Amber Archive May 2002: By Thread

Amber7 compilation on IBM sp3 machine Soonmin Jang (Tue Apr 30 2002 - 21:33:05 PDT)
AMBER 7 - more problems with leap Mark Beardsell (Wed May 01 2002 - 05:17:46 PDT)
Re: about ew_legal.h David Case (Wed May 01 2002 - 09:10:36 PDT)
Amber7 nmode Sue Heavner (Wed May 01 2002 - 10:23:19 PDT)
- Re: Amber7 nmode David Case (Wed May 01 2002 - 10:55:07 PDT)
Re: NTT=5? Jake Isaacs (Wed May 01 2002 - 12:47:09 PDT)
Carnal BUG?? William Wei (Wed May 01 2002 - 20:19:03 PDT)
RE: Problems with AMBER7 and Multiple Processors on SGI servers Vincent BOSQUIER (Thu May 02 2002 - 01:55:45 PDT)
RE: Carnal BUG?? --- How can I get the correct residue number? William Wei (Thu May 02 2002 - 09:09:21 PDT)
- RE: Carnal BUG?? --- How can I get the correct residue number? William Wei (Thu May 02 2002 - 10:48:10 PDT)
Compilation on RedHat-7.2 with MPICH Vincent BOSQUIER (Thu May 02 2002 - 09:29:32 PDT)
new RNA residues Vlad Cojocaru (Thu May 02 2002 - 12:07:32 PDT)
Re: How can I get the correct residue number? Bill Ross (Thu May 02 2002 - 13:26:45 PDT)
Re: How can I get the correct residue number? Bill Ross (Thu May 02 2002 - 13:38:24 PDT)
Help/suggestions needed with PROFEC Salinthip Thipayang (Fri May 03 2002 - 07:40:41 PDT)
help/suggestions needed with PROFEC Salinthip Thipayang (Fri May 03 2002 - 08:03:47 PDT)
TI integration Joe Fernandez (Sat May 04 2002 - 06:59:57 PDT)
Thanks to all Albert Codony (Sat May 04 2002 - 08:38:12 PDT)
crdgrow Vlad Cojocaru (Sat May 04 2002 - 13:06:32 PDT)
missing residues Mark Hsieh (Sun May 05 2002 - 00:15:31 PDT)
topology file generation Sanjeev B.S. (Sun May 05 2002 - 22:36:36 PDT)
- Re: topology file generation Andreas Svrcek-Seiler (Mon May 06 2002 - 05:11:54 PDT)
  - Re: topology file generation Sanjeev B.S. (Mon May 06 2002 - 05:24:30 PDT)
- Re: topology file generation Carlos Simmerling (Mon May 06 2002 - 05:27:06 PDT)
- (no subject) Sophia Kondratova (Mon May 06 2002 - 06:13:53 PDT)
- TI using sander on cluster Joe Fernandez (Mon May 06 2002 - 07:52:50 PDT)
- "Unit 5 Error" with a Linux/MPICH Amber7 Vincent BOSQUIER (Mon May 06 2002 - 08:50:07 PDT)
  - Re: "Unit 5 Error" with a Linux/MPICH Amber7 David Case (Mon May 06 2002 - 09:18:24 PDT)
  - Re: "Unit 5 Error" with a Linux/MPICH Amber7 Stéphane Teletchéa (Mon May 06 2002 - 09:22:42 PDT)
  - RE: "Unit 5 Error" with a Linux/MPICH Amber7 Vincent BOSQUIER (Mon May 06 2002 - 09:44:09 PDT)
Problems with parallel computing in Amber7 Vincent BOSQUIER (Tue May 14 2002 - 07:28:10 PDT)
NMR refinement Jake Isaacs (Tue May 14 2002 - 12:16:37 PDT)
- Re: NMR refinement David Case (Wed May 15 2002 - 10:09:27 PDT)
- Re: NMR refinement A. Hungie (Thu May 16 2002 - 08:02:17 PDT)
Topology file format in AMBER 7 Joffre Heredia (Tue May 14 2002 - 14:14:55 PDT)
- Re: Topology file format in AMBER 7 David Case (Tue May 14 2002 - 14:33:15 PDT)
- question Masamichi Fujinami 4029 (Tue May 14 2002 - 22:49:03 PDT)
- Energy problem during dynamics with amber 7 Florence CASSET (Wed May 15 2002 - 02:48:23 PDT)
  - Re: Energy problem during dynamics with amber 7 David Case (Wed May 15 2002 - 10:29:55 PDT)
  - Sander, Setup for Parallel SMP Linux Cluster Jianhui Wu (Wed May 15 2002 - 12:02:27 PDT)
    - Re: Sander, Setup for Parallel SMP Linux Cluster Tru (Wed May 15 2002 - 12:40:45 PDT)
    - Re: Sander, Setup for Parallel SMP Linux Cluster Joffre Heredia (Thu May 16 2002 - 11:01:16 PDT)
    - Mutations - Molecular Dynamics William Wei (Thu May 16 2002 - 16:11:36 PDT)
    - RE: Mutations - Molecular Dynamics William Wei (Mon May 27 2002 - 08:21:04 PDT)
    - igb=2,gbsa=1,antechamber,bad atom type Jianhui Wu (Fri May 17 2002 - 12:20:14 PDT)
RE: automated rescoring of ligands Vickie Tsui (Tue May 14 2002 - 14:23:29 PDT)
Re: help: nmode compile question!!! Andreas Svrcek-Seiler (Wed May 15 2002 - 04:30:12 PDT)
Re: About the box info read error Bill Ross (Fri May 17 2002 - 13:33:51 PDT)
Re: Anal in AMBER7 David Case (Sun May 19 2002 - 18:44:38 PDT)
- Re: Anal in AMBER7 Ting Wang (Tue May 21 2002 - 05:48:48 PDT)
- (no subject) Sophia Kondratova (Tue May 21 2002 - 11:37:24 PDT)
- ptraj problem Jake Isaacs (Tue May 21 2002 - 14:20:02 PDT)
  - Re: ptraj problem Prabal Maiti (Tue May 21 2002 - 16:51:22 PDT)
  - Re: Junmei et al. 1999 Michal Otyepka (Wed May 22 2002 - 00:57:11 PDT)
    - Re: Junmei et al. 1999 Lepsa (Wed May 22 2002 - 01:58:41 PDT)
    - Re: Junmei et al. 1999 Yuguang Mu (Wed May 22 2002 - 02:30:29 PDT)
    - Re: Junmei et al. 1999 David Case (Wed May 22 2002 - 08:05:23 PDT)
    - antechamber Giulio Rastelli (Wed May 22 2002 - 03:56:25 PDT)
    - Re: antechamber David Case (Wed May 22 2002 - 08:03:50 PDT)
vanadium Natasja Brooijmans (Sun May 19 2002 - 19:35:27 PDT)
about sander_classic AMBER6.0 Nikolai Smolin (Mon May 20 2002 - 06:08:14 PDT)
helix analysis Prabal Maiti (Mon May 20 2002 - 12:20:45 PDT)
mm_pbsa X. Tan (Mon May 20 2002 - 16:04:52 PDT)
- Fw: mm_pbsa Lepsa (Fri May 24 2002 - 07:27:21 PDT)
- subdomain moving as a rigid unit during MD Marcela Madrid (Fri May 24 2002 - 08:59:40 PDT)
Energy conservation in NVE simulation ? Soonmin Jang (Mon May 20 2002 - 22:42:40 PDT)
Re: Protonate doesn-t recognize my pdb input file Stéphane Teletchéa (Wed May 22 2002 - 04:41:08 PDT)
again about sander_classic Amber 6.0 Nikolai Smolin (Wed May 22 2002 - 04:42:50 PDT)
- Re: again about sander_classic Amber 6.0 David Case (Wed May 22 2002 - 08:15:06 PDT)
- still having ptraj problems Jake Isaacs (Wed May 22 2002 - 08:19:06 PDT)
  - Re: still having ptraj problems Jake Isaacs (Wed May 22 2002 - 08:50:11 PDT)
this is a test of the amber reflector. Please ignore. Marcela Marcela Madrid (Wed May 22 2002 - 06:59:24 PDT)
Protonate doesn-t recognize by pdb input file David Case (Wed May 22 2002 - 09:20:20 PDT)
- Re: Protonate doesn-t recognize by pdb input file Stéphane Teletchéa (Thu May 23 2002 - 05:23:31 PDT)
- charges Marcela Madrid (Thu May 23 2002 - 13:25:43 PDT)
  - Re: charges David Case (Thu May 23 2002 - 13:54:38 PDT)
  - helix analysis (fwd) Prabal Maiti (Thu May 23 2002 - 14:30:33 PDT)
    - Re: helix analysis (fwd) David Case (Thu May 23 2002 - 14:41:00 PDT)
TIP4P water with AMBER6 Noriaki Okimoto (Wed May 22 2002 - 11:01:35 PDT)
- Re: TIP4P water with AMBER6 jim caldwell (Wed May 22 2002 - 13:25:00 PDT)
- ambpdb in AMBER7 Matthew Lee (Wed May 22 2002 - 13:42:34 PDT)
  - Re: ambpdb in AMBER7 David Case (Wed May 22 2002 - 14:09:32 PDT)
  - this is a test for amber reflector - please ignore Asif Rahaman (Wed May 22 2002 - 15:17:29 PDT)
  - Problem with 2D Gibbs run Asif Rahaman (Wed May 22 2002 - 15:32:49 PDT)
  - This is a test for amber reflector - please ignore Lorenzo Gontrani (Thu May 23 2002 - 01:34:38 PDT)
  - CARNAL Vlad Cojocaru (Thu May 23 2002 - 03:35:29 PDT)
Re: compilation of sander on Alpha/Linux clusters jim caldwell (Fri May 24 2002 - 14:41:00 PDT)
PME & cutoff A. Hungie (Sat May 25 2002 - 06:12:48 PDT)
- Re: PME & cutoff darden (Sun May 26 2002 - 10:03:30 PDT)
- compilation for Hitachi SR8000 A. Hungie (Sun May 26 2002 - 10:25:17 PDT)
- Charge export from Leap is rounded off jeff dyason (Sun May 26 2002 - 17:06:36 PDT)
- Linux Parallel compilation Linux Mpich PGI Fabrice Yerly (Mon May 27 2002 - 05:31:09 PDT)
  - Re: Linux Parallel compilation Linux Mpich PGI Viktor Hornak (Mon May 27 2002 - 07:56:24 PDT)
parallel sander on T3E Peter Gannett (Sat May 25 2002 - 07:46:37 PDT)
- Re: parallel sander on T3E Natasja Brooijmans (Sat May 25 2002 - 08:44:34 PDT)
glucose Yuguang Mu (Tue May 28 2002 - 08:05:10 PDT)
- Re: glucose Carlos Simmerling (Tue May 28 2002 - 08:50:59 PDT)
- RESP charges for phosphorylated residues Uwe Richter (Tue May 28 2002 - 09:05:05 PDT)
- xleap Marcela Madrid (Tue May 28 2002 - 14:21:39 PDT)
- Cyclodextrin Toshikazu Matsuoka (Tue May 28 2002 - 23:48:19 PDT)
- minimization to fix up hydrogen positions yuann (Wed May 29 2002 - 00:33:23 PDT)
- SHAKE troubles Arvid Soederhaell (Wed May 29 2002 - 03:07:17 PDT)
  - Re: SHAKE troubles Stéphane Teletchéa (Wed May 29 2002 - 03:50:12 PDT)
  - Re: SHAKE troubles Yong Duan (Wed May 29 2002 - 05:33:14 PDT)
  - MPich error Fabrice Yerly (Wed May 29 2002 - 05:46:29 PDT)
    - Re: MPich error Stéphane Teletchéa (Wed May 29 2002 - 07:00:44 PDT)
  - Re: SHAKE troubles Lepsa (Wed May 29 2002 - 07:02:15 PDT)
  - xLeap problem Donald Thomas (Wed May 29 2002 - 21:42:04 PDT)
    - Re: xLeap problem John Bushnell (Wed May 29 2002 - 22:53:05 PDT)
    - sander_classic, erratic on IBM Giovanni Fossati (Wed May 29 2002 - 23:17:07 PDT)
    - Re: sander_classic, erratic on IBM David Case (Thu May 30 2002 - 07:13:44 PDT)
    - Re: sander_classic, erratic on IBM Giovanni Fossati (Thu May 30 2002 - 10:05:22 PDT)
    - (no subject) SPEROLEEM_at_aol.com (Thu May 30 2002 - 15:51:26 PDT)
    - GROUP Specification - Error decoding variable yuann (Thu May 30 2002 - 00:43:02 PDT)
    - Re: GROUP Specification - Error decoding variable Yongjun Jiang (Thu May 30 2002 - 01:23:57 PDT)
    - TIP4P SEKIJIMA Masakazu (Thu May 30 2002 - 01:43:14 PDT)
    - Re: TIP4P SEKIJIMA Masakazu (Fri May 31 2002 - 00:32:08 PDT)
    - Re: TIP4P David Case (Fri May 31 2002 - 07:44:19 PDT)
    - H-bond Dmitry Pavlov (Fri May 31 2002 - 01:01:42 PDT)
    - Intel ifc Compiler Joachim Reichelt (Thu May 30 2002 - 02:23:21 PDT)
    - Re: Intel ifc Compiler Robert Duke (Thu May 30 2002 - 06:13:59 PDT)
    - Comparing simulations using Amber 5 and Amber 6 Rebecca Perlow (Thu May 30 2002 - 07:18:36 PDT)
    - Re: Intel ifc Compiler David Case (Thu May 30 2002 - 07:00:55 PDT)
    - Re: Intel ifc Compiler David Case (Fri May 31 2002 - 07:51:21 PDT)
    - AMBER7 Michael Sattler (Thu May 30 2002 - 05:59:11 PDT)
  - Re: SHAKE troubles Arvid Soederhaell (Fri May 31 2002 - 01:50:01 PDT)
    - Re: SHAKE troubles Stéphane Teletchéa (Fri May 31 2002 - 02:45:48 PDT)
Fwd: NPT-MD Antonio J. Díaz Quintana (Fri May 31 2002 - 02:17:55 PDT)
- Re: Fwd: NPT-MD David Case (Fri May 31 2002 - 07:56:43 PDT)

Amber Archive May 2002 By Thread