Amber Archive Jun 2006: By Thread

AMBER: offset? Tonda March (Wed May 31 2006 - 23:12:19 PDT)
- Re: AMBER: offset? Angelo (Thu Jun 01 2006 - 02:39:20 PDT)
AMBER: Bond Force Conctants in Amber Force Fields åÇÏÒÏ× ä.á. (Wed May 31 2006 - 22:22:01 PDT)
Re: AMBER: Different results for TI calculation David A. Case (Thu Jun 01 2006 - 07:33:32 PDT)
- AMBER: Amber 8 QMMM tests fail on AIX Shan-ho Tsai (Thu Jun 01 2006 - 08:08:26 PDT)
  - RE: AMBER: Amber 8 QMMM tests fail on AIX Ross Walker (Thu Jun 01 2006 - 09:27:24 PDT)
    - RE: AMBER: Amber 8 QMMM tests fail on AIX Shan-ho Tsai (Thu Jun 01 2006 - 10:31:08 PDT)
Re: AMBER: AMBER mdcrd file bigger than 2GB snoze pa (Thu Jun 01 2006 - 08:41:02 PDT)
- Re: AMBER: AMBER mdcrd file bigger than 2GB Thomas Cheatham (Thu Jun 01 2006 - 09:25:19 PDT)
Re: AMBER: Installation of Amber8 on Fedora Core 5. . Don.Bashford.stjude.org (Thu Jun 01 2006 - 09:23:11 PDT)
- Re: AMBER: Installation of Amber8 on Fedora Core 5. . David A. Case (Fri Jun 02 2006 - 12:27:59 PDT)
AMBER: Another Installation Problem Seth Lilavivat (Thu Jun 01 2006 - 16:01:13 PDT)
- RE: AMBER: Another Installation Problem Ross Walker (Thu Jun 01 2006 - 22:02:03 PDT)
  - Re: AMBER: Another Installation Problem Scott Pendley (Fri Jun 02 2006 - 09:21:09 PDT)
AMBER: compile error with pgf90 Evan Kelly (Thu Jun 01 2006 - 22:33:21 PDT)
- RE: AMBER: compile error with pgf90 Ross Walker (Fri Jun 02 2006 - 08:15:01 PDT)
AMBER: some questions and problems about antechamber and divcon Zhihong Yu (Fri Jun 02 2006 - 00:11:22 PDT)
- Re: AMBER: some questions and problems about antechamber and divcon Martin Peters (Fri Jun 02 2006 - 06:07:03 PDT)
- Re: AMBER: some questions and problems about antechamber and divcon David A. Case (Fri Jun 02 2006 - 17:12:42 PDT)
AMBER: How to analyze the trajectory generated by LES simulation pang zhao (Fri Jun 02 2006 - 00:08:03 PDT)
- Re: AMBER: How to analyze the trajectory generated by LES simulation Vlad Cojocaru (Fri Jun 02 2006 - 02:54:20 PDT)
AMBER: attachments for my last mail Zhihong Yu (Fri Jun 02 2006 - 00:30:30 PDT)
AMBER: Programes to calculate ligand RMSD nag raj (Fri Jun 02 2006 - 03:59:04 PDT)
- Re: AMBER: Programes to calculate ligand RMSD Carlos Simmerling (Fri Jun 02 2006 - 04:45:17 PDT)
AMBER: individual torsion/bond energies from a minimization Thomas Pochapsky (Fri Jun 02 2006 - 06:25:33 PDT)
- Re: AMBER: individual torsion/bond energies from a minimization David A. Case (Mon Jun 05 2006 - 07:21:40 PDT)
AMBER: distance restraints Myunggi Yi (Fri Jun 02 2006 - 08:06:38 PDT)
AMBER: bugfix for frcmod.ff03 in Amber 9 David A. Case (Fri Jun 02 2006 - 09:45:29 PDT)
AMBER: NMR restraint Myunggi Yi (Fri Jun 02 2006 - 11:11:51 PDT)
- Re: AMBER: NMR restraint Myunggi Yi (Fri Jun 02 2006 - 12:15:41 PDT)
  - Re: AMBER: NMR restraint Myunggi Yi (Fri Jun 02 2006 - 12:23:28 PDT)
  - Re: AMBER: NMR restraint David A. Case (Fri Jun 02 2006 - 17:28:16 PDT)
    - Re: AMBER: NMR restraint Myunggi Yi (Sat Jun 03 2006 - 06:25:26 PDT)
Re: AMBER: Thermodynamic integration using the amber 9 Ilyas Yildirim (Fri Jun 02 2006 - 13:12:18 PDT)
Re: AMBER: Namelists in input files David A. Case (Fri Jun 02 2006 - 13:48:42 PDT)
AMBER: trouble adding mdcrd files together Adam Pelzer (Fri Jun 02 2006 - 15:22:46 PDT)
- Re: AMBER: trouble adding mdcrd files together Carlos Simmerling (Fri Jun 02 2006 - 15:37:54 PDT)
- Re: AMBER: trouble adding mdcrd files together David A. Case (Fri Jun 02 2006 - 16:30:20 PDT)
  - Re: AMBER: trouble adding mdcrd files together Carlos Simmerling (Fri Jun 02 2006 - 16:45:16 PDT)
- Re: AMBER: trouble adding mdcrd files together Adam Pelzer (Sat Jun 03 2006 - 17:40:28 PDT)
AMBER: manual docking mathew k varghese (Fri Jun 02 2006 - 20:39:13 PDT)
AMBER: manual docking mathew k varghese (Fri Jun 02 2006 - 20:50:03 PDT)
- Re: AMBER: manual docking linfu (Sat Jun 03 2006 - 00:39:44 PDT)
  - Re: AMBER: manual docking snoze pa (Sun Jun 04 2006 - 21:46:05 PDT)
AMBER: How to use the prmtop and inpcrd files of ligand in a complex system? Zhihong Yu (Sat Jun 03 2006 - 00:00:23 PDT)
- Re: AMBER: How to use the prmtop and inpcrd files of ligand in a complex system? Navnit Kumar Mishra (Mon Jun 05 2006 - 01:08:12 PDT)
Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system? Zhihong Yu (Mon Jun 05 2006 - 01:57:44 PDT)
- Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system? Navnit Kumar Mishra (Mon Jun 05 2006 - 02:22:33 PDT)
AMBER: MM-PBSA and first solvation shell Andrea Bortolato (Mon Jun 05 2006 - 02:42:39 PDT)
- Re: AMBER: MM-PBSA and first solvation shell Thomas Cheatham (Mon Jun 05 2006 - 10:23:58 PDT)
AMBER: process_mdout Navnit Kumar Mishra (Mon Jun 05 2006 - 05:00:40 PDT)
- RE: AMBER: process_mdout Ross Walker (Mon Jun 05 2006 - 08:19:47 PDT)
AMBER: Amber: Segfault while running sander sethl.gatech.edu (Mon Jun 05 2006 - 11:19:33 PDT)
- RE: AMBER: Amber: Segfault while running sander Ross Walker (Mon Jun 05 2006 - 11:31:35 PDT)
  - AMBER: Amber: Can't get sander to run sethl.gatech.edu (Tue Jun 06 2006 - 11:15:14 PDT)
    - Re: AMBER: Amber: Can't get sander to run David A. Case (Tue Jun 06 2006 - 13:31:56 PDT)
AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA. linfu (Mon Jun 05 2006 - 19:24:17 PDT)
- Re: AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA. David A. Case (Wed Jun 07 2006 - 15:22:41 PDT)
AMBER: How to submit a job in cluster pkb bioinfo (Tue Jun 06 2006 - 01:46:21 PDT)
AMBER: calculating box dimensions during MD Vlad Cojocaru (Tue Jun 06 2006 - 07:13:14 PDT)
- Re: AMBER: calculating box dimensions during MD Ananda Rama Krishnan Selvaraj (Tue Jun 06 2006 - 07:31:32 PDT)
AMBER: antechamber and FMN David Mobley (Tue Jun 06 2006 - 10:47:03 PDT)
AMBER: xleap problem Hashem Taha (Tue Jun 06 2006 - 11:29:31 PDT)
- Re: AMBER: xleap problem Myunggi Yi (Tue Jun 06 2006 - 16:32:16 PDT)
  - Re: AMBER: xleap problem Myunggi Yi (Tue Jun 06 2006 - 16:42:34 PDT)
  - Re: AMBER: xleap problem Ilyas Yildirim (Tue Jun 06 2006 - 23:49:04 PDT)
    - Re: AMBER: xleap problem Myunggi Yi (Wed Jun 07 2006 - 07:22:12 PDT)
AMBER: compiler error for Amber9 Weihua Li (Wed Jun 07 2006 - 07:34:49 PDT)
- Re: AMBER: compiler error for Amber9 Robert Duke (Wed Jun 07 2006 - 08:03:15 PDT)
- RE: AMBER: compiler error for Amber9 Ross Walker (Wed Jun 07 2006 - 08:34:20 PDT)
- Re: AMBER: compiler error for Amber9 David A. Case (Wed Jun 07 2006 - 08:52:14 PDT)
AMBER: antechamber Steve Seibold (Wed Jun 07 2006 - 09:16:47 PDT)
- Re: AMBER: antechamber Myunggi Yi (Wed Jun 07 2006 - 09:31:46 PDT)
- RE: AMBER: antechamber Ross Walker (Wed Jun 07 2006 - 09:56:01 PDT)
AMBER: RE: antechamber and FMN Junmei Wang (Wed Jun 07 2006 - 13:39:48 PDT)
AMBER: pmemd_parallel_ins_prob pkmukher (Wed Jun 07 2006 - 14:00:20 PDT)
- Re: AMBER: pmemd_parallel_ins_prob Robert Duke (Wed Jun 07 2006 - 14:21:28 PDT)
- Re: AMBER: pmemd_parallel_ins_prob pkmukher (Thu Jun 08 2006 - 11:09:00 PDT)
- Re: AMBER: pmemd_parallel_ins_prob Amber admin (Thu Jun 15 2006 - 12:08:46 PDT)
AMBER: problem with amber 9 and igb=5 M. Scott Shell (Wed Jun 07 2006 - 18:06:02 PDT)
- Re: AMBER: problem with amber 9 and igb=5 Carlos Simmerling (Wed Jun 07 2006 - 19:02:34 PDT)
  - Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Thu Jun 08 2006 - 09:05:10 PDT)
    - AMBER: GB and protein backbone parameters Carlos Simmerling (Thu Jun 08 2006 - 09:27:47 PDT)
- Re: AMBER: problem with amber 9 and igb=5 John Mongan (Wed Jun 07 2006 - 19:04:59 PDT)
  - Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Thu Jun 08 2006 - 08:55:36 PDT)
    - Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Thu Jun 08 2006 - 22:15:56 PDT)
    - Re: AMBER: problem with amber 9 and igb=5 David A. Case (Fri Jun 09 2006 - 14:58:02 PDT)
    - Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Sat Jun 10 2006 - 11:40:05 PDT)
    - RE: AMBER: problem with amber 9 and igb=5 Ross Walker (Sat Jun 10 2006 - 12:31:26 PDT)
AMBER: How to build N-terminal of alanine : NH2 jitrayut jitonnom (Thu Jun 08 2006 - 00:59:34 PDT)
- Re: AMBER: How to build N-terminal of alanine : NH2 FyD (Thu Jun 08 2006 - 01:27:58 PDT)
  - Fwd: AMBER: How to build N-terminal of alanine : NH2 jitrayut jitonnom (Thu Jun 08 2006 - 05:32:22 PDT)
    - Re: Fwd: AMBER: How to build N-terminal of alanine : NH2 FyD (Thu Jun 08 2006 - 23:45:27 PDT)
AMBER: save coordinates during SANDER minimisation Hannes Barsch (Thu Jun 08 2006 - 02:34:51 PDT)
- Re: AMBER: save coordinates during SANDER minimisation Ilyas Yildirim (Thu Jun 08 2006 - 03:22:24 PDT)
- Re: AMBER: save coordinates during SANDER minimisation David A. Case (Thu Jun 08 2006 - 15:39:01 PDT)
AMBER: Ask for help in pbsa error in AMBER9 Cheng Luo, Ph.D. (Thu Jun 08 2006 - 09:08:10 PDT)
- Re: AMBER: Ask for help in pbsa error in AMBER9 Ray Luo (Thu Jun 08 2006 - 12:01:06 PDT)
AMBER: software to visualize normal modes Douali, Latifa (Thu Jun 08 2006 - 10:03:26 PDT)
- RE: AMBER: software to visualize normal modes Ross Walker (Thu Jun 08 2006 - 10:07:41 PDT)
  - Re: AMBER: software to visualize normal modes David A. Case (Thu Jun 08 2006 - 10:46:38 PDT)
AMBER: AMD 64 Installation / configuration clarification sethl.gatech.edu (Thu Jun 08 2006 - 12:09:50 PDT)
- Re: AMBER: AMD 64 Installation / configuration clarification David LeBard (Thu Jun 08 2006 - 12:57:18 PDT)
  - Re: AMBER: AMD 64 Installation / configuration clarification sethl.gatech.edu (Thu Jun 08 2006 - 13:23:51 PDT)
    - Re: AMBER: AMD 64 Installation / configuration clarification David LeBard (Thu Jun 08 2006 - 16:52:57 PDT)
AMBER: COM khn _ (Thu Jun 08 2006 - 17:13:27 PDT)
- Re: AMBER: COM Thomas Cheatham (Thu Jun 08 2006 - 17:34:03 PDT)
AMBER: charmm force field in amber9 soo (Thu Jun 08 2006 - 21:23:26 PDT)
- Re: AMBER: charmm force field in amber9 David A. Case (Fri Jun 09 2006 - 07:02:03 PDT)
AMBER: Problem with Leap jitrayut jitonnom (Thu Jun 08 2006 - 21:40:52 PDT)
AMBER: use ptraj and two differenct prmtop file to analyze LES trajectory pang zhao (Fri Jun 09 2006 - 01:56:57 PDT)
AMBER: MMPBSA problem jitrayut jitonnom (Fri Jun 09 2006 - 02:48:50 PDT)
- Re: AMBER: MMPBSA problem Thomas Steinbrecher (Fri Jun 09 2006 - 08:06:34 PDT)
AMBER: ptraj Marcela Madrid (Fri Jun 09 2006 - 14:19:54 PDT)
AMBER: Why the result from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? Yongmei Pan (Fri Jun 09 2006 - 20:03:26 PDT)
AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? Yongmei Pan (Fri Jun 09 2006 - 19:57:42 PDT)
- Re: AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? David A. Case (Sat Jun 10 2006 - 10:06:49 PDT)
AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? linfu (Fri Jun 09 2006 - 20:25:24 PDT)
- Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? Ray Luo (Sat Jun 10 2006 - 10:45:17 PDT)
- Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? David A. Case (Sat Jun 10 2006 - 11:24:29 PDT)
AMBER: MD stopped Miguel Ferreira (Sat Jun 10 2006 - 02:33:05 PDT)
- RE: AMBER: MD stopped Ross Walker (Mon Jun 12 2006 - 08:50:34 PDT)
AMBER: Umbrella sampling Atsutoshi Okabe (Sat Jun 10 2006 - 03:42:34 PDT)
- Re: AMBER: Umbrella sampling Ilyas Yildirim (Sat Jun 10 2006 - 07:53:41 PDT)
  - RE: AMBER: Umbrella sampling Atsutoshi Okabe (Sun Jun 18 2006 - 03:14:10 PDT)
    - RE: AMBER: Umbrella sampling Ilyas Yildirim (Sun Jun 18 2006 - 09:57:09 PDT)
AMBER: parmchk error Evan Kelly (Sat Jun 10 2006 - 20:30:11 PDT)
- RE: AMBER: parmchk error Ross Walker (Mon Jun 12 2006 - 08:31:59 PDT)
  - Re: AMBER: parmchk error Evan Kelly (Mon Jun 12 2006 - 22:42:16 PDT)
    - Re: AMBER: parmchk error David A. Case (Wed Jun 14 2006 - 20:28:20 PDT)
- RE: AMBER: parmchk error Junmei Wang (Thu Jun 15 2006 - 08:16:10 PDT)
Re: Re: AMBER:it seems that The SAS in MMPBSA is SES , not SAS. ???? linfu (Sat Jun 10 2006 - 20:27:20 PDT)
AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra (Sun Jun 11 2006 - 22:59:06 PDT)
- Re: AMBER: mm_pbsa calculation for calcium Scott Pendley (Mon Jun 12 2006 - 14:42:59 PDT)
  - Re: AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra (Tue Jun 13 2006 - 00:45:32 PDT)
    - Re: AMBER: mm_pbsa calculation for calcium Scott Pendley (Tue Jun 13 2006 - 09:20:42 PDT)
    - Re: AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra (Tue Jun 13 2006 - 10:26:56 PDT)
    - Re: AMBER: mm_pbsa calculation for calcium Scott Pendley (Tue Jun 13 2006 - 13:03:17 PDT)
AMBER: switching function for electrostatic interactions Fabien Cailliez (Mon Jun 12 2006 - 04:38:22 PDT)
- RE: AMBER: switching function for electrostatic interactions Ross Walker (Mon Jun 12 2006 - 08:28:19 PDT)
- Re: AMBER: switching function for electrostatic interactions Thomas Cheatham (Mon Jun 12 2006 - 09:12:28 PDT)
AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom (Mon Jun 12 2006 - 09:41:52 PDT)
- Re: AMBER: How to calculate the mmpbsa for explicit MD ? Thomas Steinbrecher (Mon Jun 12 2006 - 09:58:33 PDT)
  - Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom (Mon Jun 12 2006 - 11:37:49 PDT)
    - Re: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? Thomas Steinbrecher (Mon Jun 12 2006 - 11:50:30 PDT)
    - Fwd: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom (Mon Jun 12 2006 - 12:15:06 PDT)
- Re: AMBER: How to calculate the mmpbsa for explicit MD ? Chris Moth (Mon Jun 12 2006 - 12:23:01 PDT)
AMBER: How to strip waters in trajectorie ? jitrayut jitonnom (Mon Jun 12 2006 - 12:50:02 PDT)
- Re: AMBER: How to strip waters in trajectorie ? Gustavo Seabra (Mon Jun 12 2006 - 12:57:30 PDT)
- Re: AMBER: How to strip waters in trajectorie ? David A. Case (Mon Jun 12 2006 - 13:06:19 PDT)
- Re: AMBER: How to strip waters in trajectorie ? simon whitehead (Tue Jun 13 2006 - 01:24:37 PDT)
AMBER: Nmode memory allocation problem JunJun Liu (Mon Jun 12 2006 - 16:45:14 PDT)
- RE: AMBER: Nmode memory allocation problem Ross Walker (Mon Jun 12 2006 - 18:34:24 PDT)
  - Re: AMBER: Nmode memory allocation problem JunJun Liu (Tue Jun 13 2006 - 08:08:25 PDT)
AMBER: SGI compiler problems Peter Gannett (Tue Jun 13 2006 - 05:46:18 PDT)
- Re: AMBER: SGI compiler problems Atro Tossavainen (Wed Jun 21 2006 - 04:30:00 PDT)
  - Re: AMBER: SGI compiler problems Roberto Gomperts (Wed Jun 21 2006 - 08:09:54 PDT)
AMBER: MMPBSA error jitrayut jitonnom (Tue Jun 13 2006 - 07:52:08 PDT)
- Re: AMBER: MMPBSA error Heike.Meiselbach.chemie.uni-erlangen.de (Tue Jun 13 2006 - 08:27:22 PDT)
  - Fwd: AMBER: MMPBSA error jitrayut jitonnom (Tue Jun 13 2006 - 09:28:43 PDT)
    - Re: Fwd: AMBER: MMPBSA error JunJun Liu (Tue Jun 13 2006 - 08:51:58 PDT)
AMBER: Difficulty loading a pdb file Kara Di Giorgio (Tue Jun 13 2006 - 11:20:41 PDT)
- Re: AMBER: Difficulty loading a pdb file Ilyas Yildirim (Tue Jun 13 2006 - 14:25:27 PDT)
- RE: AMBER: Difficulty loading a pdb file Ross Walker (Wed Jun 14 2006 - 07:05:34 PDT)
AMBER: LEaP Warning ... when do NH2-neutral fragment jitrayut jitonnom (Tue Jun 13 2006 - 11:40:47 PDT)
- Re: AMBER: LEaP Warning ... when do NH2-neutral fragment FyD (Tue Jun 13 2006 - 12:20:52 PDT)
- Re: AMBER: LEaP Warning ... when do NH2-neutral fragment Ilyas Yildirim (Tue Jun 13 2006 - 14:23:18 PDT)
  - AMBER: Problem of Ptraj in AMBER9 Chunhu Tan (Tue Jun 13 2006 - 15:24:26 PDT)
AMBER: compiler requirement for SGI Fuel To install AMBER9 S.Sundar Raman (Tue Jun 13 2006 - 23:45:40 PDT)
AMBER: How to simplify this big system rationally to perform MD studies Zhihong Yu (Wed Jun 14 2006 - 03:43:59 PDT)
Fwd: Fwd: AMBER: MMPBSA error jitrayut jitonnom (Wed Jun 14 2006 - 04:27:51 PDT)
AMBER: problems on mm_pbsa Giovanni (Wed Jun 14 2006 - 05:05:03 PDT)
- Re: AMBER: problems on mm_pbsa Ray Luo (Tue Jun 13 2006 - 22:04:28 PDT)
  - AMBER: Review. Chunhu Tan (Mon Jun 26 2006 - 12:37:22 PDT)
AMBER: saveamberparams error in Amber9 Weihua Li (Wed Jun 14 2006 - 06:28:43 PDT)
- Re: AMBER: saveamberparams error in Amber9 Thomas Steinbrecher (Wed Jun 14 2006 - 08:07:28 PDT)
  - Re: AMBER: saveamberparams error in Amber9 Weihua Li (Wed Jun 14 2006 - 19:15:03 PDT)
- Re: AMBER: saveamberparams error in Amber9 David A. Case (Wed Jun 14 2006 - 20:15:05 PDT)
  - Re: AMBER: saveamberparams error in Amber9 Weihua Li (Wed Jun 14 2006 - 23:48:52 PDT)
AMBER: ptraj: rms per residue simon whitehead (Wed Jun 14 2006 - 07:14:28 PDT)
- Re: AMBER: ptraj: rms per residue Mingfeng Yang (Wed Jun 14 2006 - 13:28:07 PDT)
AMBER: Fully QM periodic runs Steven Winfield (Wed Jun 14 2006 - 09:03:43 PDT)
- RE: AMBER: Fully QM periodic runs Ross Walker (Wed Jun 14 2006 - 09:41:58 PDT)
  - Re: AMBER: Fully QM periodic runs Wei Zhang (Wed Jun 14 2006 - 09:58:51 PDT)
    - Re: AMBER: Fully QM periodic runs Gustavo Seabra (Wed Jun 14 2006 - 10:44:37 PDT)
- Re: AMBER: Fully QM periodic runs Ken Merz (Thu Jun 15 2006 - 07:10:13 PDT)
Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Kara Di Giorgio (Wed Jun 14 2006 - 10:20:40 PDT)
- Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Ilyas Yildirim (Wed Jun 14 2006 - 11:46:22 PDT)
  - Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Knut Langsetmo (Wed Jun 14 2006 - 12:55:56 PDT)
    - RE: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Ross Walker (Wed Jun 14 2006 - 13:06:49 PDT)
    - Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Kara Di Giorgio (Thu Jun 15 2006 - 09:27:45 PDT)
- Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Mengjuei Hsieh (Sun Jun 25 2006 - 21:15:26 PDT)
AMBER: best way to customize linkages sethl.gatech.edu (Wed Jun 14 2006 - 13:25:07 PDT)
AMBER: Re: Problem in compiling sander with MMTSB Scott Brozell (Wed Jun 14 2006 - 20:29:57 PDT)
AMBER: RMS FLUCTUATIONS Jiang Jianwen (Thu Jun 15 2006 - 04:37:24 PDT)
- RE: AMBER: RMS FLUCTUATIONS Yong Duan (Thu Jun 15 2006 - 07:49:16 PDT)
  - RE: AMBER: RMS FLUCTUATIONS Jiang Jianwen (Fri Jun 16 2006 - 00:01:10 PDT)
- Re: AMBER: RMS FLUCTUATIONS David A. Case (Thu Jun 15 2006 - 21:09:53 PDT)
AMBER: GBSA of nonstandard cations Martin LEPSIK (Thu Jun 15 2006 - 15:46:16 PDT)
AMBER: Re: Problem in compiling sander with MMTSB Scott Brozell (Thu Jun 15 2006 - 16:28:27 PDT)
AMBER: repeat use of a trimer lib file Eric Hu (Thu Jun 15 2006 - 16:35:39 PDT)
AMBER: MPICH and Sander Andrew Box (Thu Jun 15 2006 - 19:07:11 PDT)
- Re: AMBER: MPICH and Sander David A. Case (Thu Jun 15 2006 - 20:47:36 PDT)
AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 06:52:33 PDT)
- Re: AMBER: LEaP error : unbalanced charge Thomas Steinbrecher (Fri Jun 16 2006 - 07:59:50 PDT)
  - Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 09:34:42 PDT)
- Re: AMBER: LEaP error : unbalanced charge FyD (Mon Jun 19 2006 - 00:03:38 PDT)
Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 10:28:08 PDT)
- Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Sat Jun 17 2006 - 13:37:46 PDT)
  - Re: Fwd: Fwd: AMBER: LEaP error : unbalanced charge Ilyas Yildirim (Sun Jun 18 2006 - 00:53:58 PDT)
    - Fwd: Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Sun Jun 18 2006 - 06:17:57 PDT)
AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand Christophe Guilbert (Fri Jun 16 2006 - 21:32:12 PDT)
- Re: AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand Ilyas Yildirim (Sat Jun 17 2006 - 01:28:55 PDT)
AMBER: Problems with restart file from pmemd sim. anna.schrey.gmx.de (Sat Jun 17 2006 - 05:30:56 PDT)
- Re: AMBER: Problems with restart file from pmemd sim. Robert Duke (Sat Jun 17 2006 - 06:10:24 PDT)
AMBER: charge in LEaP step jitrayut jitonnom (Sat Jun 17 2006 - 11:14:24 PDT)
AMBER: Non bond list overflow in amber8.0 program. nag raj (Sun Jun 18 2006 - 21:54:04 PDT)
AMBER: Post-MD minimization sangeeta.bioinfo.ernet.in (Mon Jun 19 2006 - 04:33:58 PDT)
- Re: AMBER: Post-MD minimization Carlos Simmerling (Mon Jun 19 2006 - 07:27:37 PDT)
- RE: AMBER: Post-MD minimization Ross Walker (Mon Jun 19 2006 - 08:20:25 PDT)
  - RE: AMBER: checkoverlap doubt [was: Post-MD minimization] sangeeta.bioinfo.ernet.in (Tue Jun 20 2006 - 06:21:11 PDT)
    - RE: AMBER: checkoverlap doubt [was: Post-MD minimization] Thomas Cheatham (Tue Jun 20 2006 - 15:28:36 PDT)
  - RE: AMBER: Post-MD minimization sangeeta.bioinfo.ernet.in (Thu Jun 22 2006 - 23:09:31 PDT)
    - RE: AMBER: Post-MD minimization Ross Walker (Fri Jun 23 2006 - 05:19:14 PDT)
    - AMBER: Can we submit jobs in sequences to amber? a a (Mon Jun 26 2006 - 00:14:05 PDT)
    - Re: AMBER: Can we submit jobs in sequences to amber? Ilyas Yildirim (Mon Jun 26 2006 - 00:22:00 PDT)
    - AMBER: Minizsation strange error message! Please help. a a (Mon Jun 26 2006 - 03:38:35 PDT)
    - Re: AMBER: Can we submit jobs in sequences to amber? Roberto Gomperts (Mon Jun 26 2006 - 03:25:03 PDT)
AMBER: Amber7-CHARMM22-TRIPOS force fields opitz.che.udel.edu (Mon Jun 19 2006 - 08:37:24 PDT)
AMBER: help with custom RNA molecule sethl.gatech.edu (Mon Jun 19 2006 - 11:55:59 PDT)
AMBER: Antechamber poorly define atom angles of a five ring system which causes NH2 and C not to be planar as expected Christophe Guilbert (Mon Jun 19 2006 - 18:00:29 PDT)
AMBER: ions+proteins Hannes Loeffler (Mon Jun 19 2006 - 18:45:57 PDT)
AMBER: RE: Antechamber poorly define atom angles of a five ring system whichcauses NH2 and C not to be planar as expected Junmei Wang (Mon Jun 19 2006 - 20:08:56 PDT)
AMBER: second derivative matrix Marie Brut (Tue Jun 20 2006 - 05:28:02 PDT)
- Re: AMBER: second derivative matrix David A. Case (Tue Jun 20 2006 - 14:37:01 PDT)
  - AMBER: Tutorial 2: Production MD. a a (Wed Jun 21 2006 - 03:19:05 PDT)
    - Re: AMBER: Tutorial 2: Production MD. Thomas Steinbrecher (Wed Jun 21 2006 - 08:37:51 PDT)
    - AMBER: kill job command? a a (Thu Jun 22 2006 - 00:47:51 PDT)
    - Re: AMBER: kill job command? JunJun Liu (Thu Jun 22 2006 - 06:13:04 PDT)
    - AMBER: Tutorial 2: Minimise and equlibrium error NaN a a (Fri Jun 23 2006 - 03:05:05 PDT)
    - RE: AMBER: Tutorial 2: Minimise and equlibrium error NaN Ross Walker (Fri Jun 23 2006 - 04:28:17 PDT)
AMBER: why has "ELE " a large fluctuation in MMP BSA? yxiong99 (Tue Jun 20 2006 - 06:47:44 PDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 14:37:52 PDT)
  - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 16:10:48 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Thomas Cheatham (Tue Jun 20 2006 - 16:48:54 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 15:55:09 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 17:18:21 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 17:19:10 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 16:45:52 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 18:54:51 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 18:08:32 PDT)
AMBER: why has "ELE " a large fluctuation in MMPBSA? JunJun Liu (Tue Jun 20 2006 - 06:56:25 PDT)
AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 09:13:54 PDT)
- Re: AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 11:20:53 PDT)
- Re: AMBER: ptraj vector Thomas Cheatham (Tue Jun 20 2006 - 12:32:17 PDT)
  - Re: AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 13:07:36 PDT)
    - Re: AMBER: ptraj vector David A. Case (Tue Jun 20 2006 - 14:36:49 PDT)
    - Re: AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 14:55:05 PDT)
    - Re: AMBER: ptraj vector Thomas Cheatham (Tue Jun 20 2006 - 15:13:06 PDT)
    - Re: AMBER: ptraj vector Thomas Cheatham (Tue Jun 20 2006 - 14:59:50 PDT)
AMBER: amber9 hostfile snoze pa (Tue Jun 20 2006 - 17:12:50 PDT)
AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test David McGiven (Wed Jun 21 2006 - 03:46:40 PDT)
- Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test Roberto Gomperts (Wed Jun 21 2006 - 07:10:44 PDT)
  - Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test David McGiven (Wed Jun 21 2006 - 08:54:44 PDT)
AMBER: MMTSB: phi-pdi-based clustering sangeeta.bioinfo.ernet.in (Wed Jun 21 2006 - 05:37:39 PDT)
AMBER: terms in mm-pbsa Lwin, ThuZar (Wed Jun 21 2006 - 08:48:37 PDT)
AMBER: openmpi snoze pa (Wed Jun 21 2006 - 10:28:28 PDT)
AMBER: problems with cpinutil.pl Abhilash Mohan (Wed Jun 21 2006 - 14:06:05 PDT)
AMBER: What's the meaning of NTYPES? JunJun Liu (Wed Jun 21 2006 - 13:27:51 PDT)
- Re: AMBER: What's the meaning of NTYPES? JunJun Liu (Wed Jun 21 2006 - 13:59:23 PDT)
  - Re: AMBER: What's the meaning of NTYPES? Wei Zhang (Thu Jun 22 2006 - 09:18:38 PDT)
AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen (Thu Jun 22 2006 - 00:25:11 PDT)
- Re: AMBER: problems about compiling a parallel version of AMBER 9 Wei Zhang (Thu Jun 22 2006 - 09:21:32 PDT)
  - Re: AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen (Mon Jun 26 2006 - 21:41:05 PDT)
- Re: AMBER: problems about compiling a parallel version of AMBER 9 Kateryna Miroshnychenko (Tue Jun 27 2006 - 01:41:21 PDT)
AMBER: Restraint internal coordinates in Amber 8.0 Guillaume Bollot (Thu Jun 22 2006 - 02:00:03 PDT)
AMBER: average struct.problem bala (Thu Jun 22 2006 - 02:11:15 PDT)
- Re: AMBER: average struct.problem Thomas Cheatham (Thu Jun 22 2006 - 07:35:45 PDT)
AMBER: can i use unusual amino acid priya priya (Thu Jun 22 2006 - 02:15:55 PDT)
- AMBER: RESP charge fitting problems with capping group hayden (Thu Jun 22 2006 - 02:51:52 PDT)
  - Re: AMBER: RESP charge fitting problems with capping group FyD (Thu Jun 22 2006 - 11:51:13 PDT)
AMBER: help creating RNA sethl.gatech.edu (Thu Jun 22 2006 - 12:14:06 PDT)
- Re: AMBER: help creating RNA Ilyas Yildirim (Thu Jun 22 2006 - 12:29:49 PDT)
- Re: AMBER: help creating RNA David A. Case (Thu Jun 22 2006 - 14:08:45 PDT)
  - Re: AMBER: help creating RNA sethl.gatech.edu (Mon Jun 26 2006 - 08:42:00 PDT)
- Re: AMBER: help creating RNA Vlad Cojocaru (Fri Jun 23 2006 - 01:14:24 PDT)
AMBER: ANN: APBS/Amber interface released Robert Konecny (Thu Jun 22 2006 - 23:23:35 PDT)
AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8 Ricardo J. F. Branco (Fri Jun 23 2006 - 00:36:44 PDT)
- RE: AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8 Ross Walker (Fri Jun 23 2006 - 04:34:47 PDT)
AMBER: references simon whitehead (Fri Jun 23 2006 - 03:35:56 PDT)
- Re: AMBER: references Ricardo J. F. Branco (Fri Jun 23 2006 - 03:47:50 PDT)
  - Re: AMBER: references simon whitehead (Fri Jun 23 2006 - 04:46:22 PDT)
- RE: AMBER: references Ross Walker (Fri Jun 23 2006 - 04:32:57 PDT)
AMBER: constant pressure equillibration simon whitehead (Fri Jun 23 2006 - 02:17:35 PDT)
- RE: AMBER: constant pressure equillibration Ross Walker (Fri Jun 23 2006 - 08:53:17 PDT)
AMBER: Implicit solvent question Anthony Cruz (Fri Jun 23 2006 - 06:49:22 PDT)
- Re: AMBER: Implicit solvent question John Mongan (Fri Jun 23 2006 - 09:09:49 PDT)
  - Re: AMBER: Implicit solvent question Anthony Cruz (Thu Jun 29 2006 - 09:44:54 PDT)
AMBER: problems with cpinutil.pl Abhilash Mohan (Fri Jun 23 2006 - 10:00:36 PDT)
AMBER: how to create 2'-5' RNA sethl.gatech.edu (Fri Jun 23 2006 - 14:13:57 PDT)
- Re: AMBER: how to create 2'-5' RNA FyD (Fri Jun 23 2006 - 23:29:43 PDT)
- Re: AMBER: how to create 2'-5' RNA Ilyas Yildirim (Mon Jun 26 2006 - 15:52:10 PDT)
AMBER: Second derivative matrix mbrut.laas.fr (Sat Jun 24 2006 - 04:21:27 PDT)
- Re: AMBER: Second derivative matrix David A. Case (Tue Jun 27 2006 - 01:36:57 PDT)
AMBER: about GBSA sishi.tang.utoronto.ca (Sun Jun 25 2006 - 11:45:11 PDT)
AMBER: periodic boundary condition in the X and Y dimensions only hbluo (Mon Jun 26 2006 - 14:58:00 PDT)
AMBER: periodic boundary condition in the X and Y dimensions only hbluo (Mon Jun 26 2006 - 15:15:51 PDT)
AMBER:Checkoverlap query sangeeta.bioinfo.ernet.in (Mon Jun 26 2006 - 05:12:56 PDT)
AMBER: Amber minimization with multiple restraints Qingning Shu (Mon Jun 26 2006 - 10:23:33 PDT)
- Re: AMBER: Amber minimization with multiple restraints Myunggi Yi (Wed Jun 28 2006 - 12:53:12 PDT)
  - Re: AMBER: Amber minimization with multiple restraints Myunggi Yi (Wed Jun 28 2006 - 12:56:49 PDT)
AMBER: Curves and Average Structures Lauren O'Neil (Mon Jun 26 2006 - 10:26:46 PDT)
- Re: AMBER: Curves and Average Structures David E. Konerding (Mon Jun 26 2006 - 12:42:05 PDT)
  - Re: AMBER: Curves and Average Structures Angelo (Tue Jun 27 2006 - 01:57:47 PDT)
AMBER: manual/prmtop/missing bonds section David Mobley (Mon Jun 26 2006 - 13:27:39 PDT)
AMBER: creating RNA, nucgen / leap sethl.gatech.edu (Mon Jun 26 2006 - 13:59:46 PDT)
AMBER: MM-PBSA and gaff atom types anna ferrari (Tue Jun 27 2006 - 02:28:03 PDT)
- Re: AMBER: MM-PBSA and gaff atom types Ray Luo (Tue Jun 27 2006 - 19:47:51 PDT)
  - Re: AMBER: MM-PBSA and gaff atom types anna ferrari (Wed Jun 28 2006 - 09:43:41 PDT)
AMBER: Leap: neutralising the charge Miguel Ferreira (Tue Jun 27 2006 - 02:49:36 PDT)
- Re: AMBER: Leap: neutralising the charge FyD (Tue Jun 27 2006 - 04:19:08 PDT)
AMBER: rgbmax--something wrong with my input file? Kenley Barrett (Tue Jun 27 2006 - 14:10:27 PDT)
- RE: AMBER: rgbmax--something wrong with my input file? Ross Walker (Tue Jun 27 2006 - 15:52:06 PDT)
- Re: AMBER: rgbmax--something wrong with my input file? tmarch.coin.org (Wed Jun 28 2006 - 14:37:19 PDT)
AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering Cenk Andac (Wed Jun 28 2006 - 03:46:49 PDT)
- Re: AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering Thomas Cheatham (Wed Jun 28 2006 - 09:22:42 PDT)
AMBER: REM test failures on IA-64 architecture Glass, Kevin A (Wed Jun 28 2006 - 08:28:07 PDT)
- Re: AMBER: REM test failures on IA-64 architecture Asim Okur (Wed Jun 28 2006 - 13:09:08 PDT)
AMBER: remlog option changed in amber9? Alik Widge (Wed Jun 28 2006 - 12:36:47 PDT)
- Re: AMBER: remlog option changed in amber9? Carlos Simmerling (Wed Jun 28 2006 - 14:11:22 PDT)
  - Re: AMBER: remlog option changed in amber9? Alik Widge (Wed Jun 28 2006 - 14:24:07 PDT)
    - Re: AMBER: remlog option changed in amber9? Carlos Simmerling (Wed Jun 28 2006 - 14:37:54 PDT)
AMBER: problem with pattern searching in mm_pbsa_calceneent.pm, Amber8, when salt>0 using delphi version 4 Lwin, ThuZar (Wed Jun 28 2006 - 17:58:14 PDT)
- AMBER: MM-PBSA questions Miguel Ferreira (Wed Jun 28 2006 - 18:26:14 PDT)
  - Re: AMBER: MM-PBSA questions Ray Luo (Thu Jun 29 2006 - 22:56:42 PDT)
AMBER: How to calculate binding free energy using MM-PBSA Xioling Chuang (Thu Jun 29 2006 - 02:38:58 PDT)
- Re: AMBER: How to calculate binding free energy using MM-PBSA Cenk Andac (Thu Jun 29 2006 - 03:38:11 PDT)
  - Re: AMBER: How to calculate binding free energy using MM-PBSA Xioling Chuang (Thu Jun 29 2006 - 21:16:48 PDT)
    - Re: AMBER: How to calculate binding free energy using MM-PBSA Cenk Andac (Fri Jun 30 2006 - 05:22:08 PDT)
AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes (Thu Jun 29 2006 - 08:58:26 PDT)
- Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Robert Duke (Thu Jun 29 2006 - 09:37:53 PDT)
  - Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes (Thu Jun 29 2006 - 10:53:23 PDT)
    - Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Robert Duke (Thu Jun 29 2006 - 11:24:14 PDT)
AMBER: Having trouble getting Iron parameters for QM/MM zachary hartman (Thu Jun 29 2006 - 12:23:06 PDT)
- Re: AMBER: Having trouble getting Iron parameters for QM/MM Ken Merz (Thu Jun 29 2006 - 12:54:45 PDT)
  - Re: AMBER: Having trouble getting Iron parameters for QM/MM FyD (Thu Jun 29 2006 - 13:55:14 PDT)
  - RE: AMBER: Having trouble getting Iron parameters for QM/MM Ross Walker (Fri Jun 30 2006 - 01:54:28 PDT)
AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl yxiong99 (Thu Jun 29 2006 - 13:49:50 PDT)
- Re: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl Ray Luo (Thu Jun 29 2006 - 17:47:13 PDT)
  - Re: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl JunJun Liu (Thu Jun 29 2006 - 16:56:34 PDT)
AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Christophe Guilbert (Thu Jun 29 2006 - 14:48:31 PDT)
- Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Bill Ross (Fri Jun 30 2006 - 11:42:53 PDT)
Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Bill Ross (Thu Jun 29 2006 - 16:46:17 PDT)
- Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Christophe Guilbert (Thu Jun 29 2006 - 18:06:29 PDT)
AMBER: general question about hydrogen bond energy vs electrostatic energy Eric Hu (Thu Jun 29 2006 - 17:58:24 PDT)
AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. Christophe Guilbert (Thu Jun 29 2006 - 18:28:31 PDT)
AMBER: GB simulation problem Anthony Cruz (Fri Jun 30 2006 - 09:49:53 PDT)
AMBER: NAMOT sethl.gatech.edu (Fri Jun 30 2006 - 12:17:46 PDT)
AMBER: Compiling / Installing Amber 8 on SUSE 10.1 Seth Lilavivat (Tue Jun 13 2006 - 20:23:25 PDT)
AMBER: Creating an Intercalation site Seth Lilavivat (Sat Jun 17 2006 - 12:25:59 PDT)

Amber Archive Jun 2006 By Thread