Amber Archive Feb 2006: By Thread

AMBER: Values of Spring Constants Sai Kumar Ramadugu (Tue Jan 31 2006 - 23:18:44 PST)
- Re: AMBER: Values of Spring Constants Carlos Simmerling (Wed Feb 01 2006 - 04:52:50 PST)
  - Re: AMBER: Values of Spring Constants Sai Kumar Ramadugu (Wed Feb 01 2006 - 07:43:05 PST)
    - Re: AMBER: Values of Spring Constants David A. Case (Wed Feb 01 2006 - 08:38:13 PST)
    - Re: AMBER: Values of Spring Constants Sai Kumar Ramadugu (Wed Feb 01 2006 - 21:00:56 PST)
    - Re: AMBER: Values of Spring Constants Carlos Simmerling (Thu Feb 02 2006 - 03:34:30 PST)
    - Re: AMBER: Values of Spring Constants Sai Kumar Ramadugu (Thu Feb 02 2006 - 20:01:44 PST)
    - Re: AMBER: Values of Spring Constants David A. Case (Fri Feb 03 2006 - 15:51:22 PST)
- Re: AMBER: Values of Spring Constants Adrian Roitberg (Wed Feb 01 2006 - 05:05:14 PST)
AMBER: Gibbs PMF Calculation Atsutoshi Okabe (Wed Feb 01 2006 - 04:31:12 PST)
- Re: AMBER: Gibbs PMF Calculation Carlos Simmerling (Wed Feb 01 2006 - 04:54:33 PST)
AMBER: prepi definitions Michael Mazanetz (Wed Feb 01 2006 - 07:56:25 PST)
- Re: AMBER: prepi definitions ivan.mmb.pcb.ub.es (Wed Feb 01 2006 - 08:33:42 PST)
Re: AMBER: lifetimes David A. Case (Wed Feb 01 2006 - 08:20:56 PST)
AMBER: protein ligand complex snoze pa (Wed Feb 01 2006 - 09:21:21 PST)
- Re: AMBER: protein ligand complex Carlos Simmerling (Wed Feb 01 2006 - 09:53:06 PST)
  - Re: AMBER: protein ligand complex snoze pa (Wed Feb 01 2006 - 10:06:39 PST)
    - Re: AMBER: protein ligand complex Carlos Simmerling (Wed Feb 01 2006 - 10:26:10 PST)
- Re: AMBER: protein ligand complex snoze pa (Wed Feb 01 2006 - 11:42:11 PST)
Re: AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com (Wed Feb 01 2006 - 11:39:04 PST)
- Re: AMBER: Problem in compiling sander with MMTSB David A. Case (Wed Feb 01 2006 - 16:05:58 PST)
  - Re: AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com (Wed Feb 01 2006 - 19:26:55 PST)
    - Re: AMBER: Problem in compiling sander with MMTSB David A. Case (Fri Feb 03 2006 - 16:31:32 PST)
    - Re: AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com (Fri Feb 03 2006 - 17:21:51 PST)
AMBER: Cannot successfully assign bond type for this molecule? snoze pa (Wed Feb 01 2006 - 12:43:53 PST)
- Re: AMBER: Cannot successfully assign bond type for this molecule? David Case (Wed Feb 01 2006 - 13:49:55 PST)
  - Re: AMBER: Cannot successfully assign bond type for this molecule? snoze pa (Wed Feb 01 2006 - 15:00:40 PST)
AMBER: basic minimize question A D (Wed Feb 01 2006 - 14:50:53 PST)
- RE: AMBER: basic minimize question Ross Walker (Wed Feb 01 2006 - 15:06:07 PST)
  - Re: AMBER: basic minimize question A D (Wed Feb 01 2006 - 15:35:38 PST)
    - Re: AMBER: basic minimize question David A. Case (Wed Feb 01 2006 - 16:09:11 PST)
    - RE: AMBER: basic minimize question Ross Walker (Wed Feb 01 2006 - 16:17:57 PST)
AMBER: Charges on atoms in protein :AMBER Varsha Goyal (Wed Feb 01 2006 - 19:00:09 PST)
- RE: AMBER: Charges on atoms in protein :AMBER Ross Walker (Wed Feb 01 2006 - 20:17:24 PST)
  - RE: AMBER: Charges on atoms in protein :AMBER Varsha Goyal (Thu Feb 02 2006 - 11:20:59 PST)
    - Re: AMBER: Charges on atoms in protein :AMBER Adrian Roitberg (Thu Feb 02 2006 - 11:50:54 PST)
    - RE: AMBER: Charges on atoms in protein :AMBER Ilyas Yildirim (Thu Feb 02 2006 - 12:14:53 PST)
- RE: AMBER: Charges on atoms in protein :AMBER Bill Ross (Thu Feb 02 2006 - 10:43:23 PST)
- RE: AMBER: Charges on atoms in protein :AMBER Bill Ross (Thu Feb 02 2006 - 11:31:28 PST)
AMBER: positional restraints & constant pressure Kateryna Miroshnychenko (Thu Feb 02 2006 - 07:40:30 PST)
- Re: AMBER: positional restraints & constant pressure David A. Case (Fri Feb 03 2006 - 08:40:53 PST)
AMBER: lib file snoze pa (Thu Feb 02 2006 - 08:55:33 PST)
- Re: AMBER: lib file Ilyas Yildirim (Thu Feb 02 2006 - 11:08:12 PST)
- Re: AMBER: lib file Ilyas Yildirim (Thu Feb 02 2006 - 12:18:28 PST)
  - Re: AMBER: lib file snoze pa (Fri Feb 03 2006 - 11:32:39 PST)
    - Re: AMBER: lib file Ilyas Yildirim (Fri Feb 03 2006 - 17:11:36 PST)
Re: AMBER: MM-PBSA David A. Case (Thu Feb 02 2006 - 11:00:23 PST)
AMBER: Amber8 parallel compilation problems on EM64T system HL Eastwood (Thu Feb 02 2006 - 11:32:32 PST)
- Re: AMBER: Amber8 parallel compilation problems on EM64T system David A. Case (Thu Feb 02 2006 - 12:28:27 PST)
  - AMBER: Amber8 parallel compilation problems on an OSCAR Cluster Aaron J. Greenwood (Thu Feb 02 2006 - 14:18:59 PST)
    - Re: AMBER: Amber8 parallel compilation problems on an OSCAR Cluster David A. Case (Thu Feb 02 2006 - 17:49:39 PST)
    - Re: AMBER: Amber8 parallel compilation problems on an OSCAR Cluster Aaron J. Greenwood (Fri Feb 03 2006 - 07:57:30 PST)
AMBER: parameter loading problem Lihua Wang (Thu Feb 02 2006 - 13:01:51 PST)
AMBER: MD of oligomer sequences Atilio I Anzellotti/O/VCU (Thu Feb 02 2006 - 14:53:28 PST)
- Re: AMBER: MD of oligomer sequences David A. Case (Thu Feb 02 2006 - 18:08:42 PST)
AMBER: simulated annealing run--temp won't rise Kenley Barrett (Thu Feb 02 2006 - 19:26:52 PST)
- Re: AMBER: simulated annealing run--temp won't rise David Case (Thu Feb 02 2006 - 22:46:00 PST)
AMBER: Re: Force Decomposition for MTS in AMBER 8. David Case (Thu Feb 02 2006 - 22:34:23 PST)
AMBER: Gibbs PMF Calculation Atsutoshi Okabe (Fri Feb 03 2006 - 00:38:55 PST)
- Re: AMBER: Gibbs PMF Calculation Carlos Simmerling (Fri Feb 03 2006 - 03:52:56 PST)
AMBER: MPICH-1.2.7 compilation problem ! Pradipta Bandyopadhyay (Fri Feb 03 2006 - 05:49:31 PST)
AMBER: AMBER 7 and cutoff's Toomas Kaevand (Fri Feb 03 2006 - 09:58:53 PST)
- Re: AMBER: AMBER 7 and cutoff's Carlos Simmerling (Fri Feb 03 2006 - 11:20:30 PST)
AMBER: Rhoad, Jonathan S. (Fri Feb 03 2006 - 11:56:37 PST)
- Re: AMBER: David A. Case (Fri Feb 03 2006 - 15:46:28 PST)
AMBER: MMPBSA: magnitude of PB calculation sishi.tang.utoronto.ca (Fri Feb 03 2006 - 15:34:10 PST)
- Re: AMBER: MMPBSA: magnitude of PB calculation Ray Luo (Thu Feb 02 2006 - 23:49:07 PST)
  - Re: AMBER: MMPBSA: magnitude of PB calculation sishi.tang.utoronto.ca (Sat Feb 04 2006 - 08:47:21 PST)
    - Re: AMBER: MMPBSA: magnitude of PB calculation Thomas Steinbrecher (Mon Feb 06 2006 - 00:54:01 PST)
    - Re: AMBER: MMPBSA: magnitude of PB calculation Natasja Brooijmans (Mon Feb 06 2006 - 04:52:36 PST)
AMBER: Pawe³ Gruszczyñski (Sat Feb 04 2006 - 01:16:10 PST)
- Re: AMBER: David Mobley (Sat Feb 04 2006 - 10:06:23 PST)
AMBER: Strange minimization output problem andy ng (Sat Feb 04 2006 - 04:39:31 PST)
- Re: AMBER: Strange minimization output problem Ananda Rama Krishnan Selvaraj (Sat Feb 04 2006 - 08:12:19 PST)
- Re: AMBER: Strange minimization output problem David A. Case (Sat Feb 04 2006 - 12:20:17 PST)
- Re: AMBER: Strange minimization output problem Andreas Svrcek-Seiler (Sun Feb 05 2006 - 07:23:03 PST)
AMBER: dihedral parameters richard dimelow (Sat Feb 04 2006 - 08:06:41 PST)
- Re: AMBER: dihedral parameters Carlos Simmerling (Sat Feb 04 2006 - 09:30:27 PST)
  - Re: AMBER: dihedral parameters richard dimelow (Mon Feb 06 2006 - 02:22:08 PST)
    - Re: AMBER: dihedral parameters Carlos Simmerling (Mon Feb 06 2006 - 04:22:03 PST)
Re: AMBER: bugfix for impropers in parmchk David A. Case (Sat Feb 04 2006 - 10:50:15 PST)
- Re: AMBER: bugfix for impropers in parmchk Kateryna Miroshnychenko (Mon Feb 06 2006 - 07:09:06 PST)
AMBER: What Viewer is best Brian Stupi (Sat Feb 04 2006 - 21:59:29 PST)
- Re: AMBER: What Viewer is best Vlad Cojocaru (Sun Feb 05 2006 - 09:01:11 PST)
  - AMBER: Error when installing Brian Stupi (Mon Feb 13 2006 - 12:19:19 PST)
    - Re: AMBER: Error when installing Brian Stupi (Mon Feb 13 2006 - 12:40:46 PST)
    - RE: AMBER: Error when installing Ross Walker (Tue Feb 14 2006 - 10:30:29 PST)
AMBER: could amber calculte the binding free energy ofonly two small ligands (no big molecules) ? linfu (Sun Feb 05 2006 - 08:49:32 PST)
AMBER: Hessian matrix Marie Brut (Mon Feb 06 2006 - 04:12:53 PST)
- Re: AMBER: Hessian matrix David A. Case (Tue Feb 07 2006 - 08:40:37 PST)
  - Re: AMBER: Hessian matrix mbrut.laas.fr (Tue Feb 07 2006 - 09:55:17 PST)
AMBER: helix content during my simulation julien (Mon Feb 06 2006 - 05:09:38 PST)
- Re: AMBER: helix content during my simulation Mingfeng Yang (Mon Feb 06 2006 - 06:03:32 PST)
  - Re: AMBER: helix content during my simulation julien (Mon Feb 06 2006 - 07:04:51 PST)
    - Re: AMBER: helix content during my simulation Mingfeng Yang (Mon Feb 06 2006 - 07:39:59 PST)
AMBER: Parallel version of Amber: error message snoze pa (Mon Feb 06 2006 - 10:55:39 PST)
- Re: AMBER: Parallel version of Amber: error message Carlos Simmerling (Mon Feb 06 2006 - 11:21:31 PST)
  - Re: AMBER: Parallel version of Amber: error message snoze pa (Mon Feb 06 2006 - 11:45:48 PST)
    - Re: AMBER: Parallel version of Amber: error message David LeBard (Mon Feb 06 2006 - 12:10:29 PST)
    - Re: AMBER: Parallel version of Amber: error message Mingfeng Yang (Mon Feb 06 2006 - 12:29:38 PST)
    - Re: AMBER: Parallel version of Amber: error message Mark Williamson (Mon Feb 06 2006 - 13:00:09 PST)
- Re: AMBER: Parallel version of Amber: error message Lihua Wang (Mon Feb 06 2006 - 12:27:40 PST)
AMBER: Parallel error in Amber 8 snoze pa (Mon Feb 06 2006 - 14:47:19 PST)
- Re: AMBER: Parallel error in Amber 8 snoze pa (Mon Feb 06 2006 - 15:02:22 PST)
- Re: AMBER: Parallel error in Amber 8 Wei Zhang (Mon Feb 06 2006 - 15:06:07 PST)
  - Re: AMBER: Parallel error in Amber 8 snoze pa (Mon Feb 06 2006 - 15:18:16 PST)
- Re: AMBER: Parallel error in Amber 8 David A. Case (Mon Feb 06 2006 - 15:37:56 PST)
  - Re: AMBER: Parallel error in Amber 8 snoze pa (Mon Feb 06 2006 - 16:16:20 PST)
AMBER: soft-core potential in amber? Lydia (Mon Feb 06 2006 - 16:13:14 PST)
- Re: AMBER: soft-core potential in amber? David Mobley (Tue Feb 07 2006 - 06:54:33 PST)
AMBER: non bond list overflow Kenley Barrett (Mon Feb 06 2006 - 19:43:06 PST)
- Re: AMBER: non bond list overflow David A. Case (Mon Feb 06 2006 - 22:37:59 PST)
  - Re: AMBER: non bond list overflow Kenley Barrett (Tue Feb 07 2006 - 08:32:18 PST)
    - Re: AMBER: non bond list overflow David A. Case (Tue Feb 07 2006 - 11:00:54 PST)
AMBER: format of qusaiharmonic eigenvector file in AMBER7 Phineus Markwick (Tue Feb 07 2006 - 03:10:44 PST)
- Re: AMBER: format of qusaiharmonic eigenvector file in AMBER7 Chris Moth (Tue Feb 07 2006 - 06:10:07 PST)
AMBER: Ask for your help to install Amber8 software Cao Tran (Wed Feb 08 2006 - 05:53:11 PST)
- Re: AMBER: Ask for your help to install Amber8 software Cenk Andac (Wed Feb 08 2006 - 06:44:30 PST)
  - RE: AMBER: Ask for your help to install Amber8 software CaoTran (Wed Feb 08 2006 - 07:03:51 PST)
  - RE: AMBER: Ask for your help to install Amber8 software Cao Tran (Fri Feb 10 2006 - 01:01:38 PST)
    - RE: AMBER: Ask for your help to install Amber8 software Cenk Andac (Fri Feb 10 2006 - 02:46:12 PST)
- RE: AMBER: Ask for your help to install Amber8 software Lei Wang (Wed Feb 08 2006 - 07:16:32 PST)
AMBER: DNA tutorial xleap help Amanda Jonsson (Wed Feb 08 2006 - 10:56:32 PST)
- Re: AMBER: DNA tutorial xleap help Wei Zhang (Wed Feb 08 2006 - 11:42:32 PST)
AMBER: desc related issue snoze pa (Wed Feb 08 2006 - 11:15:19 PST)
Re: AMBER: DNA tutorial xleap help Bill Ross (Wed Feb 08 2006 - 11:56:25 PST)
AMBER: PMED in AMBER snoze pa (Wed Feb 08 2006 - 17:07:40 PST)
AMBER: Acetyl CoA Satyan Sharma (Thu Feb 09 2006 - 09:55:19 PST)
AMBER: Distortion in parallelploied Varsha Goyal (Thu Feb 09 2006 - 17:39:06 PST)
- Re: AMBER: Distortion in parallelploied David A. Case (Fri Feb 10 2006 - 09:04:13 PST)
- Re: AMBER: Distortion in parallelploied Angelo Pugliese (Mon Feb 13 2006 - 07:40:40 PST)
AMBER: EAMBER Mingfeng Yang (Thu Feb 09 2006 - 19:56:04 PST)
- Re: AMBER: EAMBER Carlos Simmerling (Thu Feb 09 2006 - 20:15:21 PST)
AMBER: PMEMD MPI_Finalize() error Mingfeng Yang (Fri Feb 10 2006 - 06:50:59 PST)
- Re: AMBER: PMEMD MPI_Finalize() error Robert Duke (Fri Feb 10 2006 - 07:15:29 PST)
  - Re: AMBER: PMEMD MPI_Finalize() error Mingfeng Yang (Fri Feb 10 2006 - 08:07:53 PST)
AMBER: minization: outputing intermediate snapshots Vlad Cojocaru (Fri Feb 10 2006 - 03:49:04 PST)
- RE: AMBER: minization: outputing intermediate snapshots Ross Walker (Tue Feb 14 2006 - 10:34:30 PST)
AMBER: minization: outputing intermediate snapshots Vlad Cojocaru (Fri Feb 10 2006 - 07:05:59 PST)
AMBER: Problem in running umbrella sampling Sai Kumar Ramadugu (Sun Feb 12 2006 - 20:28:09 PST)
- Re: AMBER: Problem in running umbrella sampling David A. Case (Sun Feb 12 2006 - 21:11:48 PST)
  - Re: AMBER: Problem in running umbrella sampling Sai Kumar Ramadugu (Sun Feb 12 2006 - 21:22:49 PST)
AMBER: shuli kang (Mon Feb 13 2006 - 04:26:07 PST)
- Re: AMBER: Scott Pendley (Mon Feb 13 2006 - 13:00:15 PST)
AMBER: MM_PBSA problem (No values for MM_GAS ) Bing Liu (Mon Feb 13 2006 - 06:40:47 PST)
- Re: AMBER: MM_PBSA problem (No values for MM_GAS ) Scott Pendley (Mon Feb 13 2006 - 12:57:27 PST)
AMBER: 2D-topology Baldoni Hector Armando (Mon Feb 13 2006 - 13:50:11 PST)
- Re: AMBER: 2D-topology David A. Case (Tue Feb 14 2006 - 13:57:45 PST)
AMBER: mm_pbsa output lucas luquitas (Mon Feb 13 2006 - 15:40:28 PST)
AMBER: script advice A D (Mon Feb 13 2006 - 18:35:35 PST)
- Re: AMBER: script advice JunJun Liu (Wed Feb 15 2006 - 07:35:44 PST)
AMBER: double stranded polyribocytidylic acid Kateryna Miroshnychenko (Tue Feb 14 2006 - 01:44:01 PST)
- Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer (Tue Feb 14 2006 - 02:54:05 PST)
- Re: AMBER: double stranded polyribocytidylic acid Kateryna Miroshnychenko (Tue Feb 14 2006 - 04:09:36 PST)
  - Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer (Tue Feb 14 2006 - 04:56:07 PST)
- Re: AMBER: double stranded polyribocytidylic acid Bill Ross (Tue Feb 14 2006 - 12:35:19 PST)
  - Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer (Wed Feb 15 2006 - 05:16:46 PST)
- Re: AMBER: double stranded polyribocytidylic acid Bill Ross (Wed Feb 15 2006 - 09:25:21 PST)
  - Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer (Wed Feb 15 2006 - 09:46:27 PST)
- Re: AMBER: double stranded polyribocytidylic acid Kateryna Miroshnychenko (Thu Feb 16 2006 - 02:41:52 PST)
- Re: AMBER: double stranded polyribocytidylic acid Bill Ross (Thu Feb 16 2006 - 10:49:20 PST)
- Re: AMBER: double stranded polyribocytidylic acid Bill Ross (Thu Feb 16 2006 - 10:53:10 PST)
AMBER: Istallation AMBER8 Dr.Rudolf Friedemann (Tue Feb 14 2006 - 02:41:39 PST)
- Re: AMBER: Istallation AMBER8 David A. Case (Tue Feb 14 2006 - 22:57:13 PST)
AMBER: paralelization and sander problems cristian obiol (Tue Feb 14 2006 - 02:24:18 PST)
- Re: AMBER: paralelization and sander problems Carlos Simmerling (Tue Feb 14 2006 - 05:59:43 PST)
  - Re: AMBER: paralelization and sander problems David A. Case (Tue Feb 14 2006 - 08:32:59 PST)
  - Re: AMBER: paralelization and sander problems cristian obiol (Fri Feb 17 2006 - 02:07:37 PST)
    - Re: AMBER: paralelization and sander problems Carlos Simmerling (Fri Feb 17 2006 - 03:59:44 PST)
    - Re: AMBER: paralelization and sander problems cristian obiol (Mon Feb 20 2006 - 04:13:58 PST)
    - Re: AMBER: paralelization and sander problems Carlos Simmerling (Tue Feb 21 2006 - 04:57:10 PST)
- RE: AMBER: paralelization and sander problems Ross Walker (Tue Feb 14 2006 - 09:48:06 PST)
AMBER: Organic molecules Marie Brut (Tue Feb 14 2006 - 08:42:23 PST)
- RE: AMBER: Organic molecules Ross Walker (Tue Feb 14 2006 - 09:44:25 PST)
AMBER: Xleap crash Scott Pendley (Tue Feb 14 2006 - 08:55:12 PST)
- Re: AMBER: Xleap crash David A. Case (Tue Feb 14 2006 - 09:36:21 PST)
  - Re: AMBER: Xleap crash Scott Pendley (Tue Feb 14 2006 - 09:53:37 PST)
    - Re: AMBER: Xleap crash Scott Pendley (Tue Feb 14 2006 - 10:08:59 PST)
    - Re: AMBER: Xleap crash David A. Case (Tue Feb 14 2006 - 11:51:53 PST)
AMBER: Absoft Pro Fortran and AMBER 8 on MacOS X 10.4.4 Jingyuan Luke (Tue Feb 14 2006 - 17:35:37 PST)
- Re: AMBER: Absoft Pro Fortran and AMBER 8 on MacOS X 10.4.4 David A. Case (Tue Feb 14 2006 - 22:12:42 PST)
AMBER: negative T_solv values Markus O Kaukonen (Wed Feb 15 2006 - 00:25:40 PST)
- Re: AMBER: negative T_solv values David A. Case (Wed Feb 15 2006 - 08:18:25 PST)
AMBER: m4 error with Amber8 on SUN Amber admin (Wed Feb 15 2006 - 14:51:38 PST)
- Re: AMBER: m4 error with Amber8 on SUN David A. Case (Wed Feb 15 2006 - 15:56:06 PST)
AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation zgleo (Wed Feb 15 2006 - 22:04:47 PST)
- Re: AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation german (Thu Feb 16 2006 - 04:04:39 PST)
AMBER: sander problem bala (Thu Feb 16 2006 - 07:57:43 PST)
- Re: AMBER: sander problem snoze pa (Thu Feb 16 2006 - 08:13:22 PST)
- Re: AMBER: sander problem Carlos Simmerling (Thu Feb 16 2006 - 08:25:20 PST)
- Re: AMBER: sander problem JunJun Liu (Thu Feb 16 2006 - 08:16:34 PST)
- RE: AMBER: sander problem Ross Walker (Thu Feb 16 2006 - 08:51:24 PST)
  - RE: AMBER: sander problem Brian Stupi (Thu Feb 16 2006 - 12:44:11 PST)
    - RE: AMBER: sander problem Thomas E. Cheatham, III (Thu Feb 16 2006 - 13:12:39 PST)
    - RE: AMBER: sander problem Ross Walker (Thu Feb 16 2006 - 13:20:45 PST)
    - AMBER: process_mdout.perl Brian Stupi (Thu Feb 16 2006 - 14:02:06 PST)
AMBER: Torsional restraints for groups of atoms Supat Jiranusornkul (Fri Feb 17 2006 - 04:14:12 PST)
AMBER: Question about renaming a residue Kara Di Giorgio (Fri Feb 17 2006 - 15:28:26 PST)
- Re: AMBER: Question about renaming a residue Thomas E. Cheatham, III (Fri Feb 17 2006 - 15:46:27 PST)
- Re: AMBER: Question about renaming a residue Ilyas Yildirim (Fri Feb 17 2006 - 18:05:37 PST)
AMBER: mm_pbsa problem in IBM-aix Jiten (Fri Feb 17 2006 - 23:36:52 PST)
- Re: AMBER: mm_pbsa problem in IBM-aix Ray Luo (Sun Feb 19 2006 - 12:22:01 PST)
AMBER: instructions for making a library file for an unusual residue? Kenley Barrett (Sat Feb 18 2006 - 14:02:42 PST)
- Re: AMBER: instructions for making a library file for an unusual residue? FyD (Sun Feb 19 2006 - 09:14:10 PST)
  - Re: AMBER: instructions for making a library file for an unusual residue? Kenley Barrett (Mon Feb 20 2006 - 16:22:22 PST)
    - Re: AMBER: instructions for making a library file for an unusual residue? Ilyas Yildirim (Mon Feb 20 2006 - 22:28:49 PST)
    - Re: AMBER: instructions for making a library file for an unusual residue? FyD (Tue Feb 21 2006 - 05:17:48 PST)
AMBER: antechamber for a database of organic molecules Yogesh Sabnis (Sun Feb 19 2006 - 07:16:23 PST)
- Re: AMBER: antechamber for a database of organic molecules FyD (Sun Feb 19 2006 - 07:51:52 PST)
- RE: AMBER: antechamber for a database of organic molecules Junmei Wang (Sun Feb 19 2006 - 19:32:22 PST)
AMBER: Phosphorylated amino acid andy ng (Sun Feb 19 2006 - 15:51:41 PST)
- Re: AMBER: Phosphorylated amino acid Tim Meyer (Mon Feb 20 2006 - 00:56:36 PST)
  - Re: AMBER: Phosphorylated amino acid andy ng (Mon Feb 20 2006 - 21:55:55 PST)
AMBER: parallel problem of amber8 linfu (Mon Feb 20 2006 - 05:01:02 PST)
- RE: AMBER: parallel problem of amber8 Ross Walker (Mon Feb 20 2006 - 09:00:26 PST)
  - AMBER: Problem with file size of sander outputs Cenk Andac (Tue Feb 21 2006 - 23:54:24 PST)
    - Re: AMBER: Problem with file size of sander outputs shuli kang (Wed Feb 22 2006 - 00:45:21 PST)
    - Re: AMBER: Problem with file size of sander outputs german (Wed Feb 22 2006 - 02:49:49 PST)
    - AMBER: Free energy perturbation Angelo Pugliese (Wed Feb 22 2006 - 08:42:06 PST)
    - Re: AMBER: Problem with file size of sander outputs JunJun Liu (Wed Feb 22 2006 - 12:58:00 PST)
    - RE: AMBER: Problem with file size of sander outputs Ross Walker (Wed Feb 22 2006 - 13:16:30 PST)
    - RE: AMBER: Problem with file size of sander outputs Cenk Andac (Wed Feb 22 2006 - 23:23:02 PST)
    - RE: AMBER: Problem with file size of sander outputs Feng X Zhou (Thu Feb 23 2006 - 09:42:22 PST)
    - RE: AMBER: Problem with file size of sander outputs Ross Walker (Thu Feb 23 2006 - 10:06:30 PST)
AMBER: charge redistribution in .prep files Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon Feb 20 2006 - 04:37:54 PST)
- Re: AMBER: charge redistribution in .prep files David A. Case (Mon Feb 20 2006 - 08:29:41 PST)
AMBER: Truncated octahedral box as triclinic lattice vectors Markus O Kaukonen (Mon Feb 20 2006 - 06:42:45 PST)
AMBER: amber 8 problem Abd Ghani Abd Aziz (Mon Feb 20 2006 - 07:08:12 PST)
- Re: AMBER: amber 8 problem JunJun Liu (Mon Feb 20 2006 - 08:05:53 PST)
  - Re: AMBER: amber 8 problem Abd Ghani Abd Aziz (Mon Feb 20 2006 - 08:17:37 PST)
- Re: AMBER: amber 8 problem Andreas Svrcek-Seiler (Mon Feb 20 2006 - 08:20:28 PST)
- Re: AMBER: amber 8 problem David A. Case (Mon Feb 20 2006 - 08:33:01 PST)
- RE: AMBER: amber 8 problem Ross Walker (Mon Feb 20 2006 - 09:05:57 PST)
  - AMBER: Ti calculations in dmso solvent Vitor Manuel Sousa F?x (Mon Feb 20 2006 - 09:55:32 PST)
    - Re: AMBER: Ti calculations in dmso solvent David Mobley (Thu Feb 23 2006 - 08:58:17 PST)
    - Re: AMBER: Ti calculations in dmso solvent David A. Case (Thu Feb 23 2006 - 10:01:26 PST)
    - Re: AMBER: Ti calculations in dmso solvent David Mobley (Thu Feb 23 2006 - 12:06:43 PST)
  - RE: AMBER: amber 8 problem Abd Ghani Abd Aziz (Mon Feb 20 2006 - 20:55:27 PST)
AMBER: Error in RST files in long simulations! lucas luquitas (Mon Feb 20 2006 - 11:59:35 PST)
- Re: AMBER: Error in RST files in long simulations! Carlos Simmerling (Mon Feb 20 2006 - 12:32:13 PST)
  - Re: AMBER: Error in RST files in long simulations! lucas luquitas (Mon Feb 20 2006 - 15:08:38 PST)
    - Re: AMBER: Error in RST files in long simulations! Carlos Simmerling (Tue Feb 21 2006 - 05:02:58 PST)
AMBER: NMR restraints and LES Sivakolundu, Sivashankar (Mon Feb 20 2006 - 17:43:38 PST)
- Re: AMBER: NMR restraints and LES David A. Case (Mon Feb 20 2006 - 18:26:17 PST)
AMBER: About WHAM Atsutoshi Okabe (Mon Feb 20 2006 - 22:22:01 PST)
AMBER: does anyone have library file for methylated histidine, 2003 ff? Kenley Barrett (Tue Feb 21 2006 - 08:27:13 PST)
AMBER: CARNAL: H-BOND Specifying side chains only Kay Kunes (Tue Feb 21 2006 - 12:47:14 PST)
Re: AMBER: CARNAL: H-BOND Specifying side chains only Bill Ross (Tue Feb 21 2006 - 13:41:25 PST)
AMBER: AMBER force field with namd Fabien Cailliez (Wed Feb 22 2006 - 09:54:23 PST)
- Re: AMBER: AMBER force field with namd Vlad Cojocaru (Thu Feb 23 2006 - 02:11:17 PST)
  - Re: AMBER: AMBER force field with namd Carlos Simmerling (Thu Feb 23 2006 - 05:41:31 PST)
    - Re: AMBER: AMBER force field with namd Vlad Cojocaru (Thu Feb 23 2006 - 06:04:51 PST)
AMBER: generating parameters for the NADH analogue H4NAD Simon Whitehead (Thu Feb 23 2006 - 10:31:02 PST)
- Re: AMBER: generating parameters for the NADH analogue H4NAD Vlad Cojocaru (Thu Feb 23 2006 - 10:53:30 PST)
- RE: AMBER: generating parameters for the NADH analogue H4NAD Ross Walker (Thu Feb 23 2006 - 11:00:30 PST)
AMBER: TI cal Steve Seibold (Thu Feb 23 2006 - 11:02:45 PST)
- RE: AMBER: TI cal Ross Walker (Thu Feb 23 2006 - 11:25:57 PST)
- RE: AMBER: TI cal Steve Seibold (Thu Feb 23 2006 - 12:08:20 PST)
AMBER: A problem with Amber force field new parameter derivation Vidana.Epa.csiro.au (Thu Feb 23 2006 - 22:16:04 PST)
- Re: AMBER: A problem with Amber force field new parameter derivation FyD (Thu Feb 23 2006 - 22:27:31 PST)
AMBER: entropic energy Nina Fischer (Fri Feb 24 2006 - 04:15:17 PST)
- Re: AMBER: entropic energy David A. Case (Fri Feb 24 2006 - 08:36:49 PST)
AMBER: Antechamber Package Announcement Junmei Wang (Fri Feb 24 2006 - 08:26:52 PST)
AMBER: Constant pressure - restart - Amber8 Jennie Thomas (Fri Feb 24 2006 - 08:59:34 PST)
- Re: AMBER: Constant pressure - restart - Amber8 David A. Case (Fri Feb 24 2006 - 09:34:46 PST)
  - Re: AMBER: Constant pressure - restart - Amber8 Jennie Thomas (Fri Feb 24 2006 - 12:18:56 PST)
    - Re: AMBER: Constant pressure - restart - Amber8 David A. Case (Fri Feb 24 2006 - 13:18:58 PST)
    - AMBER: dynamic memory allocation problem in nmode Cenk Andac (Sun Feb 26 2006 - 00:58:14 PST)
    - Re: AMBER: dynamic memory allocation problem in nmode Cenk Andac (Sun Feb 26 2006 - 01:26:23 PST)
    - Re: AMBER: dynamic memory allocation problem in nmode Jiten (Sun Feb 26 2006 - 07:07:23 PST)
    - Re: AMBER: dynamic memory allocation problem in nmode David A. Case (Sun Feb 26 2006 - 20:21:02 PST)
    - Re: AMBER: Constant pressure - restart - Amber8 Jennie Thomas (Sun Feb 26 2006 - 17:56:59 PST)
AMBER: specifying RSOLV when calculating 2003 force field charges Kenley Barrett (Fri Feb 24 2006 - 12:50:07 PST)
AMBER: How to explain the meaning of the mmpbsa/DC result? zhli_2000.126.com (Sat Feb 25 2006 - 23:01:04 PST)
AMBER: ptraj atomicfluct: is it possible to calculate atomic fluctations from a reference structure Magne Olufsen (Sun Feb 26 2006 - 11:00:23 PST)
AMBER: Sulfonamides and GAFF Varsha Goyal (Sun Feb 26 2006 - 17:16:18 PST)
AMBER: ptraj warning while loading reference Vlad Cojocaru (Mon Feb 27 2006 - 04:45:28 PST)
- Re: AMBER: ptraj warning while loading reference David A. Case (Mon Feb 27 2006 - 08:44:52 PST)
  - Re: AMBER: ptraj warning while loading reference Vlad Cojocaru (Mon Feb 27 2006 - 09:00:43 PST)
AMBER: MD job stopped without any error information? ying xiong (Mon Feb 27 2006 - 00:29:50 PST)
- Re: AMBER: MD job stopped without any error information? Melinda Layten (Mon Feb 27 2006 - 07:18:09 PST)
- Re: AMBER: MD job stopped without any error information? Guanglei Cui (Mon Feb 27 2006 - 07:55:47 PST)
- RE: AMBER: MD job stopped without any error information? Ross Walker (Mon Feb 27 2006 - 08:22:25 PST)
AMBER: RE: about compiling errors for Leap Ross Walker (Mon Feb 27 2006 - 08:17:27 PST)
AMBER: sander testing problem mdione.fcq.unc.edu.ar (Mon Feb 27 2006 - 13:53:23 PST)
AMBER: mask issues Claire Zerafa (Tue Feb 28 2006 - 04:46:12 PST)
- Re: AMBER: mask issues Vlad Cojocaru (Tue Feb 28 2006 - 05:03:16 PST)
AMBER: failed to save prm and xyz using ff96 Abd Ghani Abd Aziz (Tue Feb 28 2006 - 07:32:49 PST)
- RE: AMBER: failed to save prm and xyz using ff96 Ross Walker (Tue Feb 28 2006 - 08:31:41 PST)
  - Re: AMBER: failed to save prm and xyz using ff96 Carlos Simmerling (Tue Feb 28 2006 - 09:24:23 PST)
    - Re: AMBER: failed to save prm and xyz using ff96 Abd Ghani Abd Aziz (Tue Feb 28 2006 - 23:49:57 PST)
  - AMBER: How to develop charge for my deprotonated glycine Jianzhong Liu (Tue Feb 28 2006 - 11:58:31 PST)
AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster Carlos Silva Lopez (Tue Feb 28 2006 - 09:30:42 PST)
- Re: AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster Wei Zhang (Tue Feb 28 2006 - 10:01:34 PST)
  - Re: AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster Carlos Silva Lopez (Tue Feb 28 2006 - 14:27:07 PST)
AMBER: Angle restraint venditti2.unisi.it (Tue Feb 28 2006 - 12:00:48 PST)
- Re: AMBER: Angle restraint David A. Case (Tue Feb 28 2006 - 15:54:40 PST)

Amber Archive Feb 2006 By Thread