Amber Archive Jan 2003: By Thread

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

Amber Archive Jan 2003 By Thread