AMBER Archive (2003) - Dec 2003 By Thread

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274 messages sorted by: [ author ] [ date ] [ subject ]
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Starting: Mon Dec 01 2003 - 07:34:40 CST
Ending: Wed Dec 31 2003 - 09:47:46 CST

Re: AMBER: missing of VdW Parameters for N3 wendy.cornell_at_pharma.novartis.com (Wed Dec 03 2003 - 09:18:23 CST)

Re: AMBER: Pseudouridine force field parameters Peter Gannett (Tue Dec 02 2003 - 06:45:01 CST)

Re: AMBER: Re: Nmode problem Wu Yingliang (Mon Dec 01 2003 - 07:34:40 CST)
- Re: AMBER: Re: Nmode problem Holger Gohlke (Mon Dec 01 2003 - 08:17:37 CST)

AMBER: NAD+ and NADH amber parameters Jiten (Mon Dec 01 2003 - 08:01:17 CST)
- Re: AMBER: NAD+ and NADH amber parameters David A. Case (Mon Dec 01 2003 - 10:35:56 CST)
  - Re: AMBER: NAD+ and NADH amber parameters Jiten (Sun Dec 07 2003 - 22:17:53 CST)
    - Re: AMBER: NAD+ and NADH amber parameters Ulf Ryde (Mon Dec 08 2003 - 05:05:25 CST)
    - AMBER: Temperature dependent properties of TIP4P and TIP5P rluo_at_uci.edu (Mon Dec 08 2003 - 11:00:21 CST)
- RE: AMBER: NAD+ and NADH amber parameters Ross Walker (Mon Dec 01 2003 - 11:07:40 CST)
- Re: AMBER: NAD+ and NADH amber parameters Ulf Ryde (Tue Dec 02 2003 - 07:20:26 CST)
- Re: AMBER: NAD+ and NADH amber parameters Ross Walker (Mon Dec 08 2003 - 00:22:56 CST)
AMBER: partial charge Li Ying (Mon Dec 01 2003 - 11:31:56 CST)
- Re: AMBER: partial charge David A. Case (Tue Dec 02 2003 - 00:46:04 CST)
  - Re: AMBER: partial charge Li Ying (Tue Dec 02 2003 - 13:19:22 CST)
    - Re: AMBER: partial charge David A. Case (Tue Dec 02 2003 - 14:06:02 CST)
    - Re: AMBER: partial charge Li Ying (Wed Dec 03 2003 - 12:08:14 CST)
AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg (Mon Dec 01 2003 - 13:17:15 CST)
- Re: AMBER: Compiling on Suse 9 Pro with ifc... David A. Case (Mon Dec 01 2003 - 14:49:33 CST)
AMBER: Sander / Anal Emmanuel Giudice (Mon Dec 01 2003 - 14:06:00 CST)
- Re: AMBER: Sander / Anal David A. Case (Mon Dec 01 2003 - 14:58:32 CST)
  - Re: AMBER: Sander / Anal Emmanuel Giudice (Fri Dec 05 2003 - 11:54:20 CST)
AMBER: basic questions Wei Wang (Mon Dec 01 2003 - 17:02:52 CST)
- Re: AMBER: basic questions David A. Case (Tue Dec 02 2003 - 00:37:59 CST)
- Re: AMBER: basic questions Wei Wang (Tue Dec 02 2003 - 10:23:13 CST)
  - Re: AMBER: basic questions David A. Case (Tue Dec 02 2003 - 10:37:42 CST)
AMBER: sander output Dave S Walker (Mon Dec 01 2003 - 20:04:31 CST)
- Re: AMBER: sander output Carlos Simmerling (Mon Dec 01 2003 - 20:37:06 CST)
  - Re: AMBER: sander output Dave S Walker (Thu Dec 04 2003 - 18:41:05 CST)
    - Re: AMBER: sander output David A. Case (Thu Dec 04 2003 - 18:51:03 CST)
AMBER: about H-bond definition for TIP3P Nikolai Smolin (Tue Dec 02 2003 - 07:44:19 CST)
AMBER: Ptraj-HBOND Taner E. Dirama (Tue Dec 02 2003 - 12:42:58 CST)
AMBER: Anal/MMPBSA Wu Yingliang (Tue Dec 02 2003 - 19:16:02 CST)
- Re: AMBER: Anal/MMPBSA David A. Case (Tue Dec 02 2003 - 19:29:46 CST)
  - AMBER: segmentation fault Do Anh Tuan (Tue Dec 02 2003 - 22:56:32 CST)
    - Re: AMBER: segmentation fault David A. Case (Wed Dec 03 2003 - 11:46:46 CST)
AMBER: GIBBS - PMFquestion Jiri Matousek (Wed Dec 03 2003 - 04:47:41 CST)
AMBER: how to calculate vibration frequency? A. Hungie (Wed Dec 03 2003 - 08:46:26 CST)
- Re: AMBER: how to calculate vibration frequency? David A. Case (Wed Dec 03 2003 - 10:59:41 CST)
AMBER: MM-PBSA question Giovanni (Wed Dec 03 2003 - 12:10:10 CST)
- Re: AMBER: MM-PBSA question Holger Gohlke (Wed Dec 03 2003 - 12:58:23 CST)
AMBER: Resp Esp charge Derive (RED v-1.0) release FyD (Wed Dec 03 2003 - 13:09:39 CST)
AMBER: Paramters for beta and gamma peptides Jagannadh B (Thu Dec 04 2003 - 06:34:43 CST)
AMBER: NO2-TYR arubin_at_unmc.edu (Thu Dec 04 2003 - 11:30:24 CST)
AMBER: Amber - compiler help Malone, Scott (Thu Dec 04 2003 - 16:11:53 CST)
- RE: AMBER: Amber - compiler help Chris Moth (Thu Dec 04 2003 - 16:45:10 CST)
- Re: AMBER: Amber - compiler help David A. Case (Thu Dec 04 2003 - 18:54:07 CST)
AMBER: initial structures Raghunadha Reddy Burri (Mon Dec 08 2003 - 09:21:28 CST)
- Re: AMBER: initial structures Carlos Simmerling (Mon Dec 08 2003 - 09:51:04 CST)
  - AMBER: Re: initial structures Raghunadha Reddy Burri (Mon Dec 08 2003 - 11:19:10 CST)
    - Re: AMBER: Re: initial structures David A. Case (Mon Dec 08 2003 - 11:30:57 CST)
AMBER: MD L Jin (Mon Dec 08 2003 - 11:45:01 CST)
- AMBER: gaff atom types for phosphor compouds astrid.maass (Tue Dec 09 2003 - 07:51:33 CST)
  - Re: AMBER: gaff atom types for phosphor compouds Junmei Wang (Tue Dec 09 2003 - 09:28:08 CST)
AMBER: Small problems L Jin (Mon Dec 08 2003 - 11:47:47 CST)
AMBER: Mg2+ parameters for RNA usage Vlad Cojocaru (Wed Dec 10 2003 - 07:38:59 CST)
- Re: AMBER: Mg2+ parameters for RNA usage Jiri Sponer (Wed Dec 10 2003 - 08:21:24 CST)
- Re: AMBER: Mg2+ parameters for RNA usage Pascal Auffinger (Wed Dec 10 2003 - 09:30:47 CST)
  - Re: AMBER: Mg2+ parameters for RNA usage Peter VARNAI (Wed Dec 10 2003 - 10:06:30 CST)
  - Re: AMBER: Mg2+ parameters for RNA usage Jiri Sponer (Wed Dec 10 2003 - 13:32:57 CST)
- Re: AMBER: Mg2+ parameters for RNA usage Bill Ross (Wed Dec 10 2003 - 12:07:49 CST)
AMBER: RESP charges Youyi Peng (Wed Dec 10 2003 - 08:34:58 CST)
- Re: AMBER: RESP charges David A. Case (Wed Dec 10 2003 - 10:31:38 CST)
  - Re: AMBER: RESP charges Youyi Peng (Wed Dec 10 2003 - 11:28:40 CST)
AMBER: About Temperature Regulation L Jin (Wed Dec 10 2003 - 09:09:00 CST)
- Re: AMBER: About Temperature Regulation David A. Case (Wed Dec 10 2003 - 10:30:24 CST)
  - Re: AMBER: About Temperature Regulation L Jin (Wed Dec 10 2003 - 11:06:25 CST)
AMBER: Antechamber & Ptraj/Rdparm L Jin (Wed Dec 10 2003 - 09:07:25 CST)
AMBER: Nitrated Tyr arubin_at_unmc.edu (Wed Dec 10 2003 - 10:36:45 CST)
AMBER: MOPAC from antechamber Beale, John (Wed Dec 10 2003 - 11:46:02 CST)
- Re: AMBER: MOPAC from antechamber Joey Harriman (Wed Dec 10 2003 - 12:08:13 CST)
Re: AMBER: Antechamber & Ptraj/Rdparm Bill Ross (Wed Dec 10 2003 - 12:17:37 CST)
- Re: AMBER: Antechamber & Ptraj/Rdparm L Jin (Fri Dec 12 2003 - 05:35:46 CST)
- Re: AMBER: Antechamber & Ptraj/Rdparm L Jin (Wed Dec 31 2003 - 05:44:00 CST)
  - Re: AMBER: Antechamber & Ptraj/Rdparm David A. Case (Wed Dec 31 2003 - 09:47:46 CST)
AMBER: a simple question about HBond energy... Florent Barbault (Thu Dec 11 2003 - 02:04:27 CST)
- Re: AMBER: a simple question about HBond energy... David A. Case (Fri Dec 12 2003 - 15:57:47 CST)
- Re: AMBER: a simple question about HBond energy... Bill Ross (Fri Dec 12 2003 - 16:16:42 CST)
AMBER: Carbohydrate connectivity Bimo Ario Tejo (Thu Dec 11 2003 - 09:14:05 CST)
- Re: AMBER: Carbohydrate connectivity Jiten (Thu Dec 11 2003 - 10:04:44 CST)
- Re: AMBER: Carbohydrate connectivity David A. Case (Thu Dec 11 2003 - 10:09:08 CST)
AMBER: How to use quasih? A. Hungie (Thu Dec 11 2003 - 10:12:23 CST)
- Re: AMBER: How to use quasih? David A. Case (Thu Dec 11 2003 - 10:34:39 CST)
AMBER: GBSA problem northrop_at_chem.ucla.edu (Thu Dec 11 2003 - 17:28:27 CST)
- Re: AMBER: GBSA problem Wu Yingliang (Thu Dec 11 2003 - 22:20:05 CST)
AMBER: lifetime in ptraj hbond Fajar Rakhman Wibowo (Fri Dec 12 2003 - 03:28:45 CST)
- Re: AMBER: lifetime in ptraj hbond Martin Lepsik (Fri Dec 12 2003 - 07:29:28 CST)
AMBER: ambpdb L Jin (Fri Dec 12 2003 - 04:43:36 CST)
- Re: AMBER: ambpdb ch cureton (Fri Dec 12 2003 - 04:47:06 CST)
  - Re: AMBER: ambpdb L Jin (Fri Dec 12 2003 - 05:24:42 CST)
    - Re: AMBER: ambpdb ch cureton (Fri Dec 12 2003 - 05:53:17 CST)
AMBER: adding extra salt Vlad Cojocaru (Fri Dec 12 2003 - 07:34:55 CST)
AMBER: Antechamber:charges missing L Jin (Fri Dec 12 2003 - 09:45:35 CST)
Re: AMBER: adding extra salt Bill Ross (Fri Dec 12 2003 - 10:44:07 CST)
- AMBER: order parameter myang (Fri Dec 12 2003 - 14:25:17 CST)
  - Re: AMBER: order parameter David A. Case (Fri Dec 12 2003 - 15:29:26 CST)
AMBER: nmode, trajectory kbyun_at_wesleyan.edu (Fri Dec 12 2003 - 11:05:08 CST)
- Re: AMBER: nmode, trajectory Holger Gohlke (Sat Dec 13 2003 - 09:42:39 CST)
AMBER: parmscan Jessica Swanson (Fri Dec 12 2003 - 12:39:19 CST)
AMBER: non-zero 10-12 coefficient Bimo Ario Tejo (Sat Dec 13 2003 - 08:44:49 CST)
- Re: AMBER: non-zero 10-12 coefficient David A. Case (Sat Dec 13 2003 - 14:48:12 CST)
AMBER: Heme and Zn parameters Vema Aparna (Sun Dec 14 2003 - 08:04:43 CST)
AMBER: Energy map L Jin (Mon Dec 15 2003 - 08:42:52 CST)
- Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 08:57:29 CST)
  - Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 09:17:31 CST)
AMBER: water neighborhood of amide hydrogens Jorge Vasquez-Kool (Mon Dec 15 2003 - 09:29:55 CST)
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 09:37:30 CST)
  - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 09:57:31 CST)
- Re: AMBER: water neighborhood of amide hydrogens Thomas E. Cheatham, III (Mon Dec 15 2003 - 11:29:00 CST)
  - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 11:47:32 CST)
- Re: AMBER: water neighborhood of amide hydrogens Bill Ross (Mon Dec 15 2003 - 13:26:29 CST)
AMBER: length of deltaG calcs Heather A.Carlson (Mon Dec 15 2003 - 09:32:48 CST)
- Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 09:37:30 CST)
  - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 09:57:31 CST)
- Re: AMBER: length of deltaG calcs David Smith (Mon Dec 15 2003 - 10:16:26 CST)
  - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 10:37:31 CST)
AMBER: question about namelist aini_at_UMDNJ.EDU (Mon Dec 15 2003 - 09:42:04 CST)
- Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 09:47:30 CST)
  - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:07:31 CST)
- Re: AMBER: question about namelist Holger Gohlke (Mon Dec 15 2003 - 10:10:05 CST)
  - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:27:32 CST)
- Re: AMBER: question about namelist Suse Broyde (Mon Dec 15 2003 - 11:37:58 CST)
  - Re: AMBER: question about namelist Ioana Cozmuta (Mon Dec 15 2003 - 13:14:40 CST)
- Re: AMBER: question about namelist Piotr Cieplak (Mon Dec 15 2003 - 16:02:33 CST)
AMBER: minimization on sander Herbert Georg (Mon Dec 15 2003 - 14:05:25 CST)
Re: AMBER: minimization on sander Bill Ross (Mon Dec 15 2003 - 14:32:39 CST)
- Re: AMBER: minimization on sander Herbert Georg (Mon Dec 15 2003 - 15:21:13 CST)
AMBER: no "Input orientation" in g98 log Lee, Matt (Mon Dec 15 2003 - 17:13:10 CST)
AMBER: Ibelly and Ewald error message when ewald should be off Ben Cossins (Tue Dec 16 2003 - 17:01:52 CST)
AMBER: Nmode analysis ptn-ligand complex Jory Zmuda (Tue Dec 16 2003 - 17:11:13 CST)
AMBER: nmode statistics kbyun_at_wesleyan.edu (Wed Dec 17 2003 - 13:52:51 CST)
- Re: AMBER: nmode statistics Holger Gohlke (Thu Dec 18 2003 - 01:09:05 CST)
AMBER: PMEMD Performance on Beowulf systems Stephen.Titmuss_at_csiro.au (Thu Dec 18 2003 - 21:19:59 CST)
- Re: AMBER: PMEMD Performance on Beowulf systems Robert Duke (Thu Dec 18 2003 - 22:35:40 CST)
  - Re: AMBER: PMEMD Performance on Beowulf systems Carlos Simmerling (Fri Dec 19 2003 - 08:53:12 CST)
- RE: RE: AMBER: PMEMD Performance on Beowulf systems Aldo Jongejan (Mon Dec 22 2003 - 01:27:41 CST)
  - Re: AMBER: PMEMD Performance on Beowulf systems Viktor Hornak (Mon Dec 22 2003 - 07:47:42 CST)
AMBER: MD: restrt L Jin (Fri Dec 19 2003 - 04:47:55 CST)
AMBER: special gaff atom types available? astrid.maass (Fri Dec 19 2003 - 05:58:30 CST)
- Re: AMBER: special gaff atom types available? David A. Case (Sat Dec 20 2003 - 10:25:14 CST)
AMBER: Ewald in Amber 7 Ben Cossins (Fri Dec 19 2003 - 09:49:11 CST)
- Re: AMBER: Ewald in Amber 7 David A. Case (Fri Dec 19 2003 - 11:30:23 CST)
AMBER: Vibration frequency of nucleobases A. Hungie (Fri Dec 19 2003 - 11:48:03 CST)
AMBER: Toolchest Shuang Ding (Fri Dec 19 2003 - 14:45:08 CST)
AMBER: initial velocity Fan Gao (Fri Dec 19 2003 - 18:56:16 CST)
- Re: AMBER: initial velocity Peter Oelschlaeger (Fri Dec 19 2003 - 20:08:43 CST)
AMBER: Curves parameters UU and PP Peter Gannett (Fri Dec 19 2003 - 22:08:02 CST)
- Re: AMBER: Curves parameters UU and PP Surjit Dixit (Sat Dec 20 2003 - 09:45:28 CST)
AMBER: vlimit? Ran Ye (Sun Dec 21 2003 - 16:15:57 CST)
- Re: AMBER: vlimit? David A. Case (Mon Dec 22 2003 - 11:24:18 CST)
  - Re: AMBER: vlimit? Ryan Ye (Tue Dec 23 2003 - 22:04:45 CST)
    - Re: AMBER: vlimit? David A. Case (Fri Dec 26 2003 - 12:18:16 CST)
Re: AMBER: vlimit? Bill Ross (Sun Dec 21 2003 - 22:04:40 CST)
AMBER: using sander without SHAKE Wayne Dawson (Mon Dec 22 2003 - 00:38:14 CST)
- Re: AMBER: using sander without SHAKE David A. Case (Mon Dec 22 2003 - 11:22:09 CST)
  - Re: AMBER: using sander without SHAKE Wayne Dawson (Wed Dec 24 2003 - 10:39:43 CST)
    - Re: AMBER: using sander without SHAKE David A. Case (Wed Dec 24 2003 - 12:06:40 CST)
- Re: AMBER: using sander without SHAKE Bill Ross (Wed Dec 24 2003 - 13:03:43 CST)
AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations? Jiri Matousek (Mon Dec 22 2003 - 03:51:25 CST)
- Re: AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations? David A. Case (Tue Dec 23 2003 - 13:18:39 CST)
AMBER: RESP charge redistribution Youyi Peng (Mon Dec 22 2003 - 15:27:13 CST)
AMBER: umbrella sampling with AMBER Mey Khalili (Mon Dec 22 2003 - 17:14:24 CST)
- Re: AMBER: umbrella sampling with AMBER David A. Case (Mon Dec 22 2003 - 19:48:30 CST)
AMBER: MSMS Salma B. Rafi (Tue Dec 23 2003 - 12:36:18 CST)
- Re: AMBER: MSMS David A. Case (Tue Dec 23 2003 - 12:56:32 CST)
AMBER: PMEMD Performance on IBM SP David Skinner (Tue Dec 23 2003 - 14:00:45 CST)
AMBER: Basic potential question: a b (Wed Dec 24 2003 - 03:29:56 CST)
- AMBER: Basic potential question: Wayne Dawson (Wed Dec 24 2003 - 09:56:37 CST)
  - Re: AMBER: Basic potential question: FyD (Wed Dec 24 2003 - 12:35:22 CST)
  - Re: AMBER: Basic potential question: Piotr Cieplak (Wed Dec 24 2003 - 12:47:57 CST)
    - Re: AMBER: Basic potential question: Wayne Dawson (Thu Dec 25 2003 - 21:04:37 CST)
AMBER: MSE Wen Li (Wed Dec 24 2003 - 10:25:33 CST)
- Re: AMBER: MSE David A. Case (Wed Dec 24 2003 - 12:08:59 CST)
AMBER: Constant temperature L Jin (Sat Dec 27 2003 - 05:29:13 CST)
- Re: AMBER: Constant temperature David A. Case (Sun Dec 28 2003 - 00:46:46 CST)
Re: AMBER: Constant temperature Bill Ross (Sat Dec 27 2003 - 11:14:00 CST)
AMBER: roar topology and coordinate files PSR04996_at_mailstudenti.unimi.it (Mon Dec 29 2003 - 03:11:28 CST)
- Re: AMBER: roar topology and coordinate files M. L. Dodson (Mon Dec 29 2003 - 07:35:42 CST)
  - Re: AMBER: roar topology and coordinate files M. L. Dodson (Mon Dec 29 2003 - 14:15:57 CST)
- Re: AMBER: roar topology and coordinate files Bill Ross (Mon Dec 29 2003 - 18:14:53 CST)
  - Re: AMBER: roar topology and coordinate files M. L. Dodson (Mon Dec 29 2003 - 18:42:49 CST)
AMBER: The restart file generated by Ptraj Ling Zhang (Mon Dec 29 2003 - 14:49:52 CST)
AMBER: The lost velocities in the restart file generated by Ptraj Ling Zhang (Mon Dec 29 2003 - 15:12:47 CST)
Re: AMBER: The lost velocities in the restart file generated by Ptraj Bill Ross (Mon Dec 29 2003 - 18:11:54 CST)
AMBER: problems with pressure control Endres, Robert G. (Tue Dec 30 2003 - 08:38:02 CST)
- Re: AMBER: problems with pressure control David A. Case (Tue Dec 30 2003 - 12:03:06 CST)

Last message date: Fri Feb 06 2004 - 10:15:04 CST
Archived on: Thu May 05 2005 - 14:17:50 CDT

274 messages sorted by: [ author ] [ date ] [ subject ]
About this archive