Amber Archive Apr 2002: By Thread

does PME function without charge neutralization? Ian R Bates (Tue Apr 02 2002 - 10:30:41 PST)
- Re: does PME function without charge neutralization? darden (Tue Apr 02 2002 - 14:23:02 PST)
- (no subject) deepak rangaswamy (Tue Apr 02 2002 - 20:52:55 PST)
- input files Monica (Wed Apr 03 2002 - 05:00:42 PST)
  - Re: input files Carlos Simmerling (Wed Apr 03 2002 - 05:40:30 PST)
  - Initial Amber 7 benchmark timings David Case (Wed Apr 03 2002 - 18:33:14 PST)
    - Re: Initial Amber 7 benchmark timings Stéphane Teletchéa (Thu Apr 04 2002 - 01:36:23 PST)
    - amber7, PME and anisotrop press. Arvid Soederhaell (Thu Apr 04 2002 - 01:46:58 PST)
    - new residues Vlad Cojocaru (Thu Apr 04 2002 - 05:03:37 PST)
    - About the sander_classic calculation Alan Leo (Thu Apr 04 2002 - 13:32:34 PST)
    - Re: About the sander_classic calculation John Bushnell (Thu Apr 04 2002 - 14:31:11 PST)
    - convergence of MD simulations Sue Heavner (Thu Apr 04 2002 - 14:24:05 PST)
    - Re: convergence of MD simulations Andreas Svrcek-Seiler (Fri Apr 05 2002 - 02:12:11 PST)
    - Sander-Gibbs Kidley N J (Mon Apr 08 2002 - 08:34:49 PDT)
    - PDB file with CONECT record Prabal Maiti (Mon Apr 08 2002 - 12:06:21 PDT)
    - Re:PDB file with CONECT record Bill Ross (Mon Apr 08 2002 - 13:02:21 PDT)
    - Re: PDB file with CONECT record Bill Ross (Tue Apr 09 2002 - 23:09:36 PDT)
    - Re: PDB file with CONECT record Prabal Maiti (Thu Apr 11 2002 - 23:27:15 PDT)
    - Re: PDB file with CONECT record Bill Ross (Fri Apr 12 2002 - 00:27:37 PDT)
    - Re: PDB file with CONECT record Miguel Angel (Fri Apr 12 2002 - 03:03:09 PDT)
    - order parameters? Arvid Soederhaell (Fri Apr 12 2002 - 05:55:33 PDT)
    - Re: PDB file with CONECT record Prabal Maiti (Mon Apr 15 2002 - 22:48:00 PDT)
    - compiling amber 6.0 in a Sun starfire ENT10000 ramon kleber da rocha (Tue Apr 16 2002 - 12:08:54 PDT)
    - 4 Medicinal and Computational Chemistry Candidates medicinal and Compuatational Chemistry Resumes and Jobs (Tue Apr 16 2002 - 14:55:48 PDT)
    - Recalculating energies John Finke (Tue Apr 16 2002 - 17:45:23 PDT)
    - Re: Recalculating energies Carlos Simmerling (Wed Apr 17 2002 - 04:39:27 PDT)
    - RESP charges Vlad Cojocaru (Wed Apr 17 2002 - 03:53:27 PDT)
    - Re: RESP charges Lepsa (Wed Apr 17 2002 - 05:26:27 PDT)
    - (no subject) Filip Ryjacek (Wed Apr 17 2002 - 09:01:48 PDT)
    - (no subject) Lepsa (Wed Apr 17 2002 - 07:38:47 PDT)
    - Minimization of pentane holding a plane of carbon atoms Hungie Hungie (Wed Apr 17 2002 - 10:32:28 PDT)
    - again...Minimization of pentane holding a plane of carbon atoms Hungie Hungie (Wed Apr 17 2002 - 11:03:23 PDT)
    - mm pbsa: generate snapshots Mark Hsieh (Wed Apr 17 2002 - 14:52:41 PDT)
    - Re: mm pbsa: generate snapshots Mathy Froeyen (Thu Apr 18 2002 - 00:19:35 PDT)
    - pentane minimization Hungie Hungie (Thu Apr 18 2002 - 02:15:33 PDT)
    - pentane minimization Hungie Hungie (Thu Apr 18 2002 - 02:16:46 PDT)
    - DNA shifts during MD; C.O.M. removing and ptraj doesn't help... Filip Ryjacek (Thu Apr 18 2002 - 08:17:12 PDT)
    - RESP cfrenz_at_aecom.yu.edu (Thu Apr 18 2002 - 08:55:55 PDT)
    - pentane minimization...again Hungie Hungie (Thu Apr 18 2002 - 09:30:15 PDT)
    - MPICH and AMBER 7 Mark Hsieh (Thu Apr 18 2002 - 16:12:58 PDT)
    - RESP-ivary Vlad Cojocaru (Fri Apr 19 2002 - 04:26:22 PDT)
    - Re: RESP-ivary Qing Zhang (Fri Apr 19 2002 - 09:15:27 PDT)
    - RE: RESP-ivary John Bushnell (Fri Apr 19 2002 - 11:16:40 PDT)
    - amber7 compilation on a beowulf cluster Peter Gannett (Fri Apr 19 2002 - 12:59:56 PDT)
    - RE: amber7 compilation on a beowulf cluster John Bushnell (Fri Apr 19 2002 - 14:48:00 PDT)
    - RE: amber7 compilation on a beowulf cluster Bill Ross (Fri Apr 19 2002 - 15:26:19 PDT)
    - mm_pbsa for uhbd Mark Hsieh (Fri Apr 19 2002 - 18:56:18 PDT)
    - Re: amber7 compilation on a beowulf cluster David Case (Fri Apr 19 2002 - 18:56:50 PDT)
    - (no subject) deepak rangaswamy (Fri Apr 19 2002 - 22:22:54 PDT)
    - Re: your mail David Case (Sat Apr 20 2002 - 09:06:32 PDT)
    - Re: your mail deepak rangaswamy (Tue Apr 30 2002 - 05:06:06 PDT)
    - valine to alanine example Sophia Kondratova (Tue Apr 30 2002 - 08:23:21 PDT)
    - heterochirical peptides ? Yuguang Mu (Tue Apr 30 2002 - 08:43:39 PDT)
    - Re: heterochirical peptides ? David Case (Tue Apr 30 2002 - 11:21:38 PDT)
    - dummy atoms. Yongjun Jiang (Sat Apr 20 2002 - 20:20:44 PDT)
    - leap bugfix Bill Ross (Sun Apr 21 2002 - 14:55:34 PDT)
    - RESP Vlad Cojocaru (Mon Apr 22 2002 - 03:17:17 PDT)
    - Re: RESP jim caldwell (Mon Apr 22 2002 - 08:04:25 PDT)
    - a problem Vlad Cojocaru (Mon Apr 22 2002 - 08:56:48 PDT)
    - RE: a problem John Bushnell (Wed Apr 24 2002 - 14:02:31 PDT)
    - (no subject) SPEROLEEM_at_aol.com (Mon Apr 22 2002 - 11:47:28 PDT)
    - a more general question Vlad Cojocaru (Tue Apr 23 2002 - 07:20:34 PDT)
    - DME and Carnal with AMBER6 Katherine W. Abold (Tue Apr 23 2002 - 07:48:04 PDT)
    - RESP tutorial Michael G Cooney (Tue Apr 23 2002 - 10:15:51 PDT)
    - Re: RESP tutorial David Case (Tue Apr 23 2002 - 17:41:49 PDT)
    - RESP on Deoxy-ADE Qing Zhang (Tue Apr 23 2002 - 18:34:23 PDT)
    - RESP on Deoxy-ADE Qing Zhang (Tue Apr 23 2002 - 18:34:23 PDT)
    - sander & prmtop file generated from antechamber input ? jeff dyason (Tue Apr 23 2002 - 20:33:58 PDT)
    - Re: sander & prmtop file generated from antechamber input ? David Case (Wed Apr 24 2002 - 08:59:14 PDT)
    - INTPRT and PMF Sophia Kondratova (Tue Apr 23 2002 - 11:23:36 PDT)
    - Re: INTPRT and PMF David Pearlman (Tue Apr 23 2002 - 13:05:12 PDT)
    - generating left-handed A-DNA Marcela Madrid (Tue Apr 23 2002 - 17:41:08 PDT)
    - Re: generating left-handed A-DNA David Case (Wed Apr 24 2002 - 09:09:07 PDT)
    - (no subject) Bill Ross (Tue Apr 23 2002 - 12:30:58 PDT)
    - parallel sander? Mark Hsieh (Tue Apr 23 2002 - 12:31:55 PDT)
    - RE: parallel sander? Mark Hsieh (Tue Apr 23 2002 - 12:35:44 PDT)
    - amber6 with parallel Khatcharin Siriwong (Mon Apr 22 2002 - 05:48:24 PDT)
    - Re: amber7 compilation on a beowulf cluster Peter Gannett (Sat Apr 20 2002 - 05:14:01 PDT)
    - To PROFEC users Salinthip Thipayang (Fri Apr 19 2002 - 07:13:11 PDT)
    - RESP charges Vlad Cojocaru (Wed Apr 17 2002 - 05:36:43 PDT)
    - RE: RESP charges Ross Walker (Wed Apr 17 2002 - 06:21:37 PDT)
    - Re: RESP charges jim caldwell (Wed Apr 17 2002 - 07:22:04 PDT)
    - RE: RESP charges Ross Walker (Wed Apr 17 2002 - 08:28:58 PDT)
    - Thanks FyD (Fri Apr 12 2002 - 00:04:53 PDT)
    - Amber7 and VMD Soonmin Jang (Wed Apr 10 2002 - 01:40:37 PDT)
    - Re: Amber7 and VMD Thomas Cheatham (Wed Apr 10 2002 - 06:55:46 PDT)
    - (no subject) Mark Hsieh (Wed Apr 10 2002 - 13:31:50 PDT)
    - (no subject) Carlos Simmerling (Sat Apr 13 2002 - 05:06:29 PDT)
    - Matching Patterns Tali (Wed Apr 10 2002 - 14:57:59 PDT)
    - DNA structure get distorted Monica (Thu Apr 11 2002 - 01:00:48 PDT)
    - Re: DNA structure get distorted David Case (Fri Apr 12 2002 - 09:27:10 PDT)
    - Compiling Amber7 on a Beowulf Cluster - Compiling Error Peter Gannett (Fri Apr 12 2002 - 16:59:38 PDT)
    - Re: Compiling Amber7 on a Beowulf Cluster - Compiling Error David Case (Fri Apr 12 2002 - 17:37:01 PDT)
    - help ..problem about antechamber Yi ming Cheng (Fri Apr 12 2002 - 22:30:26 PDT)
    - Re: Compiling Amber7 on a Beowulf Cluster - Compiling Error Peter Gannett (Sat Apr 13 2002 - 06:59:29 PDT)
    - Vulgar Models Do Everything And Love It!!! telesales (Mon Apr 15 2002 - 17:03:45 PDT)
    - noesy intensity input in DNA Monica (Thu Apr 11 2002 - 01:03:50 PDT)
    - Follow distances during MD Francois Dupradeau (Thu Apr 11 2002 - 03:19:02 PDT)
    - Re: Follow distances during MD Raik Grunberg (Thu Apr 11 2002 - 05:49:16 PDT)
    - (no subject) Mark Beardsell (Thu Apr 11 2002 - 06:36:29 PDT)
    - Re: your mail Andreas Svrcek-Seiler (Thu Apr 11 2002 - 07:33:22 PDT)
    - Save from LEaP to a PDBQ file ? jeff dyason (Thu Apr 11 2002 - 20:50:32 PDT)
    - Re: Save from LEaP to a PDBQ file ? Bill Ross (Thu Apr 11 2002 - 23:16:28 PDT)
    - Re: convergence of MD simulations darden (Mon Apr 08 2002 - 13:08:10 PDT)
    - PDB file with CONECT record (fwd) Prabal Maiti (Tue Apr 09 2002 - 18:04:50 PDT)
    - Re: PDB file with CONECT record (fwd) David Case (Tue Apr 09 2002 - 20:30:38 PDT)
    - Roar 2.1 with Amber7 Soonmin Jang (Tue Apr 09 2002 - 20:39:07 PDT)
    - RE: Roar 2.1 with Amber7 Ross Walker (Tue Apr 09 2002 - 22:48:43 PDT)
Re: Help! Sander run error: Bus error David Case (Mon Apr 15 2002 - 22:32:16 PDT)
Amber in a distributed environment Peter Gannett (Wed Apr 17 2002 - 05:07:56 PDT)
- Re: Amber in a distributed environment Sudhakar Pamidighantam (Wed Apr 17 2002 - 06:55:34 PDT)
Re: amber7 and tip5p David Case (Wed Apr 24 2002 - 14:04:05 PDT)
Number of WATBOX yuann (Wed Apr 24 2002 - 22:54:02 PDT)
- Re: Number of WATBOX David Smith (Thu Apr 25 2002 - 06:25:40 PDT)
- PMF calculations Sophia Kondratova (Thu Apr 25 2002 - 06:30:11 PDT)
  - Re: PMF calculations David Smith (Thu Apr 25 2002 - 08:13:23 PDT)
    - Re: PMF calculations David Pearlman (Thu Apr 25 2002 - 11:36:41 PDT)
    - sander mpich hangs Mark Hsieh (Thu Apr 25 2002 - 15:01:26 PDT)
    - Re: sander mpich hangs Stéphane Teletchéa (Fri Apr 26 2002 - 04:54:01 PDT)
    - RE: sander mpich hangs Mark Hsieh (Fri Apr 26 2002 - 12:08:48 PDT)
    - max_rstack requested Albert Codony (Sun Apr 28 2002 - 15:39:58 PDT)
    - parmjoin Vlad Cojocaru (Mon Apr 29 2002 - 09:53:01 PDT)
    - Re: parmjoin David Case (Mon Apr 29 2002 - 11:26:26 PDT)
    - Fail message:Segmantation fault and Bus error? William Wei (Mon Apr 29 2002 - 12:38:48 PDT)
    - NTT=5? Jung-Hsing Lin (Mon Apr 29 2002 - 16:10:30 PDT)
    - Re: NTT=5? David Case (Mon Apr 29 2002 - 22:32:20 PDT)
    - Re: NTT=5? Jung-Hsing Lin (Tue Apr 30 2002 - 09:10:46 PDT)
    - Re: NTT=5? David Case (Tue Apr 30 2002 - 11:16:04 PDT)
    - Re: NTT=5? Jung-Hsing Lin (Tue Apr 30 2002 - 13:36:45 PDT)
    - about ew_legal.h X. Tan (Tue Apr 30 2002 - 17:12:01 PDT)
    - IFBOX=0 error in amber7 Eva Darian (Tue Apr 30 2002 - 21:43:31 PDT)
    - Re: IFBOX=0 error in amber7 Bill Ross (Tue Apr 30 2002 - 22:15:05 PDT)
    - install leap not working nepenthes_at_vplaces.net (Tue Apr 30 2002 - 00:52:07 PDT)
    - Re: install leap not working Bill Ross (Tue Apr 30 2002 - 12:21:01 PDT)
    - NaCl concentration Peter Gannett (Tue Apr 30 2002 - 12:34:38 PDT)
    - How to run the leap module param_at_ibab.ac.in (Tue Apr 30 2002 - 02:34:32 PDT)
    - Re: How to run the leap module Sanjeev B.S. (Tue Apr 30 2002 - 03:37:11 PDT)
    - Re: How to run the leap module John Bushnell (Tue Apr 30 2002 - 10:46:35 PDT)
    - TIP4P parameters Ge Zhou (Mon Apr 29 2002 - 19:03:54 PDT)
    - Re: TIP4P parameters David Case (Mon Apr 29 2002 - 22:17:49 PDT)
    - Problems with AMBER7 and Multiple Processors on SGI servers Vincent BOSQUIER (Fri Apr 26 2002 - 01:39:35 PDT)
    - Re: Problems with AMBER7 and Multiple Processors on SGI servers Carlos Simmerling (Fri Apr 26 2002 - 05:05:52 PDT)
    - Re: Problems with AMBER7 and Multiple Processors on SGI servers Ian bates (Fri Apr 26 2002 - 08:17:52 PDT)
    - RE: Problems with AMBER7 and Multiple Processors on SGI servers Vincent BOSQUIER (Tue Apr 30 2002 - 02:59:11 PDT)
    - Re: Problems with AMBER7 and Multiple Processors on SGI servers David Case (Tue Apr 30 2002 - 09:02:30 PDT)
  - About Group in Carnal William Wei (Thu Apr 25 2002 - 08:50:08 PDT)
  - Re: PMF calculations David Pearlman (Thu Apr 25 2002 - 11:30:24 PDT)

Amber Archive Apr 2002 By Thread