AMBER Archive (2002) - Jun 2002 By Author

Starting: Sun Jun 02 2002 - 22:29:38 CDT
Ending: Sun Jun 30 2002 - 17:40:39 CDT

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

Last message date: Tue Dec 31 2002 - 15:51:31 CST
Archived on: Thu May 05 2005 - 14:17:26 CDT