Amber Archive Sep 2004: By Thread

RE: AMBER: Increase lastrst in the &cntrl namelist Osman Gani (Tue Aug 31 2004 - 23:51:32 PDT)
- RE: AMBER: Increase lastrst in the &cntrl namelist Sichun Yang (Wed Sep 01 2004 - 10:19:18 PDT)
  - Re: AMBER: Increase lastrst in the &cntrl namelist Carlos Simmerling (Wed Sep 01 2004 - 10:54:37 PDT)
  - Re: AMBER: Increase lastrst in the &cntrl namelist David A. Case (Wed Sep 01 2004 - 11:22:07 PDT)
AMBER: question on mm-pbsa cailliez (Wed Sep 01 2004 - 02:48:54 PDT)
- Re: AMBER: question on mm-pbsa Holger Gohlke (Wed Sep 01 2004 - 11:55:50 PDT)
AMBER: [0] MPI Abort by user Aborting program ! tang kwa (Wed Sep 01 2004 - 05:07:51 PDT)
- Re: AMBER: [0] MPI Abort by user Aborting program ! Melinda Layten (Wed Sep 01 2004 - 08:04:15 PDT)
AMBER: Setting up thermodynamic integration david.evans.ulsop.ac.uk (Wed Sep 01 2004 - 07:31:10 PDT)
- Re: AMBER: Setting up thermodynamic integration david.evans.ulsop.ac.uk (Wed Sep 01 2004 - 10:24:40 PDT)
AMBER: Re. HSG Convention jwcraft.uh.edu (Wed Sep 01 2004 - 08:48:41 PDT)
- Re: AMBER: Re. HSG Convention David A. Case (Wed Sep 01 2004 - 09:01:44 PDT)
Re: AMBER: Pulling versus Distance Restraints Furse, Kristina Elisabet (Wed Sep 01 2004 - 10:08:49 PDT)
Re: AMBER: About tree structure of TRP residue David A. Case (Wed Sep 01 2004 - 10:48:34 PDT)
AMBER: parameters-DGnp John (Wed Sep 01 2004 - 17:25:03 PDT)
AMBER: error in installing amber8 anshul.imtech.res.in (Thu Sep 02 2004 - 15:37:12 PDT)
- Re: AMBER: error in installing amber8 David A. Case (Thu Sep 02 2004 - 08:31:02 PDT)
- Re: AMBER: error in installing amber8 Scott Brozell (Thu Sep 02 2004 - 08:56:50 PDT)
  - Re: AMBER: error in installing amber8 anshul.imtech.res.in (Wed Sep 08 2004 - 14:39:27 PDT)
    - Re: AMBER: error in installing amber8 David A. Case (Wed Sep 08 2004 - 09:23:04 PDT)
- Re: AMBER: error in installing amber8 Bill Ross (Wed Sep 08 2004 - 07:49:11 PDT)
AMBER: loading frcmod.mod_phipsi.1 bybaker.itsa.ucsf.edu (Thu Sep 02 2004 - 14:12:04 PDT)
AMBER: Water Box & MD bybaker.itsa.ucsf.edu (Thu Sep 02 2004 - 14:48:00 PDT)
Re: AMBER: loading frcmod.mod_phipsi.1 Bill Ross (Thu Sep 02 2004 - 15:07:44 PDT)
- Re: AMBER: loading frcmod.mod_phipsi.1 bybaker.itsa.ucsf.edu (Thu Sep 02 2004 - 15:18:07 PDT)
Re: AMBER: Differences in RESP charges for G in RG and DG residues FyD (Sat Sep 04 2004 - 03:12:33 PDT)
AMBER: Amber7 tleap problem Ed Pate (Sat Sep 04 2004 - 12:03:47 PDT)
- Re: AMBER: Amber7 tleap problem David A. Case (Sat Sep 04 2004 - 13:11:39 PDT)
AMBER: general questions Marsita M (Mon Sep 06 2004 - 08:58:34 PDT)
- Re: AMBER: general questions Stefano.Pieraccini.unimi.it (Tue Sep 07 2004 - 04:11:01 PDT)
AMBER: Electrostatic potential from the trajectory ! Pradipta Bandyopadhyay (Tue Sep 07 2004 - 04:40:09 PDT)
- RE: AMBER: Electrostatic potential from the trajectory ! Ross Walker (Wed Sep 08 2004 - 04:32:58 PDT)
AMBER: is it a bug in mmpbsa Shan, Jufang (Tue Sep 07 2004 - 07:29:27 PDT)
AMBER: xLeap menus not working properly Hannes Barsch (Wed Sep 08 2004 - 01:14:38 PDT)
- Re: AMBER: xLeap menus not working properly Heike.Meiselbach.chemie.uni-erlangen.de (Wed Sep 08 2004 - 02:19:13 PDT)
AMBER: Amber: BOMB Helios (Wed Sep 08 2004 - 05:18:11 PDT)
- RE: AMBER: Amber: BOMB Ross Walker (Wed Sep 08 2004 - 07:42:53 PDT)
- Re: AMBER: Amber: BOMB David A. Case (Wed Sep 08 2004 - 07:55:04 PDT)
AMBER: Spike in energy and RMS Balvinder Singh (Wed Sep 08 2004 - 15:49:04 PDT)
- RE: AMBER: Spike in energy and RMS Ross Walker (Wed Sep 08 2004 - 07:37:26 PDT)
- Re: AMBER: Spike in energy and RMS Andreas Svrcek-Seiler (Thu Sep 09 2004 - 02:37:57 PDT)
AMBER: REST Yanze Zhang (Wed Sep 08 2004 - 13:09:31 PDT)
- Re: AMBER: REST Melinda Layten (Wed Sep 08 2004 - 13:51:30 PDT)
AMBER: Nucgen and PNA? opitz.che.udel.edu (Wed Sep 08 2004 - 14:14:42 PDT)
- Re: AMBER: Nucgen and PNA? Rhonda Torres (Wed Sep 08 2004 - 14:22:30 PDT)
- Re: AMBER: Nucgen and PNA? opitz.che.udel.edu (Thu Sep 09 2004 - 06:36:25 PDT)
AMBER: Antechamber Failure Johnson Agbo (Wed Sep 08 2004 - 14:56:58 PDT)
- Re: AMBER: Antechamber Failure David A. Case (Wed Sep 08 2004 - 15:48:41 PDT)
AMBER: Amber:how to increase the memory allocation? Helios (Wed Sep 08 2004 - 20:35:14 PDT)
- Re: AMBER: Amber:how to increase the memory allocation? David A. Case (Thu Sep 09 2004 - 08:38:12 PDT)
AMBER: REM make test Sergio E. Wong (Thu Sep 09 2004 - 15:50:50 PDT)
- Re: AMBER: REM make test David A. Case (Thu Sep 09 2004 - 16:40:13 PDT)
  - Re: AMBER: REM make test Sergio E. Wong (Thu Sep 09 2004 - 17:55:49 PDT)
  - AMBER: GB and langevin dynamics Sergio E. Wong (Thu Sep 09 2004 - 22:41:18 PDT)
    - Re: AMBER: GB and langevin dynamics David A. Case (Mon Sep 13 2004 - 12:59:31 PDT)
    - Re: AMBER: GB and langevin dynamics Sergio E. Wong (Wed Sep 15 2004 - 12:38:43 PDT)
    - Re: AMBER: GB and langevin dynamics David A. Case (Wed Sep 15 2004 - 15:01:31 PDT)
    - AMBER: amber8 performance problem on Itanium II's Sergio E. Wong (Thu Sep 16 2004 - 21:18:47 PDT)
    - Re: AMBER: amber8 performance problem on Itanium II's Andreas Svrcek-Seiler (Fri Sep 17 2004 - 01:52:53 PDT)
    - Re: AMBER: amber8 performance problem on Itanium II's Sergio E. Wong (Fri Sep 17 2004 - 11:23:18 PDT)
- Re: AMBER: REM make test Carlos Simmerling (Fri Sep 10 2004 - 06:35:18 PDT)
AMBER: MAC Based Beowulf Cluster Peter Gannett (Thu Sep 09 2004 - 16:17:14 PDT)
AMBER: How many ions? Volodymyr Zloy (Fri Sep 10 2004 - 04:23:38 PDT)
AMBER: make install error Abd Ghani Bin Abd Aziz (Fri Sep 10 2004 - 04:21:15 PDT)
- RE: AMBER: make install error Ross Walker (Fri Sep 10 2004 - 15:41:02 PDT)
AMBER: Monte Carlo simulation tang kwa (Fri Sep 10 2004 - 05:15:35 PDT)
- Re: AMBER: Monte Carlo simulation David A. Case (Fri Sep 10 2004 - 14:56:20 PDT)
AMBER: MPICH problem Abd Ghani Bin Abd Aziz (Fri Sep 10 2004 - 05:33:45 PDT)
- RE: AMBER: MPICH problem Ross Walker (Sun Sep 12 2004 - 03:12:05 PDT)
AMBER: Test Calculation of atomic charges (RESP) for RNA bases Vlad Cojocaru (Fri Sep 10 2004 - 06:41:26 PDT)
- Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases FyD (Fri Sep 10 2004 - 17:35:09 PDT)
AMBER: re:your message to amber... hj zou (Fri Sep 10 2004 - 06:46:58 PDT)
AMBER: Amber7 - mm_pbsa/molsurf Nadine Homeyer (Fri Sep 10 2004 - 05:25:20 PDT)
- Re: AMBER: Amber7 - mm_pbsa/molsurf Oliver Hucke (Fri Sep 10 2004 - 11:03:57 PDT)
Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases Piotr Cieplak (Fri Sep 10 2004 - 10:28:25 PDT)
- Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases Vlad Cojocaru (Mon Sep 13 2004 - 03:10:48 PDT)
  - Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases FyD (Mon Sep 13 2004 - 14:59:11 PDT)
AMBER: An question about PTRAJ b86203054.ntu.edu.tw (Fri Sep 10 2004 - 18:29:17 PDT)
- Re: AMBER: An question about PTRAJ Stef (Sat Sep 11 2004 - 01:01:52 PDT)
  - Re: AMBER: An question about PTRAJ b86203054.ntu.edu.tw (Mon Sep 13 2004 - 10:37:00 PDT)
- Re: AMBER: An question about PTRAJ Thomas E. Cheatham, III (Sat Sep 11 2004 - 12:06:05 PDT)
  - Re: AMBER: An question about PTRAJ b86203054.ntu.edu.tw (Mon Sep 13 2004 - 10:35:51 PDT)
AMBER: make install error Abd Ghani Bin Abd Aziz (Sat Sep 11 2004 - 02:56:40 PDT)
- RE: AMBER: make install error Ross Walker (Sun Sep 12 2004 - 03:15:03 PDT)
- RE: AMBER: make install error Abd Ghani Bin Abd Aziz (Sun Sep 12 2004 - 04:25:19 PDT)
  - Re: AMBER: make install error Robert Duke (Sun Sep 12 2004 - 04:52:48 PDT)
- Re: AMBER: make install error Abd Ghani Bin Abd Aziz (Sun Sep 12 2004 - 05:40:42 PDT)
  - Re: AMBER: make install error Robert Duke (Sun Sep 12 2004 - 05:46:30 PDT)
- Re: AMBER: make install error Abd Ghani Bin Abd Aziz (Sun Sep 12 2004 - 05:53:52 PDT)
- Re: AMBER: make install error Abd Ghani Bin Abd Aziz (Tue Sep 14 2004 - 08:23:37 PDT)
AMBER: mmpbsa: can not generate coordinates/snapshots Magne Olufsen (Mon Sep 13 2004 - 03:37:54 PDT)
AMBER: AMBER7 : update gaff and parm99 force field Guillaume Bollot (Mon Sep 13 2004 - 06:35:01 PDT)
- Re: AMBER: AMBER7 : update gaff and parm99 force field David A. Case (Mon Sep 13 2004 - 12:59:12 PDT)
AMBER: Compilation Problem in Amber 7 Stephen P. Molnar, Ph.D. (Mon Sep 13 2004 - 08:54:27 PDT)
- RE: AMBER: Compilation Problem in Amber 7 Ross Walker (Mon Sep 13 2004 - 21:05:35 PDT)
AMBER: AMBER7 : Hybrid macromolecule Guillaume Bollot (Mon Sep 13 2004 - 08:54:28 PDT)
- Re: AMBER: AMBER7 : Hybrid macromolecule david.evans.ulsop.ac.uk (Mon Sep 13 2004 - 09:30:43 PDT)
AMBER: target rmsd William Andrew McLaughlin (Mon Sep 13 2004 - 13:35:51 PDT)
- Re: AMBER: target rmsd Carlos Simmerling (Mon Sep 13 2004 - 13:49:30 PDT)
  - Re: AMBER: target rmsd Viktor Hornak (Mon Sep 13 2004 - 13:57:07 PDT)
    - Re: AMBER: target rmsd William Andrew McLaughlin (Mon Sep 13 2004 - 14:40:24 PDT)
    - Re: AMBER: target rmsd Viktor Hornak (Mon Sep 13 2004 - 15:15:56 PDT)
AMBER: bond between two polypeptides Jagdish Rai (Tue Sep 14 2004 - 01:19:48 PDT)
- Re: AMBER: bond between two polypeptides David A. Case (Tue Sep 14 2004 - 09:20:23 PDT)
AMBER: mm_pbsa for Delphi Helios Chen (Tue Sep 14 2004 - 02:28:28 PDT)
AMBER: Re: to Francois Vlad Cojocaru (Tue Sep 14 2004 - 04:35:13 PDT)
- Re: AMBER: R.E.D. II to Vlad FyD (Wed Sep 15 2004 - 09:25:44 PDT)
AMBER: MM binding energy with ANAL Ben Cossins (Tue Sep 14 2004 - 05:56:37 PDT)
- Re: AMBER: MM binding energy with ANAL David A. Case (Tue Sep 14 2004 - 15:32:48 PDT)
AMBER: amber 8 Abd Ghani Bin Abd Aziz (Tue Sep 14 2004 - 06:17:56 PDT)
- RE: AMBER: amber 8 Ross Walker (Tue Sep 14 2004 - 08:09:31 PDT)
- RE: AMBER: amber 8 Abd Ghani Bin Abd Aziz (Tue Sep 14 2004 - 08:28:47 PDT)
  - RE: AMBER: amber 8 Ross Walker (Tue Sep 14 2004 - 08:40:26 PDT)
AMBER: want to generate ammonium ion..where to start? Grace Li (Tue Sep 14 2004 - 09:48:20 PDT)
AMBER: TI with sander Oliver Hucke (Tue Sep 14 2004 - 11:58:01 PDT)
- Re: AMBER: TI with sander David A. Case (Tue Sep 14 2004 - 12:20:49 PDT)
AMBER: Restraints in sander.QMMM Joseph Fernandez (Tue Sep 14 2004 - 13:54:07 PDT)
- Re: AMBER: Restraints in sander.QMMM David A. Case (Tue Sep 14 2004 - 15:21:07 PDT)
AMBER: restrain on the distance between two molecules. Qiang Lu (Tue Sep 14 2004 - 14:18:00 PDT)
- Re: AMBER: restrain on the distance between two molecules. Nhat-hang Duong (Tue Sep 14 2004 - 14:34:49 PDT)
AMBER: nmode Carsten Detering (Tue Sep 14 2004 - 15:29:49 PDT)
- Re: AMBER: nmode David A. Case (Tue Sep 14 2004 - 16:13:14 PDT)
  - AMBER: trajectory Wen Li (Thu Sep 23 2004 - 06:35:21 PDT)
AMBER: Intel Fortran Compiler Problem Stephen P. Molnar, Ph.D. (Wed Sep 15 2004 - 07:52:55 PDT)
- Re: AMBER: Intel Fortran Compiler Problem Viktor Hornak (Wed Sep 15 2004 - 07:33:44 PDT)
  - Re: AMBER: Intel Fortran Compiler Problem Stephen P. Molnar, Ph.D. (Wed Sep 15 2004 - 08:13:49 PDT)
    - Re: AMBER: Intel Fortran Compiler Problem Robert Duke (Wed Sep 15 2004 - 07:52:50 PDT)
    - Re: AMBER: Intel Fortran Compiler Problem Viktor Hornak (Wed Sep 15 2004 - 07:52:04 PDT)
    - Re: AMBER: Intel Fortran Compiler Problem Stephen P. Molnar, Ph.D. (Wed Sep 15 2004 - 08:38:11 PDT)
    - Re: AMBER: Intel Fortran Compiler Problem Viktor Hornak (Wed Sep 15 2004 - 08:18:01 PDT)
    - Re: AMBER: Intel Fortran Compiler Problem Robert Duke (Wed Sep 15 2004 - 08:30:11 PDT)
    - Re: AMBER: Intel Fortran Compiler Problem Robert Duke (Wed Sep 15 2004 - 08:38:03 PDT)
    - Re: AMBER: Intel Fortran Compiler Problem Stephen P. Molnar, Ph.D. (Wed Sep 15 2004 - 09:23:30 PDT)
    - Re: AMBER: Intel Fortran Compiler Problem David A. Case (Wed Sep 15 2004 - 09:08:04 PDT)
    - Re: AMBER: Intel Fortran Compiler Problem Robert Duke (Wed Sep 15 2004 - 09:12:46 PDT)
- RE: AMBER: Intel Fortran Compiler Problem Ross Walker (Thu Sep 16 2004 - 21:00:30 PDT)
AMBER: F90 compiler for linux ppc64 Guanglei Cui (Wed Sep 15 2004 - 07:42:12 PDT)
- Re: AMBER: F90 compiler for linux ppc64 Carlos P. Sosa (Wed Sep 15 2004 - 08:10:32 PDT)
  - Re: AMBER: F90 compiler for linux ppc64 Guanglei Cui (Wed Sep 15 2004 - 08:28:17 PDT)
AMBER: principal axis Alberto Perez (Wed Sep 15 2004 - 06:36:37 PDT)
- Re: AMBER: principal axis Thomas E. Cheatham, III (Wed Sep 15 2004 - 08:41:37 PDT)
AMBER: bond constraints in nmode richard dimelow (Wed Sep 15 2004 - 08:15:05 PDT)
- Re: AMBER: bond constraints in nmode David A. Case (Wed Sep 15 2004 - 09:03:09 PDT)
  - AMBER: extra points richard dimelow (Thu Sep 16 2004 - 09:21:05 PDT)
    - Re: AMBER: extra points David A. Case (Thu Sep 16 2004 - 10:26:09 PDT)
AMBER: md problem Volodymyr Zloy (Wed Sep 15 2004 - 09:03:29 PDT)
- Re: AMBER: md problem Furse, Kristina Elisabet (Wed Sep 15 2004 - 12:53:23 PDT)
- RE: AMBER: md problem Ross Walker (Thu Sep 16 2004 - 07:43:19 PDT)
  - RE: AMBER: md problem Volodymyr Zloy (Mon Sep 20 2004 - 11:05:25 PDT)
AMBER: A tool for building coordinates of huge macromolecules Hwankyu Lee (Wed Sep 15 2004 - 09:28:19 PDT)
- Re: AMBER: A tool for building coordinates of huge macromolecules Joachim Reichelt (Wed Sep 15 2004 - 09:37:05 PDT)
AMBER: back interpret Joshua Hicks (Wed Sep 15 2004 - 14:49:57 PDT)
- Re: AMBER: back interpret Carlos Simmerling (Wed Sep 15 2004 - 15:08:40 PDT)
- Re: AMBER: back interpret David A. Case (Wed Sep 15 2004 - 15:23:18 PDT)
  - AMBER: Sander TI with NTR = 1. Chunhu Tan (Wed Sep 15 2004 - 16:33:47 PDT)
    - Re: AMBER: Sander TI with NTR = 1. David A. Case (Thu Sep 16 2004 - 07:56:48 PDT)
AMBER: VDWAALS error during minimisation anita pachaimuthu (Thu Sep 16 2004 - 07:42:34 PDT)
- RE: AMBER: VDWAALS error during minimisation Ross Walker (Thu Sep 16 2004 - 08:20:34 PDT)
AMBER: restraining internal coordinates Taner E. Dirama (Thu Sep 16 2004 - 09:53:51 PDT)
- Re: AMBER: restraining internal coordinates Carlos Simmerling (Thu Sep 16 2004 - 10:04:14 PDT)
AMBER: Force Compiling AMBER8 for an SGI O2 Justin Sanders (Thu Sep 16 2004 - 11:34:12 PDT)
AMBER: Amber 7 Compiling Problem Stephen P. Molnar, Ph.D. (Fri Sep 17 2004 - 08:33:15 PDT)
- Re: AMBER: Amber 7 Compiling Problem David A. Case (Fri Sep 17 2004 - 09:29:58 PDT)
  - Re: AMBER: Amber 7 Compiling Problem Stephen P. Molnar, Ph.D. (Fri Sep 17 2004 - 10:33:47 PDT)
    - Re: AMBER: Amber 7 Compiling Problem David A. Case (Fri Sep 17 2004 - 10:23:23 PDT)
    - Re: AMBER: Amber 7 Compiling Problem Stephen P. Molnar, Ph.D. (Fri Sep 17 2004 - 11:24:52 PDT)
    - Re: AMBER: Amber 7 Compiling Problem Stephen P. Molnar, Ph.D. (Fri Sep 17 2004 - 11:32:02 PDT)
AMBER: Problem with MacroMolecule to AMBER7 Guillaume Bollot (Fri Sep 17 2004 - 08:56:22 PDT)
- Re: AMBER: Problem with MacroMolecule to AMBER7 Sébastien Osborne (Fri Sep 17 2004 - 09:04:48 PDT)
AMBER: PMEMD Greg Kellogg (Fri Sep 17 2004 - 09:20:00 PDT)
- Re: AMBER: PMEMD Robert Duke (Fri Sep 17 2004 - 09:56:01 PDT)
AMBER: Moil-view & Amber trajectory opitz.che.udel.edu (Fri Sep 17 2004 - 13:41:42 PDT)
- Re: AMBER: Moil-view & Amber trajectory Carlos Simmerling (Fri Sep 17 2004 - 14:01:37 PDT)
- Re: AMBER: Moil-view & Amber trajectory Thomas E. Cheatham, III (Fri Sep 17 2004 - 14:23:14 PDT)
- Re: AMBER: Moil-view & Amber trajectory opitz.che.udel.edu (Mon Sep 20 2004 - 14:59:39 PDT)
  - Re: AMBER: Moil-view & Amber trajectory Carlos Simmerling (Tue Sep 21 2004 - 09:17:59 PDT)
AMBER: mm_pbsa nmode problem Fang, Jianwen (Fri Sep 17 2004 - 15:28:47 PDT)
AMBER: Re: Delphi PATH question hj zou (Fri Sep 17 2004 - 23:22:08 PDT)
AMBER: about PARALLEL run on SGI. Ji Changge (Fri Sep 17 2004 - 23:47:38 PDT)
- Re: AMBER: about PARALLEL run on SGI. David A. Case (Sun Sep 19 2004 - 17:49:30 PDT)
Re: AMBER: About binding energy Oliver Hucke (Sat Sep 18 2004 - 21:53:36 PDT)
AMBER: More details about free energy Xiao He (Sun Sep 19 2004 - 01:02:53 PDT)
AMBER: ifort installation mathew k varghese (Sun Sep 19 2004 - 01:46:57 PDT)
- Re: AMBER: ifort installation Nhat-hang Duong (Sun Sep 19 2004 - 12:03:32 PDT)
AMBER: Questions on simulating dendrimer in AMBER. Hwankyu Lee (Sun Sep 19 2004 - 20:21:03 PDT)
AMBER: The question about SAS calculation in MM_PBSA Jack Lei (Mon Sep 20 2004 - 10:19:29 PDT)
- Re: AMBER: The question about SAS calculation in MM_PBSA David A. Case (Wed Sep 22 2004 - 11:29:52 PDT)
RE: AMBER: Trajectory file conversion between Amber & Charmm CK Sim (Mon Sep 20 2004 - 10:45:09 PDT)
- Re: AMBER: Trajectory file conversion between Amber & Charmm Carlos Simmerling (Mon Sep 20 2004 - 10:59:41 PDT)
- RE: AMBER: Trajectory file conversion between Amber & Charmm Thomas E. Cheatham, III (Mon Sep 20 2004 - 11:18:46 PDT)
AMBER: RESP problem... FyD (Mon Sep 20 2004 - 12:59:04 PDT)
AMBER: sander8 compile: myrinet and mpigm Guanglei Cui (Mon Sep 20 2004 - 13:42:14 PDT)
AMBER: about MM-PBSA Xiao He (Mon Sep 20 2004 - 22:40:16 PDT)
- RE: AMBER: about MM-PBSA S. Frank Yan (Mon Sep 20 2004 - 22:59:02 PDT)
  - Re: RE: AMBER: about MM-PBSA Xiao He (Tue Sep 21 2004 - 00:49:24 PDT)
    - Re: AMBER: about MM-PBSA Ray Luo (Mon Sep 20 2004 - 19:26:52 PDT)
    - Re: Re: AMBER: about MM-PBSA Xiao He (Tue Sep 21 2004 - 20:44:51 PDT)
    - AMBER: compressed files Jessica Koplin (Wed Sep 22 2004 - 09:56:27 PDT)
    - RE: AMBER: compressed files Ross Walker (Wed Sep 22 2004 - 10:20:18 PDT)
AMBER: Ptraj data Steve Seibold (Tue Sep 21 2004 - 11:13:49 PDT)
- Re: AMBER: Ptraj data Viktor Hornak (Tue Sep 21 2004 - 11:43:44 PDT)
- Re: AMBER: Ptraj data Thomas E. Cheatham, III (Tue Sep 21 2004 - 11:59:58 PDT)
  - Re: AMBER: Ptraj data Elijah Gregory (Tue Sep 21 2004 - 15:04:45 PDT)
AMBER: MAXRING Antechamber problem Karl N. Kirschner (Tue Sep 21 2004 - 12:37:44 PDT)
- RE: AMBER: MAXRING Antechamber problem Ross Walker (Tue Sep 21 2004 - 12:49:51 PDT)
  - RE: AMBER: MAXRING Antechamber problem Karl N. Kirschner (Wed Sep 22 2004 - 13:17:31 PDT)
AMBER: Question about Parallel Compilation David LeBard (Tue Sep 21 2004 - 16:12:54 PDT)
- Re: AMBER: Question about Parallel Compilation David A. Case (Wed Sep 22 2004 - 09:49:02 PDT)
  - Re: AMBER: Question about Parallel Compilation David LeBard (Wed Sep 22 2004 - 19:49:47 PDT)
AMBER: amber8 installation mathew k varghese (Wed Sep 22 2004 - 00:07:50 PDT)
- Re: AMBER: amber8 installation Andreas Svrcek-Seiler (Wed Sep 22 2004 - 04:05:02 PDT)
AMBER: all_nucleic02 and all_nucleic94 Vlad Cojocaru (Wed Sep 22 2004 - 03:40:10 PDT)
- Re: AMBER: all_nucleic02 and all_nucleic94 David A. Case (Wed Sep 22 2004 - 09:59:01 PDT)
AMBER: Re: Re: Delphi PATH question hj zou (Wed Sep 22 2004 - 06:40:23 PDT)
- Re: AMBER: Re: Re: Delphi PATH question Xiao He (Wed Sep 22 2004 - 08:47:47 PDT)
AMBER: amber8 tests mathew k varghese (Wed Sep 22 2004 - 07:30:09 PDT)
- Re: AMBER: amber8 tests David A. Case (Wed Sep 22 2004 - 11:28:34 PDT)
AMBER: all_nucleic94 versus all_nucleic02 Vlad Cojocaru (Wed Sep 22 2004 - 08:15:12 PDT)
- Re: AMBER: all_nucleic94 versus all_nucleic02 Jiten (Wed Sep 22 2004 - 08:45:36 PDT)
- RE: AMBER: all_nucleic94 versus all_nucleic02 Ross Walker (Wed Sep 22 2004 - 08:53:49 PDT)
- RE: AMBER: all_nucleic94 versus all_nucleic02 Ross Walker (Wed Sep 22 2004 - 10:11:21 PDT)
AMBER: building parameters with Amber Amber admin (Wed Sep 22 2004 - 09:41:38 PDT)
- Re: AMBER: building parameters with Amber Furse, Kristina Elisabet (Wed Sep 22 2004 - 11:36:41 PDT)
AMBER: mm_pbsa.pl nmode entropy estimating problem jwfang (Wed Sep 22 2004 - 12:30:21 PDT)
- Re: AMBER: mm_pbsa.pl nmode entropy estimating problem David A. Case (Wed Sep 22 2004 - 13:29:04 PDT)
AMBER: RESTARTED DUE TO LINMIN FAILURE ... ying xiong (Thu Sep 23 2004 - 01:24:13 PDT)
- Re: AMBER: RESTARTED DUE TO LINMIN FAILURE ... cailliez (Thu Sep 23 2004 - 01:42:31 PDT)
AMBER: Jiten (Thu Sep 23 2004 - 01:44:49 PDT)
- RE: AMBER: Ross Walker (Thu Sep 23 2004 - 10:36:45 PDT)
AMBER: replica exchange with thermodynamic integration david.evans.ulsop.ac.uk (Thu Sep 23 2004 - 04:18:44 PDT)
- Re: AMBER: replica exchange with thermodynamic integration David A. Case (Fri Sep 24 2004 - 08:44:01 PDT)
AMBER: question about J. Am. Chem. Soc. 2001, 123, 5221 paper jwfang (Thu Sep 23 2004 - 08:15:36 PDT)
AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 08:44:39 PDT)
- Re: AMBER: Amber job submission using PBS Guanglei Cui (Thu Sep 23 2004 - 08:52:01 PDT)
  - Re: AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 09:11:41 PDT)
    - Re: AMBER: Amber job submission using PBS Guanglei Cui (Thu Sep 23 2004 - 09:20:30 PDT)
    - Re: AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 09:57:35 PDT)
    - Re: AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 10:04:36 PDT)
    - Re: AMBER: Amber job submission using PBS Guanglei Cui (Thu Sep 23 2004 - 10:49:35 PDT)
    - Re: AMBER: Amber job submission using PBS Thomas E. Cheatham, III (Thu Sep 23 2004 - 10:59:00 PDT)
    - Re: AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 21:05:39 PDT)
    - Re: AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 23:21:27 PDT)
    - Re: AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 21:09:06 PDT)
- RE: AMBER: Amber job submission using PBS Ross Walker (Thu Sep 23 2004 - 10:44:04 PDT)
- RE: AMBER: Amber job submission using PBS Bill Ross (Thu Sep 23 2004 - 12:18:37 PDT)
AMBER: Amber 8 installation error on Xeon 2-CPU Kei ODAI (Thu Sep 23 2004 - 16:11:15 PDT)
- RE: AMBER: Amber 8 installation error on Xeon 2-CPU Ross Walker (Thu Sep 23 2004 - 16:32:49 PDT)
AMBER: ptraj problem Marsita M (Thu Sep 23 2004 - 16:53:53 PDT)
Re: AMBER: Amber 8 installation error on Xeon 2-CPU Bill Ross (Thu Sep 23 2004 - 17:17:17 PDT)
AMBER: about mm_pbsa parameter Xiao He (Thu Sep 23 2004 - 20:56:04 PDT)
- Re: AMBER: about mm_pbsa parameter Oliver Hucke (Fri Sep 24 2004 - 08:49:22 PDT)
AMBER: nbflag cailliez (Thu Sep 23 2004 - 23:44:22 PDT)
- Re: AMBER: nbflag David A. Case (Fri Sep 24 2004 - 08:15:20 PDT)
  - Re: AMBER: nbflag cailliez (Fri Sep 24 2004 - 08:20:13 PDT)
AMBER: phosphoserine library component jwcraft.uh.edu (Fri Sep 24 2004 - 07:01:28 PDT)
- Re: AMBER: phosphoserine library component Jiten (Fri Sep 24 2004 - 07:25:24 PDT)
- Re: AMBER: phosphoserine library component David A. Case (Fri Sep 24 2004 - 08:25:10 PDT)
- Re: AMBER: phosphoserine library component FyD (Fri Sep 24 2004 - 10:10:40 PDT)
AMBER: regular ewald sum in Amber8 Jianwen Jiang (Fri Sep 24 2004 - 09:15:34 PDT)
- Re: AMBER: regular ewald sum in Amber8 David A. Case (Fri Sep 24 2004 - 12:12:30 PDT)
AMBER: Parameters for Inosine yuqin cai (Fri Sep 24 2004 - 11:51:40 PDT)
- Re: AMBER: Parameters for Inosine Jiri Sponer (Fri Sep 24 2004 - 13:02:59 PDT)
AMBER: Question Amber8 install errer with Windows Amber admin (Fri Sep 24 2004 - 12:46:06 PDT)
- Re: AMBER: Question Amber8 install errer with Windows David A. Case (Fri Sep 24 2004 - 13:41:18 PDT)
AMBER: nmode error Xiao He (Fri Sep 24 2004 - 19:17:24 PDT)
- Re: AMBER: nmode error David A. Case (Sat Sep 25 2004 - 11:44:37 PDT)
AMBER: Analysis mm_pbsa result Xiao He (Fri Sep 24 2004 - 19:53:08 PDT)
AMBER: output of mm_pbsa.log Xiao He (Sat Sep 25 2004 - 02:30:16 PDT)
AMBER: minimization problem hj zou (Sat Sep 25 2004 - 02:30:11 PDT)
- Re: AMBER: minimization problem David A. Case (Sat Sep 25 2004 - 11:43:49 PDT)
AMBER: Abd Ghani Bin Abd Aziz (Sat Sep 25 2004 - 03:16:39 PDT)
AMBER: radius of gyration Marsita M (Sat Sep 25 2004 - 19:13:25 PDT)
- Re: AMBER: radius of gyration Sanjeev B.S. (Sat Sep 25 2004 - 20:28:32 PDT)
- Re: AMBER: radius of gyration Marsita M (Sat Sep 25 2004 - 23:40:24 PDT)
  - Re: AMBER: radius of gyration Sanjeev B.S. (Sun Sep 26 2004 - 00:04:51 PDT)
- Re: AMBER: radius of gyration Bill Ross (Sun Sep 26 2004 - 20:41:58 PDT)
- Re: AMBER: radius of gyration Bill Ross (Sun Sep 26 2004 - 20:49:40 PDT)
AMBER: amber 8 error on installation Abd Ghani Bin Abd Aziz (Sun Sep 26 2004 - 05:55:07 PDT)
- Re: AMBER: amber 8 error on installation Carlos Simmerling (Sun Sep 26 2004 - 06:24:08 PDT)
- Re: AMBER: amber 8 error on installation Abd Ghani Bin Abd Aziz (Sun Sep 26 2004 - 06:47:04 PDT)
AMBER: dihedral hj zou (Sun Sep 26 2004 - 18:08:20 PDT)
- Re: AMBER: dihedral Thomas E. Cheatham, III (Sun Sep 26 2004 - 19:13:42 PDT)
AMBER: Atom distance bybaker.itsa.ucsf.edu (Sun Sep 26 2004 - 23:59:05 PDT)
- Re: AMBER: Atom distance Tomas Linhart (Mon Sep 27 2004 - 00:12:59 PDT)
- Re: AMBER: Atom distance bybaker.itsa.ucsf.edu (Mon Sep 27 2004 - 13:39:49 PDT)
  - Re: AMBER: Atom distance Thomas E. Cheatham, III (Mon Sep 27 2004 - 13:48:11 PDT)
AMBER: Principal Component Analysis Vlad Cojocaru (Mon Sep 27 2004 - 05:09:50 PDT)
AMBER: unformatted md problem richard dimelow (Mon Sep 27 2004 - 06:13:40 PDT)
- Re: AMBER: unformatted md problem David A. Case (Mon Sep 27 2004 - 08:06:05 PDT)
AMBER: Great help:Analysis mm_pbsa result Xiao He (Mon Sep 27 2004 - 07:44:03 PDT)
AMBER: how to visualize modes from PCA Vlad Cojocaru (Mon Sep 27 2004 - 09:05:35 PDT)
- Re: AMBER: how to visualize modes from PCA Carlos Simmerling (Mon Sep 27 2004 - 09:13:10 PDT)
AMBER: Amber-7:Bugfix.47 sachin patil (Mon Sep 27 2004 - 12:32:21 PDT)
- Re: AMBER: Amber-7:Bugfix.47 David A. Case (Mon Sep 27 2004 - 13:20:20 PDT)
- RE: AMBER: Amber-7:Bugfix.47 Ross Walker (Mon Sep 27 2004 - 13:34:36 PDT)
AMBER: intramolecular energies Guanglei Cui (Mon Sep 27 2004 - 14:17:11 PDT)
- Re: AMBER: intramolecular energies David A. Case (Mon Sep 27 2004 - 16:27:25 PDT)
  - Re: AMBER: intramolecular energies Guanglei Cui (Mon Sep 27 2004 - 18:55:41 PDT)
    - Re: AMBER: intramolecular energies David A. Case (Tue Sep 28 2004 - 08:43:11 PDT)
    - Re: AMBER: intramolecular energies Guanglei Cui (Tue Sep 28 2004 - 09:11:10 PDT)
    - Re: AMBER: intramolecular energies David A. Case (Tue Sep 28 2004 - 10:11:57 PDT)
    - Re: AMBER: intramolecular energies Guanglei Cui (Tue Sep 28 2004 - 10:38:16 PDT)
AMBER: Re: Atom distance bybaker.itsa.ucsf.edu (Mon Sep 27 2004 - 18:21:20 PDT)
AMBER: question about delphi and UHBD xhu1.memphis.edu (Tue Sep 28 2004 - 09:19:32 PDT)
- Re: AMBER: question about delphi and UHBD Ray Luo (Tue Sep 28 2004 - 10:58:11 PDT)
  - Re: AMBER: question about delphi and UHBD Thomas E. Cheatham, III (Tue Sep 28 2004 - 12:34:59 PDT)
- Re: AMBER: question about delphi and UHBD xhu1.memphis.edu (Tue Sep 28 2004 - 13:32:51 PDT)
  - Re: AMBER: question about delphi and UHBD Carlos Simmerling (Tue Sep 28 2004 - 13:46:43 PDT)
- Re: AMBER: question about delphi and UHBD xhu1.memphis.edu (Tue Sep 28 2004 - 15:06:12 PDT)
  - Re: AMBER: question about delphi and UHBD Ray Luo (Tue Sep 28 2004 - 15:19:59 PDT)
- Re: AMBER: question about delphi and UHBD xhu1.memphis.edu (Wed Sep 29 2004 - 12:11:47 PDT)
- Re: AMBER: question about delphi and UHBD xhu1.memphis.edu (Thu Sep 30 2004 - 09:52:01 PDT)
AMBER: Ahammadunny Pathiaseril (Tue Sep 28 2004 - 11:05:44 PDT)
- Re: AMBER: Ray Luo (Tue Sep 28 2004 - 11:30:10 PDT)
AMBER: The convergence of energy minimisation Binbin Liu (Tue Sep 28 2004 - 12:10:56 PDT)
AMBER: Amber bybaker.itsa.ucsf.edu (Tue Sep 28 2004 - 12:28:32 PDT)
- Re: AMBER: Amber Thomas E. Cheatham, III (Tue Sep 28 2004 - 12:37:25 PDT)
- Re: AMBER: Amber Tomas Linhart (Tue Sep 28 2004 - 12:50:28 PDT)
AMBER: Phosphoserine parameters Venkata S Koppuravuri (Tue Sep 28 2004 - 13:41:23 PDT)
- Re: AMBER: Phosphoserine parameters Oliver Hucke (Tue Sep 28 2004 - 16:53:27 PDT)
- Re: AMBER: Phosphoserine parameters Joseph Nachman (Wed Sep 29 2004 - 08:50:24 PDT)
AMBER: Re: Amber bybaker.itsa.ucsf.edu (Tue Sep 28 2004 - 14:35:01 PDT)
AMBER: scaling 1-4 NB interaction for rings j-shimada.az.jp.nec.com (Wed Sep 29 2004 - 07:16:38 PDT)
- Re: AMBER: scaling 1-4 NB interaction for rings David A. Case (Wed Sep 29 2004 - 08:11:02 PDT)
AMBER: (no subject) Rasha Radwan (Wed Sep 29 2004 - 07:24:25 PDT)
- Re: AMBER: (no subject) Jiten (Wed Sep 29 2004 - 08:23:55 PDT)
- Re: AMBER: (no subject) M. L. Dodson (Wed Sep 29 2004 - 08:39:12 PDT)
- Re: AMBER: (no subject) David A. Case (Wed Sep 29 2004 - 08:39:43 PDT)
- Re: AMBER: (no subject) Anselm Horn (Wed Sep 29 2004 - 08:00:43 PDT)
AMBER: impose: Illegal angle internal definition Madalin Giambasu (Wed Sep 29 2004 - 09:34:18 PDT)
- Re: AMBER: impose: Illegal angle internal definition David A. Case (Wed Sep 29 2004 - 12:13:36 PDT)
AMBER: resp error message Andre Farias de Moura (Wed Sep 29 2004 - 09:25:07 PDT)
- Re: AMBER: resp error message FyD (Wed Sep 29 2004 - 12:55:26 PDT)
  - Re: AMBER: resp error message Andre Farias de Moura (Wed Sep 29 2004 - 10:41:05 PDT)
    - Re: AMBER: resp error message FyD (Wed Sep 29 2004 - 13:54:12 PDT)
    - Re: AMBER: resp error message Andre Farias de Moura (Thu Sep 30 2004 - 06:58:38 PDT)
    - Re: AMBER: resp error message FyD (Thu Sep 30 2004 - 09:54:33 PDT)
AMBER: Compiling AMBER8 Justin Sanders (Thu Sep 30 2004 - 07:54:05 PDT)
- Re: AMBER: Compiling AMBER8 David A. Case (Thu Sep 30 2004 - 08:59:42 PDT)
AMBER: Testing Delphi for mm_pbsa Scott Pendley (Thu Sep 30 2004 - 10:20:15 PDT)
AMBER: anal error Guanglei Cui (Thu Sep 30 2004 - 13:28:35 PDT)

Amber Archive Sep 2004 By Thread