Amber Archive Jun 2002: by author

A. Hungie
- propeller twist of ideal B-DNA (Wed Jun 19 2002 - 09:37:29 PDT)
- vlimit exceeded (Wed Jun 12 2002 - 02:49:44 PDT)
- benchmark for Amber7 (Fri Jun 07 2002 - 07:37:07 PDT)
- Machine_file for Hitachi SR8000 (Wed Jun 05 2002 - 04:09:03 PDT)
Amesh Patel
- minimization probs (Tue Jun 11 2002 - 08:57:12 PDT)
Andreas Svrcek-Seiler
- Re: van der Waals, hydrogen bond energy (Sat Jun 29 2002 - 05:29:38 PDT)
Andrew Petersen
- Protonated database (Tue Jun 11 2002 - 12:12:28 PDT)
Arvid Soederhaell
- SHAKE... (Mon Jun 24 2002 - 04:25:05 PDT)
- even more van der Waals explosion (Fri Jun 21 2002 - 02:23:17 PDT)
- more van der Waals explosion (Fri Jun 21 2002 - 02:00:59 PDT)
- van der Waals explosion (Fri Jun 21 2002 - 01:54:05 PDT)
- Re: turning PME off in AMBER7 (Thu Jun 20 2002 - 06:45:25 PDT)
- no mdcrd, no mden file (Fri Jun 07 2002 - 04:43:30 PDT)
- Re: SHAKE troubles (Tue Jun 04 2002 - 01:22:40 PDT)
Asif Rahaman
- analysis of Gibbs 2D run (Thu Jun 06 2002 - 21:46:34 PDT)
- Problem with Gibbs 2D run (Sun Jun 02 2002 - 20:29:38 PDT)
Asim Okur
- Re: cold belly run error (Mon Jun 10 2002 - 21:58:30 PDT)
bdodson_at_scms.utmb.EDU
- Running amber7 and nab on FreeBSD (Wed Jun 05 2002 - 13:31:24 PDT)
Bill Ross
- xmkmf: not found (Thu Jun 27 2002 - 15:29:08 PDT)
- Re: transferring structures (Wed Jun 26 2002 - 12:47:02 PDT)
- Re: SHAKE (actually: new atom types) (Mon Jun 24 2002 - 12:22:02 PDT)
- Re: how to keep aromatic ring flat (Fri Jun 14 2002 - 16:34:42 PDT)
- Re: Floating Invalid (Mon Jun 10 2002 - 22:36:16 PDT)
- Re:xaLeap make fails on AIX (Mon Jun 10 2002 - 11:19:47 PDT)
- Re: Suggestion to Bill and Case (Fri Jun 07 2002 - 13:16:30 PDT)
Bjorn-Olav Brandsdal
- Parameters for hexachloroethane (Wed Jun 05 2002 - 02:13:54 PDT)
Carlos Simmerling
- Re: van der Waals, hydrogen bond energy (Fri Jun 28 2002 - 16:41:11 PDT)
- Re: box size & 1st equilibrium (Fri Jun 28 2002 - 04:56:09 PDT)
- Re: partial charges (Mon Jun 24 2002 - 18:38:35 PDT)
- Re: The atom number mismatch in coord and topology file. (Thu Jun 13 2002 - 15:27:38 PDT)
- Re: vlimit exceeded (Wed Jun 12 2002 - 04:42:14 PDT)
- Re: Reorder water in amber7 (Tue Jun 11 2002 - 04:36:04 PDT)
case
- RE: minimization probs (Tue Jun 11 2002 - 10:36:57 PDT)
- RE: entropy calculation (Tue Jun 11 2002 - 06:56:37 PDT)
- RE: Reorder water in amber7 (Tue Jun 11 2002 - 06:53:59 PDT)
- amber on MAC OSX (Thu Jun 06 2002 - 17:22:44 PDT)
- Re: Intel Kernel Math Library (Thu Jun 06 2002 - 08:02:25 PDT)
Christian.Pilger_at_bc.boehringer-ingelheim.com
- WG: (Mon Jun 17 2002 - 22:48:01 PDT)
- (no subject) (Mon Jun 17 2002 - 03:09:11 PDT)
- (no subject) (Thu Jun 13 2002 - 22:30:15 PDT)
Craig A Bayse
- question (Tue Jun 18 2002 - 15:04:47 PDT)
David A. Case
- Re: mopac (Thu Jun 27 2002 - 11:34:34 PDT)
- Re: problems compiling Amber 7 (Thu Jun 27 2002 - 11:27:09 PDT)
- Re: dummy torsional parameters (Thu Jun 27 2002 - 08:38:49 PDT)
- Re: xleap problem (Thu Jun 27 2002 - 08:33:16 PDT)
- Re: partial charges (Mon Jun 24 2002 - 18:52:47 PDT)
- Re: taupt: time constant for heat bath coupling for the SOLUTE (Fri Jun 21 2002 - 17:28:38 PDT)
- Re: van der Waals explosion (Fri Jun 21 2002 - 07:55:26 PDT)
- Re: j3 coupling (Fri Jun 21 2002 - 07:49:40 PDT)
- Re: turning PME off in AMBER7 (Thu Jun 20 2002 - 06:49:33 PDT)
David Case
- Re: Problem in amber (Thu Jun 27 2002 - 07:38:30 PDT)
- Re: mm_pbsa in parallel system (Mon Jun 03 2002 - 07:49:08 PDT)
David Smith
- Re: PME box ? (Wed Jun 05 2002 - 07:15:44 PDT)
David.Rilett_at_astrazeneca.com
- mopac (Thu Jun 27 2002 - 10:50:41 PDT)
Dov Barak
- Compilation ov Amber 7 (Fri Jun 21 2002 - 09:40:58 PDT)
Emma.Sigfridsson_at_astrazeneca.com
- igb problem in sander (Wed Jun 12 2002 - 02:11:20 PDT)
- Amber protein-ion problem (Tue Jun 11 2002 - 04:41:29 PDT)
eric hu
- Re: sander parallel (Thu Jun 13 2002 - 15:05:13 PDT)
- sander parallel (Wed Jun 12 2002 - 14:11:24 PDT)
- Re: cold belly run error (Tue Jun 11 2002 - 12:42:19 PDT)
- Re: cold belly run error (Tue Jun 11 2002 - 10:41:47 PDT)
- cold belly run error (Sun Jun 09 2002 - 15:55:47 PDT)
- Re: cap water (Fri Jun 07 2002 - 11:39:22 PDT)
- cap water (Wed Jun 05 2002 - 17:14:10 PDT)
Fabrice Yerly
- Amber PGF77 comilation error + MPICH problem (Wed Jun 05 2002 - 01:31:26 PDT)
FyD
- xleap problem (Thu Jun 27 2002 - 01:20:53 PDT)
- plep question (Wed Jun 26 2002 - 00:28:23 PDT)
Giulio Rastelli
- dummy torsional parameters (Thu Jun 27 2002 - 03:31:50 PDT)
Ishita sharma
- (no subject) (Mon Jun 03 2002 - 04:07:38 PDT)
Jake Isaacs
- solvated time-averaged restraint refinement of DNA (Wed Jun 19 2002 - 09:52:35 PDT)
Jianhui Wu
- Amber7, sander, restart, blast up (Wed Jun 05 2002 - 10:07:51 PDT)
- Re: mm_pbsa in parallel system (fwd) (Mon Jun 03 2002 - 09:03:12 PDT)
jim caldwell
- Re: van der Waals, hydrogen bond energy (Fri Jun 28 2002 - 17:24:21 PDT)
- Re: question (Tue Jun 18 2002 - 15:52:19 PDT)
- Re: Floating Invalid (Tue Jun 11 2002 - 07:43:49 PDT)
Jiyoung Heo
- model molecules for getting charges of DNA (Sat Jun 08 2002 - 17:20:10 PDT)
Joachim Reichelt
- Re: Intel ifc Compiler (Sun Jun 02 2002 - 23:51:54 PDT)
Joffre Heredia
- Re: sander parallel (Thu Jun 13 2002 - 10:39:55 PDT)
- Intel Kernel Math Library (Thu Jun 06 2002 - 12:46:32 PDT)
Jones de Andrade
- C=C=C bending parameters (Sun Jun 09 2002 - 13:55:33 PDT)
Karen Haskell
- tleap error for systems with 64-bit pointers (Fri Jun 14 2002 - 12:55:16 PDT)
kiyean.nam_at_pharma.novartis.com
- Interaction table from minimization (Fri Jun 28 2002 - 14:40:59 PDT)
lamon_at_lav.Boehringer-Ingelheim.com
- turning PME off in AMBER7 (Thu Jun 20 2002 - 06:28:30 PDT)
- re: parameters for zn2+ bond to cys- (Thu Jun 20 2002 - 06:17:38 PDT)
lifang xu
- RE: Floating Invalid (Wed Jun 12 2002 - 20:02:21 PDT)
Ling Zhang
- The crystal water is solute or solvent during solvation (Fri Jun 28 2002 - 11:58:08 PDT)
- iwrap set in sander of Amber6 (Thu Jun 27 2002 - 13:43:41 PDT)
- Using a trucated octahedral box in Amber6 (Wed Jun 26 2002 - 18:28:46 PDT)
- The atom number mismatch in coord and topology file in AMBER6. (Fri Jun 14 2002 - 07:58:45 PDT)
- The atom number mismatch in coord and topology file. (Thu Jun 13 2002 - 14:41:08 PDT)
- How to set the dielctric constant equals 1, when running MD simulations in real solvent water? (Thu Jun 13 2002 - 13:54:53 PDT)
Long Hai
- Re: PME box ? (Wed Jun 05 2002 - 09:07:29 PDT)
Mao Xiang
- perturbed type DH not found (Wed Jun 12 2002 - 03:47:19 PDT)
Marcela Madrid
- charges for peptides (Fri Jun 07 2002 - 08:14:59 PDT)
- reference (Wed Jun 05 2002 - 08:48:55 PDT)
Marcelo Roitburd
- Re: Fwd: Re: probelms in install of amber (fwd) (Thu Jun 27 2002 - 15:47:41 PDT)
- Re: Fwd: Re: probelms in install of amber (fwd) (Thu Jun 27 2002 - 15:23:29 PDT)
- Re: Fwd: Re: probelms in install of amber (fwd) (Thu Jun 27 2002 - 13:59:35 PDT)
Matt Hartings
- Re: transferring structures (Wed Jun 26 2002 - 13:58:11 PDT)
- transferring structures (Wed Jun 26 2002 - 10:24:23 PDT)
mdk7p_at_cms.mail.virginia.edu
- Zn/Mg Counterion placement around DNA (Fri Jun 28 2002 - 12:46:11 PDT)
mer_at_chem.wayne.edu
- Analysis of LES simulation (Sun Jun 30 2002 - 15:40:39 PDT)
Michael Jakusch
- EWALD BOMB (The system has extended beyond ...) (Fri Jun 28 2002 - 02:17:20 PDT)
- antechamber charges don't sum up to zero (Mon Jun 24 2002 - 12:38:15 PDT)
Miguel de Federico
- RESP Multiconformer Fitting (Thu Jun 20 2002 - 16:05:11 PDT)
Monica
- error in rMD (Fri Jun 28 2002 - 06:35:34 PDT)
Monica
- Problem in amber (Wed Jun 26 2002 - 22:28:21 PDT)
- New Residue (Mon Jun 24 2002 - 08:01:42 PDT)
- Application of Amber (Wed Jun 12 2002 - 08:24:49 PDT)
navjot_at_bioinfo.ernet.in
- Mn parameters!!! (Mon Jun 17 2002 - 02:19:12 PDT)
Nikolai Smolin
- minimum image cut-off (Wed Jun 26 2002 - 04:05:08 PDT)
Nitin Kumar Singh
- Query regarding Gamess (Tue Jun 25 2002 - 08:23:09 PDT)
Osvaldo Santos-Filho
- partial charges (Mon Jun 24 2002 - 17:33:15 PDT)
Pascal Bonnet
- Re: mopac (Fri Jun 28 2002 - 01:49:11 PDT)
Peter VARNAI
- Re: remove COM velocity in Amber7 (Thu Jun 20 2002 - 05:03:07 PDT)
- remove COM velocity in Amber7 (Mon Jun 17 2002 - 05:16:27 PDT)
- Re: Reorder water in amber7 (Tue Jun 11 2002 - 10:16:00 PDT)
- Reorder water in amber7 (Tue Jun 11 2002 - 01:38:32 PDT)
Qing Zhang
- van der Waals, hydrogen bond energy (Fri Jun 28 2002 - 15:57:10 PDT)
- taupt: time constant for heat bath coupling for the SOLUTE (Fri Jun 21 2002 - 16:44:55 PDT)
- how to keep aromatic ring flat (Fri Jun 14 2002 - 16:00:51 PDT)
- free energy for binding (Fri Jun 14 2002 - 15:50:54 PDT)
- Re: model molecules for getting charges of DNA (Sun Jun 09 2002 - 12:47:04 PDT)
R.Sathyapriya
- Clarification (Tue Jun 04 2002 - 00:45:19 PDT)
ramon kleber da rocha
- problems compiling Amber 7 (Thu Jun 27 2002 - 10:18:50 PDT)
Randy M. Wadkins
- Re: sander input for a newbie (Wed Jun 12 2002 - 06:04:55 PDT)
- sander input for a newbie (Tue Jun 11 2002 - 16:21:22 PDT)
- Re: amber on MAC OSX (Fri Jun 07 2002 - 12:29:58 PDT)
- Mac OS X compiliation? (Thu Jun 06 2002 - 14:58:18 PDT)
rino ragno
- Amber tutorial (Sat Jun 15 2002 - 02:53:53 PDT)
Robert Duke
- Re: The atom number mismatch in coord and topology file in AMBER6. (Fri Jun 14 2002 - 09:27:00 PDT)
Rudesh Toofanny
- Periodic water box (Fri Jun 14 2002 - 05:41:01 PDT)
S. Yamasaki
- Using TIP4P water (Thu Jun 13 2002 - 18:05:48 PDT)
Sanjeev B.S.
- Re: Compilation ov Amber 7 (Sun Jun 30 2002 - 10:42:28 PDT)
Snyder, James
- (no subject) (Sun Jun 09 2002 - 17:45:03 PDT)
St�phane Teletch�a
- Re: sander parallel (Fri Jun 14 2002 - 01:58:53 PDT)
Thomas A. Spraggins
- Passing arguments with SP2 LoadLeveler (Mon Jun 24 2002 - 07:41:26 PDT)
- bug in .../sander/egb.f ? (Thu Jun 20 2002 - 10:45:28 PDT)
- RE: xaLeap make fails on AIX (Mon Jun 10 2002 - 09:13:01 PDT)
- Parallel Amber on Solaris 2.6 (Mon Jun 03 2002 - 07:49:45 PDT)
Thomas Cheatham
- Re: ptraj problem (Mon Jun 24 2002 - 10:24:30 PDT)
- Re: Periodic water box (Wed Jun 19 2002 - 20:57:04 PDT)
- Re: vlimit exceeded (Wed Jun 12 2002 - 12:35:53 PDT)
TL Poulos
- Question (Wed Jun 05 2002 - 08:49:10 PDT)
Tru
- Re: amber on MAC OSX (Mon Jun 10 2002 - 02:18:03 PDT)
Vlad Cojocaru
- a problem with AMBER7 (Thu Jun 27 2002 - 03:12:58 PDT)
- ptraj problem (Mon Jun 24 2002 - 08:54:32 PDT)
William Gropp
- Re: Parallel Amber on Solaris 2.6 (Mon Jun 03 2002 - 12:20:26 PDT)
William Wei
- Suggestion to Bill and Case (Fri Jun 07 2002 - 13:49:10 PDT)
X. Tan
- parameters for Zn2+ bond to CYS- (Wed Jun 19 2002 - 17:23:16 PDT)
- entropy calculation (Mon Jun 10 2002 - 16:42:59 PDT)
Yi ming Cheng
- PME box ? (Wed Jun 05 2002 - 05:11:15 PDT)
Yongjun Jiang
- test of mm_pbsa (Tue Jun 11 2002 - 20:08:23 PDT)
yuann
- box size & 1st equilibrium (Thu Jun 27 2002 - 23:16:51 PDT)
Yuguang Mu
- j3 coupling (Fri Jun 21 2002 - 03:38:31 PDT)

Amber Archive Jun 2002 by author