Amber Archive Jun 2002: By Thread

Problem with Gibbs 2D run Asif Rahaman (Sun Jun 02 2002 - 20:29:38 PDT)
Re: Intel ifc Compiler Joachim Reichelt (Sun Jun 02 2002 - 23:51:54 PDT)
(no subject) Ishita sharma (Mon Jun 03 2002 - 04:07:38 PDT)
Re: mm_pbsa in parallel system David Case (Mon Jun 03 2002 - 07:49:08 PDT)
Parallel Amber on Solaris 2.6 Thomas A. Spraggins (Mon Jun 03 2002 - 07:49:45 PDT)
- Re: Parallel Amber on Solaris 2.6 William Gropp (Mon Jun 03 2002 - 12:20:26 PDT)
Re: mm_pbsa in parallel system (fwd) Jianhui Wu (Mon Jun 03 2002 - 09:03:12 PDT)
Clarification R.Sathyapriya (Tue Jun 04 2002 - 00:45:19 PDT)
Re: SHAKE troubles Arvid Soederhaell (Tue Jun 04 2002 - 01:22:40 PDT)
Amber PGF77 comilation error + MPICH problem Fabrice Yerly (Wed Jun 05 2002 - 01:31:26 PDT)
Parameters for hexachloroethane Bjorn-Olav Brandsdal (Wed Jun 05 2002 - 02:13:54 PDT)
Machine_file for Hitachi SR8000 A. Hungie (Wed Jun 05 2002 - 04:09:03 PDT)
PME box ? Yi ming Cheng (Wed Jun 05 2002 - 05:11:15 PDT)
- Re: PME box ? David Smith (Wed Jun 05 2002 - 07:15:44 PDT)
  - Re: PME box ? Long Hai (Wed Jun 05 2002 - 09:07:29 PDT)
  - Amber7, sander, restart, blast up Jianhui Wu (Wed Jun 05 2002 - 10:07:51 PDT)
  - Running amber7 and nab on FreeBSD bdodson_at_scms.utmb.EDU (Wed Jun 05 2002 - 13:31:24 PDT)
  - cap water eric hu (Wed Jun 05 2002 - 17:14:10 PDT)
    - Re: cap water eric hu (Fri Jun 07 2002 - 11:39:22 PDT)
- reference Marcela Madrid (Wed Jun 05 2002 - 08:48:55 PDT)
- Question TL Poulos (Wed Jun 05 2002 - 08:49:10 PDT)
Suggestion to Bill and Case William Wei (Fri Jun 07 2002 - 13:49:10 PDT)
- Re: Suggestion to Bill and Case Bill Ross (Fri Jun 07 2002 - 13:16:30 PDT)
- model molecules for getting charges of DNA Jiyoung Heo (Sat Jun 08 2002 - 17:20:10 PDT)
  - Re: model molecules for getting charges of DNA Qing Zhang (Sun Jun 09 2002 - 12:47:04 PDT)
  - C=C=C bending parameters Jones de Andrade (Sun Jun 09 2002 - 13:55:33 PDT)
  - cold belly run error eric hu (Sun Jun 09 2002 - 15:55:47 PDT)
    - Re: cold belly run error Asim Okur (Mon Jun 10 2002 - 21:58:30 PDT)
    - Re: cold belly run error eric hu (Tue Jun 11 2002 - 10:41:47 PDT)
    - Re: cold belly run error eric hu (Tue Jun 11 2002 - 12:42:19 PDT)
    - sander input for a newbie Randy M. Wadkins (Tue Jun 11 2002 - 16:21:22 PDT)
    - Re: sander input for a newbie Randy M. Wadkins (Wed Jun 12 2002 - 06:04:55 PDT)
    - Application of Amber Monica (Wed Jun 12 2002 - 08:24:49 PDT)
    - test of mm_pbsa Yongjun Jiang (Tue Jun 11 2002 - 20:08:23 PDT)
    - igb problem in sander Emma.Sigfridsson_at_astrazeneca.com (Wed Jun 12 2002 - 02:11:20 PDT)
    - vlimit exceeded A. Hungie (Wed Jun 12 2002 - 02:49:44 PDT)
    - Re: vlimit exceeded Carlos Simmerling (Wed Jun 12 2002 - 04:42:14 PDT)
    - Re: vlimit exceeded Thomas Cheatham (Wed Jun 12 2002 - 12:35:53 PDT)
    - sander parallel eric hu (Wed Jun 12 2002 - 14:11:24 PDT)
    - Re: sander parallel Joffre Heredia (Thu Jun 13 2002 - 10:39:55 PDT)
    - How to set the dielctric constant equals 1, when running MD simulations in real solvent water? Ling Zhang (Thu Jun 13 2002 - 13:54:53 PDT)
    - The atom number mismatch in coord and topology file. Ling Zhang (Thu Jun 13 2002 - 14:41:08 PDT)
    - Re: The atom number mismatch in coord and topology file. Carlos Simmerling (Thu Jun 13 2002 - 15:27:38 PDT)
    - Using TIP4P water S. Yamasaki (Thu Jun 13 2002 - 18:05:48 PDT)
    - (no subject) Christian.Pilger_at_bc.boehringer-ingelheim.com (Thu Jun 13 2002 - 22:30:15 PDT)
    - Re: sander parallel eric hu (Thu Jun 13 2002 - 15:05:13 PDT)
    - Re: sander parallel Stéphane Teletchéa (Fri Jun 14 2002 - 01:58:53 PDT)
    - free energy for binding Qing Zhang (Fri Jun 14 2002 - 15:50:54 PDT)
    - how to keep aromatic ring flat Qing Zhang (Fri Jun 14 2002 - 16:00:51 PDT)
    - Re: how to keep aromatic ring flat Bill Ross (Fri Jun 14 2002 - 16:34:42 PDT)
    - remove COM velocity in Amber7 Peter VARNAI (Mon Jun 17 2002 - 05:16:27 PDT)
    - Re: remove COM velocity in Amber7 Peter VARNAI (Thu Jun 20 2002 - 05:03:07 PDT)
    - WG: Christian.Pilger_at_bc.boehringer-ingelheim.com (Mon Jun 17 2002 - 22:48:01 PDT)
    - question Craig A Bayse (Tue Jun 18 2002 - 15:04:47 PDT)
    - Re: question jim caldwell (Tue Jun 18 2002 - 15:52:19 PDT)
    - propeller twist of ideal B-DNA A. Hungie (Wed Jun 19 2002 - 09:37:29 PDT)
    - solvated time-averaged restraint refinement of DNA Jake Isaacs (Wed Jun 19 2002 - 09:52:35 PDT)
    - parameters for Zn2+ bond to CYS- X. Tan (Wed Jun 19 2002 - 17:23:16 PDT)
    - Amber tutorial rino ragno (Sat Jun 15 2002 - 02:53:53 PDT)
    - Mn parameters!!! navjot_at_bioinfo.ernet.in (Mon Jun 17 2002 - 02:19:12 PDT)
    - (no subject) Christian.Pilger_at_bc.boehringer-ingelheim.com (Mon Jun 17 2002 - 03:09:11 PDT)
    - Periodic water box Rudesh Toofanny (Fri Jun 14 2002 - 05:41:01 PDT)
    - Re: Periodic water box Thomas Cheatham (Wed Jun 19 2002 - 20:57:04 PDT)
    - The atom number mismatch in coord and topology file in AMBER6. Ling Zhang (Fri Jun 14 2002 - 07:58:45 PDT)
    - Re: The atom number mismatch in coord and topology file in AMBER6. Robert Duke (Fri Jun 14 2002 - 09:27:00 PDT)
    - tleap error for systems with 64-bit pointers Karen Haskell (Fri Jun 14 2002 - 12:55:16 PDT)
    - perturbed type DH not found Mao Xiang (Wed Jun 12 2002 - 03:47:19 PDT)
    - Protonated database Andrew Petersen (Tue Jun 11 2002 - 12:12:28 PDT)
  - (no subject) Snyder, James (Sun Jun 09 2002 - 17:45:03 PDT)
RE: xaLeap make fails on AIX Thomas A. Spraggins (Mon Jun 10 2002 - 09:13:01 PDT)
Re:xaLeap make fails on AIX Bill Ross (Mon Jun 10 2002 - 11:19:47 PDT)
entropy calculation X. Tan (Mon Jun 10 2002 - 16:42:59 PDT)
- RE: entropy calculation case (Tue Jun 11 2002 - 06:56:37 PDT)
Re: Floating Invalid Bill Ross (Mon Jun 10 2002 - 22:36:16 PDT)
- Re: Floating Invalid jim caldwell (Tue Jun 11 2002 - 07:43:49 PDT)
Reorder water in amber7 Peter Varnai (Tue Jun 11 2002 - 01:38:32 PDT)
- Re: Reorder water in amber7 Carlos Simmerling (Tue Jun 11 2002 - 04:36:04 PDT)
  - Re: Reorder water in amber7 Peter VARNAI (Tue Jun 11 2002 - 10:16:00 PDT)
- Amber protein-ion problem Emma.Sigfridsson_at_astrazeneca.com (Tue Jun 11 2002 - 04:41:29 PDT)
- RE: Reorder water in amber7 case (Tue Jun 11 2002 - 06:53:59 PDT)
minimization probs Amesh Patel (Tue Jun 11 2002 - 08:57:12 PDT)
- RE: minimization probs case (Tue Jun 11 2002 - 10:36:57 PDT)
RE: Floating Invalid lifang xu (Wed Jun 12 2002 - 20:02:21 PDT)
re: parameters for zn2+ bond to cys- lamon_at_lav.Boehringer-Ingelheim.com (Thu Jun 20 2002 - 06:17:38 PDT)
turning PME off in AMBER7 lamon_at_lav.Boehringer-Ingelheim.com (Thu Jun 20 2002 - 06:28:30 PDT)
- Re: turning PME off in AMBER7 Arvid Soederhaell (Thu Jun 20 2002 - 06:45:25 PDT)
- Re: turning PME off in AMBER7 David A. Case (Thu Jun 20 2002 - 06:49:33 PDT)
bug in .../sander/egb.f ? Thomas A. Spraggins (Thu Jun 20 2002 - 10:45:28 PDT)
RESP Multiconformer Fitting Miguel de Federico (Thu Jun 20 2002 - 16:05:11 PDT)
van der Waals explosion Arvid Soederhaell (Fri Jun 21 2002 - 01:54:05 PDT)
- Re: van der Waals explosion David A. Case (Fri Jun 21 2002 - 07:55:26 PDT)
  - taupt: time constant for heat bath coupling for the SOLUTE Qing Zhang (Fri Jun 21 2002 - 16:44:55 PDT)
    - Re: taupt: time constant for heat bath coupling for the SOLUTE David A. Case (Fri Jun 21 2002 - 17:28:38 PDT)
    - SHAKE... Arvid Soederhaell (Mon Jun 24 2002 - 04:25:05 PDT)
- Compilation ov Amber 7 Dov Barak (Fri Jun 21 2002 - 09:40:58 PDT)
  - Re: Compilation ov Amber 7 Sanjeev B.S. (Sun Jun 30 2002 - 10:42:28 PDT)
more van der Waals explosion Arvid Soederhaell (Fri Jun 21 2002 - 02:00:59 PDT)
even more van der Waals explosion Arvid Soederhaell (Fri Jun 21 2002 - 02:23:17 PDT)
j3 coupling Yuguang Mu (Fri Jun 21 2002 - 03:38:31 PDT)
- Re: j3 coupling David A. Case (Fri Jun 21 2002 - 07:49:40 PDT)
Passing arguments with SP2 LoadLeveler Thomas A. Spraggins (Mon Jun 24 2002 - 07:41:26 PDT)
New Residue Monica (Mon Jun 24 2002 - 08:01:42 PDT)
ptraj problem Vlad Cojocaru (Mon Jun 24 2002 - 08:54:32 PDT)
- Re: ptraj problem Thomas Cheatham (Mon Jun 24 2002 - 10:24:30 PDT)
Re: SHAKE (actually: new atom types) Bill Ross (Mon Jun 24 2002 - 12:22:02 PDT)
antechamber charges don't sum up to zero Michael Jakusch (Mon Jun 24 2002 - 12:38:15 PDT)
partial charges Osvaldo Santos-Filho (Mon Jun 24 2002 - 17:33:15 PDT)
- Re: partial charges Carlos Simmerling (Mon Jun 24 2002 - 18:38:35 PDT)
- Re: partial charges David A. Case (Mon Jun 24 2002 - 18:52:47 PDT)
- Query regarding Gamess Nitin Kumar Singh (Tue Jun 25 2002 - 08:23:09 PDT)
- plep question FyD (Wed Jun 26 2002 - 00:28:23 PDT)
- minimum image cut-off Nikolai Smolin (Wed Jun 26 2002 - 04:05:08 PDT)
- transferring structures Matt Hartings (Wed Jun 26 2002 - 10:24:23 PDT)
  - Re: transferring structures Bill Ross (Wed Jun 26 2002 - 12:47:02 PDT)
  - Re: transferring structures Matt Hartings (Wed Jun 26 2002 - 13:58:11 PDT)
Using a trucated octahedral box in Amber6 Ling Zhang (Wed Jun 26 2002 - 18:28:46 PDT)
Problem in amber Monica (Wed Jun 26 2002 - 22:28:21 PDT)
- Re: Problem in amber David Case (Thu Jun 27 2002 - 07:38:30 PDT)
xleap problem FyD (Thu Jun 27 2002 - 01:20:53 PDT)
- Re: xleap problem David A. Case (Thu Jun 27 2002 - 08:33:16 PDT)
a problem with AMBER7 Vlad Cojocaru (Thu Jun 27 2002 - 03:12:58 PDT)
dummy torsional parameters Giulio Rastelli (Thu Jun 27 2002 - 03:31:50 PDT)
- Re: dummy torsional parameters David A. Case (Thu Jun 27 2002 - 08:38:49 PDT)
- problems compiling Amber 7 ramon kleber da rocha (Thu Jun 27 2002 - 10:18:50 PDT)
  - Re: problems compiling Amber 7 David A. Case (Thu Jun 27 2002 - 11:27:09 PDT)
- mopac David.Rilett_at_astrazeneca.com (Thu Jun 27 2002 - 10:50:41 PDT)
  - Re: mopac David A. Case (Thu Jun 27 2002 - 11:34:34 PDT)
    - Re: mopac Pascal Bonnet (Fri Jun 28 2002 - 01:49:11 PDT)
    - van der Waals, hydrogen bond energy Qing Zhang (Fri Jun 28 2002 - 15:57:10 PDT)
    - Re: van der Waals, hydrogen bond energy Carlos Simmerling (Fri Jun 28 2002 - 16:41:11 PDT)
    - Re: van der Waals, hydrogen bond energy jim caldwell (Fri Jun 28 2002 - 17:24:21 PDT)
    - Re: van der Waals, hydrogen bond energy Andreas Svrcek-Seiler (Sat Jun 29 2002 - 05:29:38 PDT)
    - EWALD BOMB (The system has extended beyond ...) Michael Jakusch (Fri Jun 28 2002 - 02:17:20 PDT)
  - iwrap set in sander of Amber6 Ling Zhang (Thu Jun 27 2002 - 13:43:41 PDT)
Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd (Thu Jun 27 2002 - 13:59:35 PDT)
- Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd (Thu Jun 27 2002 - 15:23:29 PDT)
- Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd (Thu Jun 27 2002 - 15:47:41 PDT)
xmkmf: not found Bill Ross (Thu Jun 27 2002 - 15:29:08 PDT)
box size & 1st equilibrium yuann (Thu Jun 27 2002 - 23:16:51 PDT)
- Re: box size & 1st equilibrium Carlos Simmerling (Fri Jun 28 2002 - 04:56:09 PDT)

Amber Archive Jun 2002 By Thread