information aram joel panay (Thu May 29 2003 - 22:45:48 CDT)
Phosphorylated Serine Library Frederico.Miranda_at_ibmb.uib.no (Fri May 30 2003 - 03:01:31 CDT)
A simple question about offset, want to make sure Huang Zunnan (Sat May 31 2003 - 11:44:46 CDT)
Re: information David A. Case (Sun Jun 01 2003 - 19:14:29 CDT)
Re: IR6 and makeDIST-RST David A. Case (Sun Jun 01 2003 - 19:14:04 CDT)
Re: antechamber read gaussian file David A. Case (Sun Jun 01 2003 - 19:18:54 CDT)
EGB problem in MMPBSA Obdulia Rabal (Mon Jun 02 2003 - 06:11:45 CDT)
Need help recompiling Peter Anderson (Mon Jun 02 2003 - 09:23:11 CDT)
Install Amber7 in linux cluster Wen Li (Mon Jun 02 2003 - 09:20:51 CDT)
Re: Install Amber7 in linux cluster Viktor Hornak (Mon Jun 02 2003 - 10:11:10 CDT)
Re: Need help recompiling caldwell_at_heimdal.compchem.ucsf.edu (Mon Jun 02 2003 - 10:14:06 CDT)
run sander? quch quch (Mon Jun 02 2003 - 11:22:35 CDT)
Re: run sander? David A. Case (Mon Jun 02 2003 - 12:52:00 CDT)
Re: run sander? quch quch (Mon Jun 02 2003 - 13:52:22 CDT)
pol_h Giulio Rastelli (Tue Jun 03 2003 - 11:34:23 CDT)
MGB RADII PARAMETRIZATION Obdulia Rabal (Tue Jun 03 2003 - 06:08:15 CDT)
Mg++ polarizability Robert Duke (Tue Jun 03 2003 - 06:39:25 CDT)
Re: run sander? Michael Crowley (Tue Jun 03 2003 - 07:42:53 CDT)
Re: pol_h David A. Case (Tue Jun 03 2003 - 11:26:41 CDT)
Nancy's leaving caldwell_at_heimdal.compchem.ucsf.edu (Tue Jun 03 2003 - 21:42:00 CDT)
solventbox at constant pressure Petrodler_at_aol.com (Wed Jun 04 2003 - 02:19:05 CDT)
angle violation in SANDER simulation XU Xingfu (Wed Jun 04 2003 - 04:11:24 CDT)
keeping pdb residues numbers ? GUILBAUD Philippe 153683 (Wed Jun 04 2003 - 07:48:50 CDT)
belly vs. position restraints Peter Anderson (Wed Jun 04 2003 - 09:17:05 CDT)
Re: solventbox at constant pressure David A. Case (Wed Jun 04 2003 - 10:13:37 CDT)
Re: angle violation in SANDER simulation David A. Case (Wed Jun 04 2003 - 10:17:32 CDT)
Re: belly vs. position restraints David A. Case (Wed Jun 04 2003 - 10:57:02 CDT)
Re: keeping pdb residues numbers ? David A. Case (Wed Jun 04 2003 - 12:40:08 CDT)
RDPARM problems (ptraj) Sophia Kondratova (Thu Jun 05 2003 - 12:13:35 CDT)
PROBLEM WITH LIBRARY Frederico.Miranda_at_ibmb.uib.no (Thu Jun 05 2003 - 15:06:27 CDT)
constant volume Shuang Ding (Thu Jun 05 2003 - 17:26:39 CDT)
unit of output velocity Yuguang Mu (Fri Jun 06 2003 - 10:33:01 CDT)
Re: unit of output velocity Holger Gohlke (Fri Jun 06 2003 - 10:46:38 CDT)
Re: unit of output velocity Satish Kumar (Fri Jun 06 2003 - 11:25:58 CDT)
Re: unit of output velocity Satish Mummadi (Fri Jun 06 2003 - 11:39:45 CDT)
Re: unit of output velocity Andreas Svrcek-Seiler (Fri Jun 06 2003 - 11:49:32 CDT)
Q) vdw radii & GBSA error Sukjoon Yoon (Fri Jun 06 2003 - 11:58:03 CDT)
Re: constant volume David A. Case (Fri Jun 06 2003 - 17:48:16 CDT)
how to use profec??? sxzheng (Sun Jun 08 2003 - 03:04:09 CDT)
mm_pbsa error message chernhoe (Sun Jun 08 2003 - 04:48:02 CDT)
Re: mm_pbsa error message Holger Gohlke (Sun Jun 08 2003 - 11:19:24 CDT)
Amber Installation on Octane Joseph Maxwell (Sun Jun 08 2003 - 16:55:55 CDT)
VdW in FEP ENikitina (Mon Jun 09 2003 - 02:06:49 CDT)
May I get you help from new user of amber? Wu Yingliang (Mon Jun 09 2003 - 09:21:49 CDT)
Re: May I get you help from new user of amber? Guanglei Cui (Mon Jun 09 2003 - 09:41:07 CDT)
Re: VdW in FEP David A. Case (Mon Jun 09 2003 - 10:05:58 CDT)
RE: May I get you help from new user of amber? Yong Duan (Mon Jun 09 2003 - 10:12:41 CDT)
Re: May I get you help from new user of amber? Satish Mummadi (Mon Jun 09 2003 - 10:28:54 CDT)
Re: May I get you help from new user of amber?(xmkmf) Satish Kumar (Mon Jun 09 2003 - 10:46:53 CDT)
saving trajectory of solute only Peter Anderson (Mon Jun 09 2003 - 11:01:53 CDT)
Re: saving trajectory of solute only Carlos Simmerling (Mon Jun 09 2003 - 11:06:01 CDT)
Re: saving trajectory of solute only David A. Case (Mon Jun 09 2003 - 11:24:03 CDT)
shake problem? Shuang Ding (Mon Jun 09 2003 - 13:33:50 CDT)
helix movement Bimo Ario Tejo (Tue Jun 10 2003 - 05:10:29 CDT)
Re: helix movement Yuguang Mu (Tue Jun 10 2003 - 05:47:42 CDT)
Re: helix movement Bimo Ario Tejo (Tue Jun 10 2003 - 06:19:05 CDT)
Re: VdW in FEP ENikitina (Tue Jun 10 2003 - 06:56:23 CDT)
PME Yuguang Mu (Tue Jun 10 2003 - 07:04:08 CDT)
Re: helix movement Andreas Svrcek-Seiler (Tue Jun 10 2003 - 07:07:49 CDT)
Re: helix movement Bimo Ario Tejo (Tue Jun 10 2003 - 07:18:14 CDT)
helix axis for A-RNA Vlad Cojocaru (Tue Jun 10 2003 - 07:25:09 CDT)
Re: helix axis for A-RNA M. L. Dodson (Tue Jun 10 2003 - 08:36:44 CDT)
Superimposed trajectory Filip Razga (Tue Jun 10 2003 - 08:59:06 CDT)
Re: Superimposed trajectory David A. Case (Tue Jun 10 2003 - 09:53:42 CDT)
Problem in separating LES copies into different trajectory Sameer P. Kawatkar (Tue Jun 10 2003 - 10:15:18 CDT)
Re: Problem in separating LES copies into different trajectory Viktor Hornak (Tue Jun 10 2003 - 10:50:36 CDT)
A question of time Darren Davies (Tue Jun 10 2003 - 10:52:31 CDT)
Re: A question of time David A. Case (Tue Jun 10 2003 - 11:34:19 CDT)
restart MD Shuang Ding (Tue Jun 10 2003 - 13:12:08 CDT)
GB model MF Yang (Tue Jun 10 2003 - 14:54:33 CDT)
Minimization does not converge. Javier Cuervo (Tue Jun 10 2003 - 22:14:43 CDT)
Re: any tool to know what functions are being called while sander is being run?? Satish Mummadi (Wed Jun 11 2003 - 00:32:11 CDT)
Re: Minimization does not converge. David A. Case (Wed Jun 11 2003 - 00:52:29 CDT)
New location for the Amber web site David A. Case (Wed Jun 11 2003 - 01:04:54 CDT)
PME Yuguang Mu (Wed Jun 11 2003 - 03:33:29 CDT)
delphi on linux chernhoe (Wed Jun 11 2003 - 04:03:13 CDT)
vlimit exceeded when sander calculate free energies using TI zsx (Wed Jun 11 2003 - 06:51:09 CDT)
Re: helix movement Yuguang Mu (Wed Jun 11 2003 - 07:47:34 CDT)
Re: PME darden (Wed Jun 11 2003 - 09:33:12 CDT)
any tool to know what functions are being called while sander is being run?? Satish Mummadi (Wed Jun 11 2003 - 08:42:58 CDT)
Re: any tool to know what functions are being called while sander is being run?? Guanglei Cui (Wed Jun 11 2003 - 08:53:45 CDT)
quasih problem Yang, Mingfeng (Wed Jun 11 2003 - 09:10:30 CDT)
Re: PME darden (Wed Jun 11 2003 - 10:21:25 CDT)
Re: quasih problem David A. Case (Wed Jun 11 2003 - 10:12:54 CDT)
Re: vlimit exceeded when sander calculate free energies using TI David A. Case (Wed Jun 11 2003 - 10:21:31 CDT)
calculated b-factor higher than x-ray Bimo Ario Tejo (Wed Jun 11 2003 - 13:23:03 CDT)
which AMBER program to use to get the e-density output? salinthip thipayang (Wed Jun 11 2003 - 14:24:40 CDT)
bugfix ptraj-6.4 (need to confirm) Bimo Ario Tejo (Thu Jun 12 2003 - 07:51:27 CDT)
jarrod Jarrod Wesley Barnes (Thu Jun 12 2003 - 09:51:33 CDT)
Re: jarrod Holger Gohlke (Thu Jun 12 2003 - 10:18:43 CDT)
install problem Dave S Walker (Thu Jun 12 2003 - 16:18:02 CDT)
Re: install problem David A. Case (Thu Jun 12 2003 - 17:26:56 CDT)
Re: install problem Dave S Walker (Thu Jun 12 2003 - 19:03:21 CDT)
Re: jarrod Matheus Froeyen (Fri Jun 13 2003 - 02:36:14 CDT)
glycam force field with amber PSR04996_at_mailstudenti.unimi.it (Fri Jun 13 2003 - 06:28:07 CDT)
Re: glycam force field with amber David A. Case (Fri Jun 13 2003 - 11:42:31 CDT)
Problem with a library Frederico.Miranda_at_ibmb.uib.no (Fri Jun 13 2003 - 15:27:36 CDT)
Re: Problem with a library David A. Case (Fri Jun 13 2003 - 16:07:37 CDT)
parallel sander jobs die with error: "MPI_COMM_RANK : Null communicator" chris switzer (Sat Jun 14 2003 - 21:00:51 CDT)
can you give me more advice about: vlimit exceeded when sander calculate free energies using TI sxzheng (Mon Jun 16 2003 - 07:47:53 CDT)
Re: can you give me more advice about: vlimit exceeded when sander calculate free energies using TI David A. Case (Mon Jun 16 2003 - 10:12:05 CDT)
LEAP compiling problem yuann (Tue Jun 17 2003 - 05:14:23 CDT)
Re: LEAP compiling problem David A. Case (Tue Jun 17 2003 - 10:51:21 CDT)
Re: LEAP compiling problem David A. Case (Tue Jun 17 2003 - 11:09:26 CDT)
CCL: Amber free energy equation Daquan Gao (Tue Jun 17 2003 - 11:33:39 CDT)
AMBER7 on linux cluster Venkata S Koppuravuri (Tue Jun 17 2003 - 11:49:06 CDT)
Re: AMBER7 on linux cluster Carlos Simmerling (Tue Jun 17 2003 - 11:54:28 CDT)
new tutorial available: introduction to ptraj David A. Case (Tue Jun 17 2003 - 13:03:54 CDT)
Sander error Yuhui Cheng (Tue Jun 17 2003 - 13:37:21 CDT)
Re: Sander error Natasja Brooijmans (Tue Jun 17 2003 - 13:44:53 CDT)
Error in minimization using sander_classic of AMBER6 dicksmit_at_umich.edu (Tue Jun 17 2003 - 15:20:03 CDT)
web link for PLEP is not available. Margaret Shun Cheung (Tue Jun 17 2003 - 15:28:40 CDT)
Re: Error in minimization using sander_classic of AMBER6 David A. Case (Tue Jun 17 2003 - 15:53:49 CDT)
Problem with LES topology file Courtney Stanton (Tue Jun 17 2003 - 17:28:10 CDT)
Re: Problem with LES topology file Carlos Simmerling (Tue Jun 17 2003 - 17:42:07 CDT)
Re: LEAP compiling problem yuann (Tue Jun 17 2003 - 20:17:56 CDT)
Flag for antechamber Nick Polfer (Wed Jun 18 2003 - 03:59:01 CDT)
VdW in FEP ENikitina (Wed Jun 18 2003 - 09:02:14 CDT)
mpirun problem: no rsh Peter Anderson (Wed Jun 18 2003 - 12:50:26 CDT)
Re: mpirun problem: no rsh Carlos Simmerling (Wed Jun 18 2003 - 12:56:48 CDT)
Re: mpirun problem: no rsh Michael Crowley (Wed Jun 18 2003 - 14:04:52 CDT)
help on solvatecap Mao Xiang (Wed Jun 18 2003 - 20:47:36 CDT)
debug sander Andrew Petersen (Thu Jun 19 2003 - 01:40:04 CDT)
Re: debug sander Satish Mummadi (Thu Jun 19 2003 - 03:32:02 CDT)
RE: debug sander Yong Duan (Thu Jun 19 2003 - 04:21:27 CDT)
constraint + restraint Jose Ramon Blas (Thu Jun 19 2003 - 18:58:41 CDT)
Re: constraint + restraint David A. Case (Thu Jun 19 2003 - 10:39:44 CDT)
NOESY restraints Teletchéa Stéphane (Fri Jun 20 2003 - 06:28:03 CDT)
Re: AMBER7 on linux cluster Venkata S Koppuravuri (Fri Jun 20 2003 - 09:53:17 CDT)
Re: AMBER7 on linux cluster Carlos Simmerling (Fri Jun 20 2003 - 09:55:10 CDT)
AMBER question David (Fri Jun 20 2003 - 11:31:55 CDT)
perl question Ioana Cozmuta (Fri Jun 20 2003 - 17:28:57 CDT)
mm_pbsa problem Peter Anderson (Fri Jun 20 2003 - 17:31:17 CDT)
Re: NOESY restraints David A. Case (Fri Jun 20 2003 - 19:49:00 CDT)
Re: AMBER question David A. Case (Fri Jun 20 2003 - 19:59:04 CDT)
RE: AMBER7 on linux cluster Yong Duan (Fri Jun 20 2003 - 20:35:04 CDT)
Re: mm_pbsa problem Holger Gohlke (Fri Jun 20 2003 - 20:47:21 CDT)
Question about defining force field FUNG WAI KEUNG (Fri Jun 20 2003 - 22:12:59 CDT)
Re: NOESY restraints Steph (Sat Jun 21 2003 - 05:27:35 CDT)
Problem with XLEaP in Mandrake 9.1 Karthikeyan Pasupathy (Sun Jun 22 2003 - 12:08:23 CDT)
RE: Problem with XLEaP in Mandrake 9.1 Ross Walker (Sun Jun 22 2003 - 12:31:02 CDT)
Re: Problem with XLEaP in Mandrake 9.1 CUI, Guanglei (Sun Jun 22 2003 - 12:44:51 CDT)
Re: Problem with XLEaP in Mandrake 9.1 John Bushnell (Sun Jun 22 2003 - 20:04:43 CDT)
1-4 vdw term in Glycam2000 yuann (Sun Jun 22 2003 - 23:24:16 CDT)
viewing movie with VMD Layi Adekoya (Mon Jun 23 2003 - 03:00:51 CDT)
Re: viewing movie with VMD Lepsa (Mon Jun 23 2003 - 03:09:29 CDT)
Running MD Balvinder Singh (Mon Jun 23 2003 - 12:33:56 CDT)
Re: Running MD Carlos Simmerling (Mon Jun 23 2003 - 07:10:23 CDT)
Re: Running MD Balvinder Singh (Mon Jun 23 2003 - 13:02:33 CDT)
Re: Running MD Carlos Simmerling (Mon Jun 23 2003 - 07:40:24 CDT)
how to restrain water Mao Xiang (Mon Jun 23 2003 - 09:59:23 CDT)
Re: how to restrain water Alfonso Garcia Sosa (Mon Jun 23 2003 - 10:14:02 CDT)
Re: how to restrain water Alfonso Garcia Sosa (Mon Jun 23 2003 - 10:42:42 CDT)
RE: viewing movie with VMD Ross Walker (Mon Jun 23 2003 - 17:36:30 CDT)
AMBER parameters D Fernandez (Tue Jun 24 2003 - 00:26:09 CDT)
ptraj question Ioana Cozmuta (Tue Jun 24 2003 - 02:59:48 CDT)
Re: AMBER parameters David A. Case (Tue Jun 24 2003 - 10:25:35 CDT)
Another mm_pbsa problem Peter Anderson (Tue Jun 24 2003 - 11:47:58 CDT)
Re: Another mm_pbsa problem Holger Gohlke (Tue Jun 24 2003 - 12:08:25 CDT)
GAFF in GUI MD apps Thomas (Tue Jun 24 2003 - 14:07:54 CDT)
electrostatic interaction energ. /delphi Tommi Kajander (Tue Jun 24 2003 - 14:39:51 CDT)
Re: electrostatic interaction energ. /delphi Natasja Brooijmans (Tue Jun 24 2003 - 14:45:22 CDT)
RE: Software Sales Pete Koladich (Tue Jun 24 2003 - 15:41:53 CDT)
Re: ptraj question Thomas Cheatham (Tue Jun 24 2003 - 15:56:51 CDT)
Memory problem Frederico.Miranda_at_ibmb.uib.no (Tue Jun 24 2003 - 19:17:40 CDT)
T in MD vs. T in wet experiments Jianhui Wu (Tue Jun 24 2003 - 20:34:31 CDT)
Sander problem Yuhui Cheng (Tue Jun 24 2003 - 21:31:28 CDT)
Question about defining force field (followup) FUNG WAI KEUNG (Tue Jun 24 2003 - 23:14:10 CDT)
Re: GAFF in GUI MD apps FyD (Wed Jun 25 2003 - 00:50:58 CDT)
unifying trajectory files Peter Anderson (Wed Jun 25 2003 - 10:57:42 CDT)
Re: unifying trajectory files Carlos Simmerling (Wed Jun 25 2003 - 11:05:57 CDT)
Re: unifying trajectory files Natasja Brooijmans (Wed Jun 25 2003 - 11:25:41 CDT)
Antechamber Shweta Sikri (Wed Jun 25 2003 - 11:47:52 CDT)
Re: Antechamber David A. Case (Wed Jun 25 2003 - 12:31:31 CDT)
Re: Antechamber Shweta Sikri (Wed Jun 25 2003 - 14:26:31 CDT)
Re: unifying trajectory files Ioana Cozmuta (Wed Jun 25 2003 - 14:58:39 CDT)
Re: Sander problem David A. Case (Wed Jun 25 2003 - 17:30:21 CDT)
pyroglutamic acid (PCA) Javier Cuervo (Wed Jun 25 2003 - 20:16:44 CDT)
Amber6 on RH 9 Yichen Cao (Thu Jun 26 2003 - 10:37:09 CDT)
Re: Amber6 on RH 9 David A. Case (Thu Jun 26 2003 - 12:31:56 CDT)
Re: pyroglutamic acid (PCA) David A. Case (Thu Jun 26 2003 - 12:34:25 CDT)
Problem with Snader Frederico.Miranda_at_ibmb.uib.no (Sat Jun 28 2003 - 08:17:12 CDT)
Re: Problem with Snader Guanglei Cui (Sat Jun 28 2003 - 09:53:59 CDT)
protonate Giulio Rastelli (Sun Jun 29 2003 - 16:31:20 CDT)
Re: Re: 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)
How do I perform an Nmode calculation on a big protein-ligand complex? Thomas Steinbrecher (Mon Jun 30 2003 - 04:31:38 CDT)
Questions about output archive and micromolecules Andrei Leitão (Mon Jun 30 2003 - 15:17:46 CDT)
Re: protonate David A. Case (Mon Jun 30 2003 - 17:44:18 CDT)
VXllig Legal geld Verdienen Ohne Risiko! Mcneils (Tue Jul 01 2003 - 02:30:43 CDT)
Nmode recompilation Thomas Steinbrecher (Tue Jul 01 2003 - 03:41:33 CDT)
g77 on 32 bits cpu (was Re: Nmode recompilation) Tru Huynh (Tue Jul 01 2003 - 04:48:15 CDT)
Re: AMBER Cutoff Darren Davies (Tue Jul 01 2003 - 05:45:05 CDT)
parallel version amber installation problem Raja Swaminathan (Tue Jul 01 2003 - 06:09:43 CDT)
(no subject) Lifang Xu (Tue Jul 01 2003 - 09:22:43 CDT)
Re: AMBER Cutoff David A. Case (Tue Jul 01 2003 - 10:00:00 CDT)
Re: your mail (IBM runtime problem) Thomas Cheatham (Tue Jul 01 2003 - 11:58:00 CDT)
Re: protonate David A. Case (Tue Jul 01 2003 - 12:29:54 CDT)
Re: Questions about output archive and micromolecules David A. Case (Tue Jul 01 2003 - 12:39:33 CDT)
Re: parallel version amber installation problem David A. Case (Tue Jul 01 2003 - 12:43:03 CDT)
input problem Herbert Georg (Tue Jul 01 2003 - 14:12:23 CDT)
Re: input problem David A. Case (Tue Jul 01 2003 - 14:24:42 CDT)
Nmode doesn't work ? Gus Carri (Tue Jul 01 2003 - 16:09:11 CDT)
about the read error Zhi Qiang ZHOU (Tue Jul 01 2003 - 21:35:41 CDT)
PMF X. Tan (Wed Jul 02 2003 - 14:02:53 CDT)
Nmanal Gus Carri (Wed Jul 02 2003 - 16:26:50 CDT)
Antechamber Shweta Sikri (Thu Jul 03 2003 - 11:29:03 CDT)
Re: Antechamber David A. Case (Thu Jul 03 2003 - 11:59:12 CDT)
Re: Antechamber Shweta Sikri (Thu Jul 03 2003 - 12:18:58 CDT)
Re: Antechamber David A. Case (Thu Jul 03 2003 - 12:36:47 CDT)
sander,ntt=5 Monika Fuxreiter (Fri Jul 04 2003 - 06:17:33 CDT)
How to do a rigid solvent model? Marco Aurelio Correia Preto (Fri Jul 04 2003 - 09:30:00 CDT)
Machine file available for ICC compiler ? Teletchéa Stéphane (Fri Jul 04 2003 - 12:08:30 CDT)
Re: sander,ntt=5 David A. Case (Fri Jul 04 2003 - 12:13:21 CDT)
Re: How to do a rigid solvent model? David A. Case (Fri Jul 04 2003 - 12:16:51 CDT)
Re: How to do a rigid solvent model? Carlos Simmerling (Fri Jul 04 2003 - 12:25:21 CDT)
Re: Machine file available for ICC compiler ? David A. Case (Fri Jul 04 2003 - 14:14:00 CDT)
vlimit exceeded Peter Anderson (Sat Jul 05 2003 - 11:39:01 CDT)
RE: How to do a rigid solvent model? Yong Duan (Sat Jul 05 2003 - 13:48:01 CDT)
Re: How to do a rigid solvent model? Carlos Simmerling (Sat Jul 05 2003 - 15:06:39 CDT)
RE: How to do a rigid solvent model? Yong Duan (Sun Jul 06 2003 - 14:59:23 CDT)
RE: How to do a rigid solvent model? Marco Aurelio Correia Preto (Mon Jul 07 2003 - 03:25:27 CDT)
parallelisation gold gunaseelan (Mon Jul 07 2003 - 08:32:00 CDT)
Re: parallelisation Carlos Simmerling (Mon Jul 07 2003 - 08:38:32 CDT)
ALAscan of Proline Martin Lepsik (Mon Jul 07 2003 - 16:14:09 CDT)
Valdiation of Latest Amber parameters Sia Meshkat (Mon Jul 07 2003 - 11:35:57 CDT)
ptraj Ioana Cozmuta (Mon Jul 07 2003 - 14:06:13 CDT)
New program available: PMEMD (Particle Mesh Ewald Molecular Dynamics) David A. Case (Mon Jul 07 2003 - 16:13:33 CDT)
correction to location of the PMEMD program David A. Case (Mon Jul 07 2003 - 16:17:44 CDT)
Re: Valdiation of Latest Amber parameters David A. Case (Mon Jul 07 2003 - 16:23:48 CDT)
RE: Valdiation of Latest Amber parameters Sia Meshkat (Mon Jul 07 2003 - 16:48:41 CDT)
RE: Valdiation of Latest Amber parameters caldwell_at_heimdal.compchem.ucsf.edu (Mon Jul 07 2003 - 16:44:53 CDT)
diffusion in ptraj Ioana Cozmuta (Mon Jul 07 2003 - 16:56:56 CDT)
Re: Valdiation of Latest Amber parameters David A. Case (Mon Jul 07 2003 - 17:04:01 CDT)
RE: Valdiation of Latest Amber parameters Sia Meshkat (Mon Jul 07 2003 - 17:19:04 CDT)
RE: Valdiation of Latest Amber parameters Yong Duan (Mon Jul 07 2003 - 18:28:41 CDT)
Re: Valdiation of Latest Amber parameters Carlos Simmerling (Mon Jul 07 2003 - 19:50:14 CDT)
RE: Valdiation of Latest Amber parameters Sia Meshkat (Mon Jul 07 2003 - 20:40:52 CDT)
constraint + restraint tang kwa (Tue Jul 08 2003 - 02:05:11 CDT)
Distribution Min with truncated octahedron box Ling Zhang (Tue Jul 08 2003 - 12:24:47 CDT)
Re: constraint + restraint David A. Case (Tue Jul 08 2003 - 12:33:35 CDT)
Re: Distribution Min with truncated octahedron box Bill Ross (Tue Jul 08 2003 - 13:24:09 CDT)
Re: Distribution Min with truncated octahedron box Ling Zhang (Tue Jul 08 2003 - 13:31:42 CDT)
carnal in big systems GUILLERMINA L ESTIU (Tue Jul 08 2003 - 13:44:21 CDT)
Re: carnal in big systems Bill Ross (Tue Jul 08 2003 - 14:22:09 CDT)
Lennard-Jones A and B coefficients Gus Carri (Tue Jul 08 2003 - 17:53:56 CDT)
memory shortage with mm_pbsa Peter Anderson (Tue Jul 08 2003 - 19:36:09 CDT)
Re: memory shortage with mm_pbsa David A. Case (Tue Jul 08 2003 - 20:47:55 CDT)
RE: Valdiation of Latest Amber parameters Yong Duan (Tue Jul 08 2003 - 22:12:27 CDT)
Ar as a solvent ENikitina (Wed Jul 09 2003 - 06:42:47 CDT)
May I get your help? Wu Yingliang (Wed Jul 09 2003 - 07:39:05 CDT)
memory problem zhaoxc_at_puccini.che.pitt.edu (Wed Jul 09 2003 - 08:34:09 CDT)
Refining a docked protein complex Wu Yingliang (Wed Jul 09 2003 - 08:59:26 CDT)
Re: Valdiation of Latest Amber parameters Jiri Sponer (Wed Jul 09 2003 - 12:03:53 CDT)
(no subject) Richard Dayton Smith (Wed Jul 09 2003 - 12:23:38 CDT)
Adding missing parameters Peter Anderson (Wed Jul 09 2003 - 13:18:33 CDT)
npscal Shuang Ding (Wed Jul 09 2003 - 15:12:04 CDT)
Temperature control Andrei Leitão (Wed Jul 09 2003 - 15:25:12 CDT)
Re: Temperature control Carlos Simmerling (Wed Jul 09 2003 - 15:38:26 CDT)
Re: Temperature control David A. Case (Wed Jul 09 2003 - 15:53:10 CDT)
Re: npscal David A. Case (Wed Jul 09 2003 - 15:53:54 CDT)
Re: Temperature control Carlos Simmerling (Wed Jul 09 2003 - 16:15:29 CDT)
RE: Valdiation of Latest Amber parameters Yong Duan (Thu Jul 10 2003 - 00:25:33 CDT)
van der Waals term David (Thu Jul 10 2003 - 01:47:34 CDT)
AMBER question David (Thu Jul 10 2003 - 01:51:31 CDT)
RE: AMBER question Marco Aurelio Correia Preto (Thu Jul 10 2003 - 03:04:08 CDT)
Amber7 on Opteron Florian Barth (Thu Jul 10 2003 - 05:46:32 CDT)
3 simultaneous simulations in one computer ptolonen_at_cc.joensuu.fi (Thu Jul 10 2003 - 06:20:15 CDT)
Opteron Experience ian r gould (Thu Jul 10 2003 - 08:29:38 CDT)
RE: 3 simultaneous simulations in one computer Ross Walker (Thu Jul 10 2003 - 07:01:57 CDT)
nab compilation Vlad Cojocaru (Thu Jul 10 2003 - 07:02:04 CDT)
RE: Amber7 on Opteron Ross Walker (Thu Jul 10 2003 - 06:58:08 CDT)
effect of forcing neutrality zhaoxc_at_puccini.che.pitt.edu (Thu Jul 10 2003 - 14:56:00 CDT)
resp for charged molecule? quch quch (Thu Jul 10 2003 - 16:09:08 CDT)
Re: Adding missing parameters David A. Case (Thu Jul 10 2003 - 21:58:21 CDT)
Re: your mail David A. Case (Thu Jul 10 2003 - 22:01:51 CDT)
Re: memory problem David A. Case (Thu Jul 10 2003 - 22:03:14 CDT)
Re: May I get your help? David A. Case (Thu Jul 10 2003 - 22:05:21 CDT)
Re: memory shortage with mm_pbsa - some more thoughts Joffre Heredia (Sat Jul 12 2003 - 05:26:39 CDT)
Comparative MD FyD (Fri Jul 11 2003 - 08:29:02 CDT)
AMBER question David (Fri Jul 11 2003 - 08:42:12 CDT)
RE: AMBER question Marco Aurelio Correia Preto (Fri Jul 11 2003 - 09:29:11 CDT)
parallelisation gold gunaseelan (Fri Jul 11 2003 - 10:06:43 CDT)
Re: AMBER question Carlos Simmerling (Fri Jul 11 2003 - 10:24:30 CDT)
RE: May I get your help? Zhijun Li (Fri Jul 11 2003 - 10:22:30 CDT)
delphi with amber 7 Noriaki Okimoto (Fri Jul 11 2003 - 13:34:34 CDT)
Re: Comparative MD Thomas Cheatham (Fri Jul 11 2003 - 14:32:35 CDT)
Re: delphi with amber 7 Guanglei Cui (Fri Jul 11 2003 - 15:44:09 CDT)
Re: delphi with amber 7 Nori (Fri Jul 11 2003 - 21:15:30 CDT)
ntx in sander dvira (Sat Jul 12 2003 - 08:00:57 CDT)
Strange F.E.P. behavior Peter Anderson (Sun Jul 13 2003 - 08:15:49 CDT)
methylphosphonate A. Hungie (Mon Jul 14 2003 - 08:20:52 CDT)
Bad atom type: f Sukjoon Yoon (Mon Jul 14 2003 - 10:28:58 CDT)
Re: effect of forcing neutrality David A. Case (Mon Jul 14 2003 - 10:49:57 CDT)
parallelisation gold gunaseelan (Mon Jul 14 2003 - 10:48:56 CDT)
Sander_classic output: NAN pantelo_at_okstate.edu (Mon Jul 14 2003 - 11:07:19 CDT)
Re: parallelisation Carlos P. Sosa (Mon Jul 14 2003 - 11:19:00 CDT)
Re: effect of forcing neutrality zhaoxc_at_puccini.che.pitt.edu (Mon Jul 14 2003 - 11:17:24 CDT)
big changes coming caldwell_at_heimdal.compchem.ucsf.edu (Mon Jul 14 2003 - 10:27:11 CDT)
mail reflector address is changing David A. Case (Mon Jul 14 2003 - 16:56:21 CDT)
Re: parallelisation David A. Case (Mon Jul 14 2003 - 17:24:34 CDT)
Re: Sander_classic output: NAN David A. Case (Mon Jul 14 2003 - 17:27:17 CDT)
AMBER: Re: memory shortage with mm_pbsa - some more thoughts Qing Zhang (Mon Jul 14 2003 - 18:10:26 CDT)
AMBER: Re: methylphosphonate David A. Case (Mon Jul 14 2003 - 19:22:28 CDT)
AMBER: question on LJ parameters for molecules Ioana Cozmuta (Mon Jul 14 2003 - 19:38:58 CDT)
Re: AMBER: Re: methylphosphonate Piotr Cieplak (Mon Jul 14 2003 - 19:43:14 CDT)
AMBER: Re: methylphosphonate Thomas E. Cheatham, III (Mon Jul 14 2003 - 21:46:06 CDT)
RE: AMBER: question on LJ parameters for molecules Yong Duan (Mon Jul 14 2003 - 22:52:27 CDT)
Re: AMBER: Re: methylphosphonate Piotr Cieplak (Tue Jul 15 2003 - 00:01:59 CDT)
AMBER: Re: methylphosphonate A. Hungie (Tue Jul 15 2003 - 03:31:52 CDT)
AMBER: PMF X. Tan (Tue Jul 15 2003 - 12:02:47 CDT)
AMBER: Questions about mm_pbsa and alanine scanning Haizhen Zhong (Tue Jul 15 2003 - 15:34:32 CDT)
Re: AMBER: Questions about mm_pbsa and alanine scanning Natasja Brooijmans (Tue Jul 15 2003 - 15:42:40 CDT)
Re: AMBER: Questions about mm_pbsa and alanine scanning Haizhen Zhong (Tue Jul 15 2003 - 16:01:47 CDT)
AMBER: Coordinate resetting (SHAKE) cannot be accomplished Anton B. Guliaev (Tue Jul 15 2003 - 16:35:59 CDT)
Re: AMBER: Coordinate resetting (SHAKE) cannot be accomplished David A. Case (Tue Jul 15 2003 - 20:25:26 CDT)
Re: AMBER: PMF David Smith (Wed Jul 16 2003 - 04:37:56 CDT)
Re: AMBER: Questions about mm_pbsa and alanine scanning Haizhen Zhong (Wed Jul 16 2003 - 08:04:30 CDT)
AMBER: neutral N- and C- termini ! Xavier Periole (Wed Jul 16 2003 - 13:52:29 CDT)
AMBER: curves nomenclature Sue Heavner (Wed Jul 16 2003 - 14:34:13 CDT)
Re: AMBER: Coordinate resetting (SHAKE) cannot be accomplished Bill Ross (Wed Jul 16 2003 - 14:46:44 CDT)
AMBER: N/C termini Xavier Periole (Wed Jul 16 2003 - 17:24:19 CDT)
Re: AMBER: curves nomenclature David A. Case (Wed Jul 16 2003 - 17:29:01 CDT)
AMBER: PMEMD and sander from AMBER6 performances Teletchéa Stéphane (Wed Jul 16 2003 - 18:37:34 CDT)
Re: AMBER: PMEMD and sander from AMBER6 performances Robert Duke (Wed Jul 16 2003 - 22:11:55 CDT)
AMBER: RADII in DELPHI Obdulia Rabal (Thu Jul 17 2003 - 03:58:57 CDT)
AMBER: Big system in Gibbs ENikitina (Thu Jul 17 2003 - 01:01:23 CDT)
Re: AMBER: Big system in Gibbs David A. Case (Thu Jul 17 2003 - 11:00:57 CDT)
Re: AMBER: RADII in DELPHI David A. Case (Thu Jul 17 2003 - 11:03:29 CDT)
Re: AMBER: neutral N- and C- termini ! David A. Case (Thu Jul 17 2003 - 11:05:00 CDT)
AMBER: question about quasih? Lishan Yao (Fri Jul 18 2003 - 17:15:32 CDT)
AMBER: Fwd: Minimizing after solvation Angela Pantelogianis (Fri Jul 18 2003 - 17:34:30 CDT)
Re: AMBER: question about quasih? Thomas E. Cheatham, III (Fri Jul 18 2003 - 17:39:15 CDT)
Re: AMBER: Fwd: Minimizing after solvation David A. Case (Sat Jul 19 2003 - 23:34:53 CDT)
AMBER: variable not in namelist for Sander input Haizhen Zhong (Mon Jul 21 2003 - 09:16:40 CDT)
RE: AMBER: variable not in namelist for Sander input Yong Duan (Mon Jul 21 2003 - 09:49:07 CDT)
Re: AMBER: variable not in namelist for Sander input Angela Pantelogianis (Mon Jul 21 2003 - 09:59:24 CDT)
Re: AMBER: variable not in namelist for Sander input Vlad Cojocaru (Mon Jul 21 2003 - 10:16:22 CDT)
Re: AMBER: Fwd: Minimizing after solvation Angela Pantelogianis (Mon Jul 21 2003 - 10:26:30 CDT)
AMBER: dielectric in sander Michele Lunelli (Mon Jul 21 2003 - 10:36:19 CDT)
Re: AMBER: Fwd: Minimizing after solvation Dr. Yong Duan (Mon Jul 21 2003 - 10:48:00 CDT)
Re: AMBER: Fwd: Minimizing after solvation David A. Case (Mon Jul 21 2003 - 10:50:35 CDT)
Re: AMBER: dielectric in sander David A. Case (Mon Jul 21 2003 - 10:52:57 CDT)
RE: AMBER: variable not in namelist for Sander input Haizhen Zhong (Mon Jul 21 2003 - 11:25:38 CDT)
Re: AMBER: variable not in namelist for Sander input Teletchéa Stéphane (Mon Jul 21 2003 - 11:35:46 CDT)
Re: AMBER: variable not in namelist for Sander input Thomas E. Cheatham, III (Mon Jul 21 2003 - 11:40:29 CDT)
Re: AMBER: variable not in namelist for Sander input Haizhen Zhong (Mon Jul 21 2003 - 13:08:39 CDT)
Re: AMBER: variable not in namelist for Sander input Thomas E. Cheatham, III (Mon Jul 21 2003 - 13:18:50 CDT)
RE: AMBER: variable not in namelist for Sander input Yong Duan (Mon Jul 21 2003 - 13:51:30 CDT)
AMBER: Odd Problem with PMEMD Chen, Ya (Mon Jul 21 2003 - 22:35:23 CDT)
Re: AMBER: Odd Problem with PMEMD Johannes Zuegg (Mon Jul 21 2003 - 23:12:37 CDT)
Re: AMBER: Odd Problem with PMEMD Robert Duke (Tue Jul 22 2003 - 06:17:25 CDT)
Re: AMBER: Big system in Gibbs ENikitina (Tue Jul 22 2003 - 10:40:07 CDT)
AMBER: (no subject) ENikitina (Tue Jul 22 2003 - 10:53:56 CDT)
Re: AMBER: (no subject) David A. Case (Tue Jul 22 2003 - 11:30:00 CDT)
AMBER: FILE UNITIO.C Obdulia Rabal (Tue Jul 22 2003 - 13:15:48 CDT)
Re: AMBER: FILE UNITIO.C David A. Case (Tue Jul 22 2003 - 13:54:14 CDT)
AMBER: Non-standard Residue Ran Ye (Tue Jul 22 2003 - 14:34:06 CDT)
Re: AMBER: Non-standard Residue David A. Case (Tue Jul 22 2003 - 16:06:50 CDT)
AMBER: HB dynamics in water and Ion solvation free energies Ioana Cozmuta (Tue Jul 22 2003 - 17:09:41 CDT)
Re: AMBER: HB dynamics in water and Ion solvation free energies David A. Case (Tue Jul 22 2003 - 21:18:51 CDT)
RE: AMBER: FILE UNITIO.C Obdulia Rabal (Wed Jul 23 2003 - 02:51:22 CDT)
Re: AMBER: FILE UNITIO.C David A. Case (Wed Jul 23 2003 - 10:04:54 CDT)
Re: AMBER: Non-standard Residue Ran Ye (Wed Jul 23 2003 - 11:08:03 CDT)
AMBER: strange problem with a small system GUILLERMINA L ESTIU (Wed Jul 23 2003 - 12:22:34 CDT)
Re: AMBER: Non-standard Residue David A. Case (Wed Jul 23 2003 - 13:31:44 CDT)
AMBER: addition to: problem with a small system GUILLERMINA L ESTIU (Wed Jul 23 2003 - 13:36:03 CDT)
Re: AMBER: strange problem with a small system David A. Case (Wed Jul 23 2003 - 13:51:59 CDT)
Re: AMBER: strange problem with a small system GUILLERMINA L ESTIU (Wed Jul 23 2003 - 14:13:47 CDT)
AMBER: /exe/teLeap does not exist Mizuguchi Mineyuki (Thu Jul 24 2003 - 02:23:55 CDT)
AMBER: water box problem Omar Wahab (Thu Jul 24 2003 - 03:32:35 CDT)
Re: AMBER: water box problem Carlos Simmerling (Thu Jul 24 2003 - 06:36:29 CDT)
AMBER: (no subject) Narang Manpreet Kaur (Thu Jul 24 2003 - 06:57:36 CDT)
Re: AMBER: (no subject) Holger Gohlke (Thu Jul 24 2003 - 10:38:15 CDT)
AMBER: question about ptraj? Lishan Yao (Thu Jul 24 2003 - 11:18:20 CDT)
Re: AMBER: (no subject) Thomas E. Cheatham, III (Thu Jul 24 2003 - 11:32:28 CDT)
Re: AMBER: question about ptraj? Thomas E. Cheatham, III (Thu Jul 24 2003 - 11:40:50 CDT)
Re: AMBER: question about ptraj? rluo_at_uci.edu (Thu Jul 24 2003 - 11:48:54 CDT)
AMBER: TEMP is not reaching 300K sd233_at_georgetown.edu (Thu Jul 24 2003 - 12:06:49 CDT)
Re: AMBER: TEMP is not reaching 300K Carlos Simmerling (Thu Jul 24 2003 - 12:35:03 CDT)
Re: AMBER: TEMP is not reaching 300K Vlad Cojocaru (Thu Jul 24 2003 - 12:35:21 CDT)
AMBER: running AMBER on an IBM P690 cluster Vlad Cojocaru (Thu Jul 24 2003 - 12:46:30 CDT)
AMBER: PMF calculation Lishan Yao (Thu Jul 24 2003 - 14:25:48 CDT)
AMBER: MOPAC509mn test jobs on linux takanori.kanazawa_at_pharma.novartis.com (Thu Jul 24 2003 - 18:54:39 CDT)
Re: AMBER: /exe/teLeap does not exist David A. Case (Thu Jul 24 2003 - 19:50:17 CDT)
Re: AMBER: (no subject) Narang Manpreet Kaur (Thu Jul 24 2003 - 23:36:54 CDT)
Re: AMBER: strange problem with a small system David A. Case (Thu Jul 24 2003 - 23:51:04 CDT)
Re: AMBER: TEMP is not reaching 300K Michele Lunelli (Fri Jul 25 2003 - 10:27:09 CDT)
AMBER: Dynamics and Simulated Annealing Narang Manpreet Kaur (Fri Jul 25 2003 - 08:03:52 CDT)
Re: AMBER: Dynamics and Simulated Annealing Carlos Simmerling (Fri Jul 25 2003 - 11:53:38 CDT)
Re: AMBER: Dynamics and Simulated Annealing Teletchéa Stéphane (Fri Jul 25 2003 - 11:57:53 CDT)
AMBER: Taisung Lee/San Diego/Accelrys is out of the office. Taisung Lee (Fri Jul 25 2003 - 12:02:29 CDT)
AMBER: DYNAMICS RUN sd233_at_georgetown.edu (Fri Jul 25 2003 - 12:47:44 CDT)
AMBER: monitor vdw along time Ling Zhang (Fri Jul 25 2003 - 12:48:26 CDT)
Re: AMBER: monitor vdw along time Holger Gohlke (Fri Jul 25 2003 - 13:56:28 CDT)
Re: AMBER: monitor vdw along time Suse Broyde (Fri Jul 25 2003 - 14:57:06 CDT)
AMBER: a note on problems with MPI and sander David A. Case (Sat Jul 26 2003 - 13:50:37 CDT)
AMBER: AMBER and NAMD Vlad Cojocaru (Sun Jul 27 2003 - 08:57:24 CDT)
Re: AMBER: AMBER and NAMD Andreas Svrcek-Seiler (Sun Jul 27 2003 - 11:10:10 CDT)
Re: AMBER: AMBER and NAMD Vlad Cojocaru (Sun Jul 27 2003 - 12:45:40 CDT)
AMBER: Impropers from Amber parm files to NAMD Vlad Cojocaru (Sun Jul 27 2003 - 12:56:47 CDT)
AMBER: please let me know if this is correct Vlad Cojocaru (Mon Jul 28 2003 - 08:58:55 CDT)
AMBER: Question about quasih analysis Lishan Yao (Mon Jul 28 2003 - 09:04:26 CDT)
Re: AMBER: PMF calculation Carlos Simmerling (Mon Jul 28 2003 - 10:09:45 CDT)
Re: AMBER: strange problem with a small system GUILLERMINA L ESTIU (Mon Jul 28 2003 - 11:00:55 CDT)
Re: AMBER: please let me know if this is correct Andreas Svrcek-Seiler (Mon Jul 28 2003 - 11:07:28 CDT)
Re: AMBER: Question about quasih analysis David A. Case (Mon Jul 28 2003 - 11:16:13 CDT)
Re: AMBER: please let me know if this is correct David A. Case (Mon Jul 28 2003 - 11:55:28 CDT)
Re: AMBER: strange problem with a small system David A. Case (Mon Jul 28 2003 - 12:12:30 CDT)
Re: AMBER: Question about quasih analysis Lishan Yao (Mon Jul 28 2003 - 12:30:26 CDT)
Re: AMBER: Question about quasih analysis David A. Case (Mon Jul 28 2003 - 13:37:20 CDT)
AMBER: ambpdb and residue number Vlad Cojocaru (Mon Jul 28 2003 - 14:47:26 CDT)
Re: AMBER: Question about quasih analysis Lishan Yao (Mon Jul 28 2003 - 15:24:19 CDT)
Re: AMBER: Question about quasih analysis David A. Case (Mon Jul 28 2003 - 16:40:48 CDT)
AMBER: H-O-H angle in TIP3P water model during minimization Vlad Cojocaru (Mon Jul 28 2003 - 19:42:10 CDT)
RE: AMBER: H-O-H angle in TIP3P water model during minimization Yong Duan (Mon Jul 28 2003 - 19:54:28 CDT)
AMBER: chemical potential Petrodler_at_aol.com (Tue Jul 29 2003 - 01:28:57 CDT)
Re: AMBER: chemical potential David A. Case (Tue Jul 29 2003 - 09:50:23 CDT)
AMBER: dynamics of isolated system Herbert Georg (Tue Jul 29 2003 - 13:19:18 CDT)
Re: AMBER: dynamics of isolated system Vlad Cojocaru (Tue Jul 29 2003 - 13:50:52 CDT)
Re: AMBER: dynamics of isolated system Dr. Yong Duan (Tue Jul 29 2003 - 14:04:42 CDT)
Re: AMBER: dynamics of isolated system Herbert Georg (Tue Jul 29 2003 - 14:05:45 CDT)
Re: AMBER: dynamics of isolated system Herbert Georg (Tue Jul 29 2003 - 14:27:15 CDT)
Re: AMBER: dynamics of isolated system Dr. Yong Duan (Tue Jul 29 2003 - 15:16:35 CDT)
AMBER: combine prep files Mi-Kyung Seo (Tue Jul 29 2003 - 16:14:52 CDT)
Re: AMBER: combine prep files David A. Case (Tue Jul 29 2003 - 19:27:57 CDT)
Re: AMBER: dynamics of isolated system David A. Case (Tue Jul 29 2003 - 19:35:03 CDT)
Re: AMBER: chemical potential Petrodler_at_aol.com (Wed Jul 30 2003 - 02:50:05 CDT)
AMBER: Ewald_Bomb Susanna Monti (Wed Jul 30 2003 - 08:37:40 CDT)
AMBER: Ewald problem Shuang Ding (Wed Jul 30 2003 - 11:08:55 CDT)
Re: AMBER: Ewald_Bomb David A. Case (Wed Jul 30 2003 - 11:30:13 CDT)
Re: AMBER: chemical potential David A. Case (Wed Jul 30 2003 - 11:31:34 CDT)
Re: AMBER: Ewald problem David A. Case (Wed Jul 30 2003 - 12:01:49 CDT)
Re: AMBER: Ewald problem Shuang Ding (Wed Jul 30 2003 - 12:28:31 CDT)
AMBER: (no subject) Mi-Kyung Seo (Wed Jul 30 2003 - 14:00:49 CDT)
Re: AMBER: (no subject) Junmei Wang (Wed Jul 30 2003 - 14:34:54 CDT)
AMBER: compile problem Shuang Ding (Wed Jul 30 2003 - 15:59:08 CDT)
AMBER: Aki Hoji (Wed Jul 30 2003 - 16:19:02 CDT)
AMBER: frequency analysis Lishan Yao (Wed Jul 30 2003 - 16:43:16 CDT)
Re: AMBER: frequency analysis Piotr Cieplak (Wed Jul 30 2003 - 16:49:08 CDT)
Re: AMBER: compile problem David A. Case (Wed Jul 30 2003 - 16:56:58 CDT)
Re: AMBER: compile problem Scott Brozell (Wed Jul 30 2003 - 16:58:55 CDT)
AMBER: question about ptraj Ioana Cozmuta (Wed Jul 30 2003 - 17:07:21 CDT)
Re: AMBER: question about ptraj Thomas E. Cheatham, III (Wed Jul 30 2003 - 17:38:52 CDT)
RE: AMBER: frequency analysis Yong Duan (Wed Jul 30 2003 - 18:04:00 CDT)
AMBER: parallelisation gold gunaseelan (Thu Jul 31 2003 - 07:42:25 CDT)
AMBER: parallelisation gold gunaseelan (Thu Jul 31 2003 - 07:42:32 CDT)
AMBER: Running Amber on MacOSX(XDarwin) Aki Hoji (Thu Jul 31 2003 - 09:10:16 CDT)
AMBER: add Ran Ye (Thu Jul 31 2003 - 15:08:30 CDT)
AMBER: chage WATBOX216 Ioana Cozmuta (Thu Jul 31 2003 - 16:10:44 CDT)
Re: AMBER: add Scott Brozell (Thu Jul 31 2003 - 16:51:46 CDT)
Re: AMBER: add Ran Ye (Thu Jul 31 2003 - 17:03:43 CDT)
Re: AMBER: add Scott Brozell (Thu Jul 31 2003 - 18:45:54 CDT)
AMBER: parallelisation gold gunaseelan (Fri Aug 01 2003 - 01:13:21 CDT)
AMBER: parallelisation gold gunaseelan (Fri Aug 01 2003 - 01:12:33 CDT)
AMBER: Amber parallelisation arun prasad (Fri Aug 01 2003 - 04:15:05 CDT)
AMBER: Problem generating .tpp and .rst files for a complex Yogesh Sabnis (Fri Aug 01 2003 - 05:57:07 CDT)
AMBER: Restrain of dihedral angle! Marco Aurelio Correia Preto (Fri Aug 01 2003 - 05:59:08 CDT)
RE: AMBER: parallelisation Yong Duan (Fri Aug 01 2003 - 07:21:36 CDT)
RE: AMBER: Amber parallelisation Yong Duan (Fri Aug 01 2003 - 07:28:31 CDT)
AMBER: RE: Restrain of dihedral angle! Yong Duan (Fri Aug 01 2003 - 08:27:04 CDT)
Re: AMBER: Amber parallelisation David A. Case (Fri Aug 01 2003 - 10:18:17 CDT)
Re: AMBER: Problem generating .tpp and .rst files for a complex David A. Case (Fri Aug 01 2003 - 10:32:24 CDT)
Re: AMBER: Restrain of dihedral angle! Luis Gracia (Fri Aug 01 2003 - 11:14:21 CDT)
AMBER: AMBER7 & mpich takanori.kanazawa_at_pharma.novartis.com (Sat Aug 02 2003 - 07:17:52 CDT)
Re: AMBER: AMBER7 & mpich Carlos Simmerling (Sat Aug 02 2003 - 07:53:26 CDT)
AMBER: AMBER7 & mpich : (no-attachment version) takanori.kanazawa_at_pharma.novartis.com (Sat Aug 02 2003 - 08:03:06 CDT)
Re: AMBER: AMBER7 & mpich : (no-attachment version) Natasja Brooijmans (Sat Aug 02 2003 - 13:24:59 CDT)
Re: AMBER: AMBER7 & mpich : (no-attachment version) David A. Case (Sat Aug 02 2003 - 15:30:00 CDT)
AMBER: xplor2amber Mahadevan Seetharaman (Sat Aug 02 2003 - 21:35:48 CDT)
AMBER: xplor2amber Mahadevan Seetharaman (Sat Aug 02 2003 - 21:34:24 CDT)
AMBER: charge method of antechamber Helios Chen (Sun Aug 03 2003 - 23:00:35 CDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 02:32:48 CDT)
RE: AMBER: Restrain of dihedral angle! Marco Aurelio Correia Preto (Mon Aug 04 2003 - 04:15:22 CDT)
AMBER: separate thermostats for different molecules Arvid Soederhaell (Mon Aug 04 2003 - 08:13:11 CDT)
Re: AMBER: charge method of antechamber Junmei Wang (Mon Aug 04 2003 - 09:39:58 CDT)
AMBER: normal mode analysis Marcela Madrid (Mon Aug 04 2003 - 13:03:23 CDT)
AMBER: Re: AMBER7 & mpich : (no-attachment version) takanori.kanazawa_at_pharma.novartis.com (Mon Aug 04 2003 - 18:51:17 CDT)
Re: AMBER: normal mode analysis David A. Case (Tue Aug 05 2003 - 00:12:36 CDT)
Re: AMBER: separate thermostats for different molecules David A. Case (Tue Aug 05 2003 - 00:19:02 CDT)
Re: AMBER: charge method of antechamber David A. Case (Tue Aug 05 2003 - 00:24:00 CDT)
AMBER: (no subject) Narang Manpreet Kaur (Tue Aug 05 2003 - 08:55:57 CDT)
AMBER: parallelisation gold gunaseelan (Tue Aug 05 2003 - 08:55:31 CDT)
AMBER: zero free energy change for nonbond leg of electrst. decoupling Alfonso Garcia Sosa (Tue Aug 05 2003 - 09:03:59 CDT)
Re: AMBER: (no subject) David A. Case (Tue Aug 05 2003 - 14:32:56 CDT)
Re: AMBER: zero free energy change for nonbond leg of electrst. decoupling David A. Case (Tue Aug 05 2003 - 14:39:22 CDT)
AMBER: compile problem? Shuang Ding (Tue Aug 05 2003 - 15:51:25 CDT)
Re: AMBER: zero free energy change for nonbond leg of electrst. decoupling Alfonso Garcia Sosa (Tue Aug 05 2003 - 16:12:10 CDT)
Re: AMBER: parallelisation Jian Zhang (Wed Aug 06 2003 - 07:39:22 CDT)
AMBER: Comparing PE of different conformations Pratul K. Agarwal (Wed Aug 06 2003 - 11:14:03 CDT)
Re: AMBER: Comparing PE of different conformations Carlos Simmerling (Wed Aug 06 2003 - 11:33:42 CDT)
Re: AMBER: Comparing PE of different conformations Pratul K. Agarwal (Wed Aug 06 2003 - 11:40:16 CDT)
Re: AMBER: Comparing PE of different conformations Carlos Simmerling (Wed Aug 06 2003 - 11:45:53 CDT)
AMBER: problem regarding surface Vikas Varshney (Wed Aug 06 2003 - 12:00:09 CDT)
AMBER: anal - memory problem sd233_at_georgetown.edu (Wed Aug 06 2003 - 12:02:44 CDT)
Re: AMBER: anal - memory problem David A. Case (Wed Aug 06 2003 - 14:00:32 CDT)
AMBER: SHAKE Problem Richard Smith (Wed Aug 06 2003 - 15:02:30 CDT)
Re: AMBER: SHAKE Problem Xavier Periole (Wed Aug 06 2003 - 15:26:05 CDT)
AMBER: Re: dynamics of isolated system (fwd) David A. Case (Wed Aug 06 2003 - 16:43:29 CDT)
Re: AMBER: SHAKE Problem David A. Case (Wed Aug 06 2003 - 16:52:21 CDT)
Re: AMBER: Re: AMBER7 & mpich : (no-attachment version) takanori.kanazawa_at_pharma.novartis.com (Wed Aug 06 2003 - 23:11:30 CDT)
AMBER: references about AMBER MD simulations sd233_at_georgetown.edu (Thu Aug 07 2003 - 00:23:35 CDT)
Re: AMBER: references about AMBER MD simulations David A. Case (Thu Aug 07 2003 - 01:21:05 CDT)
Re: AMBER: Re: AMBER7 & mpich : (no-attachment version) Scott Brozell (Thu Aug 07 2003 - 02:40:06 CDT)
AMBER: about the npscal, box size changes and rms Haizhen Zhong (Thu Aug 07 2003 - 09:05:08 CDT)
RE: AMBER: SHAKE Problem Richard Smith (Thu Aug 07 2003 - 09:42:56 CDT)
AMBER: 2D periodic box Vikas Varshney (Thu Aug 07 2003 - 09:50:20 CDT)
AMBER: one more line about the npscal, box size changes and rms Haizhen Zhong (Thu Aug 07 2003 - 09:58:31 CDT)
Re: AMBER: references about AMBER MD simulations sd233_at_georgetown.edu (Thu Aug 07 2003 - 10:04:39 CDT)
Re: AMBER: one more line about the npscal, box size changes and rms Andy Purkiss (Thu Aug 07 2003 - 10:30:25 CDT)
a bug? Re: AMBER: one more line about the npscal, box size changes and rms Dr. Yong Duan (Thu Aug 07 2003 - 10:49:10 CDT)
Re: AMBER: 2D periodic box David A. Case (Thu Aug 07 2003 - 11:28:09 CDT)
Re: AMBER: 2D periodic box Teletchéa Stéphane (Thu Aug 07 2003 - 11:52:01 CDT)
Re: AMBER: PMEMD and sander from AMBER6 performances Teletchéa Stéphane (Thu Aug 07 2003 - 11:55:03 CDT)
Re: AMBER: 2D periodic box Ioana Cozmuta (Thu Aug 07 2003 - 12:00:22 CDT)
Re: a bug? Re: AMBER: one more line about the npscal, box size changes and rms Haizhen Zhong (Thu Aug 07 2003 - 12:54:17 CDT)
AMBER: mpi in mm-pbsa Shuang Ding (Thu Aug 07 2003 - 12:57:03 CDT)
Re: AMBER: Comparing PE of different conformations Pratul K. Agarwal (Thu Aug 07 2003 - 13:21:07 CDT)
Re: a bug? Re: AMBER: one more line about the npscal, box size changes and rms David A. Case (Thu Aug 07 2003 - 13:35:46 CDT)
RE: a bug? Re: AMBER: one more line about the npscal, box size changes and rms Yong Duan (Thu Aug 07 2003 - 13:49:39 CDT)
Re: AMBER: PMEMD and sander from AMBER6 performances Robert Duke (Thu Aug 07 2003 - 14:01:39 CDT)
AMBER: import pdb file in xleap Mi-Kyung Seo (Thu Aug 07 2003 - 14:07:17 CDT)
Re: AMBER: import pdb file in xleap Vikas Varshney (Thu Aug 07 2003 - 14:21:32 CDT)
Re: AMBER: mpi in mm-pbsa Holger Gohlke (Thu Aug 07 2003 - 14:22:53 CDT)
AMBER: more than 100,000 atoms ? David Smith (Thu Aug 07 2003 - 14:44:23 CDT)
Re: AMBER: Comparing PE of different conformations Carlos Simmerling (Thu Aug 07 2003 - 14:57:11 CDT)
Re: AMBER: mpi in mm-pbsa Shuang Ding (Thu Aug 07 2003 - 15:14:53 CDT)
Re: AMBER: more than 100,000 atoms ? Robert Duke (Thu Aug 07 2003 - 15:33:36 CDT)
Re: AMBER: more than 100,000 atoms ? darden (Thu Aug 07 2003 - 16:23:25 CDT)
AMBER: PMEMD and EAMBER Kristina Furse (Thu Aug 07 2003 - 15:32:45 CDT)
Re: AMBER: PMEMD and EAMBER Robert Duke (Thu Aug 07 2003 - 16:06:11 CDT)
AMBER: About the limitation of characters on one line in carnal input fi le Ming Lei (Thu Aug 07 2003 - 16:16:26 CDT)
Re: AMBER: import pdb file in xleap David A. Case (Thu Aug 07 2003 - 16:30:51 CDT)
Re: AMBER: About the limitation of characters on one line in carnal input fi le Bill Ross (Thu Aug 07 2003 - 17:01:40 CDT)
AMBER: Insight pdb file in xleap Mi-Kyung Seo (Thu Aug 07 2003 - 18:09:47 CDT)
Re: AMBER: import pdb file in xleap Scott Brozell (Thu Aug 07 2003 - 18:25:18 CDT)
Re: AMBER: Insight pdb file in xleap Rhonda Torres (Thu Aug 07 2003 - 18:29:47 CDT)
RE: AMBER: Insight pdb file in xleap Yong Duan (Thu Aug 07 2003 - 18:35:03 CDT)
Re: AMBER: About the limitation of characters on one line in carnal input fi le Bill Ross (Thu Aug 07 2003 - 16:31:39 CDT)
AMBER: Insight pdb file in xleap Wayne Dawson (Thu Aug 07 2003 - 21:33:26 CDT)
AMBER: saveamberprep in xLeap Mi-Kyung Seo (Thu Aug 07 2003 - 22:38:24 CDT)
Re: AMBER: Insight pdb file in xleap Gaurav Sahni (Fri Aug 08 2003 - 01:25:42 CDT)
AMBER: derive corresponding torsional parameters yuann (Fri Aug 08 2003 - 05:25:31 CDT)
AMBER: Reference for Amber7 heme parameters Ross Walker (Fri Aug 08 2003 - 06:41:30 CDT)
Re: AMBER: derive corresponding torsional parameters David Smith (Fri Aug 08 2003 - 08:39:57 CDT)
AMBER: water model tianxiao yang (Fri Aug 08 2003 - 10:10:04 CDT)
Re: AMBER: more than 100,000 atoms ? David Smith (Fri Aug 08 2003 - 10:17:39 CDT)
Re: AMBER: Reference for Amber7 heme parameters David A. Case (Fri Aug 08 2003 - 10:23:46 CDT)
Re[2]: AMBER: derive corresponding torsional parameters sychen (Fri Aug 08 2003 - 10:43:43 CDT)
Re: Re[2]: AMBER: derive corresponding torsional parameters David Smith (Fri Aug 08 2003 - 11:20:32 CDT)
Re: AMBER: saveamberprep in xLeap David A. Case (Fri Aug 08 2003 - 11:38:34 CDT)
AMBER: saveamberprep and saveoff in xLeap Mi-Kyung Seo (Fri Aug 08 2003 - 12:39:37 CDT)
RE: AMBER: more than 100,000 atoms ? Kristina Furse (Fri Aug 08 2003 - 13:14:10 CDT)
RE: AMBER: PMEMD and EAMBER Kristina Furse (Fri Aug 08 2003 - 13:33:28 CDT)
AMBER: PMEMD NMR Restraints fix Robert Duke (Fri Aug 08 2003 - 17:13:08 CDT)
AMBER: MD simulation with ATP and MG Thomas Steinbrecher (Mon Aug 11 2003 - 04:45:08 CDT)
Re: AMBER: MD simulation with ATP and MG Heather A.Carlson (Mon Aug 11 2003 - 07:11:27 CDT)
Re: Fw: AMBER: PMEMD and EAMBER Robert Duke (Mon Aug 11 2003 - 08:49:36 CDT)
AMBER: machine dependent? Shuang Ding (Mon Aug 11 2003 - 13:39:10 CDT)
Re: AMBER: machine dependent? David A. Case (Mon Aug 11 2003 - 15:46:14 CDT)
AMBER: GLYCAM Herbert Georg (Mon Aug 11 2003 - 15:57:37 CDT)
AMBER: How to develop parameters for metallic atoms Gustavo A. Carri (Mon Aug 11 2003 - 16:11:19 CDT)
Re: AMBER: machine dependent? Shuang Ding (Mon Aug 11 2003 - 17:01:38 CDT)
AMBER: "irstrnt=1"in input file for RESP Mi-Kyung Seo (Mon Aug 11 2003 - 17:26:30 CDT)
Re: AMBER: machine dependent? Michael Crowley (Tue Aug 12 2003 - 09:24:58 CDT)
Re: AMBER: machine dependent? Shuang Ding (Tue Aug 12 2003 - 13:48:00 CDT)
AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Margaret S. Cheung (Tue Aug 12 2003 - 13:56:47 CDT)
Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. David A. Case (Tue Aug 12 2003 - 14:23:55 CDT)
Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Thomas E. Cheatham, III (Tue Aug 12 2003 - 14:32:36 CDT)
AMBER: constant energy simulation Lishan Yao (Tue Aug 12 2003 - 14:38:49 CDT)
Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Margaret S. Cheung (Tue Aug 12 2003 - 14:46:24 CDT)
Re: AMBER: constant energy simulation Xavier Periole (Tue Aug 12 2003 - 14:51:24 CDT)
Re: AMBER: constant energy simulation Lishan Yao (Tue Aug 12 2003 - 17:25:37 CDT)
Re: AMBER: constant energy simulation Xavier Periole (Tue Aug 12 2003 - 17:39:29 CDT)
AMBER: Antechamber functionality, MOL2 files bigbrainstorm (Tue Aug 12 2003 - 21:50:40 CDT)
AMBER: secondary structure Yuguang Mu (Wed Aug 13 2003 - 07:37:08 CDT)
Re: AMBER: constant energy simulation Lishan Yao (Wed Aug 13 2003 - 08:00:20 CDT)
Re: AMBER: constant energy simulation Andreas Svrcek-Seiler (Wed Aug 13 2003 - 08:50:32 CDT)
Re: AMBER: secondary structure Holger Gohlke (Wed Aug 13 2003 - 09:55:22 CDT)
Re: AMBER: constant energy simulation Lishan Yao (Wed Aug 13 2003 - 10:07:29 CDT)
Re: AMBER: Antechamber functionality, MOL2 files Junmei Wang (Wed Aug 13 2003 - 10:06:47 CDT)
Re: AMBER: constant energy simulation David A. Case (Wed Aug 13 2003 - 10:46:52 CDT)
Re: AMBER: constant energy simulation Lishan Yao (Wed Aug 13 2003 - 11:09:14 CDT)
Re: AMBER: Antechamber functionality, MOL2 files Junmei Wang (Wed Aug 13 2003 - 11:28:03 CDT)
Re: AMBER: Antechamber functionality, MOL2 files bigbrainstorm (Wed Aug 13 2003 - 11:20:09 CDT)
AMBER: amber-on-cheetah-question Endres, Robert G. (Wed Aug 13 2003 - 14:20:10 CDT)
AMBER: ANAL component sd233_at_georgetown.edu (Wed Aug 13 2003 - 16:36:56 CDT)
AMBER: Atom type in prepin file Yong-Liang Zhu (Wed Aug 13 2003 - 17:21:28 CDT)
Re: AMBER: Atom type in prepin file Rhonda Torres (Wed Aug 13 2003 - 17:38:26 CDT)
AMBER: complete pdb structure Mi-Kyung Seo (Wed Aug 13 2003 - 17:41:52 CDT)
Re: AMBER: ANAL component David A. Case (Wed Aug 13 2003 - 17:45:36 CDT)
Re: AMBER: constant energy simulation David A. Case (Wed Aug 13 2003 - 17:52:56 CDT)
RE: AMBER: Atom type in prepin file - new problem Yong-Liang Zhu (Wed Aug 13 2003 - 18:05:01 CDT)
RE: AMBER: Atom type in prepin file - new problem John Bushnell (Wed Aug 13 2003 - 19:01:21 CDT)
Re: AMBER: complete pdb structure David A. Case (Thu Aug 14 2003 - 00:30:08 CDT)
AMBER: modelling a Ca binding site Karsten Suhre (Thu Aug 14 2003 - 04:36:53 CDT)
AMBER: simulating a crystal using the unit cell Sarah Wittkopp (Thu Aug 14 2003 - 06:09:07 CDT)
Re: AMBER: simulating a crystal using the unit cell David A. Case (Thu Aug 14 2003 - 10:40:42 CDT)
Re: AMBER: constant energy simulation Lishan Yao (Thu Aug 14 2003 - 10:53:13 CDT)
Re: AMBER: simulating a crystal using the unit cell Joseph Nachman (Thu Aug 14 2003 - 11:01:34 CDT)
Re: AMBER: modelling a Ca binding site Xavier Periole (Thu Aug 14 2003 - 12:07:26 CDT)
AMBER: minimization error Venkata S Koppuravuri (Thu Aug 14 2003 - 13:23:39 CDT)
Re: AMBER: minimization error Xavier Periole (Thu Aug 14 2003 - 13:38:39 CDT)
Re: AMBER: minimization error David A. Case (Thu Aug 14 2003 - 13:41:43 CDT)
AMBER: How to add new atom type. Yong-Liang Zhu (Thu Aug 14 2003 - 14:49:49 CDT)
RE: AMBER: minimization error Yong Duan (Thu Aug 14 2003 - 15:56:54 CDT)
AMBER: Problems with extra points on parralellized linux and sgi machine Sarah Wittkopp (Fri Aug 15 2003 - 02:07:11 CDT)
Re: AMBER: modelling a Ca binding site Karsten Suhre (Fri Aug 15 2003 - 04:44:09 CDT)
AMBER: Hydrogen bond plot from carnal Layi Adekoya (Fri Aug 15 2003 - 05:16:02 CDT)
AMBER: Gibbs pmf calculation Lishan Yao (Fri Aug 15 2003 - 10:35:51 CDT)
Re: AMBER: Problems with extra points on parralellized linux and sgi machine David A. Case (Fri Aug 15 2003 - 11:17:15 CDT)
Re: AMBER: Gibbs pmf calculation David A. Case (Fri Aug 15 2003 - 11:51:07 CDT)
AMBER: protonation states of small molecules Lee, Matthew (Fri Aug 15 2003 - 13:33:40 CDT)
AMBER: NTX 5 or 7 after equilibration in constant pressure? Majid moghaddam (Sat Aug 16 2003 - 02:08:38 CDT)
AMBER: Is NTC=2 correct for minimization when hydrogens are added? Majid moghaddam (Sat Aug 16 2003 - 03:00:04 CDT)
Re: AMBER: Is NTC=2 correct for minimization when hydrogens are added? Alexey Onufriev (Sat Aug 16 2003 - 11:37:35 CDT)
AMBER: minimum image convention mystery Martin Mucha (Sat Aug 16 2003 - 15:42:37 CDT)
Re: AMBER: minimum image convention mystery David A. Case (Sat Aug 16 2003 - 19:02:03 CDT)
Re: AMBER: NTX 5 or 7 after equilibration in constant pressure? David A. Case (Sat Aug 16 2003 - 19:04:18 CDT)
AMBER: large changes in xyz coordinates Sivakolundu, Sivashankar (Sat Aug 16 2003 - 20:06:14 CDT)
Re: AMBER: large changes in xyz coordinates David A. Case (Sat Aug 16 2003 - 23:07:25 CDT)
Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Ioana Cozmuta (Sun Aug 17 2003 - 22:08:00 CDT)
AMBER: AMBER 7_make install Krishna Bisetty (Mon Aug 18 2003 - 02:36:37 CDT)
AMBER: Hydrogen bond plot from carnal Layi Adekoya (Mon Aug 18 2003 - 02:51:51 CDT)
Re: AMBER: Problems with extra points on parralellized linux and sgi machine Sarah Wittkopp (Mon Aug 18 2003 - 02:33:36 CDT)
AMBER: united atom weiner force field sohail qamar (Mon Aug 18 2003 - 05:46:18 CDT)
Re: AMBER: charge method of antechamber Helios Chen (Mon Aug 18 2003 - 07:39:18 CDT)
AMBER: MM-GB/PBSA:Main-chain/side-chain decomposition in ligands Martin Lepsik (Mon Aug 18 2003 - 08:12:51 CDT)
Re: AMBER: charge method of antechamber(it's ok) Helios Chen (Mon Aug 18 2003 - 08:15:28 CDT)
Re: AMBER: charge method of antechamber(it's ok) Junmei Wang (Mon Aug 18 2003 - 09:26:41 CDT)
Re: AMBER: Problems with extra points on parralellized linux and sgi machine David A. Case (Mon Aug 18 2003 - 10:08:57 CDT)
Re: AMBER: AMBER 7_make install David A. Case (Mon Aug 18 2003 - 10:16:20 CDT)
AMBER: pmemd james tomomi macdonald (Mon Aug 18 2003 - 10:18:47 CDT)
Re: AMBER: united atom weiner force field David A. Case (Mon Aug 18 2003 - 10:21:03 CDT)
Re: AMBER: pmemd Robert Duke (Mon Aug 18 2003 - 10:45:47 CDT)
Re: AMBER: MM-GB/PBSA:Main-chain/side-chain decomposition in ligands Holger Gohlke (Mon Aug 18 2003 - 10:50:49 CDT)
Re: AMBER: pmemd james tomomi macdonald (Mon Aug 18 2003 - 11:05:20 CDT)
Re: AMBER: united atom weiner force field Bill Ross (Mon Aug 18 2003 - 11:12:49 CDT)
Re: AMBER: pmemd Robert Duke (Mon Aug 18 2003 - 11:51:16 CDT)
AMBER: tleap under amber6 Qiang Lu (Mon Aug 18 2003 - 12:32:05 CDT)
AMBER: nmanal in amber7 Qiang Lu (Mon Aug 18 2003 - 12:41:42 CDT)
RE: AMBER: large changes in xyz coordinates Sivakolundu, Sivashankar (Mon Aug 18 2003 - 12:51:49 CDT)
AMBER: ptraj problem Lishan Yao (Mon Aug 18 2003 - 13:22:43 CDT)
RE: AMBER: large changes in xyz coordinates Kristina Furse (Mon Aug 18 2003 - 13:26:27 CDT)
RE: AMBER: large changes in xyz coordinates james tomomi macdonald (Mon Aug 18 2003 - 13:35:18 CDT)
Re: AMBER: nmanal in amber7 David A. Case (Mon Aug 18 2003 - 13:44:20 CDT)
Re: AMBER: tleap under amber6 David A. Case (Mon Aug 18 2003 - 13:48:19 CDT)
Re[2]: AMBER: nmanal in amber7 Qiang Lu (Mon Aug 18 2003 - 14:17:30 CDT)
Re: AMBER: pmemd james tomomi macdonald (Mon Aug 18 2003 - 14:52:32 CDT)
Re: AMBER: nmanal in amber7 David A. Case (Mon Aug 18 2003 - 14:54:04 CDT)
AMBER: overlap problem Ioana Cozmuta (Mon Aug 18 2003 - 16:26:57 CDT)
AMBER: nmanal's error message Qiang Lu (Mon Aug 18 2003 - 17:23:20 CDT)
Re: AMBER: nmanal's error message David Case (Mon Aug 18 2003 - 18:24:11 CDT)
Re[2]: AMBER: nmanal's error message Qiang Lu (Mon Aug 18 2003 - 19:10:29 CDT)
AMBER: prepin file Helios Chen (Tue Aug 19 2003 - 01:53:27 CDT)
AMBER: temperature does not reach to temp0 Majid moghaddam (Tue Aug 19 2003 - 07:32:43 CDT)
AMBER: ptraj problem Lishan Yao (Tue Aug 19 2003 - 16:08:02 CDT)
AMBER: nmanal's rvec file Qiang Lu (Tue Aug 19 2003 - 18:19:27 CDT)
Re: AMBER: nmanal's rvec file David A. Case (Tue Aug 19 2003 - 21:00:19 CDT)
Re: AMBER: prepin file David A. Case (Tue Aug 19 2003 - 10:45:30 CDT)
Re: AMBER: temperature does not reach to temp0 David A. Case (Tue Aug 19 2003 - 10:47:15 CDT)
Re: AMBER: overlap problem Xavier Periole (Tue Aug 19 2003 - 11:23:45 CDT)
AMBER: minimization termination sd233_at_georgetown.edu (Tue Aug 19 2003 - 12:40:53 CDT)
AMBER: PARMSET problem Yichen Cao (Wed Aug 20 2003 - 12:07:29 CDT)
Re: AMBER: PARMSET problem Junmei Wang (Wed Aug 20 2003 - 13:06:00 CDT)
AMBER: PMEMD 3.01 Update available Robert Duke (Wed Aug 20 2003 - 13:36:56 CDT)
AMBER: antechamber problem Qiang Lu (Wed Aug 20 2003 - 13:56:14 CDT)
Re: AMBER: ptraj problem Thomas E. Cheatham, III (Wed Aug 20 2003 - 14:00:57 CDT)
AMBER: gibbs pmf calculation Lishan Yao (Wed Aug 20 2003 - 14:24:29 CDT)
Re: AMBER: antechamber problem David A. Case (Wed Aug 20 2003 - 17:07:30 CDT)
Re: AMBER: gibbs pmf calculation David A. Case (Wed Aug 20 2003 - 17:13:23 CDT)
Re[2]: AMBER: antechamber problem Qiang Lu (Wed Aug 20 2003 - 17:17:30 CDT)
Re[2]: AMBER: antechamber problem Natasja Brooijmans (Wed Aug 20 2003 - 17:26:58 CDT)
AMBER: NTT Herbert Georg (Thu Aug 21 2003 - 11:31:06 CDT)
Re: AMBER: NTT Herbert Georg (Thu Aug 21 2003 - 14:48:17 CDT)
Re: Re[2]: AMBER: antechamber problem Junmei Wang (Thu Aug 21 2003 - 15:16:02 CDT)
Re: Re[2]: AMBER: antechamber problem David A. Case (Thu Aug 21 2003 - 18:34:17 CDT)
AMBER: The FCAP parameter in amber7 Thomas Steinbrecher (Fri Aug 22 2003 - 04:21:35 CDT)
Re: Re[2]: AMBER: antechamber problem Junmei Wang (Fri Aug 22 2003 - 10:03:23 CDT)
AMBER: problems with pmemd james tomomi macdonald (Fri Aug 22 2003 - 10:37:34 CDT)
Re: AMBER: problems with pmemd Robert Duke (Fri Aug 22 2003 - 11:45:47 CDT)
AMBER: PMEMD BUG ALERT!!! Robert Duke (Fri Aug 22 2003 - 15:50:02 CDT)
AMBER: Spartan and AMBER7 Peter Oelschlaeger (Fri Aug 22 2003 - 21:52:21 CDT)
AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Chen, Ya (Fri Aug 22 2003 - 23:47:21 CDT)
Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Robert Duke (Sat Aug 23 2003 - 07:41:49 CDT)
Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Robert Duke (Sat Aug 23 2003 - 09:41:42 CDT)
Fw: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Robert Duke (Sat Aug 23 2003 - 22:44:06 CDT)
Re: AMBER: gibbs pmf calculation Lishan Yao (Mon Aug 25 2003 - 08:16:03 CDT)
Re: AMBER: ptraj problem Lishan Yao (Mon Aug 25 2003 - 08:23:10 CDT)
AMBER: temperature problem Lishan Yao (Mon Aug 25 2003 - 08:37:01 CDT)
AMBER: CARNAL Wen Li (Mon Aug 25 2003 - 09:30:19 CDT)
Re: AMBER: gibbs pmf calculation David A. Case (Mon Aug 25 2003 - 10:25:27 CDT)
RE: AMBER: CARNAL Ming Lei (Mon Aug 25 2003 - 14:27:42 CDT)
RE: AMBER: CARNAL Bill Ross (Mon Aug 25 2003 - 14:40:29 CDT)
Re: AMBER: ptraj problem Bill Ross (Mon Aug 25 2003 - 14:14:23 CDT)
RE: AMBER: CARNAL Ming Lei (Mon Aug 25 2003 - 15:12:50 CDT)
AMBER: Re: apparent PMEMD bug -- NTWPRT > 0 & IWRAP = 1 Robert Duke (Mon Aug 25 2003 - 14:20:48 CDT)
AMBER: Apparent PMEMD bug -- NTWPRT > 0 & IWRAP = 1 Robert Duke (Mon Aug 25 2003 - 15:41:08 CDT)
RE: AMBER: CARNAL Bill Ross (Mon Aug 25 2003 - 15:45:13 CDT)
Re: AMBER: gibbs pmf calculation Lishan Yao (Mon Aug 25 2003 - 16:06:29 CDT)
Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Robert Duke (Mon Aug 25 2003 - 16:33:38 CDT)
Re: AMBER: gibbs pmf calculation David A. Case (Mon Aug 25 2003 - 18:07:16 CDT)
Re: AMBER: The FCAP parameter in amber7 David A. Case (Mon Aug 25 2003 - 18:59:45 CDT)
Re: AMBER: CARNAL Bill Ross (Mon Aug 25 2003 - 14:04:56 CDT)
AMBER: Antechamber formal charges with Gasteiger method Lee, Matthew (Tue Aug 26 2003 - 13:07:14 CDT)
Re: AMBER: Antechamber formal charges with Gasteiger method Junmei Wang (Tue Aug 26 2003 - 14:55:14 CDT)
AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space zhaoxc_at_puccini.che.pitt.edu (Tue Aug 26 2003 - 18:17:00 CDT)
AMBER: xleap memory issue Terry Downing (Tue Aug 26 2003 - 19:30:06 CDT)
Re: AMBER: xleap memory issue Bill Ross (Tue Aug 26 2003 - 19:52:40 CDT)
Re: AMBER: xleap memory issue David A. Case (Tue Aug 26 2003 - 20:25:29 CDT)
Re: AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space David A. Case (Tue Aug 26 2003 - 20:32:20 CDT)
Re: AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space Robert Duke (Tue Aug 26 2003 - 20:53:06 CDT)
AMBER: LEaP not compiling Niko Jukarainen (Wed Aug 27 2003 - 09:50:01 CDT)
Re: AMBER: gibbs pmf calculation Lishan Yao (Wed Aug 27 2003 - 10:34:02 CDT)
Re: AMBER: LEaP not compiling David A. Case (Wed Aug 27 2003 - 10:42:49 CDT)
AMBER: Antechamber Problem Yuhui Cheng (Wed Aug 27 2003 - 11:31:43 CDT)
AMBER: target MD simulation Lishan Yao (Wed Aug 27 2003 - 13:01:46 CDT)
Re: AMBER: target MD simulation Carlos Simmerling (Wed Aug 27 2003 - 14:59:09 CDT)
RE: AMBER: LEaP not compiling John Bushnell (Wed Aug 27 2003 - 16:56:32 CDT)
AMBER: PMF calculation with gibbs Xiao Jian Tan (Wed Aug 27 2003 - 17:34:16 CDT)
RE: AMBER: LEaP not compiling Niko Jukarainen (Wed Aug 27 2003 - 10:58:52 CDT)
Re: AMBER: target MD simulation David A. Case (Wed Aug 27 2003 - 15:39:31 CDT)
AMBER: RESP calculation Yuhui Cheng (Wed Aug 27 2003 - 21:04:57 CDT)
RE: AMBER: LEaP not compiling Niko Jukarainen (Wed Aug 27 2003 - 23:58:24 CDT)
AMBER: "ATTN, need revision" atobak_at_eden.rutgers.edu (Thu Aug 28 2003 - 11:31:05 CDT)
Re: AMBER: "ATTN, need revision" Junmei Wang (Thu Aug 28 2003 - 12:06:46 CDT)
Re: AMBER: Antechamber Problem Junmei Wang (Thu Aug 28 2003 - 12:16:24 CDT)
AMBER: forces estimation Ioana Cozmuta (Thu Aug 28 2003 - 13:54:52 CDT)
AMBER: what can't I use ibelly? nie beining (Thu Aug 28 2003 - 14:30:23 CDT)
Re: AMBER: what can't I use ibelly? David A. Case (Thu Aug 28 2003 - 14:40:55 CDT)
AMBER: Could you please give me an example? Thanks! nie beining (Thu Aug 28 2003 - 15:04:00 CDT)
AMBER: Fxnal form of NMR-style restraints Kristina Furse (Thu Aug 28 2003 - 16:41:56 CDT)
AMBER: usability of mm_pbsa with ligand - membrane protein - complex Frank Boeckler (Thu Aug 28 2003 - 17:20:09 CDT)
Re: AMBER: Fxnal form of NMR-style restraints Holger Gohlke (Thu Aug 28 2003 - 17:41:04 CDT)
Re: AMBER: usability of mm_pbsa with ligand - membrane protein - complex Holger Gohlke (Thu Aug 28 2003 - 18:01:11 CDT)
AMBER: AmberFFC v1.3 released FyD (Fri Aug 29 2003 - 11:35:12 CDT)
AMBER: sander minimization atobak_at_eden.rutgers.edu (Fri Aug 29 2003 - 15:39:58 CDT)
Re: AMBER: sander minimization Qiang Lu (Fri Aug 29 2003 - 16:13:53 CDT)
Re: AMBER: sander minimization David A. Case (Fri Aug 29 2003 - 16:32:55 CDT)
AMBER: processors Herbert Georg (Mon Sep 01 2003 - 14:30:04 CDT)
title card? Re: AMBER: what can't I use ibelly? nie beining (Mon Sep 01 2003 - 21:39:06 CDT)
Re: title card? Re: AMBER: what can't I use ibelly? David A. Case (Mon Sep 01 2003 - 23:18:12 CDT)
AMBER: MIPS R14000 and Machine-file Antonio J.Díaz Quintana (Tue Sep 02 2003 - 03:14:33 CDT)
AMBER: MIPS R14000 and Machine-file Antonio J.Díaz Quintana (Tue Sep 02 2003 - 06:49:37 CDT)
Re: AMBER: MIPS R14000 and Machine-file Sanjeev B.S. (Tue Sep 02 2003 - 07:48:33 CDT)
Re: AMBER: MIPS R14000 and Machine-file David A. Case (Tue Sep 02 2003 - 09:56:26 CDT)
AMBER: error message is the same after I added a title nie beining (Tue Sep 02 2003 - 10:20:11 CDT)
AMBER: PMF ethane example: Can someone correct the INPUT? Thanks. Christophe L M J Verlinde (Tue Sep 02 2003 - 12:57:52 CDT)
AMBER: GLYCAM/AMBER Configurator ayongye_at_sunchem.chem.uga.edu (Tue Sep 02 2003 - 13:36:51 CDT)
AMBER: surften value in mm_gbsa/mm_pbsa calculations Sergio E. Wong (Tue Sep 02 2003 - 14:34:22 CDT)
Re: AMBER: surften value in mm_gbsa/mm_pbsa calculations Holger Gohlke (Tue Sep 02 2003 - 15:30:15 CDT)
AMBER: atomic clash or structure size? atobak_at_eden.rutgers.edu (Tue Sep 02 2003 - 16:08:51 CDT)
Re: AMBER: atomic clash or structure size? Qiang Lu (Tue Sep 02 2003 - 16:20:32 CDT)
Re: AMBER: atomic clash or structure size? David A. Case (Wed Sep 03 2003 - 10:32:42 CDT)
Re: AMBER: PMF ethane example: Can someone correct the INPUT? Thanks. David A. Case (Wed Sep 03 2003 - 10:38:56 CDT)
Re: AMBER: processors Scott Brozell (Thu Sep 04 2003 - 11:50:10 CDT)
AMBER: charge of IRON in HEME!! Pradipta Bandyopadhyay (Thu Sep 04 2003 - 19:28:11 CDT)
Re: AMBER: charge of IRON in HEME!! Qiang Lu (Thu Sep 04 2003 - 19:40:48 CDT)
AMBER: problems with periodic boundary conditions Monika Fuxreiter (Fri Sep 05 2003 - 04:17:40 CDT)
AMBER: DNA helix is not in z-direction A. Hungie (Fri Sep 05 2003 - 04:35:50 CDT)
AMBER: IG value SEKIJIMA Masakazu (Fri Sep 05 2003 - 06:50:05 CDT)
Re: AMBER: IG value Carlos Simmerling (Fri Sep 05 2003 - 06:57:07 CDT)
Re: AMBER: problems with periodic boundary conditions Michael Crowley (Fri Sep 05 2003 - 09:32:29 CDT)
Re: AMBER: problems with periodic boundary conditions David A. Case (Fri Sep 05 2003 - 09:43:29 CDT)
Re: AMBER: IG value David A. Case (Fri Sep 05 2003 - 09:46:58 CDT)
AMBER: Accuracy of PB solvation energy Qing Zhang (Fri Sep 05 2003 - 12:15:15 CDT)
Re: AMBER: Accuracy of PB solvation energy Jiri Sponer (Fri Sep 05 2003 - 12:46:04 CDT)
AMBER: Using NWCHEM for esp? David E. Konerding DSD Staff (Fri Sep 05 2003 - 12:59:45 CDT)
RE: AMBER: charge of IRON in HEME!! Ming Lei (Fri Sep 05 2003 - 13:15:32 CDT)
AMBER: 'ho' vDW parameters Lee, Matthew (Fri Sep 05 2003 - 17:33:12 CDT)
Re: AMBER: DNA helix is not in z-direction David A. Case (Fri Sep 05 2003 - 19:37:20 CDT)
Re: AMBER: Using NWCHEM for esp? Peter Oelschlaeger (Fri Sep 05 2003 - 23:03:29 CDT)
AMBER: solvatebox-solvateshell Majid moghaddam (Sat Sep 06 2003 - 06:42:55 CDT)
AMBER: charge definition Khanh KIm Dao (Sat Sep 06 2003 - 13:40:31 CDT)
Re: AMBER: charge definition Holger Gohlke (Sat Sep 06 2003 - 14:00:01 CDT)
Re: AMBER: solvatebox-solvateshell David A. Case (Sat Sep 06 2003 - 14:56:39 CDT)
AMBER: update to answer about solvateShell David A. Case (Sat Sep 06 2003 - 15:00:50 CDT)
Re: AMBER: solvatebox-solvateshell Thomas E. Cheatham, III (Sat Sep 06 2003 - 15:16:38 CDT)
Re: AMBER: Using NWCHEM for esp? FyD (Sun Sep 07 2003 - 16:19:33 CDT)
AMBER: dielectric constant for blends Taner E. Dirama (Mon Sep 08 2003 - 09:21:11 CDT)
Re: AMBER: dielectric constant for blends David A. Case (Mon Sep 08 2003 - 10:23:34 CDT)
AMBER: parm. and top. for sugars, charmm? Endres, Robert G. (Mon Sep 08 2003 - 11:05:00 CDT)
Re: AMBER: 'ho' vDW parameters Junmei Wang (Mon Sep 08 2003 - 15:01:25 CDT)
Re: AMBER: 'ho' vDW parameters Carlos Simmerling (Mon Sep 08 2003 - 15:10:13 CDT)
RE: AMBER: 'ho' vDW parameters Yong Duan (Mon Sep 08 2003 - 15:27:48 CDT)
Re: AMBER: solvatebox-solvateshell Xavier Periole (Mon Sep 08 2003 - 16:46:00 CDT)
AMBER: Compiling 64-bit version on AIX Pratul K. Agarwal (Mon Sep 08 2003 - 21:00:55 CDT)
Re: AMBER: parm. and top. for sugars, charmm? Itziar Maestre Asenjo (Tue Sep 09 2003 - 00:57:27 CDT)
Re: AMBER: Compiling 64-bit version on AIX Nicolas Grima (Tue Sep 09 2003 - 02:11:03 CDT)
AMBER: radial distribution-function by Ptraj Petrodler_at_aol.com (Tue Sep 09 2003 - 04:15:10 CDT)
AMBER: reporting atoms clashed during simple energy minimization jackie_at_ibms.sinica.edu.tw (Tue Sep 09 2003 - 05:19:36 CDT)
AMBER: SHAKE poblem with dummy atoms Itziar Maestre Asenjo (Tue Sep 09 2003 - 05:06:57 CDT)
Re: AMBER: reporting atoms clashed during simple energy minimization Dr. Yong Duan (Tue Sep 09 2003 - 07:18:44 CDT)
AMBER: PMF calculations Sébastien Canneaux (Tue Sep 09 2003 - 07:29:36 CDT)
AMBER: TIP5P Ulf Johansson (Tue Sep 09 2003 - 08:27:27 CDT)
Re: AMBER: TIP5P David A. Case (Tue Sep 09 2003 - 10:32:58 CDT)
Re: AMBER: reporting atoms clashed during simple energy minimization David A. Case (Tue Sep 09 2003 - 10:36:29 CDT)
Re: AMBER: SHAKE poblem with dummy atoms David A. Case (Tue Sep 09 2003 - 10:38:49 CDT)
Re: AMBER: Compiling 64-bit version on AIX Pratul K. Agarwal (Tue Sep 09 2003 - 10:45:58 CDT)
Re: AMBER: Compiling 64-bit version on AIX Carlos P. Sosa (Tue Sep 09 2003 - 11:06:39 CDT)
Re: AMBER: Compiling 64-bit version on AIX David A. Case (Tue Sep 09 2003 - 11:36:12 CDT)
Re: AMBER: Compiling 64-bit version on AIX Pratul K. Agarwal (Tue Sep 09 2003 - 12:01:13 CDT)
Re: AMBER: TIP5P Ulf Johansson (Wed Sep 10 2003 - 02:37:36 CDT)
Re: AMBER: TIP5P David A. Case (Wed Sep 10 2003 - 10:14:18 CDT)
AMBER: Re: torsional energy David A. Case (Wed Sep 10 2003 - 17:15:34 CDT)
AMBER: altering mass in .top file hagop demirdjian (Thu Sep 11 2003 - 04:07:02 CDT)
Re: AMBER: altering mass in .top file Pascal Bonnet (Thu Sep 11 2003 - 05:05:15 CDT)
AMBER: EWALD BOMB and solvent density problem northrop_at_chem.ucla.edu (Thu Sep 11 2003 - 13:28:51 CDT)
AMBER: ptraj question Lishan Yao (Thu Sep 11 2003 - 14:48:08 CDT)
AMBER: gaff parameters astrid.maass (Fri Sep 12 2003 - 04:10:32 CDT)
AMBER: DMSO box Dalmaris, John (Fri Sep 12 2003 - 04:25:21 CDT)
Re: AMBER: gaff parameters Kazuo Koyano (Fri Sep 12 2003 - 05:31:33 CDT)
AMBER: FF parameters for BOC - group Balvinder Singh (Fri Sep 12 2003 - 12:38:34 CDT)
Re: AMBER: FF parameters for BOC - group Martin Lepsik (Fri Sep 12 2003 - 09:57:24 CDT)
AMBER: minimization error Venkata S Koppuravuri (Fri Sep 12 2003 - 14:00:05 CDT)
Re: AMBER: minimization error Scott Brozell (Fri Sep 12 2003 - 14:24:37 CDT)
Re: AMBER: minimization error David A. Case (Fri Sep 12 2003 - 16:19:48 CDT)
Re: AMBER: gaff parameters Junmei Wang (Fri Sep 12 2003 - 16:46:24 CDT)
Re: AMBER: DMSO box Jiten (Fri Sep 12 2003 - 20:05:46 CDT)
AMBER: AMBER on LINUX ?? (fwd) sangeeta_at_bioinfo.ernet.in (Mon Sep 15 2003 - 01:57:20 CDT)
Re: AMBER: AMBER on LINUX ?? (fwd) Sanjeev B.S. (Mon Sep 15 2003 - 04:17:01 CDT)
AMBER: AMBER error in CHALANGE sd233_at_georgetown.edu (Mon Sep 15 2003 - 10:58:31 CDT)
Re: AMBER: AMBER error in CHALANGE Carlos Simmerling (Mon Sep 15 2003 - 11:04:26 CDT)
AMBER: sander on cygwin Lee, Matthew (Mon Sep 15 2003 - 13:14:40 CDT)
Re: AMBER: sander on cygwin David E. Konerding DSD Staff (Mon Sep 15 2003 - 13:24:29 CDT)
AMBER: performance vs number of processors GUILLERMINA L ESTIU (Mon Sep 15 2003 - 13:58:37 CDT)
Re: AMBER: performance vs number of processors zhaoxc_at_puccini.che.pitt.edu (Mon Sep 15 2003 - 14:41:20 CDT)
Re: AMBER: performance vs number of processors David A. Case (Mon Sep 15 2003 - 14:53:32 CDT)
Re: AMBER: sander on cygwin David A. Case (Mon Sep 15 2003 - 15:03:23 CDT)
Re: AMBER: AMBER error in CHALANGE David A. Case (Mon Sep 15 2003 - 15:06:21 CDT)
Re: AMBER: AMBER on LINUX ?? (fwd) David A. Case (Mon Sep 15 2003 - 15:08:56 CDT)
AMBER: Benchmark of AMBER on Apple G5 machine Mengjuei Hsieh (Mon Sep 15 2003 - 15:56:43 CDT)
Re: AMBER: sander on cygwin David E. Konerding DSD Staff (Mon Sep 15 2003 - 16:21:57 CDT)
AMBER: PMEMD: dual XEON vs SGI cluster Chris Moth (Tue Sep 16 2003 - 16:46:45 CDT)
Re: AMBER: PMEMD: dual XEON vs SGI cluster Robert Duke (Mon Sep 15 2003 - 17:55:28 CDT)
Re: AMBER: PMEMD: dual XEON vs SGI cluster Johannes Zuegg (Mon Sep 15 2003 - 18:45:27 CDT)
RE: AMBER: PMEMD: dual XEON vs SGI cluster Chris Moth (Mon Sep 15 2003 - 20:55:46 CDT)
AMBER: MD simulations on small molecules immersed in sparse water shell Junmei Wang (Tue Sep 16 2003 - 11:42:56 CDT)
Re: AMBER: MD simulations on small molecules immersed in sparse water shell Alfonso Garcia Sosa (Tue Sep 16 2003 - 12:08:24 CDT)
Re: AMBER: MD simulations on small molecules immersed in sparse water shell rluo_at_uci.edu (Tue Sep 16 2003 - 13:16:41 CDT)
Re: AMBER: MD simulations on small molecules immersed in sparse water shell Carlos Simmerling (Tue Sep 16 2003 - 13:23:53 CDT)
Re: AMBER: MD simulations on small molecules immersed in sparse water shell rluo_at_uci.edu (Tue Sep 16 2003 - 14:07:03 CDT)
Re: AMBER: MD simulations on small molecules immersed in sparse water shell Carlos Simmerling (Tue Sep 16 2003 - 14:21:18 CDT)
AMBER: MD problem! Pradipta Bandyopadhyay (Tue Sep 16 2003 - 19:33:17 CDT)
AMBER: Compiling sander with single precision rluo_at_uci.edu (Tue Sep 16 2003 - 20:37:01 CDT)
Re: AMBER: Compiling sander with single precision Scott Brozell (Tue Sep 16 2003 - 20:59:25 CDT)
Re: AMBER: MD problem! darden (Wed Sep 17 2003 - 10:29:50 CDT)
AMBER: mfef90 - installation problem Joseph Maxwell (Wed Sep 17 2003 - 11:34:18 CDT)
Re: AMBER: mfef90 - installation problem Michael Crowley (Wed Sep 17 2003 - 12:28:19 CDT)
Re: AMBER: mfef90 - installation problem Joseph Maxwell (Wed Sep 17 2003 - 13:11:58 CDT)
AMBER: leap/frcmod problem Joseph Nachman (Wed Sep 17 2003 - 15:08:37 CDT)
Re: AMBER: leap/frcmod problem David A. Case (Wed Sep 17 2003 - 15:57:18 CDT)
Re: AMBER: Compiling sander with single precision Mengjuei Hsieh (Wed Sep 17 2003 - 16:56:34 CDT)
AMBER: Scyld cluster amber 7 compile problems Bengt Svensson (Wed Sep 17 2003 - 20:11:04 CDT)
AMBER: Amber 7 - bugfix 42 problem. Bengt Svensson (Wed Sep 17 2003 - 20:21:08 CDT)
AMBER: Suggestion regarding long simulation. uddhavesh bhaskar sonavane (Thu Sep 18 2003 - 01:50:37 CDT)
AMBER: Calculating solvation energies for MM-PBSA use Thomas Steinbrecher (Thu Sep 18 2003 - 07:43:37 CDT)
Re: AMBER: Calculating solvation energies for MM-PBSA use samantha hughes (Thu Sep 18 2003 - 08:13:04 CDT)
AMBER: FEP problem Itziar Maestre Asenjo (Thu Sep 18 2003 - 07:35:37 CDT)
Re: AMBER: FEP problem David A. Case (Thu Sep 18 2003 - 10:08:18 CDT)
AMBER: re: MD problem!! Pradipta Bandyopadhyay (Thu Sep 18 2003 - 12:36:59 CDT)
Re: AMBER: Scyld cluster amber 7 compile problems Scott Brozell (Thu Sep 18 2003 - 12:50:08 CDT)
AMBER: Generalized Born parameters Peter VARNAI (Thu Sep 18 2003 - 13:51:24 CDT)
RE: AMBER: re: MD problem!! Yong Duan (Thu Sep 18 2003 - 14:32:49 CDT)
AMBER: MD problem!! Pradipta Bandyopadhyay (Thu Sep 18 2003 - 15:35:36 CDT)
Re: AMBER: MD problem!! yduan_at_udel.edu (Thu Sep 18 2003 - 16:21:22 CDT)
Re: AMBER: Suggestion regarding long simulation. Johannes Zuegg (Thu Sep 18 2003 - 17:56:39 CDT)
RE: AMBER: Suggestion regarding long simulation. Yong Duan (Thu Sep 18 2003 - 19:33:30 CDT)
Re: AMBER: Suggestion regarding long simulation. Carlos Simmerling (Thu Sep 18 2003 - 21:12:20 CDT)
Re: AMBER: Suggestion regarding long simulation. Carlos Simmerling (Fri Sep 19 2003 - 07:05:58 CDT)
AMBER: no defined type for atom N atom Wu Yingliang (Fri Sep 19 2003 - 07:57:12 CDT)
AMBER: no defined type for atom N atom Wu Yingliang (Fri Sep 19 2003 - 08:02:31 CDT)
Re: AMBER: no defined type for atom N atom David A. Case (Fri Sep 19 2003 - 12:01:29 CDT)
Re: AMBER: Amber 7 - bugfix 42 problem. David A. Case (Fri Sep 19 2003 - 13:17:10 CDT)
AMBER: xLEAP Problem Stephen P. Molnar, Ph.D. (Fri Sep 19 2003 - 15:07:14 CDT)
AMBER: 'high' temp. simulation!! Pradipta Bandyopadhyay (Fri Sep 19 2003 - 15:09:05 CDT)
AMBER: double bonds in prmtop Herbert Georg (Fri Sep 19 2003 - 15:09:16 CDT)
Re: AMBER: double bonds in prmtop Ioana Cozmuta (Fri Sep 19 2003 - 15:24:18 CDT)
RE: AMBER: xLEAP Problem Niko Jukarainen (Fri Sep 19 2003 - 16:18:30 CDT)
Re: AMBER: double bonds in prmtop Herbert Georg (Fri Sep 19 2003 - 16:27:53 CDT)
Re: AMBER: double bonds in prmtop David A. Case (Fri Sep 19 2003 - 17:42:23 CDT)
AMBER: C-alpha RMS Do Anh Tuan (Sat Sep 20 2003 - 01:39:42 CDT)
AMBER: AMBER Carnal files Frederico.Miranda_at_ibmb.uib.no (Sat Sep 20 2003 - 17:24:12 CDT)
RE: AMBER: AMBER Carnal files Yong Duan (Sat Sep 20 2003 - 17:44:44 CDT)
RE: AMBER: AMBER Carnal files Frederico.Miranda_at_ibmb.uib.no (Sun Sep 21 2003 - 19:09:01 CDT)
RE: AMBER: AMBER Carnal files Yong Duan (Sun Sep 21 2003 - 21:02:40 CDT)
Re: AMBER: xLEAP Problem Kazuo Koyano (Sun Sep 21 2003 - 21:18:49 CDT)
Re: AMBER: xLEAP Problem Donald Thomas (Sun Sep 21 2003 - 21:37:23 CDT)
AMBER: slow simulation nie beining (Mon Sep 22 2003 - 01:46:21 CDT)
Re: AMBER: C-alpha RMS Kun Song (Mon Sep 22 2003 - 08:45:20 CDT)
Re: AMBER: slow simulation David A. Case (Mon Sep 22 2003 - 09:54:46 CDT)
AMBER: plane angle. Pascal Bonnet (Mon Sep 22 2003 - 10:14:44 CDT)
AMBER: slower simulation nie beining (Mon Sep 22 2003 - 10:43:24 CDT)
Re: AMBER: slower simulation Carlos Simmerling (Mon Sep 22 2003 - 10:59:02 CDT)
AMBER: Antechamber problem Shafinaz (Mon Sep 22 2003 - 11:33:58 CDT)
AMBER: Slower simulation and pair-range cutoff? nie beining (Mon Sep 22 2003 - 12:11:11 CDT)
Re: AMBER: plane angle. Bill Ross (Mon Sep 22 2003 - 13:42:40 CDT)
AMBER: increase size of NATOM or NRES for "ambpdb" Wen Li (Mon Sep 22 2003 - 14:14:36 CDT)
Re: AMBER: increase size of NATOM or NRES for "ambpdb" David A. Case (Mon Sep 22 2003 - 14:24:12 CDT)
AMBER: Re: xLEAP Problem Stephen P. Molnar, Ph.D. (Mon Sep 22 2003 - 11:36:48 CDT)
AMBER: Carnal Input file Frederico.Miranda_at_ibmb.uib.no (Mon Sep 22 2003 - 18:06:55 CDT)
Re: AMBER: Carnal Input file Bill Ross (Mon Sep 22 2003 - 18:23:27 CDT)
RE: AMBER: Carnal Input file Ming Lei (Mon Sep 22 2003 - 22:34:05 CDT)
Re: AMBER: Antechamber problem David A. Case (Tue Sep 23 2003 - 10:19:54 CDT)
AMBER: How can I set ntx=7, but exclude the velocity? Margaret S. Cheung (Tue Sep 23 2003 - 10:30:28 CDT)
Re: AMBER: How can I set ntx=7, but exclude the velocity? Carlos Simmerling (Tue Sep 23 2003 - 10:35:28 CDT)
AMBER: pair-cutoff nie beining (Tue Sep 23 2003 - 10:40:32 CDT)
Re: AMBER: pair-cutoff David A. Case (Tue Sep 23 2003 - 10:59:01 CDT)
AMBER: mm_pbsa - ?small bugs? Chris Moth (Wed Sep 24 2003 - 12:37:37 CDT)
AMBER: GROUP Atchara Wijitkosoom (Tue Sep 23 2003 - 15:04:20 CDT)
AMBER: ?small bugs? - 2nd suggestion Chris Moth (Wed Sep 24 2003 - 15:23:41 CDT)
AMBER: residues and molecules GUILLERMINA L ESTIU (Tue Sep 23 2003 - 16:56:01 CDT)
AMBER: PMEMD 3.03 Update available Robert Duke (Tue Sep 23 2003 - 21:13:57 CDT)
AMBER: cd-c-os and c3-cd-c angle parameters Vikas Varshney (Wed Sep 24 2003 - 10:10:09 CDT)
Re: AMBER: cd-c-os and c3-cd-c angle parameters Junmei Wang (Wed Sep 24 2003 - 13:16:18 CDT)
Re: AMBER: residues and molecules David A. Case (Wed Sep 24 2003 - 13:45:40 CDT)
AMBER: problem with file format Shafinaz (Wed Sep 24 2003 - 14:05:23 CDT)
Re: AMBER: problem with file format David A. Case (Wed Sep 24 2003 - 14:28:22 CDT)
Re: AMBER: residues and molecules Robert Duke (Wed Sep 24 2003 - 14:53:20 CDT)
AMBER: NaCl ion pairs in TIP3P water box Nathan A. Baker (Wed Sep 24 2003 - 15:13:11 CDT)
RE: AMBER: problem with file format Shafinaz (Wed Sep 24 2003 - 15:29:10 CDT)
RE: AMBER: problem with file format Junmei Wang (Wed Sep 24 2003 - 15:34:14 CDT)
Re: AMBER: NaCl ion pairs in TIP3P water box Bill Ross (Wed Sep 24 2003 - 15:53:39 CDT)
Re: AMBER: NaCl ion pairs in TIP3P water box David A. Case (Wed Sep 24 2003 - 16:09:06 CDT)
Re: AMBER: NaCl ion pairs in TIP3P water box Jiri Sponer (Wed Sep 24 2003 - 16:41:27 CDT)
Re: AMBER: NaCl ion pairs in TIP3P water box Bill Ross (Wed Sep 24 2003 - 17:13:47 CDT)
Re: AMBER: NaCl ion pairs in TIP3P water box Ioana Cozmuta (Wed Sep 24 2003 - 17:30:26 CDT)
Re: AMBER: NaCl ion pairs in TIP3P water box M. L. Dodson (Wed Sep 24 2003 - 18:53:22 CDT)
Re: AMBER: NaCl ion pairs in TIP3P water box Nathan A. Baker (Wed Sep 24 2003 - 20:14:47 CDT)
AMBER: MM_PBSA(GBSA) Examples Kazuo Koyano (Thu Sep 25 2003 - 05:35:50 CDT)
Re: AMBER: NaCl ion pairs in TIP3P water box Jiri Sponer (Thu Sep 25 2003 - 06:59:51 CDT)
Re: AMBER: NaCl ion pairs in TIP3P water box Pascal Auffinger (Thu Sep 25 2003 - 08:30:08 CDT)
AMBER: MM_PBSA(GBSA) Examples Chris Moth (Thu Sep 25 2003 - 10:56:23 CDT)
AMBER: Online model of 2C9 Peter Gannett (Thu Sep 25 2003 - 14:23:22 CDT)
AMBER: MeCNBOX northrop_at_chem.ucla.edu (Thu Sep 25 2003 - 14:35:03 CDT)
Re: AMBER: MeCNBOX David A. Case (Thu Sep 25 2003 - 15:25:23 CDT)
Re: AMBER: MeCNBOX northrop_at_chem.ucla.edu (Thu Sep 25 2003 - 15:40:37 CDT)
Re: AMBER: MeCNBOX northrop_at_chem.ucla.edu (Thu Sep 25 2003 - 15:47:03 CDT)
Re: AMBER: MeCNBOX James W. Caldwell (Thu Sep 25 2003 - 16:04:03 CDT)
AMBER: Re:MeCNBOX Pradipta Bandyopadhyay (Thu Sep 25 2003 - 16:23:09 CDT)
AMBER: about the mopac7 installation. Yong Wang (Fri Sep 26 2003 - 02:07:16 CDT)
Re: AMBER: MeCNBOX Pascal Bonnet (Fri Sep 26 2003 - 03:38:03 CDT)
Re: AMBER: MM_PBSA(GBSA) Examples Kazuo Koyano (Fri Sep 26 2003 - 05:37:40 CDT)
AMBER: Zn in antechamber Lishan Yao (Fri Sep 26 2003 - 08:48:44 CDT)
Re: AMBER: Zn in antechamber Junmei Wang (Fri Sep 26 2003 - 09:47:45 CDT)
Re: AMBER: Zn in antechamber Lishan Yao (Fri Sep 26 2003 - 10:01:41 CDT)
AMBER: non-bonded cutoffs Michael Dolan (Fri Sep 26 2003 - 10:17:16 CDT)
Re: AMBER: non-bonded cutoffs David A. Case (Fri Sep 26 2003 - 10:32:09 CDT)
Re: AMBER: non-bonded cutoffs Michael Dolan (Fri Sep 26 2003 - 10:39:34 CDT)
AMBER: Phase for torsion angle different of 0 or 180 ? Teletchéa Stéphane (Fri Sep 26 2003 - 11:27:34 CDT)
Re: AMBER: Zn in antechamber Junmei Wang (Fri Sep 26 2003 - 12:00:11 CDT)
Re: AMBER: Zn in antechamber Rhonda Torres (Fri Sep 26 2003 - 12:24:16 CDT)
Re: AMBER: Zn in antechamber Lishan Yao (Fri Sep 26 2003 - 14:15:21 CDT)
AMBER: FW: Residual dipolar couplings McAteer, Kathleen (Fri Sep 26 2003 - 14:44:57 CDT)
Re: AMBER: Zn in antechamber Junmei Wang (Fri Sep 26 2003 - 15:24:46 CDT)
Re: AMBER: FW: Residual dipolar couplings David A. Case (Fri Sep 26 2003 - 15:36:25 CDT)
Re: AMBER: Phase for torsion angle different of 0 or 180 ? David A. Case (Fri Sep 26 2003 - 15:41:35 CDT)
AMBER: polarizability and PME Martin Mucha (Sat Sep 27 2003 - 09:46:08 CDT)
Re: AMBER: polarizability and PME David A. Case (Sat Sep 27 2003 - 11:17:46 CDT)
Re: AMBER: Zn in antechamber Lishan Yao (Mon Sep 29 2003 - 10:13:42 CDT)
Re: AMBER: Zn in antechamber Junmei Wang (Mon Sep 29 2003 - 10:32:52 CDT)
Re: AMBER: Zn in antechamber Lishan Yao (Mon Sep 29 2003 - 10:59:09 CDT)
Re: AMBER: Zn in antechamber Junmei Wang (Mon Sep 29 2003 - 11:38:09 CDT)
AMBER: AMBER quasih question(s) Rachel Ward (Mon Sep 29 2003 - 14:39:17 CDT)
Re: AMBER: Zn in antechamber Lishan Yao (Mon Sep 29 2003 - 15:15:04 CDT)
AMBER: nstlim Amber Administration (Mon Sep 29 2003 - 18:55:42 CDT)
Re: AMBER: nstlim Robert Duke (Mon Sep 29 2003 - 20:40:24 CDT)
AMBER: A problem about xleap Jiang Pengju (Mon Sep 29 2003 - 21:04:14 CDT)
AMBER: density equilibrium & harmonic restrain yuann (Mon Sep 29 2003 - 21:59:50 CDT)
AMBER: iam a newbie !!! Karthikeyan Pasupathy (Mon Sep 29 2003 - 23:25:05 CDT)
AMBER: following salt and waterbridges during a simulation Karsten Suhre (Tue Sep 30 2003 - 01:33:31 CDT)
AMBER: TTF parameters northrop_at_chem.ucla.edu (Tue Sep 30 2003 - 01:49:20 CDT)
Re: AMBER: iam a newbie !!! Vlad Cojocaru (Tue Sep 30 2003 - 04:12:43 CDT)
Re: AMBER: A problem about xleap John Bushnell (Tue Sep 30 2003 - 12:13:06 CDT)
AMBER: improper Li Ying (Tue Sep 30 2003 - 15:08:11 CDT)
Re: AMBER: improper Bill Ross (Tue Sep 30 2003 - 15:15:28 CDT)
Re: AMBER: improper ya ya (Wed Oct 01 2003 - 09:59:16 CDT)
Re: Re: AMBER: nstlim uddhavesh bhaskar sonavane (Wed Oct 01 2003 - 10:32:27 CDT)
Re: Re: AMBER: nstlim Robert Duke (Wed Oct 01 2003 - 11:32:48 CDT)
Re: AMBER: improper Bill Ross (Wed Oct 01 2003 - 12:21:03 CDT)
AMBER: Added water and mm_pbsa Yong-Liang Zhu (Wed Oct 01 2003 - 12:29:37 CDT)
Re: AMBER: improper Bill Ross (Wed Oct 01 2003 - 12:38:08 CDT)
AMBER: addions/xleap question FyD (Wed Oct 01 2003 - 15:39:47 CDT)
Re: AMBER: addions/xleap question Rhonda Torres (Wed Oct 01 2003 - 16:10:00 CDT)
Re: AMBER: addions/xleap question Bill Ross (Wed Oct 01 2003 - 16:10:44 CDT)
Re: AMBER: addions/xleap question FyD (Wed Oct 01 2003 - 16:24:38 CDT)
AMBER: constant pressure in GB aini_at_UMDNJ.EDU (Wed Oct 01 2003 - 20:19:12 CDT)
RE: AMBER: constant pressure in GB Yong Duan (Wed Oct 01 2003 - 20:45:04 CDT)
Re: AMBER: AMBER quasih question(s) David Case (Thu Oct 02 2003 - 06:34:18 CDT)
Re: AMBER: density equilibrium & harmonic restrain David Case (Thu Oct 02 2003 - 06:39:05 CDT)
Re: AMBER: constant pressure in GB David Case (Thu Oct 02 2003 - 06:53:32 CDT)
AMBER: regarding trajectory input and output with ptraj or Carnal Vlad Cojocaru (Thu Oct 02 2003 - 07:37:19 CDT)
Re: AMBER: regarding trajectory input and output with ptraj or Carnal David Case (Thu Oct 02 2003 - 07:54:11 CDT)
AMBER: calculation of LJ 12-6 from .dat file (fwd) Michal Otyepka (Thu Oct 02 2003 - 09:53:27 CDT)
Re: AMBER: regarding trajectory input and output with ptraj or Carnal Bill Ross (Thu Oct 02 2003 - 11:28:41 CDT)
AMBER: SHAKE for TIP4P! Pradipta Bandyopadhyay (Thu Oct 02 2003 - 18:25:49 CDT)
Re: AMBER: SHAKE for TIP4P! David Case (Fri Oct 03 2003 - 02:43:43 CDT)
Re: AMBER: calculation of LJ 12-6 from .dat file (fwd) Martin Lepsik (Fri Oct 03 2003 - 04:53:50 CDT)
Re: AMBER: calculation of LJ 12-6 from .dat file (fwd)-CORRECTION!!! Martin Lepsik (Fri Oct 03 2003 - 04:56:07 CDT)
AMBER: Compiling antechamber on amber 8 Mengjuei Hsieh (Fri Oct 03 2003 - 05:10:35 CDT)
Re: AMBER: Compiling antechamber on amber 8 Junmei Wang (Fri Oct 03 2003 - 09:50:01 CDT)
AMBER: H-bond analysis RAJA SWAMINATHAN (Fri Oct 03 2003 - 11:11:17 CDT)
RE: AMBER: H-bond analysis myang (Fri Oct 03 2003 - 13:08:49 CDT)
AMBER: ibelly Amber Administration (Fri Oct 03 2003 - 13:55:02 CDT)
Re: AMBER: Compiling antechamber on amber 8 Mengjuei Hsieh (Fri Oct 03 2003 - 19:42:32 CDT)
AMBER: surface code in Amber John Lee (Sun Oct 05 2003 - 16:13:43 CDT)
AMBER: output frequency GUILLERMINA L ESTIU (Mon Oct 06 2003 - 08:43:26 CDT)
RE: AMBER: output frequency Yong Duan (Mon Oct 06 2003 - 09:08:21 CDT)
AMBER: mgbjsb Radii in GBSA Giulio Rastelli (Tue Oct 07 2003 - 09:42:34 CDT)
AMBER: Atomic charges and internal H-bond Martin Lepsik (Tue Oct 07 2003 - 06:41:19 CDT)
Re: AMBER: Atomic charges and internal H-bond Jiri Sponer (Tue Oct 07 2003 - 09:12:27 CDT)
Re: AMBER: Atomic charges and internal H-bond Piotr Cieplak (Tue Oct 07 2003 - 12:41:49 CDT)
AMBER: Re:atomic charges and internal H-bond Pradipta Bandyopadhyay (Tue Oct 07 2003 - 13:24:18 CDT)
AMBER: Resp Problem Vikas Varshney (Tue Oct 07 2003 - 10:18:39 CDT)
Re: AMBER: Re:atomic charges and internal H-bond Jiri Sponer (Tue Oct 07 2003 - 15:48:00 CDT)
Re: AMBER: Re:atomic charges and internal H-bond Piotr Cieplak (Tue Oct 07 2003 - 16:36:10 CDT)
Re: AMBER: Re:atomic charges and internal H-bond Jiri Sponer (Tue Oct 07 2003 - 17:08:09 CDT)
Re: AMBER: Atomic charges and internal H-bond Martin Lepsik (Wed Oct 08 2003 - 03:44:21 CDT)
AMBER: Addles Mark K. Dean (Wed Oct 08 2003 - 09:46:41 CDT)
Re: AMBER: Addles xiaolin cheng (Wed Oct 08 2003 - 10:56:18 CDT)
AMBER: mopac lil_at_umbi.umd.edu (Wed Oct 08 2003 - 11:19:18 CDT)
Re: AMBER: mopac Junmei Wang (Wed Oct 08 2003 - 12:15:18 CDT)
AMBER: Compiling AMBER franck (Thu Oct 09 2003 - 09:16:17 CDT)
AMBER: question about ewald Lishan Yao (Thu Oct 09 2003 - 11:03:44 CDT)
Re: AMBER: question about ewald Scott Brozell (Thu Oct 09 2003 - 13:11:21 CDT)
Re: AMBER: question about ewald darden (Thu Oct 09 2003 - 15:38:10 CDT)
AMBER: mm_pbsa example Jory Zmuda (Thu Oct 09 2003 - 15:35:21 CDT)
Re: AMBER: mm_pbsa example Rhonda Torres (Thu Oct 09 2003 - 16:09:33 CDT)
Re: AMBER: Compiling AMBER, ie, number of atoms limit Scott Brozell (Thu Oct 09 2003 - 16:30:02 CDT)
AMBER: Not getting restrt file on running sanders Vikas Varshney (Thu Oct 09 2003 - 16:40:15 CDT)
RE: AMBER: Not getting restrt file on running sanders Asim Okur (Thu Oct 09 2003 - 16:53:37 CDT)
Re: AMBER: Compiling AMBER, ie, number of atoms limit Robert Duke (Thu Oct 09 2003 - 17:18:27 CDT)
RE: AMBER: Not getting restrt file on running sanders Scott Brozell (Thu Oct 09 2003 - 18:25:11 CDT)
AMBER: Freezing the residues Vikas Varshney (Thu Oct 09 2003 - 22:37:11 CDT)
Re: AMBER: Freezing the residues zhaoxc_at_puccini.che.pitt.edu (Fri Oct 10 2003 - 07:30:38 CDT)
AMBER: is there a good program to quantitatively analyze hydration effect? zhaoxc_at_puccini.che.pitt.edu (Fri Oct 10 2003 - 07:36:08 CDT)
AMBER: monte carlo Vlad Cojocaru (Fri Oct 10 2003 - 08:40:11 CDT)
Re: AMBER: monte carlo Andreas Svrcek-Seiler (Fri Oct 10 2003 - 09:19:41 CDT)
AMBER: input/output error Dalmaris, John (Fri Oct 10 2003 - 11:32:15 CDT)
Re: AMBER: Freezing the residues Scott Brozell (Fri Oct 10 2003 - 14:25:04 CDT)
Re: AMBER: Freezing the residues Bill Ross (Fri Oct 10 2003 - 14:43:38 CDT)
Re: AMBER: input/output error Scott Brozell (Fri Oct 10 2003 - 17:10:08 CDT)
AMBER: nmanal projection Qiang Lu (Fri Oct 10 2003 - 17:22:48 CDT)
Re: AMBER: surface code in Amber Alexey Onufriev (Fri Oct 10 2003 - 18:25:45 CDT)
AMBER: MeCNBOX & EWALD bomb northrop_at_chem.ucla.edu (Fri Oct 10 2003 - 19:31:46 CDT)
Re: AMBER: MeCNBOX & EWALD bomb Jiten (Fri Oct 10 2003 - 22:29:04 CDT)
AMBER: Water as part of protein in mm_pbsa calculation Yong-Liang Zhu (Sat Oct 11 2003 - 22:20:12 CDT)
AMBER: force field for hybrid systems Ioana Cozmuta (Sun Oct 12 2003 - 12:58:41 CDT)
AMBER: problem with pdb files Mithun Mitra (Sun Oct 12 2003 - 15:12:45 CDT)
AMBER: sander: vlimit problem Vikas Varshney (Sun Oct 12 2003 - 21:19:41 CDT)
Re: AMBER: problem with pdb files Vlad Cojocaru (Mon Oct 13 2003 - 03:35:04 CDT)
AMBER: Re:mm_pbsa problem Itziar Maestre Asenjo (Mon Oct 13 2003 - 04:18:38 CDT)
AMBER: Reverse TI run Martin Lepsik (Mon Oct 13 2003 - 11:55:03 CDT)
Re: AMBER: problem with pdb files Bill Ross (Mon Oct 13 2003 - 12:12:41 CDT)
AMBER: mm_pbsa crg file kbyun_at_wesleyan.edu (Mon Oct 13 2003 - 12:24:15 CDT)
AMBER: mm_pbsa rna/dna charges kbyun_at_wesleyan.edu (Mon Oct 13 2003 - 15:45:37 CDT)
AMBER: antechamber lil_at_umbi.umd.edu (Mon Oct 13 2003 - 18:30:25 CDT)
Re: AMBER: antechamber Bill Ross (Mon Oct 13 2003 - 19:38:24 CDT)
AMBER: Amber charge problem Yuhui Cheng (Mon Oct 13 2003 - 19:25:58 CDT)
Re: AMBER: Amber charge problem Bill Ross (Mon Oct 13 2003 - 20:21:00 CDT)
Re: AMBER: Reverse TI run Martin Lepsik (Tue Oct 14 2003 - 08:02:22 CDT)
AMBER: running sander_classic on multiple processors Richard Smith (Tue Oct 14 2003 - 08:48:23 CDT)
Re: AMBER: mm_pbsa crg file kbyun_at_wesleyan.edu (Tue Oct 14 2003 - 09:09:35 CDT)
AMBER: mm_pbsa with amber7 Itziar Maestre Asenjo (Tue Oct 14 2003 - 11:22:18 CDT)
AMBER: infinitely long DNA & moil-view? Endres, Robert G. (Tue Oct 14 2003 - 13:57:43 CDT)
Re: AMBER: infinitely long DNA & moil-view? Carlos Simmerling (Tue Oct 14 2003 - 14:18:30 CDT)
Re: AMBER: infinitely long DNA & moil-view? bishop (Tue Oct 14 2003 - 14:24:52 CDT)
AMBER: 'vlimit exceeded' Vikas Varshney (Tue Oct 14 2003 - 14:36:19 CDT)
RE: AMBER: infinitely long DNA & moil-view? Yong Duan (Tue Oct 14 2003 - 15:15:29 CDT)
RE: AMBER: infinitely long DNA & moil-view? Bill Ross (Tue Oct 14 2003 - 15:36:56 CDT)
Re: AMBER: nmanal projection David A. Case (Tue Oct 14 2003 - 17:11:29 CDT)
Re: AMBER: MeCNBOX & EWALD bomb David A. Case (Tue Oct 14 2003 - 17:12:42 CDT)
Re: AMBER: sander: vlimit problem David A. Case (Tue Oct 14 2003 - 17:15:02 CDT)
Re: AMBER: sander: vlimit problem Bill Ross (Tue Oct 14 2003 - 17:23:59 CDT)
AMBER: tru64 alpha Mu Yuguang (Dr) (Tue Oct 14 2003 - 20:19:06 CDT)
AMBER: Restraints to maintain base pair planarity Mahadevan Seetharaman (Tue Oct 14 2003 - 22:10:29 CDT)
RE: AMBER: tru64 alpha Mu Yuguang (Dr) (Wed Oct 15 2003 - 02:07:45 CDT)
AMBER: a problem with xleap Ye Mei (Wed Oct 15 2003 - 03:03:36 CDT)
Re: AMBER: Reverse TI run Michael Crowley (Wed Oct 15 2003 - 04:55:39 CDT)
AMBER: STREAM problems : segmentation fault with CARNAL Jean-François Taly (Wed Oct 15 2003 - 05:03:35 CDT)
Re: AMBER: Restraints to maintain base pair planarity David A. Case (Wed Oct 15 2003 - 09:18:10 CDT)
Re: AMBER: tru64 alpha David A. Case (Wed Oct 15 2003 - 09:25:03 CDT)
Re: AMBER: a problem with xleap David A. Case (Wed Oct 15 2003 - 09:31:06 CDT)
RE: AMBER: tru64 alpha Bill Ross (Wed Oct 15 2003 - 09:38:45 CDT)
Re: AMBER: Restraints to maintain base pair planarity Andreas Svrcek-Seiler (Wed Oct 15 2003 - 11:51:12 CDT)
RE: AMBER: running sander_classic on multiple processors Richard Smith (Wed Oct 15 2003 - 14:09:57 CDT)
Re: Re: AMBER: a problem with xleap Ye Mei (Wed Oct 15 2003 - 20:34:51 CDT)
Re: AMBER: tru64 alpha Robert Duke (Wed Oct 15 2003 - 21:51:20 CDT)
RE: AMBER: tru64 alpha Mu Yuguang (Dr) (Wed Oct 15 2003 - 21:59:29 CDT)
Re: AMBER: tru64 alpha Robert Duke (Wed Oct 15 2003 - 22:41:57 CDT)
Re: AMBER: tru64 alpha Robert Duke (Thu Oct 16 2003 - 09:17:00 CDT)
AMBER: charmm force field in amber Hyonseok Hwang (Thu Oct 16 2003 - 13:05:36 CDT)
Re: AMBER: a problem with xleap Scott Brozell (Thu Oct 16 2003 - 13:19:29 CDT)
Re: AMBER: a problem with xleap Bill Ross (Thu Oct 16 2003 - 13:22:42 CDT)
RE: AMBER: charmm force field in amber myang (Thu Oct 16 2003 - 15:57:47 CDT)
RE: AMBER: tru64 alpha Mu Yuguang (Dr) (Thu Oct 16 2003 - 19:40:56 CDT)
Re: AMBER: tru64 alpha Robert Duke (Thu Oct 16 2003 - 20:18:41 CDT)
Re: AMBER: tru64 alpha Robert Duke (Thu Oct 16 2003 - 20:27:27 CDT)
RE: AMBER: tru64 alpha Mu Yuguang (Dr) (Thu Oct 16 2003 - 20:52:41 CDT)
RE: AMBER: tru64 alpha Yong Duan (Thu Oct 16 2003 - 21:00:04 CDT)
RE: AMBER: tru64 alpha Mu Yuguang (Dr) (Thu Oct 16 2003 - 21:08:14 CDT)
Re: AMBER: tru64 alpha Robert Duke (Thu Oct 16 2003 - 21:50:08 CDT)
RE: AMBER: tru64 alpha Yong Duan (Fri Oct 17 2003 - 06:53:39 CDT)
AMBER: problem in tleap aini_at_UMDNJ.EDU (Fri Oct 17 2003 - 10:41:27 CDT)
AMBER: Implicit precision in sander vs architecture Teletchéa Stéphane (Fri Oct 17 2003 - 10:42:41 CDT)
Re: AMBER: problem in tleap David A. Case (Fri Oct 17 2003 - 10:59:27 CDT)
Re: AMBER: Implicit precision in sander vs architecture David A. Case (Fri Oct 17 2003 - 11:05:15 CDT)
Re: AMBER: Implicit precision in sander vs architecture Teletchéa Stéphane (Fri Oct 17 2003 - 11:15:13 CDT)
RE: AMBER: Implicit precision in sander vs architecture Yong Duan (Fri Oct 17 2003 - 11:30:31 CDT)
Re: AMBER: Implicit precision in sander vs architecture David E. Konerding (Fri Oct 17 2003 - 12:05:14 CDT)
Re: AMBER: Implicit precision in sander vs architecture Bill Ross (Fri Oct 17 2003 - 13:10:46 CDT)
AMBER: a question Pingna Xu (Fri Oct 17 2003 - 16:01:12 CDT)
AMBER: ibelly in AMBER 6 Qing Zhang (Fri Oct 17 2003 - 17:32:21 CDT)
Re: AMBER: a question David A. Case (Fri Oct 17 2003 - 17:36:08 CDT)
Re: AMBER: ibelly in AMBER 6 David A. Case (Fri Oct 17 2003 - 19:51:29 CDT)
Re: AMBER: ibelly in AMBER 6 David A. Case (Sat Oct 18 2003 - 11:48:16 CDT)
AMBER: one more question Pingna Xu (Sat Oct 18 2003 - 13:01:32 CDT)
RE: AMBER: one more question myang (Sat Oct 18 2003 - 13:51:33 CDT)
AMBER: torsional restraints for groups of atoms Anonymous (Sun Oct 19 2003 - 12:42:59 CDT)
AMBER: carnal Frederico.Miranda_at_ibmb.uib.no (Sun Oct 19 2003 - 14:48:06 CDT)
RE: AMBER: carnal Yong Duan (Sun Oct 19 2003 - 15:00:11 CDT)
AMBER: more questions about igb Pingna Xu (Sun Oct 19 2003 - 22:54:49 CDT)
Re: AMBER: Implicit precision in sander vs architecture Teletchéa Stéphane (Mon Oct 20 2003 - 03:45:04 CDT)
Re: AMBER: Implicit precision in sander vs architecture Robert Duke (Mon Oct 20 2003 - 08:01:47 CDT)
AMBER: stable protein Do Anh Tuan (Mon Oct 20 2003 - 12:30:45 CDT)
Re: AMBER: stable protein Carlos Simmerling (Mon Oct 20 2003 - 12:48:03 CDT)
Re: AMBER: Implicit precision in sander vs architecture Amber Administration (Mon Oct 20 2003 - 18:18:02 CDT)
Re: AMBER: more questions about igb David A. Case (Mon Oct 20 2003 - 18:47:35 CDT)
Re: AMBER: Implicit precision in sander vs architecture David A. Case (Mon Oct 20 2003 - 19:13:15 CDT)
Re: AMBER: Implicit precision in sander vs architecture Robert Duke (Mon Oct 20 2003 - 20:06:22 CDT)
AMBER: what is the unit for the energy calculated from MM_PBSA? zhaoxc_at_puccini.che.pitt.edu (Mon Oct 20 2003 - 20:08:51 CDT)
RE: AMBER: what is the unit for the energy calculated from MM_PBSA? Rhonda Torres (Mon Oct 20 2003 - 20:19:09 CDT)
AMBER: ECC vs non-ECC (non-amber issue) Yong Duan (Mon Oct 20 2003 - 21:04:37 CDT)
Re: AMBER: ECC vs non-ECC (non-amber issue) Robert Duke (Mon Oct 20 2003 - 21:40:24 CDT)
AMBER: memory SC45 Mu Yuguang (Dr) (Mon Oct 20 2003 - 21:39:29 CDT)
Re: AMBER: memory SC45 Robert Duke (Mon Oct 20 2003 - 22:17:25 CDT)
Re: AMBER: memory SC45 Bill Ross (Mon Oct 20 2003 - 22:19:37 CDT)
RE: AMBER: memory SC45 Mu Yuguang (Dr) (Mon Oct 20 2003 - 22:46:50 CDT)
RE: AMBER: memory SC45 Bill Ross (Mon Oct 20 2003 - 23:09:01 CDT)
Re: AMBER: Implicit precision in sander vs architecture Teletchéa Stéphane (Tue Oct 21 2003 - 03:42:54 CDT)
Re: AMBER: memory SC45 Robert Duke (Tue Oct 21 2003 - 07:55:22 CDT)
Re: AMBER: memory SC45 Robert Duke (Tue Oct 21 2003 - 08:20:59 CDT)
AMBER: how to mend the peptide with missing residues? Ye Mei (Tue Oct 21 2003 - 10:07:14 CDT)
RE: AMBER: how to mend the peptide with missing residues? Yong Duan (Tue Oct 21 2003 - 10:15:53 CDT)
AMBER: frozen x unfrozen Herbert Georg (Tue Oct 21 2003 - 14:04:44 CDT)
Re: AMBER: frozen x unfrozen Bill Ross (Tue Oct 21 2003 - 14:52:55 CDT)
RE: AMBER: memory SC45 Mu Yuguang (Dr) (Tue Oct 21 2003 - 20:19:45 CDT)
Re: AMBER: memory SC45 Robert Duke (Tue Oct 21 2003 - 21:12:31 CDT)
AMBER: antechamber and bond type Herbert Georg (Wed Oct 22 2003 - 07:56:15 CDT)
Re: AMBER: frozen x unfrozen David A. Case (Wed Oct 22 2003 - 18:58:41 CDT)
Re: AMBER: torsional restraints for groups of atoms David A. Case (Wed Oct 22 2003 - 19:00:16 CDT)
Re: AMBER: torsional restraints for groups of atoms xiaolin cheng (Wed Oct 22 2003 - 19:30:33 CDT)
Re: AMBER: frozen x unfrozen Herbert Georg (Thu Oct 23 2003 - 09:25:20 CDT)
AMBER: Simulation of small protein Endres, Robert G. (Thu Oct 23 2003 - 10:52:52 CDT)
AMBER: frozen x unfrozen and the gibbs tragedy David Smith (Thu Oct 23 2003 - 10:56:00 CDT)
Re: AMBER: Simulation of small protein Carlos Simmerling (Thu Oct 23 2003 - 11:13:09 CDT)
RE: AMBER: Simulation of small protein Endres, Robert G. (Thu Oct 23 2003 - 12:27:45 CDT)
AMBER: correlated motion Jory L. Zmuda (Thu Oct 23 2003 - 13:17:01 CDT)
AMBER: Simulation of small protein (MD Display tips) Chris Moth (Fri Oct 24 2003 - 13:56:38 CDT)
AMBER: mddisplay Anonymous (Thu Oct 23 2003 - 15:57:37 CDT)
AMBER: mddisplay Chris Moth (Fri Oct 24 2003 - 16:22:18 CDT)
AMBER: SHAKE question Herbert Georg (Thu Oct 23 2003 - 17:17:45 CDT)
Re: AMBER: SHAKE question Bill Ross (Thu Oct 23 2003 - 17:24:20 CDT)
Re: AMBER: Simulation of small protein Carlos Simmerling (Thu Oct 23 2003 - 17:59:58 CDT)
RE: AMBER: Simulation of small protein Yong Duan (Thu Oct 23 2003 - 20:11:02 CDT)
RE: AMBER: Simulation of small protein Endres, Robert G. (Thu Oct 23 2003 - 20:28:21 CDT)
RE: AMBER: Simulation of small protein Yong Duan (Thu Oct 23 2003 - 20:51:12 CDT)
AMBER: carnal iteration deviation from original crd file Dalmaris, John (Fri Oct 24 2003 - 06:11:36 CDT)
Re: AMBER: carnal iteration deviation from original crd file Vlad Cojocaru (Fri Oct 24 2003 - 06:32:17 CDT)
RE: AMBER: carnal iteration deviation from original crd file Dalmaris, John (Fri Oct 24 2003 - 07:29:28 CDT)
Re: AMBER: carnal iteration deviation from original crd file Vlad Cojocaru (Fri Oct 24 2003 - 07:42:24 CDT)
Re: AMBER: carnal iteration deviation from original crd file aini_at_UMDNJ.EDU (Fri Oct 24 2003 - 08:11:30 CDT)
AMBER: prmtop file format Herbert Georg (Fri Oct 24 2003 - 09:37:42 CDT)
RE: AMBER: prmtop file format Yong Duan (Fri Oct 24 2003 - 10:05:35 CDT)
Re: AMBER: carnal iteration deviation from original crd file Bill Ross (Fri Oct 24 2003 - 10:31:17 CDT)
RE: AMBER: carnal iteration deviation from original crd file Bill Ross (Fri Oct 24 2003 - 10:35:53 CDT)
AMBER: Pressure in NVT ensemble Shiang-Tai Lin (Fri Oct 24 2003 - 12:44:21 CDT)
Re: AMBER: prmtop file format Herbert Georg (Fri Oct 24 2003 - 13:51:50 CDT)
RE: AMBER: prmtop file format Yong Duan (Fri Oct 24 2003 - 14:19:16 CDT)
Re: AMBER: problem in tleap aini_at_UMDNJ.EDU (Fri Oct 24 2003 - 14:23:33 CDT)
Re: AMBER: problem in tleap Scott Brozell (Fri Oct 24 2003 - 21:05:33 CDT)
AMBER: RMSD and Radius of Gyration Endres, Robert G. (Sat Oct 25 2003 - 17:24:07 CDT)
Re: AMBER: RMSD and Radius of Gyration Carlos Simmerling (Sat Oct 25 2003 - 18:28:28 CDT)
RE: AMBER: RMSD and Radius of Gyration Yong Duan (Sat Oct 25 2003 - 20:40:07 CDT)
Re: AMBER: antechamber and bond type David A. Case (Sat Oct 25 2003 - 21:49:05 CDT)
Re: AMBER: Pressure in NVT ensemble David A. Case (Sat Oct 25 2003 - 22:16:37 CDT)
Re: AMBER: problem in tleap David A. Case (Sat Oct 25 2003 - 22:56:29 CDT)
AMBER: MD simulation: enzyme and its substrate Do Anh Tuan (Sat Oct 25 2003 - 23:51:20 CDT)
Re[2]: AMBER: surface code in Amber John Lee (Sun Oct 26 2003 - 20:06:56 CST)
Re: AMBER: surface code in Amber David A. Case (Mon Oct 27 2003 - 00:45:18 CST)
AMBER: comparing versions 6.0 and 7.0 of AMBER Therese Malliavin (Mon Oct 27 2003 - 03:30:21 CST)
AMBER: amber 7 for industrial application Jose Gallego (Mon Oct 27 2003 - 07:18:16 CST)
AMBER: solute images Sandro Fornili (Mon Oct 27 2003 - 09:28:34 CST)
Re: AMBER: surface code in Amber David E. Konerding (Mon Oct 27 2003 - 09:32:41 CST)
Re: AMBER: Pressure in NVT ensemble Shiang-Tai Lin (Mon Oct 27 2003 - 11:48:48 CST)
AMBER: Implicit MD simulations in Amber7 Joey Harriman (Mon Oct 27 2003 - 12:53:01 CST)
Re: AMBER: Implicit MD simulations in Amber7 Scott Brozell (Mon Oct 27 2003 - 14:20:14 CST)
Re: AMBER: solute images Scott Brozell (Mon Oct 27 2003 - 14:39:21 CST)
AMBER: Removal of Rotational and Translational Motion in AMBER6 Richard Smith (Mon Oct 27 2003 - 14:51:59 CST)
AMBER: aminoacid mutation Ioana Cozmuta (Mon Oct 27 2003 - 18:46:13 CST)
RE: AMBER: carnal iteration deviation from original crd file John (Mon Oct 27 2003 - 19:05:28 CST)
AMBER: SC45 Mu Yuguang (Dr) (Mon Oct 27 2003 - 19:12:29 CST)
RE: AMBER: aminoacid mutation Yong Duan (Mon Oct 27 2003 - 20:09:02 CST)
RE: AMBER: aminoacid mutation Endres, Robert G. (Mon Oct 27 2003 - 21:02:15 CST)
AMBER: Radius of Gyration and RMSD Jagannadh B (Tue Oct 28 2003 - 03:36:55 CST)
RE: AMBER: aminoacid mutation Bill Ross (Mon Oct 27 2003 - 23:09:23 CST)
AMBER: aminoacid mutation Wayne Dawson (Mon Oct 27 2003 - 23:47:25 CST)
Re: AMBER: amber 7 for industrial application David A. Case (Tue Oct 28 2003 - 00:21:35 CST)
Re[2]: AMBER: surface code in Amber John Lee (Tue Oct 28 2003 - 00:53:49 CST)
Re[2]: AMBER: surface code in Amber Dr. Yong Duan (Tue Oct 28 2003 - 08:46:32 CST)
RE: AMBER: Radius of Gyration and RMSD Endres, Robert G. (Tue Oct 28 2003 - 08:36:27 CST)
RE: AMBER: amber 7 for industrial application Jose Gallego (Tue Oct 28 2003 - 08:45:19 CST)
RE: AMBER: aminoacid mutation Sivakolundu, Sivashankar (Tue Oct 28 2003 - 09:43:38 CST)
RE: AMBER: amber 7 for industrial application Junmei Wang (Tue Oct 28 2003 - 09:58:43 CST)
Re: AMBER: surface code in Amber David E. Konerding (Tue Oct 28 2003 - 10:38:56 CST)
RE: AMBER: surface code in Amber Yong Duan (Tue Oct 28 2003 - 11:01:33 CST)
AMBER: how to measure the minor groove widths of a DNA? zhaoxc_at_puccini.che.pitt.edu (Tue Oct 28 2003 - 11:16:06 CST)
RE: AMBER: Radius of Gyration and RMSD Bill Ross (Tue Oct 28 2003 - 11:21:10 CST)
AMBER: ibelly problem Vikas Varshney (Tue Oct 28 2003 - 13:34:00 CST)
Re: AMBER: how to measure the minor groove widths of a DNA? Peter Gannett (Tue Oct 28 2003 - 13:43:22 CST)
RE: AMBER: aminoacid mutation Ioana Cozmuta (Tue Oct 28 2003 - 14:25:53 CST)
Re: AMBER: aminoacid mutation Osmar Norberto de Souza (Tue Oct 28 2003 - 14:38:00 CST)
Re: AMBER: aminoacid mutation Amber Administration (Tue Oct 28 2003 - 16:34:47 CST)
AMBER: Installation Problem, xleap can't load pdb files Jonathan Neidigh (Tue Oct 28 2003 - 17:19:59 CST)
Re: AMBER: surface code in Amber David A. Case (Tue Oct 28 2003 - 18:15:33 CST)
AMBER: mddisplay Anonymous (Tue Oct 28 2003 - 18:21:04 CST)
RE: AMBER: mddisplay Kristina Furse (Tue Oct 28 2003 - 18:48:30 CST)
Re: AMBER: Installation Problem, xleap can't load pdb files Jonathan Neidigh (Wed Oct 29 2003 - 09:54:18 CST)
RE: AMBER: amber 7 for industrial application Bayly, Christopher (Wed Oct 29 2003 - 10:45:27 CST)
Re: AMBER: ibelly problem Thomas E. Cheatham, III (Wed Oct 29 2003 - 11:23:12 CST)
Re: AMBER: how to measure the minor groove widths of a DNA? Thomas E. Cheatham, III (Wed Oct 29 2003 - 11:31:09 CST)
AMBER: mddisplay Chris Moth (Thu Oct 30 2003 - 12:29:12 CST)
AMBER: reduce box and delete excess solvent Endres, Robert G. (Wed Oct 29 2003 - 13:31:52 CST)
AMBER: MD simulation: enzyme and its substrate Do Anh Tuan (Wed Oct 29 2003 - 13:52:24 CST)
Re: AMBER: MD simulation: enzyme and its substrate!! Pradipta Bandyopadhyay (Wed Oct 29 2003 - 14:26:17 CST)
AMBER: JAC on NCSA titan (Itanium 2 833MHZ) Qiang Lu (Wed Oct 29 2003 - 16:09:56 CST)
AMBER: wangf2 (Thu Oct 30 2003 - 10:00:15 CST)
Re: AMBER: David A. Case (Thu Oct 30 2003 - 11:23:12 CST)
AMBER: minimize a covalently bounded protein-ligand complex Eric Hu (Thu Oct 30 2003 - 17:36:53 CST)
Re: AMBER: minimize a covalently bounded protein-ligand complex David A. Case (Thu Oct 30 2003 - 17:50:11 CST)
AMBER: What does this error message mean? nie beining (Fri Oct 31 2003 - 09:34:40 CST)
AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD Robert Duke (Fri Oct 31 2003 - 09:40:37 CST)
Re: AMBER: What does this error message mean? Ioana Cozmuta (Fri Oct 31 2003 - 09:46:46 CST)
Re: AMBER: What does this error message mean? Jose Ramon Blas (Fri Oct 31 2003 - 18:29:19 CST)
Re: AMBER: What does this error message mean? nie beining (Fri Oct 31 2003 - 11:41:27 CST)
AMBER: Freezing of water with TIP3P potential. Mahesh Chandran (Mon Nov 03 2003 - 05:41:21 CST)
AMBER: question about input files for small molecule with fluorine aini_at_rwja.umdnj.edu (Mon Nov 03 2003 - 09:45:10 CST)
Re: AMBER: question about input files for small molecule with fluorine Carlos Simmerling (Mon Nov 03 2003 - 09:53:49 CST)
AMBER: large file for carnal volodya (Sat Oct 04 2003 - 12:12:37 CDT)
Re: AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD David E. Konerding (Mon Nov 03 2003 - 12:41:08 CST)
AMBER: distrance restraints for alpha carbons Sheldon Holder (Mon Nov 03 2003 - 13:27:48 CST)
Re: AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD Robert Duke (Mon Nov 03 2003 - 13:31:34 CST)
Re: AMBER: distrance restraints for alpha carbons Sheldon Holder (Mon Nov 03 2003 - 13:56:49 CST)
Re: AMBER: large file for carnal Bill Ross (Mon Nov 03 2003 - 14:14:30 CST)
Re: AMBER: make clean doesn't clean leap David A. Case (Mon Nov 03 2003 - 16:58:38 CST)
Re: AMBER: distrance restraints for alpha carbons David A. Case (Mon Nov 03 2003 - 17:06:57 CST)
AMBER: MD Equil Chenglong Li (Mon Nov 03 2003 - 17:07:56 CST)
Re: AMBER: make clean doesn't clean leap Karen Haskell (Mon Nov 03 2003 - 17:19:23 CST)
AMBER: make clean doesn't clean leap Karen Haskell (Mon Nov 03 2003 - 16:47:22 CST)
Re: AMBER: MD Equil David A. Case (Mon Nov 03 2003 - 18:55:59 CST)
Re: AMBER: large file for carnal volodya (Sun Oct 05 2003 - 06:23:44 CDT)
RE: AMBER: make clean doesn't clean leap Ming Lei (Tue Nov 04 2003 - 10:01:26 CST)
Re: AMBER: large file for carnal Bill Ross (Tue Nov 04 2003 - 11:03:44 CST)
AMBER: Restart a simulation Frederico.Miranda_at_ibmb.uib.no (Tue Nov 04 2003 - 13:21:03 CST)
Re: AMBER: large file for carnal Bill Ross (Tue Nov 04 2003 - 14:19:19 CST)
AMBER: atomtypenumber Rajendra P. OJHA (Tue Nov 04 2003 - 15:07:20 CST)
AMBER: RESP fitting limit? yuann (Tue Nov 04 2003 - 22:46:10 CST)
AMBER: How to estimate SD of the delta delta G between two mm_pbsa runs Zheng Suxin (Wed Nov 05 2003 - 07:41:34 CST)
AMBER: absolute vs. relative binding free energy Qing Zhang (Wed Nov 05 2003 - 18:24:45 CST)
Re: AMBER: absolute vs. relative binding free energy David A. Case (Wed Nov 05 2003 - 19:45:54 CST)
AMBER: shake constraint on all bonds Jian Zhang, Dr (Wed Nov 05 2003 - 21:34:24 CST)
RE: AMBER: shake constraint on all bonds Yong Duan (Wed Nov 05 2003 - 22:08:44 CST)
Re: AMBER: How to estimate SD of the delta delta G between two mm_pbsa runs Holger Gohlke (Thu Nov 06 2003 - 01:24:42 CST)
Re: AMBER: large file for carnal volodya (Tue Oct 07 2003 - 07:52:04 CDT)
AMBER: RMSd per residue volodya (Tue Oct 07 2003 - 07:58:20 CDT)
AMBER: parmchk on MAC Kaushik Raha (Thu Nov 06 2003 - 10:19:52 CST)
AMBER: handling non neutral systems hagop demirdjian (Thu Nov 06 2003 - 09:31:19 CST)
AMBER: Restraints Steve Seibold (Thu Nov 06 2003 - 14:28:09 CST)
Re: AMBER: Restraints David A. Case (Thu Nov 06 2003 - 17:26:47 CST)
AMBER: Can use mm_pbsa_statistics.pl to calculate each snapshot's Delta Delta G, then give the SD Zheng Suxin (Thu Nov 06 2003 - 21:41:12 CST)
Re: AMBER: Can use mm_pbsa_statistics.pl to calculate each snapshot's Delta Delta G, then give the SD Holger Gohlke (Fri Nov 07 2003 - 02:23:29 CST)
AMBER: fix some area Helios Chen (Fri Nov 07 2003 - 03:06:06 CST)
Re: AMBER: fix some area Carlos Simmerling (Fri Nov 07 2003 - 06:27:38 CST)
AMBER: restrain Vlad Cojocaru (Fri Nov 07 2003 - 09:53:52 CST)
Re: AMBER: restrain David A. Case (Fri Nov 07 2003 - 10:34:21 CST)
RE: AMBER: infinitely long DNA (to Yong Duan) Endres, Robert G. (Fri Nov 07 2003 - 14:50:17 CST)
Re: AMBER: infinitely long DNA (to Yong Duan) bishop (Fri Nov 07 2003 - 15:59:46 CST)
RE: AMBER: infinitely long DNA (to Yong Duan) Yong Duan (Fri Nov 07 2003 - 16:24:41 CST)
AMBER: mpich problem Qiang Lu (Sat Nov 08 2003 - 02:25:08 CST)
AMBER: mpich problem Qiang Lu (Sat Nov 08 2003 - 02:23:50 CST)
Re: AMBER: mpich problem David E. Konerding (Sat Nov 08 2003 - 11:15:34 CST)
Re[2]: AMBER: mpich problem Qiang Lu (Sun Nov 09 2003 - 16:27:47 CST)
Re[3]: AMBER: mpich problem Qiang Lu (Sun Nov 09 2003 - 18:28:37 CST)
Re: AMBER: mpich problem Viktor Hornak (Sun Nov 09 2003 - 18:06:53 CST)
RE: AMBER: mpich problem Yong Duan (Sun Nov 09 2003 - 18:13:13 CST)
Re: AMBER: fix some area Helios Chen (Sun Nov 09 2003 - 19:21:42 CST)
Re[2]: AMBER: mpich problem Qiang Lu (Sun Nov 09 2003 - 20:27:09 CST)
Re[2]: AMBER: mpich problem Qiang Lu (Sun Nov 09 2003 - 20:24:20 CST)
Re: AMBER: fix some area Carlos Simmerling (Sun Nov 09 2003 - 19:50:17 CST)
AMBER: a problem with antechamber and leap Ye Mei (Sun Nov 09 2003 - 23:02:04 CST)
Re: AMBER: a problem with antechamber and leap David A. Case (Mon Nov 10 2003 - 01:24:41 CST)
Re: Re: AMBER: a problem with antechamber and leap Ye Mei (Mon Nov 10 2003 - 03:15:06 CST)
AMBER: mgbjsb radii in GBSA Giulio Rastelli (Mon Nov 10 2003 - 10:39:18 CST)
AMBER: AM1-BCC in Amber7 Joey Harriman (Mon Nov 10 2003 - 06:56:23 CST)
Re: AMBER: AM1-BCC in Amber7 Ye Mei (Mon Nov 10 2003 - 07:37:05 CST)
Re: AMBER: AM1-BCC in Amber7 Joey Harriman (Mon Nov 10 2003 - 08:15:25 CST)
Re: AMBER: mgbjsb radii in GBSA David A. Case (Mon Nov 10 2003 - 10:10:17 CST)
Re: AMBER: AM1-BCC in Amber7 David A. Case (Mon Nov 10 2003 - 10:12:07 CST)
Re: AMBER: mgbjsb radii in GBSA Giulio Rastelli (Mon Nov 10 2003 - 17:02:00 CST)
AMBER: change force constants Obdulia Rabal (Mon Nov 10 2003 - 11:27:23 CST)
AMBER: Re: AM1-BCC in Amber7 Rhonda Torres (Mon Nov 10 2003 - 12:22:19 CST)
Re[2]: AMBER: mpich problem Qiang Lu (Mon Nov 10 2003 - 18:07:06 CST)
Re: AMBER: change force constants David A. Case (Mon Nov 10 2003 - 17:56:59 CST)
AMBER: restraints and reordering water Vlad Cojocaru (Tue Nov 11 2003 - 03:42:04 CST)
AMBER: Protein Rotation Frederico.Miranda_at_ibmb.uib.no (Tue Nov 11 2003 - 06:47:44 CST)
Re: AMBER: Protein Rotation Carlos Simmerling (Tue Nov 11 2003 - 07:02:32 CST)
Re: AMBER: Protein Rotation volodya (Sun Oct 12 2003 - 08:40:07 CDT)
Re: AMBER: Protein Rotation Frederico.Miranda_at_ibmb.uib.no (Tue Nov 11 2003 - 08:52:44 CST)
Re: AMBER: Protein Rotation Carlos Simmerling (Tue Nov 11 2003 - 09:11:40 CST)
Re: AMBER: Protein Rotation Bill Ross (Tue Nov 11 2003 - 10:06:33 CST)
Re: AMBER: RMSd per residue Bill Ross (Tue Nov 11 2003 - 10:20:20 CST)
Re: AMBER: Protein Rotation Bill Ross (Tue Nov 11 2003 - 10:35:08 CST)
Re: AMBER: restraints and reordering water David A. Case (Tue Nov 11 2003 - 11:21:10 CST)
AMBER: GB/SA Yichen Cao (Tue Nov 11 2003 - 13:02:41 CST)
Re: AMBER: GB/SA Chris Moth (Wed Nov 12 2003 - 14:30:33 CST)
Re: AMBER: GB/SA Holger Gohlke (Tue Nov 11 2003 - 14:47:59 CST)
Re: AMBER: AM1-BCC in Amber7 Junmei Wang (Tue Nov 11 2003 - 15:49:31 CST)
Re: AMBER: mgbjsb radii in GBSA Junmei Wang (Tue Nov 11 2003 - 16:12:08 CST)
Re: Re: AMBER: a problem with antechamber and leap Junmei Wang (Tue Nov 11 2003 - 16:33:02 CST)
Re: Re: AMBER: a problem with antechamber and leap Junmei Wang (Tue Nov 11 2003 - 16:38:32 CST)
Re: Re: AMBER: a problem with antechamber and leap David A. Case (Tue Nov 11 2003 - 19:01:39 CST)
AMBER: Separation of a Water molecules nabe (Tue Nov 11 2003 - 18:59:22 CST)
Re: AMBER: Separation of a Water molecules Carlos Simmerling (Tue Nov 11 2003 - 20:15:53 CST)
Re: AMBER: Separation of a Water molecules Thomas E. Cheatham, III (Tue Nov 11 2003 - 22:13:41 CST)
Re: AMBER: Separation of a Water molecules nabe (Wed Nov 12 2003 - 02:43:59 CST)
Re: Re: Re: AMBER: a problem with antechamber and leap Ye Mei (Wed Nov 12 2003 - 02:48:06 CST)
Re: AMBER: Correction [Separation of a Water molecules] nabe (Wed Nov 12 2003 - 02:53:49 CST)
Re: AMBER: Separation of a Water molecules Carlos Simmerling (Wed Nov 12 2003 - 06:47:20 CST)
AMBER: antechamber mopac7 parameters Joey Harriman (Wed Nov 12 2003 - 09:06:41 CST)
AMBER: average coordinates Frederico.Miranda_at_ibmb.uib.no (Wed Nov 12 2003 - 11:47:33 CST)
Re: AMBER: average coordinates Bill Ross (Wed Nov 12 2003 - 12:12:20 CST)
Re: AMBER: average coordinates Bill Ross (Wed Nov 12 2003 - 12:24:18 CST)
AMBER: about some of the cards in Sander 7 Pingna Xu (Wed Nov 12 2003 - 14:09:12 CST)
Re: AMBER: about some of the cards in Sander 7 Rhonda Torres (Wed Nov 12 2003 - 14:35:43 CST)
Re: AMBER: about some of the cards in Sander 7 Vlad Cojocaru (Wed Nov 12 2003 - 14:38:39 CST)
Re: Re: AMBER: a problem with antechamber and leap Junmei Wang (Wed Nov 12 2003 - 14:46:02 CST)
Re: Re: Re: AMBER: a problem with antechamber and leap Junmei Wang (Wed Nov 12 2003 - 14:51:05 CST)
Re: AMBER: Separation of a Water molecules nabe (Wed Nov 12 2003 - 20:32:45 CST)
Re: AMBER: Separation of a Water molecules Thomas E. Cheatham, III (Wed Nov 12 2003 - 22:16:38 CST)
Re: AMBER: Separation of a Water molecules Dr. Yong Duan (Wed Nov 12 2003 - 23:43:26 CST)
Re: Re: Re: Re: AMBER: a problem with antechamber and leap Ye Mei (Thu Nov 13 2003 - 00:52:38 CST)
AMBER: atmtypenumbers for halogens Thomas.Fox_at_bc.boehringer-ingelheim.com (Thu Nov 13 2003 - 02:53:38 CST)
AMBER: ndfmin in belly runs John (Thu Nov 13 2003 - 04:50:52 CST)
AMBER: RNA and Protein questions (also some general questions) a b (Thu Nov 13 2003 - 04:55:07 CST)
Re: AMBER: RNA and Protein questions (also some general questions) Balvinder Singh (Thu Nov 13 2003 - 11:21:49 CST)
AMBER: GIBBS - PMF problem: Lambda has not changed Jiri Matousek (Thu Nov 13 2003 - 06:32:01 CST)
Re: AMBER: Separation of a Water molecules Carlos Simmerling (Thu Nov 13 2003 - 07:48:28 CST)
Re: AMBER: RNA and Protein questions (also some general questions) Dr. Yong Duan (Thu Nov 13 2003 - 09:57:41 CST)
Re: AMBER: GIBBS - PMF problem: Lambda has not changed David Smith (Thu Nov 13 2003 - 08:00:48 CST)
Re: AMBER: ndfmin in belly runs David A. Case (Thu Nov 13 2003 - 10:07:14 CST)
AMBER: high temperature, 498K, unfolding simulations james tomomi macdonald (Thu Nov 13 2003 - 10:19:05 CST)
AMBER: Nmode Problem Yuqin Cai (Thu Nov 13 2003 - 10:26:25 CST)
Re: AMBER: RNA and Protein questions (also some general questions) FyD (Thu Nov 13 2003 - 10:45:33 CST)
Re: AMBER: high temperature, 498K, unfolding simulations Andreas Svrcek-Seiler (Thu Nov 13 2003 - 11:05:46 CST)
Re: AMBER: GIBBS - PMF problem: Lambda has not changed Jiri Matousek (Thu Nov 13 2003 - 11:09:49 CST)
Re: AMBER: RNA and Protein questions (also some general questions) Piotr Cieplak (Thu Nov 13 2003 - 11:37:14 CST)
Re: AMBER: Nmode Problem Holger Gohlke (Thu Nov 13 2003 - 13:13:45 CST)
AMBER: water prep file needed Youyi Peng (Thu Nov 13 2003 - 15:37:36 CST)
AMBER: Any correct way to image a molecule ? Teletchéa Stéphane (Thu Nov 13 2003 - 15:37:40 CST)
Re: AMBER: water prep file needed David A. Case (Thu Nov 13 2003 - 15:36:38 CST)
Re: AMBER: Any correct way to image a molecule ? Thomas E. Cheatham, III (Thu Nov 13 2003 - 15:58:38 CST)
Re: AMBER: Any correct way to image a molecule ? Teletchéa Stéphane (Thu Nov 13 2003 - 16:46:48 CST)
Re: AMBER: Any correct way to image a molecule ? Carlos Simmerling (Thu Nov 13 2003 - 18:35:19 CST)
Re: AMBER: atmtypenumbers for halogens Giulio Rastelli (Fri Nov 14 2003 - 09:00:41 CST)
Re: AMBER: Any correct way to image a molecule ? Teletchéa Stéphane (Fri Nov 14 2003 - 03:55:36 CST)
Re: AMBER: Any correct way to image a molecule ? Carlos Simmerling (Fri Nov 14 2003 - 04:27:18 CST)
Re: AMBER: GIBBS - PMF problem: Lambda has not changed David Smith (Fri Nov 14 2003 - 04:50:01 CST)
AMBER: Problems restarting with sander raist_at_mmb.pcb.ub.es (Fri Nov 14 2003 - 15:26:07 CST)
AMBER: rotation removal in sander GB Mu Yuguang (Dr) (Fri Nov 14 2003 - 09:40:56 CST)
Re: AMBER: Problems restarting with sander David A. Case (Fri Nov 14 2003 - 10:31:12 CST)
Re: AMBER: rotation removal in sander GB David A. Case (Fri Nov 14 2003 - 10:34:06 CST)
Re: AMBER: Problems restarting with sander raist_at_mmb.pcb.ub.es (Fri Nov 14 2003 - 19:14:42 CST)
AMBER: update of BOX dim. Endres, Robert G. (Fri Nov 14 2003 - 13:53:21 CST)
RE: AMBER: update of BOX dim. Endres, Robert G. (Fri Nov 14 2003 - 14:23:14 CST)
AMBER: sander lastist Frederico.Miranda_at_ibmb.uib.no (Sat Nov 15 2003 - 04:01:57 CST)
Re: AMBER: mgbjsb radii in GBSA Giulio Rastelli (Sat Nov 15 2003 - 11:05:49 CST)
Re: AMBER: sander lastist David A. Case (Sat Nov 15 2003 - 11:40:13 CST)
Re: AMBER: mgbjsb radii in GBSA David A. Case (Sat Nov 15 2003 - 11:58:35 CST)
AMBER: Diffusion constant franck (Sat Nov 15 2003 - 13:00:56 CST)
Re: AMBER: Diffusion constant David A. Case (Sat Nov 15 2003 - 14:45:56 CST)
AMBER: a problem with memory size Ye Mei (Sun Nov 16 2003 - 09:45:39 CST)
AMBER: MM_pbsa Rajendra P. OJHA (Sun Nov 16 2003 - 11:35:23 CST)
AMBER: dual processor Rajendra P. OJHA (Sun Nov 16 2003 - 11:45:40 CST)
AMBER: Pressure during MD João Barroso (Sun Nov 16 2003 - 12:12:18 CST)
Re: AMBER: a problem with memory size David A. Case (Sun Nov 16 2003 - 16:49:30 CST)
Re: AMBER: Pressure during MD David A. Case (Sun Nov 16 2003 - 16:52:36 CST)
Re: AMBER: Pressure during MD João Barroso (Mon Nov 17 2003 - 03:36:41 CST)
AMBER: Restarting MD amber7 raist_at_mmb.pcb.ub.es (Mon Nov 17 2003 - 12:54:32 CST)
Re: AMBER: Restarting MD amber7 Carlos Simmerling (Sun Nov 16 2003 - 08:39:03 CST)
AMBER: RESP charge Youyi Peng (Mon Nov 17 2003 - 08:46:32 CST)
AMBER: ptraj and charmm files Endres, Robert G. (Mon Nov 17 2003 - 09:25:04 CST)
Re: AMBER: ptraj and charmm files Thomas E. Cheatham, III (Mon Nov 17 2003 - 09:50:22 CST)
AMBER: Lone pairs and resp Perdita Barran (Mon Nov 17 2003 - 10:49:35 CST)
AMBER: Lone pairs and resp Perdita Barran (Mon Nov 17 2003 - 10:55:05 CST)
AMBER: antechamber test failure Meg McCarrick (Mon Nov 17 2003 - 14:39:58 CST)
Re: AMBER: RESP charge FyD (Mon Nov 17 2003 - 16:27:25 CST)
AMBER: amber on mac cluster yu275197_at_yorku.ca (Mon Nov 17 2003 - 19:58:34 CST)
Re: AMBER: Lone pairs and resp FyD (Mon Nov 17 2003 - 20:06:57 CST)
Re: AMBER: Pressure during MD David A. Case (Mon Nov 17 2003 - 21:03:47 CST)
Re: AMBER: antechamber test failure David A. Case (Mon Nov 17 2003 - 21:03:56 CST)
AMBER: Compiling AMBER7 on Suse Herbert Georg (Tue Nov 18 2003 - 07:08:06 CST)
AMBER: Zinc parameters Annette Höglund (Tue Nov 18 2003 - 07:19:28 CST)
Re: AMBER: Compiling AMBER7 on Suse Andreas Svrcek-Seiler (Tue Nov 18 2003 - 07:41:47 CST)
AMBER: Problem with MPI_Finalize Thomas.Fox_at_bc.boehringer-ingelheim.com (Tue Nov 18 2003 - 08:10:02 CST)
Re: AMBER: Problem with MPI_Finalize Robert Duke (Tue Nov 18 2003 - 08:54:36 CST)
AW: AMBER: Problem with MPI_Finalize Thomas.Fox_at_bc.boehringer-ingelheim.com (Tue Nov 18 2003 - 09:34:36 CST)
RE: AMBER: antechamber test failure Meg McCarrick (Tue Nov 18 2003 - 11:06:12 CST)
Re: AMBER: Problem with MPI_Finalize Bill Ross (Tue Nov 18 2003 - 12:06:13 CST)
Re: AMBER: Compiling AMBER7 on Suse Bill Ross (Tue Nov 18 2003 - 12:27:25 CST)
AMBER: molsuf failure with too many intersecting cusps Lee, Matthew (Tue Nov 18 2003 - 14:24:29 CST)
RE: AMBER: Zinc parameters Ross Walker (Tue Nov 18 2003 - 15:26:49 CST)
Re: AMBER: antechamber test failure David A. Case (Tue Nov 18 2003 - 16:22:16 CST)
AMBER: Cutress %cmass error Jory Zmuda (Wed Nov 19 2003 - 09:17:08 CST)
AMBER: MM_PB/GB/SA Chenglong Li (Wed Nov 19 2003 - 12:44:19 CST)
Re: AMBER: Cutress %cmass error Bill Ross (Wed Nov 19 2003 - 13:51:04 CST)
Re: AMBER: MM_PB/GB/SA Holger Gohlke (Thu Nov 20 2003 - 06:36:30 CST)
[Fwd: AMBER: MM_PB/GB/SA] Chenglong Li (Thu Nov 20 2003 - 12:07:19 CST)
AMBER: missing of VdW Parameters for N3 Nikolai Smolin (Fri Nov 21 2003 - 03:45:09 CST)
Re: AMBER: missing of VdW Parameters for N3 David A. Case (Fri Nov 21 2003 - 10:08:07 CST)
Re: AMBER: missing of VdW Parameters for N3 Piotr Cieplak (Fri Nov 21 2003 - 12:56:53 CST)
AMBER: Why I get the same TSTRA for different strucutures from Nmode calculation? Yuqin Cai (Fri Nov 21 2003 - 14:54:54 CST)
AMBER: Compaq Tru64 Unix Herbert de Castro Georg (Fri Nov 21 2003 - 15:37:07 CST)
Re: AMBER: Compaq Tru64 Unix David A. Case (Fri Nov 21 2003 - 17:34:43 CST)
Re: AMBER: Why I get the same TSTRA for different strucutures from Nmode calculation? David A. Case (Fri Nov 21 2003 - 17:33:38 CST)
AMBER: mm_pbsa and antechamber Rajendra P. OJHA (Sat Nov 22 2003 - 13:03:34 CST)
AMBER: structure refinement using CNS vs. AMBER a b (Sat Nov 22 2003 - 15:27:06 CST)
AMBER: Fluorine in GBSA aini_at_UMDNJ.EDU (Mon Nov 24 2003 - 08:38:38 CST)
AMBER: protein MD - problem RAJA SWAMINATHAN (Mon Nov 24 2003 - 08:47:53 CST)
Re: AMBER: protein MD - problem Carlos Simmerling (Mon Nov 24 2003 - 08:52:53 CST)
Re: AMBER: protein MD - problem David A. Case (Mon Nov 24 2003 - 10:27:08 CST)
AMBER: water mediated contacts Vlad Cojocaru (Mon Nov 24 2003 - 10:42:12 CST)
AMBER: Re: AMBER water mediated contacts Rhonda Torres (Mon Nov 24 2003 - 11:51:31 CST)
Re: AMBER: mm_pbsa and antechamber Holger Gohlke (Mon Nov 24 2003 - 13:37:02 CST)
AMBER: torsion problems of dummy atoms Difei Wang (Mon Nov 24 2003 - 14:24:11 CST)
Re: AMBER: torsion problems of dummy atoms Bill Ross (Mon Nov 24 2003 - 17:58:21 CST)
AMBER: saveamberparm Atchara Wijitkosoom (Mon Nov 24 2003 - 19:20:36 CST)
Re: AMBER: saveamberparm Bill Ross (Mon Nov 24 2003 - 19:31:51 CST)
Re: AMBER: saveamberparm David A. Case (Mon Nov 24 2003 - 19:32:22 CST)
AMBER: charge fitting Itziar Maestre Asenjo (Tue Nov 25 2003 - 02:28:05 CST)
Re: AMBER: charge fitting FyD (Tue Nov 25 2003 - 10:42:56 CST)
AMBER: 1 fs timestep for GB? Peter VARNAI (Tue Nov 25 2003 - 11:48:35 CST)
Re: AMBER: charge fitting Piotr Cieplak (Tue Nov 25 2003 - 11:59:59 CST)
AMBER: image question Li Ying (Tue Nov 25 2003 - 12:13:21 CST)
Re: AMBER: 1 fs timestep for GB? Andreas Svrcek-Seiler (Tue Nov 25 2003 - 12:32:15 CST)
RE: AMBER: image question Rhonda Torres (Tue Nov 25 2003 - 12:50:36 CST)
Re: AMBER: 1 fs timestep for GB? Alexey Onufriev (Tue Nov 25 2003 - 15:19:04 CST)
Re: AMBER: Fluorine in GBSA Alexey Onufriev (Tue Nov 25 2003 - 15:33:43 CST)
AMBER: intermolecular force Dave S Walker (Tue Nov 25 2003 - 17:19:15 CST)
AMBER: gaff errors? Difei Wang (Tue Nov 25 2003 - 18:53:43 CST)
AMBER: compiling amber using gcc on SGI Unix machines Wayne Dawson (Wed Nov 26 2003 - 07:15:57 CST)
Re: AMBER: gaff errors? David A. Case (Wed Nov 26 2003 - 10:40:37 CST)
AMBER: restart MD program Do Anh Tuan (Wed Nov 26 2003 - 11:12:50 CST)
Re: AMBER: restart MD program Carlos Simmerling (Wed Nov 26 2003 - 11:23:06 CST)
AMBER: restarted MD and ptraj Frederico.Miranda_at_ibmb.uib.no (Wed Nov 26 2003 - 19:35:35 CST)
Re: AMBER: charge fitting Itziar Maestre Asenjo (Thu Nov 27 2003 - 03:00:58 CST)
AMBER: Nmode problem Wu Yingliang (Fri Nov 28 2003 - 07:52:31 CST)
Re: AMBER: Nmode problem Holger Gohlke (Fri Nov 28 2003 - 09:11:49 CST)
Re: AMBER: charge fitting FyD (Fri Nov 28 2003 - 12:45:21 CST)
AMBER: Hello Rajendra P. OJHA (Sat Nov 29 2003 - 09:51:21 CST)
AMBER: Pseudouridine force field parameters Peter Gannett (Sat Nov 29 2003 - 18:27:38 CST)
Re: AMBER: Pseudouridine force field parameters David A. Case (Sat Nov 29 2003 - 18:48:59 CST)
AMBER: Re: Nmode problem Wu Yingliang (Sat Nov 29 2003 - 21:52:15 CST)
AMBER: Re: Nmode problem Holger Gohlke (Sun Nov 30 2003 - 09:24:50 CST)
Re: AMBER: Pseudouridine force field parameters Pascal Auffinger (Sun Nov 30 2003 - 09:58:30 CST)
Re: AMBER: Pseudouridine force field parameters Peter Gannett (Sun Nov 30 2003 - 09:56:28 CST)
Re: AMBER: Re: Nmode problem Wu Yingliang (Mon Dec 01 2003 - 07:34:40 CST)
AMBER: NAD+ and NADH amber parameters Jiten (Mon Dec 01 2003 - 08:01:17 CST)
Re: AMBER: Re: Nmode problem Holger Gohlke (Mon Dec 01 2003 - 08:17:37 CST)
Re: AMBER: NAD+ and NADH amber parameters David A. Case (Mon Dec 01 2003 - 10:35:56 CST)
RE: AMBER: NAD+ and NADH amber parameters Ross Walker (Mon Dec 01 2003 - 11:07:40 CST)
AMBER: partial charge Li Ying (Mon Dec 01 2003 - 11:31:56 CST)
AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg (Mon Dec 01 2003 - 13:17:15 CST)
AMBER: Sander / Anal Emmanuel Giudice (Mon Dec 01 2003 - 14:06:00 CST)
Re: AMBER: Compiling on Suse 9 Pro with ifc... David A. Case (Mon Dec 01 2003 - 14:49:33 CST)
Re: AMBER: Sander / Anal David A. Case (Mon Dec 01 2003 - 14:58:32 CST)
AMBER: basic questions Wei Wang (Mon Dec 01 2003 - 17:02:52 CST)
AMBER: sander output Dave S Walker (Mon Dec 01 2003 - 20:04:31 CST)
Re: AMBER: sander output Carlos Simmerling (Mon Dec 01 2003 - 20:37:06 CST)
Re: AMBER: basic questions David A. Case (Tue Dec 02 2003 - 00:37:59 CST)
Re: AMBER: partial charge David A. Case (Tue Dec 02 2003 - 00:46:04 CST)
Re: AMBER: Pseudouridine force field parameters Peter Gannett (Tue Dec 02 2003 - 06:45:01 CST)
Re: AMBER: NAD+ and NADH amber parameters Ulf Ryde (Tue Dec 02 2003 - 07:20:26 CST)
AMBER: about H-bond definition for TIP3P Nikolai Smolin (Tue Dec 02 2003 - 07:44:19 CST)
Re: AMBER: basic questions Wei Wang (Tue Dec 02 2003 - 10:23:13 CST)
Re: AMBER: basic questions David A. Case (Tue Dec 02 2003 - 10:37:42 CST)
AMBER: Ptraj-HBOND Taner E. Dirama (Tue Dec 02 2003 - 12:42:58 CST)
Re: AMBER: partial charge Li Ying (Tue Dec 02 2003 - 13:19:22 CST)
Re: AMBER: partial charge David A. Case (Tue Dec 02 2003 - 14:06:02 CST)
AMBER: Anal/MMPBSA Wu Yingliang (Tue Dec 02 2003 - 19:16:02 CST)
Re: AMBER: Anal/MMPBSA David A. Case (Tue Dec 02 2003 - 19:29:46 CST)
AMBER: segmentation fault Do Anh Tuan (Tue Dec 02 2003 - 22:56:32 CST)
AMBER: GIBBS - PMFquestion Jiri Matousek (Wed Dec 03 2003 - 04:47:41 CST)
AMBER: how to calculate vibration frequency? A. Hungie (Wed Dec 03 2003 - 08:46:26 CST)
Re: AMBER: missing of VdW Parameters for N3 wendy.cornell_at_pharma.novartis.com (Wed Dec 03 2003 - 09:18:23 CST)
Re: AMBER: how to calculate vibration frequency? David A. Case (Wed Dec 03 2003 - 10:59:41 CST)
AMBER: MM-PBSA question Giovanni (Wed Dec 03 2003 - 12:10:10 CST)
Re: AMBER: segmentation fault David A. Case (Wed Dec 03 2003 - 11:46:46 CST)
Re: AMBER: partial charge Li Ying (Wed Dec 03 2003 - 12:08:14 CST)
Re: AMBER: MM-PBSA question Holger Gohlke (Wed Dec 03 2003 - 12:58:23 CST)
AMBER: Resp Esp charge Derive (RED v-1.0) release FyD (Wed Dec 03 2003 - 13:09:39 CST)
AMBER: Paramters for beta and gamma peptides Jagannadh B (Thu Dec 04 2003 - 06:34:43 CST)
RE: Re: AMBER: ANAL/MMPBSA Wu Yingliang (Thu Dec 04 2003 - 01:53:25 CST)
Re: AMBER: ANAL/MMPBSA Holger Gohlke (Thu Dec 04 2003 - 02:42:06 CST)
AMBER: TFE solvent box John (Thu Dec 04 2003 - 05:16:33 CST)
Re: AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg (Wed Dec 03 2003 - 07:26:07 CST)
Re: AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg (Wed Dec 03 2003 - 08:04:30 CST)
Re: AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg (Wed Dec 03 2003 - 13:13:42 CST)
Re: AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg (Thu Dec 04 2003 - 06:56:55 CST)
Re: Re: AMBER: ANAL/MMPBSA Wu Yingliang (Thu Dec 04 2003 - 07:29:41 CST)
Re: AMBER: Compiling on Suse 9 Pro with ifc... David A. Case (Thu Dec 04 2003 - 10:42:15 CST)
AMBER: NO2-TYR arubin_at_unmc.edu (Thu Dec 04 2003 - 11:30:24 CST)
AMBER: Amber - compiler help Malone, Scott (Thu Dec 04 2003 - 16:11:53 CST)
RE: AMBER: Amber - compiler help Chris Moth (Thu Dec 04 2003 - 16:45:10 CST)
Re: AMBER: sander output Dave S Walker (Thu Dec 04 2003 - 18:41:05 CST)
Re: AMBER: sander output David A. Case (Thu Dec 04 2003 - 18:51:03 CST)
Re: AMBER: Amber - compiler help David A. Case (Thu Dec 04 2003 - 18:54:07 CST)
AMBER: TFE solvent box RAJA SWAMINATHAN (Thu Dec 04 2003 - 22:34:03 CST)
RE: AMBER: TFE solvent box John (Fri Dec 05 2003 - 08:25:42 CST)
Re: AMBER: Sander / Anal Emmanuel Giudice (Fri Dec 05 2003 - 11:54:20 CST)
Re: Re: AMBER: Compiling on Suse 9 Pro with ifc... Ye Mei (Fri Dec 05 2003 - 22:44:49 CST)
Re: AMBER: NAD+ and NADH amber parameters Jiten (Sun Dec 07 2003 - 22:17:53 CST)
Re: AMBER: NAD+ and NADH amber parameters Ross Walker (Mon Dec 08 2003 - 00:22:56 CST)
Re: AMBER: NAD+ and NADH amber parameters Ulf Ryde (Mon Dec 08 2003 - 05:05:25 CST)
AMBER: initial structures Raghunadha Reddy Burri (Mon Dec 08 2003 - 09:21:28 CST)
Re: AMBER: initial structures Carlos Simmerling (Mon Dec 08 2003 - 09:51:04 CST)
AMBER: Temperature dependent properties of TIP4P and TIP5P rluo_at_uci.edu (Mon Dec 08 2003 - 11:00:21 CST)
AMBER: Re: initial structures Raghunadha Reddy Burri (Mon Dec 08 2003 - 11:19:10 CST)
Re: AMBER: Re: initial structures David A. Case (Mon Dec 08 2003 - 11:30:57 CST)
AMBER: MD L Jin (Mon Dec 08 2003 - 11:45:01 CST)
AMBER: Small problems L Jin (Mon Dec 08 2003 - 11:47:47 CST)
AMBER: gaff atom types for phosphor compouds astrid.maass (Tue Dec 09 2003 - 07:51:33 CST)
Re: AMBER: gaff atom types for phosphor compouds Junmei Wang (Tue Dec 09 2003 - 09:28:08 CST)
AMBER: xleap-N/C terminus John (Wed Dec 10 2003 - 06:34:13 CST)
Re: AMBER: xleap-N/C terminus Jiten (Wed Dec 10 2003 - 07:10:15 CST)
AMBER: Mg2+ parameters for RNA usage Vlad Cojocaru (Wed Dec 10 2003 - 07:38:59 CST)
Re: AMBER: Mg2+ parameters for RNA usage Jiri Sponer (Wed Dec 10 2003 - 08:21:24 CST)
AMBER: RESP charges Youyi Peng (Wed Dec 10 2003 - 08:34:58 CST)
AMBER: About Temperature Regulation L Jin (Wed Dec 10 2003 - 09:09:00 CST)
AMBER: Antechamber & Ptraj/Rdparm L Jin (Wed Dec 10 2003 - 09:07:25 CST)
Re: AMBER: Mg2+ parameters for RNA usage Pascal Auffinger (Wed Dec 10 2003 - 09:30:47 CST)
RE: AMBER: xleap-N/C terminus John (Wed Dec 10 2003 - 09:46:22 CST)
Re: AMBER: Mg2+ parameters for RNA usage Peter VARNAI (Wed Dec 10 2003 - 10:06:30 CST)
Re: AMBER: About Temperature Regulation David A. Case (Wed Dec 10 2003 - 10:30:24 CST)
Re: AMBER: xleap-N/C terminus David A. Case (Wed Dec 10 2003 - 10:33:52 CST)
Re: AMBER: RESP charges David A. Case (Wed Dec 10 2003 - 10:31:38 CST)
AMBER: Nitrated Tyr arubin_at_unmc.edu (Wed Dec 10 2003 - 10:36:45 CST)
Re: AMBER: About Temperature Regulation L Jin (Wed Dec 10 2003 - 11:06:25 CST)
Re: AMBER: RESP charges Youyi Peng (Wed Dec 10 2003 - 11:28:40 CST)
AMBER: MOPAC from antechamber Beale, John (Wed Dec 10 2003 - 11:46:02 CST)
Re: AMBER: RESP charges Jiten (Wed Dec 10 2003 - 11:55:51 CST)
Re: AMBER: RESP charges Joey Harriman (Wed Dec 10 2003 - 12:05:44 CST)
Re: AMBER: Mg2+ parameters for RNA usage Bill Ross (Wed Dec 10 2003 - 12:07:49 CST)
Re: AMBER: MOPAC from antechamber Joey Harriman (Wed Dec 10 2003 - 12:08:13 CST)
Re: AMBER: xleap-N/C terminus Bill Ross (Wed Dec 10 2003 - 12:14:06 CST)
Re: AMBER: Antechamber & Ptraj/Rdparm Bill Ross (Wed Dec 10 2003 - 12:17:37 CST)
Re: AMBER: RESP charges David A. Case (Wed Dec 10 2003 - 12:28:00 CST)
Re: AMBER: RESP charges Junmei Wang (Wed Dec 10 2003 - 12:38:15 CST)
Re: AMBER: Mg2+ parameters for RNA usage Jiri Sponer (Wed Dec 10 2003 - 13:32:57 CST)
Re: AMBER: RESP charges Youyi Peng (Wed Dec 10 2003 - 14:57:56 CST)
Re: AMBER: RESP charges Junmei Wang (Wed Dec 10 2003 - 15:07:24 CST)
Re: AMBER: RESP charges Youyi Peng (Wed Dec 10 2003 - 16:48:05 CST)
Re: AMBER: RESP charges Youyi Peng (Wed Dec 10 2003 - 16:50:46 CST)
Re: AMBER: RESP charges Junmei Wang (Wed Dec 10 2003 - 17:29:19 CST)
AMBER: a simple question about HBond energy... Florent Barbault (Thu Dec 11 2003 - 02:04:27 CST)
AMBER: Carbohydrate connectivity Bimo Ario Tejo (Thu Dec 11 2003 - 09:14:05 CST)
Re: AMBER: Carbohydrate connectivity Jiten (Thu Dec 11 2003 - 10:04:44 CST)
Re: AMBER: Carbohydrate connectivity David A. Case (Thu Dec 11 2003 - 10:09:08 CST)
AMBER: How to use quasih? A. Hungie (Thu Dec 11 2003 - 10:12:23 CST)
Re: AMBER: How to use quasih? David A. Case (Thu Dec 11 2003 - 10:34:39 CST)
Re: AMBER: RESP charges Youyi Peng (Thu Dec 11 2003 - 10:41:45 CST)
Re: AMBER: RESP charges Junmei Wang (Thu Dec 11 2003 - 10:55:21 CST)
RE: AMBER: xleap-N/C terminus Dalmaris, John (Thu Dec 11 2003 - 12:01:35 CST)
RE: AMBER: xleap-N/C terminus Bill Ross (Thu Dec 11 2003 - 12:33:09 CST)
AMBER: GBSA problem northrop_at_chem.ucla.edu (Thu Dec 11 2003 - 17:28:27 CST)
Re: AMBER: GBSA problem Wu Yingliang (Thu Dec 11 2003 - 22:20:05 CST)
AMBER: lifetime in ptraj hbond Fajar Rakhman Wibowo (Fri Dec 12 2003 - 03:28:45 CST)
AMBER: ambpdb L Jin (Fri Dec 12 2003 - 04:43:36 CST)
Re: AMBER: ambpdb ch cureton (Fri Dec 12 2003 - 04:47:06 CST)
Re: AMBER: ambpdb L Jin (Fri Dec 12 2003 - 05:24:42 CST)
Re: AMBER: Antechamber & Ptraj/Rdparm L Jin (Fri Dec 12 2003 - 05:35:46 CST)
Re: AMBER: ambpdb ch cureton (Fri Dec 12 2003 - 05:53:17 CST)
Re: AMBER: lifetime in ptraj hbond Martin Lepsik (Fri Dec 12 2003 - 07:29:28 CST)
AMBER: adding extra salt Vlad Cojocaru (Fri Dec 12 2003 - 07:34:55 CST)
AMBER: Antechamber:charges missing L Jin (Fri Dec 12 2003 - 09:45:35 CST)
Re: AMBER: adding extra salt Bill Ross (Fri Dec 12 2003 - 10:44:07 CST)
AMBER: nmode, trajectory kbyun_at_wesleyan.edu (Fri Dec 12 2003 - 11:05:08 CST)
AMBER: parmscan Jessica Swanson (Fri Dec 12 2003 - 12:39:19 CST)
AMBER: order parameter myang (Fri Dec 12 2003 - 14:25:17 CST)
Re: AMBER: order parameter David A. Case (Fri Dec 12 2003 - 15:29:26 CST)
Re: AMBER: a simple question about HBond energy... David A. Case (Fri Dec 12 2003 - 15:57:47 CST)
Re: AMBER: a simple question about HBond energy... Bill Ross (Fri Dec 12 2003 - 16:16:42 CST)
AMBER: non-zero 10-12 coefficient Bimo Ario Tejo (Sat Dec 13 2003 - 08:44:49 CST)
Re: AMBER: nmode, trajectory Holger Gohlke (Sat Dec 13 2003 - 09:42:39 CST)
Re: AMBER: non-zero 10-12 coefficient David A. Case (Sat Dec 13 2003 - 14:48:12 CST)
AMBER: Heme and Zn parameters Vema Aparna (Sun Dec 14 2003 - 08:04:43 CST)
AMBER: Energy map L Jin (Mon Dec 15 2003 - 08:42:52 CST)
Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 08:57:29 CST)
AMBER: water neighborhood of amide hydrogens Jorge Vasquez-Kool (Mon Dec 15 2003 - 09:29:55 CST)
Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 09:17:31 CST)
AMBER: length of deltaG calcs Heather A.Carlson (Mon Dec 15 2003 - 09:32:48 CST)
AMBER: question about namelist aini_at_UMDNJ.EDU (Mon Dec 15 2003 - 09:42:04 CST)
Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 09:37:30 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 09:37:30 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 09:37:30 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 09:47:30 CST)
Re: AMBER: question about namelist Holger Gohlke (Mon Dec 15 2003 - 10:10:05 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 09:57:31 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 09:57:31 CST)
Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 09:57:31 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:07:31 CST)
Re: AMBER: length of deltaG calcs David Smith (Mon Dec 15 2003 - 10:16:26 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 10:27:32 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:27:32 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 10:27:32 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:27:32 CST)
Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 10:27:32 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 10:37:31 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 10:47:32 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:47:32 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:47:32 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 10:47:32 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 10:57:31 CST)
Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 10:57:31 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 11:07:32 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 11:07:32 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 11:07:32 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 11:17:32 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 11:17:32 CST)
Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 11:17:32 CST)
Re: AMBER: water neighborhood of amide hydrogens Thomas E. Cheatham, III (Mon Dec 15 2003 - 11:29:00 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 11:27:32 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 11:27:32 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 11:37:32 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 11:37:32 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 11:37:32 CST)
Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 11:37:32 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 11:47:32 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 11:47:32 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 11:47:32 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 11:57:33 CST)
Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 11:57:32 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 11:57:32 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 11:57:32 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 12:07:32 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 12:07:32 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 12:07:32 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 12:17:33 CST)
Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 12:17:33 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 12:17:33 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 12:27:33 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 12:27:33 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 12:27:33 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 12:27:33 CST)
Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 12:37:33 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 12:37:33 CST)
Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 12:37:33 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 12:47:34 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 12:47:34 CST)
Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 12:47:34 CST)
Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 12:47:34 CST)
Re: AMBER: question about namelist Suse Broyde (Mon Dec 15 2003 - 11:37:58 CST)
Re: AMBER: question about namelist Ioana Cozmuta (Mon Dec 15 2003 - 13:14:40 CST)
Re: AMBER: water neighborhood of amide hydrogens Bill Ross (Mon Dec 15 2003 - 13:26:29 CST)
AMBER: minimization on sander Herbert Georg (Mon Dec 15 2003 - 14:05:25 CST)
Re: AMBER: minimization on sander Bill Ross (Mon Dec 15 2003 - 14:32:39 CST)
Re: AMBER: minimization on sander Herbert Georg (Mon Dec 15 2003 - 15:21:13 CST)
Re: AMBER: question about namelist Piotr Cieplak (Mon Dec 15 2003 - 16:02:33 CST)
AMBER: no "Input orientation" in g98 log Lee, Matt (Mon Dec 15 2003 - 17:13:10 CST)
AMBER: Ibelly and Ewald error message when ewald should be off Ben Cossins (Tue Dec 16 2003 - 17:01:52 CST)
AMBER: Nmode analysis ptn-ligand complex Jory Zmuda (Tue Dec 16 2003 - 17:11:13 CST)
AMBER: nmode statistics kbyun_at_wesleyan.edu (Wed Dec 17 2003 - 13:52:51 CST)
Re: AMBER: nmode statistics Holger Gohlke (Thu Dec 18 2003 - 01:09:05 CST)
Re: AMBER: RESP charges Youyi Peng (Thu Dec 18 2003 - 09:20:43 CST)
Re: AMBER: RESP charges Junmei Wang (Thu Dec 18 2003 - 15:17:28 CST)
Re: AMBER: RESP charges Youyi Peng (Thu Dec 18 2003 - 17:31:51 CST)
Re: AMBER: RESP charges Junmei Wang (Thu Dec 18 2003 - 20:29:45 CST)
AMBER: PMEMD Performance on Beowulf systems Stephen.Titmuss_at_csiro.au (Thu Dec 18 2003 - 21:19:59 CST)
Re: AMBER: PMEMD Performance on Beowulf systems Robert Duke (Thu Dec 18 2003 - 22:35:40 CST)
AMBER: MD: restrt L Jin (Fri Dec 19 2003 - 04:47:55 CST)
AMBER: special gaff atom types available? astrid.maass (Fri Dec 19 2003 - 05:58:30 CST)
AMBER: Ewald in Amber 7 Ben Cossins (Fri Dec 19 2003 - 09:49:11 CST)
Re: AMBER: PMEMD Performance on Beowulf systems Carlos Simmerling (Fri Dec 19 2003 - 08:53:12 CST)
Re: AMBER: Ewald in Amber 7 David A. Case (Fri Dec 19 2003 - 11:30:23 CST)
AMBER: Vibration frequency of nucleobases A. Hungie (Fri Dec 19 2003 - 11:48:03 CST)
AMBER: Toolchest Shuang Ding (Fri Dec 19 2003 - 14:45:08 CST)
AMBER: initial velocity Fan Gao (Fri Dec 19 2003 - 18:56:16 CST)
Re: AMBER: initial velocity Peter Oelschlaeger (Fri Dec 19 2003 - 20:08:43 CST)
AMBER: Curves parameters UU and PP Peter Gannett (Fri Dec 19 2003 - 22:08:02 CST)
Re: AMBER: Curves parameters UU and PP Surjit Dixit (Sat Dec 20 2003 - 09:45:28 CST)
Re: AMBER: special gaff atom types available? David A. Case (Sat Dec 20 2003 - 10:25:14 CST)
AMBER: vlimit? Ran Ye (Sun Dec 21 2003 - 16:15:57 CST)
Re: AMBER: vlimit? Bill Ross (Sun Dec 21 2003 - 22:04:40 CST)
AMBER: using sander without SHAKE Wayne Dawson (Mon Dec 22 2003 - 00:38:14 CST)
RE: RE: AMBER: PMEMD Performance on Beowulf systems Aldo Jongejan (Mon Dec 22 2003 - 01:27:41 CST)
AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations? Jiri Matousek (Mon Dec 22 2003 - 03:51:25 CST)
Re: AMBER: PMEMD Performance on Beowulf systems Viktor Hornak (Mon Dec 22 2003 - 07:47:42 CST)
Re: AMBER: PMEMD Performance on Beowulf systems David E. Konerding (Mon Dec 22 2003 - 09:53:20 CST)
Re: AMBER: PMEMD Performance on Beowulf systems Carlos Simmerling (Mon Dec 22 2003 - 10:12:37 CST)
Re: AMBER: PMEMD Performance on Beowulf systems Robert Duke (Mon Dec 22 2003 - 10:44:47 CST)
Re: AMBER: PMEMD Performance on Beowulf systems David E. Konerding (Mon Dec 22 2003 - 10:57:23 CST)
Re: AMBER: PMEMD Performance on Beowulf systems David E. Konerding (Mon Dec 22 2003 - 11:04:03 CST)
Re: AMBER: PMEMD Performance on Beowulf systems Carlos Simmerling (Mon Dec 22 2003 - 11:06:39 CST)
Re: AMBER: using sander without SHAKE David A. Case (Mon Dec 22 2003 - 11:22:09 CST)
Re: AMBER: vlimit? David A. Case (Mon Dec 22 2003 - 11:24:18 CST)
AMBER: HT vs no HT John Mongan (Mon Dec 22 2003 - 13:18:31 CST)
AMBER: RESP charge redistribution Youyi Peng (Mon Dec 22 2003 - 15:27:13 CST)
AMBER: umbrella sampling with AMBER Mey Khalili (Mon Dec 22 2003 - 17:14:24 CST)
Re: AMBER: umbrella sampling with AMBER David A. Case (Mon Dec 22 2003 - 19:48:30 CST)
AMBER: MSMS Salma B. Rafi (Tue Dec 23 2003 - 12:36:18 CST)
Re: AMBER: MSMS David A. Case (Tue Dec 23 2003 - 12:56:32 CST)
Re: AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations? David A. Case (Tue Dec 23 2003 - 13:18:39 CST)
AMBER: PMEMD Performance on IBM SP David Skinner (Tue Dec 23 2003 - 14:00:45 CST)
Re: AMBER: vlimit? Ryan Ye (Tue Dec 23 2003 - 22:04:45 CST)
AMBER: Basic potential question: a b (Wed Dec 24 2003 - 03:29:56 CST)
AMBER: Basic potential question: Wayne Dawson (Wed Dec 24 2003 - 09:56:37 CST)
AMBER: MSE Wen Li (Wed Dec 24 2003 - 10:25:33 CST)
Re: AMBER: using sander without SHAKE Wayne Dawson (Wed Dec 24 2003 - 10:39:43 CST)
Re: AMBER: using sander without SHAKE David A. Case (Wed Dec 24 2003 - 12:06:40 CST)
Re: AMBER: MSE David A. Case (Wed Dec 24 2003 - 12:08:59 CST)
Re: AMBER: Basic potential question: FyD (Wed Dec 24 2003 - 12:35:22 CST)
Re: AMBER: Basic potential question: Piotr Cieplak (Wed Dec 24 2003 - 12:47:57 CST)
Re: AMBER: using sander without SHAKE Bill Ross (Wed Dec 24 2003 - 13:03:43 CST)
Re: AMBER: Basic potential question: Wayne Dawson (Thu Dec 25 2003 - 21:04:37 CST)
Re: AMBER: vlimit? David A. Case (Fri Dec 26 2003 - 12:18:16 CST)
AMBER: Constant temperature L Jin (Sat Dec 27 2003 - 05:29:13 CST)
Re: AMBER: Constant temperature Bill Ross (Sat Dec 27 2003 - 11:14:00 CST)
Re: AMBER: Constant temperature David A. Case (Sun Dec 28 2003 - 00:46:46 CST)
AMBER: roar topology and coordinate files PSR04996_at_mailstudenti.unimi.it (Mon Dec 29 2003 - 03:11:28 CST)
Re: AMBER: roar topology and coordinate files M. L. Dodson (Mon Dec 29 2003 - 07:35:42 CST)
Re: AMBER: roar topology and coordinate files M. L. Dodson (Mon Dec 29 2003 - 14:15:57 CST)
AMBER: The restart file generated by Ptraj Ling Zhang (Mon Dec 29 2003 - 14:49:52 CST)
AMBER: The lost velocities in the restart file generated by Ptraj Ling Zhang (Mon Dec 29 2003 - 15:12:47 CST)
Re: AMBER: The lost velocities in the restart file generated by Ptraj Bill Ross (Mon Dec 29 2003 - 18:11:54 CST)
Re: AMBER: roar topology and coordinate files Bill Ross (Mon Dec 29 2003 - 18:14:53 CST)
Re: AMBER: roar topology and coordinate files M. L. Dodson (Mon Dec 29 2003 - 18:42:49 CST)
AMBER: problems with pressure control Endres, Robert G. (Tue Dec 30 2003 - 08:38:02 CST)
Re: AMBER: problems with pressure control David A. Case (Tue Dec 30 2003 - 12:03:06 CST)
Re: AMBER: Antechamber & Ptraj/Rdparm L Jin (Wed Dec 31 2003 - 05:44:00 CST)
Re: AMBER: Antechamber & Ptraj/Rdparm David A. Case (Wed Dec 31 2003 - 09:47:46 CST)
DON'T DELETE THIS MESSAGE -- FOLDER INTERNAL DATA Mail System Internal Data (Fri Feb 06 2004 - 10:15:04 CST)

Last message date: Fri Feb 06 2004 - 10:15:04 CST
Archived on: Thu May 05 2005 - 14:17:43 CDT

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