AMBER Archive (2008) - By Thread

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Starting: Tue Jan 01 2008 - 19:53:35 CST
Ending: Wed Dec 31 2008 - 22:47:27 CST

AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine John Chodera (Tue Jan 01 2008 - 19:44:34 CST)
- Re: AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine FyD (Wed Jan 02 2008 - 02:52:15 CST)
- Re: AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine FyD (Fri Jan 04 2008 - 04:34:00 CST)
Re: AMBER: a question of ptraj WANG,YING (Wed Jan 02 2008 - 12:04:24 CST)
AMBER: Help reg. input file snoze pa (Wed Jan 02 2008 - 12:34:56 CST)
- Re: AMBER: Help reg. input file FyD (Wed Jan 02 2008 - 13:34:40 CST)
  - Re: AMBER: Help reg. input file snoze pa (Wed Jan 02 2008 - 13:50:50 CST)
    - Re: AMBER: Help reg. input file FyD (Wed Jan 02 2008 - 14:21:03 CST)
AMBER: AMBER-8 parallel installation - test run failure brmeher_at_iitg.ernet.in (Thu Jan 03 2008 - 04:10:58 CST)
- Re: AMBER: AMBER-8 parallel installation - test run failure Ming Lei (Thu Jan 03 2008 - 08:08:46 CST)
AMBER: question about antechamber Lynn (Thu Jan 03 2008 - 08:32:56 CST)
- Re: AMBER: question about antechamber Junmei Wang (Thu Jan 03 2008 - 09:18:34 CST)
AMBER: Thermodynamic integration with positional restraint? Cen Gao (Thu Jan 03 2008 - 10:43:32 CST)
- Re: AMBER: Thermodynamic integration with positional restraint? David A. Case (Thu Jan 03 2008 - 11:31:19 CST)
AMBER: Combine mdcrd files Francesco Pietra (Thu Jan 03 2008 - 17:01:47 CST)
- Re: AMBER: Combine mdcrd files Carlos Simmerling (Thu Jan 03 2008 - 17:09:23 CST)
- RE: AMBER: Combine mdcrd files Ross Walker (Fri Jan 04 2008 - 10:35:23 CST)
AMBER: MM-PBSA problem stephane acoca (Thu Jan 03 2008 - 21:45:10 CST)
- Re: AMBER: MM-PBSA problem Jack Lei (Fri Jan 04 2008 - 19:31:05 CST)
  - Re: AMBER: MM-PBSA problem David A. Case (Fri Jan 04 2008 - 20:07:07 CST)
AMBER: check COM velocity Pankaj R. Daga (Fri Jan 04 2008 - 10:06:26 CST)
- Re: AMBER: check COM velocity David A. Case (Fri Jan 04 2008 - 10:29:09 CST)
- Re: AMBER: check COM velocity Lars Skjærven (Fri Jan 04 2008 - 10:36:53 CST)
AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 10:37:07 CST)
- Re: AMBER: Combine mdcrd Carlos Simmerling (Fri Jan 04 2008 - 10:44:55 CST)
  - Re: AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 11:07:15 CST)
AMBER: FW: AMBER vs Gaussian : zero VDW parameters? Ross Walker (Fri Jan 04 2008 - 11:01:14 CST)
Fwd: Re: AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 11:23:45 CST)
- Re: Re: AMBER: Combine mdcrd Carlos Simmerling (Fri Jan 04 2008 - 11:30:31 CST)
Fwd: Re: AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 11:36:49 CST)
- Re: Re: AMBER: Combine mdcrd Carlos Simmerling (Fri Jan 04 2008 - 11:56:04 CST)
  - Re: Re: AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 15:26:32 CST)
AMBER: Combining multiple structures into single pdb Seth Lilavivat (Fri Jan 04 2008 - 14:21:58 CST)
AMBER: mm/pbsa and saltcon effect Christopher Gaughan (Fri Jan 04 2008 - 15:40:17 CST)
AMBER: amber :antechamber problem jani sahil (Fri Jan 04 2008 - 21:51:56 CST)
- Re: AMBER: amber :antechamber problem Wei Chen (Mon Jan 07 2008 - 10:14:53 CST)
- Re: AMBER: amber :antechamber problem Florian Haberl (Mon Jan 07 2008 - 10:33:02 CST)
AMBER: antechamber problems jani sahil (Fri Jan 04 2008 - 21:49:10 CST)
- Re: AMBER: antechamber problems Junmei Wang (Sat Jan 05 2008 - 23:35:04 CST)
AMBER: About RAMD Francesco Pietra (Sat Jan 05 2008 - 04:39:44 CST)
- Re: AMBER: About RAMD Carlos Simmerling (Sat Jan 05 2008 - 10:12:40 CST)
  - Re: AMBER: About RAMD Francesco Pietra (Sat Jan 05 2008 - 10:26:01 CST)
AMBER: NMROPT=1 in minimisation Binbin Liu (Sat Jan 05 2008 - 17:38:51 CST)
- Re: AMBER: NMROPT=1 in minimisation David A. Case (Sun Jan 06 2008 - 14:59:03 CST)
AMBER: temperature spikes Sally Pias (Sun Jan 06 2008 - 00:26:55 CST)
- Re: AMBER: temperature spikes Adrian Roitberg (Sun Jan 06 2008 - 10:41:50 CST)
AMBER: MD of protein-ligand comlex umbrita itl (Sun Jan 06 2008 - 14:54:47 CST)
- Re: AMBER: MD of protein-ligand comlex Syed Tarique Moin (Mon Jan 07 2008 - 00:18:20 CST)
- Re: AMBER: MD of protein-ligand comlex Chris Moth (Mon Jan 07 2008 - 06:10:23 CST)
AMBER: Cluster analysis Francesco Pietra (Mon Jan 07 2008 - 10:00:40 CST)
- Re: AMBER: Cluster analysis Carlos Simmerling (Mon Jan 07 2008 - 10:18:22 CST)
AMBER: Structure comparison-NMR and X-ray structure using AMBER9 Prem Prakash Pathak (Mon Jan 07 2008 - 10:11:22 CST)
- Re: AMBER: Structure comparison-NMR and X-ray structure using AMBER9 Carlos Simmerling (Mon Jan 07 2008 - 10:16:16 CST)
AMBER: offset residue numbering Brendan Duggan (Mon Jan 07 2008 - 14:14:30 CST)
- Re: AMBER: offset residue numbering David A. Case (Sat Jan 12 2008 - 01:10:08 CST)
AMBER: Torsional Forcing to generate PES? Praveena Gopal (Mon Jan 07 2008 - 22:42:04 CST)
- Re: AMBER: Torsional Forcing to generate PES? Chris Moth (Tue Jan 08 2008 - 11:08:12 CST)
AMBER: Nudged Elastic Band initial heating problem Mike Wykes (Tue Jan 08 2008 - 04:42:09 CST)
- Re: AMBER: Nudged Elastic Band initial heating problem Keith Van Nostrand (Tue Jan 08 2008 - 07:32:31 CST)
- RE: AMBER: Nudged Elastic Band initial heating problem Ross Walker (Tue Jan 08 2008 - 17:00:59 CST)
AMBER: Problem about antechamber ÀÌÃ« Óæ (Tue Jan 08 2008 - 10:09:03 CST)
AMBER: solvateBox/solvateDontClip darkcz_at_tlen.pl (Tue Jan 08 2008 - 10:02:19 CST)
AMBER: A problem about antechamber ÀÌÃ« Óæ (Tue Jan 08 2008 - 10:03:49 CST)
- Re: AMBER: A problem about antechamber Junmei Wang (Tue Jan 08 2008 - 16:19:15 CST)
AMBER: connectivity problem rams rams (Wed Jan 09 2008 - 08:53:55 CST)
- Re: AMBER: connectivity problem Junmei Wang (Wed Jan 09 2008 - 09:51:05 CST)
  - Re: AMBER: connectivity problem rams rams (Wed Jan 09 2008 - 23:04:41 CST)
    - Re: AMBER: connectivity problem Junmei Wang (Thu Jan 10 2008 - 09:27:07 CST)
AMBER: The energy minimization of SIngle RNA chain backy (Thu Jan 10 2008 - 02:33:20 CST)
AMBER: input options for replica exchange simulations rebeca_at_mmb.pcb.ub.es (Thu Jan 10 2008 - 10:46:42 CST)
- Re: AMBER: input options for replica exchange simulations Carlos Simmerling (Thu Jan 10 2008 - 10:57:12 CST)
  - Re: AMBER: input options for replica exchange simulations Adrian Roitberg (Thu Jan 10 2008 - 11:28:50 CST)
    - Re: AMBER: input options for replica exchange simulations rebeca_at_mmb.pcb.ub.es (Thu Jan 10 2008 - 12:00:10 CST)
    - Re: AMBER: input options for replica exchange simulations Carlos Simmerling (Thu Jan 10 2008 - 14:50:18 CST)
AMBER: using hydrogen bond facility to monitor ion pair interaction Zhenwei Lu (Thu Jan 10 2008 - 11:09:09 CST)
- Re: AMBER: using hydrogen bond facility to monitor ion pair interaction Thomas Cheatham III (Thu Jan 10 2008 - 11:21:10 CST)
  - Re: AMBER: using hydrogen bond facility to monitor ion pair interaction Zhenwei Lu (Thu Jan 10 2008 - 12:16:57 CST)
AMBER: antechamber problem gurpreet singh (Thu Jan 10 2008 - 11:49:15 CST)
- Re: AMBER: antechamber problem Junmei Wang (Thu Jan 10 2008 - 12:29:23 CST)
  - Re: AMBER: antechamber problem gurpreet singh (Thu Jan 10 2008 - 22:05:38 CST)
AMBER: ANTECHAMBER NAMING Shozeb Haider (Thu Jan 10 2008 - 15:19:18 CST)
- Re: AMBER: ANTECHAMBER NAMING David A. Case (Thu Jan 10 2008 - 21:32:30 CST)
  - Re: AMBER: ANTECHAMBER NAMING FyD (Fri Jan 11 2008 - 01:53:04 CST)
AMBER: graphite Boutheina Kerkeni (Fri Jan 11 2008 - 05:26:58 CST)
AMBER: chromophore parameters for Molecular Dynamics Anthony Cruz (Fri Jan 11 2008 - 09:32:31 CST)
- Re: AMBER: chromophore parameters for Molecular Dynamics FyD (Fri Jan 11 2008 - 14:57:19 CST)
  - Re: AMBER: chromophore parameters for Molecular Dynamics Anthony Cruz (Wed Jan 16 2008 - 07:47:42 CST)
    - Re: AMBER: chromophore parameters for Molecular Dynamics FyD (Wed Jan 16 2008 - 08:59:31 CST)
AMBER: problems with restart of MD Vijay Singh (Fri Jan 11 2008 - 11:29:31 CST)
- Re: AMBER: problems with restart of MD Age.Skjevik_at_student.uib.no (Fri Jan 11 2008 - 12:16:00 CST)
- RE: AMBER: problems with restart of MD Pankaj R. Daga (Fri Jan 11 2008 - 12:34:13 CST)
- RE: AMBER: problems with restart of MD Ross Walker (Fri Jan 11 2008 - 13:56:16 CST)
  - Re: AMBER: problems with restart of MD Vijay Singh (Fri Jan 11 2008 - 14:04:39 CST)
AMBER: Visualizing Electrostatic Potential Seth Lilavivat (Fri Jan 11 2008 - 13:57:31 CST)
AMBER: Amber DNA Model for X-ray Crystallography Hopkins, Robert (Fri Jan 11 2008 - 17:32:00 CST)
AMBER: Unable to create the top & crd files for a protein+ligand pdb structure abiram abiram (Sat Jan 12 2008 - 01:54:01 CST)
- Re: AMBER: Unable to create the top & crd files for a protein+ligand pdb structure Jiten (Sat Jan 12 2008 - 02:21:01 CST)
AMBER: connectivity lose during the minimizations rams rams (Sat Jan 12 2008 - 05:40:21 CST)
- Re: AMBER: connectivity lose during the minimizations David A. Case (Sat Jan 12 2008 - 14:28:37 CST)
AMBER: build RNA by nucgen Å·ÑôµÂ·½ (Sat Jan 12 2008 - 20:26:44 CST)
- Re: AMBER: build RNA by nucgen David A. Case (Sun Jan 13 2008 - 11:56:32 CST)
  - AMBER: Back on track Mike Summers (Mon Jan 28 2008 - 19:39:32 CST)
    - Re: AMBER: Back on track David A. Case (Wed Jan 30 2008 - 19:33:46 CST)
AMBER: problem:capping jani sahil (Sat Jan 12 2008 - 20:53:24 CST)
- Re: AMBER: problem:capping David A. Case (Sun Jan 13 2008 - 11:10:55 CST)
AMBER: problem in neturalization jani sahil (Sat Jan 12 2008 - 21:27:31 CST)
AMBER: Distorsion in protein and ligand during MD Francesco Pietra (Sun Jan 13 2008 - 03:46:23 CST)
AMBER: Fwd: Distorsion in protein and ligand during MD Francesco Pietra (Sun Jan 13 2008 - 03:57:43 CST)
AMBER: ELAN_EXCEPTION @ --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) Neko Maryam. (Sun Jan 13 2008 - 23:44:10 CST)
- Re: AMBER: ELAN_EXCEPTION @ --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) David A. Case (Mon Jan 14 2008 - 00:16:31 CST)
  - Re: AMBER: ELAN_EXCEPTION @ --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) Neko Maryam. (Mon Jan 14 2008 - 00:23:58 CST)
    - Re: AMBER: ELAN_EXCEPTION @ --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) Neko Maryam. (Mon Jan 14 2008 - 00:54:28 CST)
AMBER: Amber : neutralizing without adding ions jani sahil (Mon Jan 14 2008 - 05:43:01 CST)
- Re: AMBER: Amber : neutralizing without adding ions Lars Skjærven (Mon Jan 14 2008 - 09:41:55 CST)
AMBER: pmemd 9.0 compilation error Raphael Chaleil (Mon Jan 14 2008 - 08:38:12 CST)
- Re: AMBER: pmemd 9.0 compilation error Robert Duke (Mon Jan 14 2008 - 09:19:51 CST)
AMBER: QM/MM Heating Steven Winfield (Mon Jan 14 2008 - 09:22:27 CST)
- Re: AMBER: QM/MM Heating Steven Winfield (Mon Jan 21 2008 - 07:48:22 CST)
  - Re: AMBER: QM/MM Heating Adrian Roitberg (Mon Jan 21 2008 - 10:13:18 CST)
- RE: AMBER: QM/MM Heating Ross Walker (Mon Jan 21 2008 - 10:41:31 CST)
  - Re: AMBER: QM/MM Heating Steven Winfield (Wed Jan 23 2008 - 06:30:11 CST)
    - RE: AMBER: QM/MM Heating Ross Walker (Tue Jan 29 2008 - 08:49:48 CST)
AMBER: Disturb you for help! ÀÌÃ« Óæ (Mon Jan 14 2008 - 10:16:37 CST)
- RE: AMBER: Disturb you for help! Yong Duan (Mon Jan 14 2008 - 14:06:11 CST)
  - »Ø¸´£º RE: AMBER: Disturb you for help !?= ÀÌÃ« Óæ (Mon Jan 14 2008 - 18:12:27 CST)
AMBER: running AMBER in NAMD Trucated Octahedron Seth Lilavivat (Mon Jan 14 2008 - 16:19:05 CST)
- Re: AMBER: running AMBER in NAMD Trucated Octahedron Jojart Balazs (Mon Jan 14 2008 - 16:31:05 CST)
AMBER: Using VMD to calculate end-to-end distance? Lili Peng (Mon Jan 14 2008 - 16:41:55 CST)
- Re: AMBER: Using VMD to calculate end-to-end distance? Keith Van Nostrand (Mon Jan 14 2008 - 21:35:42 CST)
AMBER: How to build a dimer using amber Reena ..... (Tue Jan 15 2008 - 01:19:45 CST)
- Re: AMBER: How to build a dimer using amber David A. Case (Tue Jan 15 2008 - 01:51:50 CST)
  - Re: AMBER: How to build a dimer using amber Reena ..... (Tue Jan 15 2008 - 03:29:03 CST)
    - Re: AMBER: How to build a dimer using amber Reena ..... (Tue Jan 15 2008 - 03:31:24 CST)
    - Re: AMBER: How to build a dimer using amber David A. Case (Tue Jan 15 2008 - 11:18:14 CST)
AMBER: NPT to NVT Age.Skjevik_at_student.uib.no (Tue Jan 15 2008 - 07:58:22 CST)
AMBER: Regarding neutral Arginine unit jani sahil (Tue Jan 15 2008 - 10:19:00 CST)
- Re: AMBER: Regarding neutral Arginine unit Carlos Simmerling (Tue Jan 15 2008 - 10:28:21 CST)
AMBER: Problem with: Increase lastrst in the &cntrl namelist rdauria_at_uci.edu (Tue Jan 15 2008 - 22:46:04 CST)
- Re: AMBER: Problem with: Increase lastrst in the &cntrl namelist David A. Case (Wed Jan 16 2008 - 10:46:35 CST)
  - Re: AMBER: Problem with: Increase lastrst in the &cntrl namelist rdauria_at_uci.edu (Wed Jan 16 2008 - 12:19:27 CST)
AMBER: DawsonSean (Wed Jan 16 2008 - 02:52:07 CST)
- Re: AMBER: Reena ..... (Wed Jan 16 2008 - 03:07:30 CST)
  - AMBER: Chris Moth (Wed Jan 16 2008 - 09:11:07 CST)
AMBER: Help in radii snoze pa (Wed Jan 16 2008 - 11:08:59 CST)
- Re: AMBER: Help in radii snoze pa (Wed Jan 16 2008 - 11:45:20 CST)
- Re: AMBER: Help in radii FyD (Wed Jan 16 2008 - 14:31:07 CST)
AMBER: diblock copolymer Z Insepov (Thu Jan 17 2008 - 09:27:47 CST)
- Re: AMBER: diblock copolymer Jed W Pitera (Tue Jan 22 2008 - 19:01:03 CST)
  - Re: AMBER: diblock copolymer Z Insepov (Tue Jan 22 2008 - 23:23:39 CST)
AMBER: Re: timestep problem Andrey Semichaevsky (Thu Jan 17 2008 - 12:24:00 CST)
- Re: AMBER: Re: timestep problem David A. Case (Thu Jan 17 2008 - 14:27:56 CST)
AMBER: PEO-PLA/PCE Z Insepov (Thu Jan 17 2008 - 14:19:47 CST)
- Re: AMBER: PEO-PLA/PCE FyD (Fri Jan 18 2008 - 14:42:06 CST)
AMBER: GAFF atom types for flavin (again) Hans Martin Senn (Thu Jan 17 2008 - 14:47:54 CST)
- Re: AMBER: GAFF atom types for flavin (again) Junmei Wang (Thu Jan 17 2008 - 23:21:21 CST)
AMBER: problems of antechamber liu junjun (Thu Jan 17 2008 - 20:15:54 CST)
- Re: AMBER: problems of antechamber Junmei Wang (Thu Jan 17 2008 - 23:24:52 CST)
  - Re: AMBER: problems of antechamber JunJun Liu (Tue Jan 22 2008 - 08:45:26 CST)
- Re: AMBER: problems of antechamber liu junjun (Sun Jan 20 2008 - 09:21:49 CST)
AMBER: NMR refinement Wenyong Tong (Thu Jan 17 2008 - 20:54:04 CST)
- Re: AMBER: NMR refinement David A. Case (Fri Jan 18 2008 - 11:11:54 CST)
  - Re: AMBER: NMR refinement David A. Case (Fri Jan 18 2008 - 11:35:37 CST)
AMBER: Tinker 4.3 Paulo Couto (Fri Jan 18 2008 - 09:22:25 CST)
- Re: AMBER: Tinker 4.3 David A. Case (Fri Jan 18 2008 - 11:07:50 CST)
AMBER: about AM1-BCC in antechamber Shun Zhu (Fri Jan 18 2008 - 16:06:30 CST)
- Re: AMBER: about AM1-BCC in antechamber David Mobley (Fri Jan 18 2008 - 16:21:44 CST)
  - Re: AMBER: about AM1-BCC in antechamber Junmei Wang (Fri Jan 18 2008 - 23:31:06 CST)
AMBER: A problem to loadup the molecular in the xleap ÀÌÃ« Óæ (Fri Jan 18 2008 - 23:28:02 CST)
- RE: AMBER: A problem to loadup the molecular in the xleap Yong Duan (Sat Jan 19 2008 - 00:17:35 CST)
  - »Ø¸´£º RE: AMBER: A problem to loadup the molecular in the xleap ÀÌÃ« Óæ (Sat Jan 19 2008 - 10:31:05 CST)
    - Re: ?????? RE: AMBER: A problem to loadup the molecular in the xleap David A. Case (Sat Jan 19 2008 - 12:17:16 CST)
    - AMBER: RE: »Ø¸´£º RE: AMBER: A problem to loadup the molecular in the xleap Yong Duan (Sat Jan 19 2008 - 14:44:25 CST)
AMBER: RMSD calculation using AMBER7 Biman Jana (Sat Jan 19 2008 - 07:16:46 CST)
- Re: AMBER: RMSD calculation using AMBER7 Carlos Simmerling (Sat Jan 19 2008 - 08:19:45 CST)
  - AMBER: convergence of free energy calculations saurabh agrawal (Tue Jan 22 2008 - 05:54:28 CST)
    - Re: AMBER: convergence of free energy calculations David Mobley (Thu Jan 24 2008 - 12:20:35 CST)
AMBER: problem with group input Ed Pate (Mon Jan 21 2008 - 00:53:28 CST)
- Re: AMBER: problem with group input anna.schrey_at_gmx.de (Mon Jan 21 2008 - 08:22:48 CST)
AMBER: Atomic restraints Marie Brut (Mon Jan 21 2008 - 07:34:42 CST)
AMBER: BCC charges Thomas Exner (Tue Jan 22 2008 - 09:47:20 CST)
- RE: AMBER: BCC charges Ross Walker (Tue Jan 22 2008 - 11:16:05 CST)
  - Re: AMBER: BCC charges Thomas Exner (Wed Jan 23 2008 - 04:11:36 CST)
AMBER: Has anyone seen a protein fall apart due to PBCs? David Cerutti (Tue Jan 22 2008 - 10:10:10 CST)
- Re: AMBER: Has anyone seen a protein fall apart due to PBCs? Thomas Cheatham III (Tue Jan 22 2008 - 10:37:03 CST)
  - RE: AMBER: Has anyone seen a protein fall apart due to PBCs? Irene Newhouse (Tue Jan 22 2008 - 11:28:44 CST)
AMBER: Systematic drift Francesco Pietra (Tue Jan 22 2008 - 16:06:46 CST)
AMBER: Installing OpenMPI Hopkins, Robert (Tue Jan 22 2008 - 17:57:49 CST)
- Re: AMBER: Installing OpenMPI David A. Case (Wed Jan 23 2008 - 11:07:46 CST)
  - Re: AMBER: Installing OpenMPI Francesco Pietra (Wed Jan 23 2008 - 12:18:44 CST)
    - Re: AMBER: Installing OpenMPI Hopkins, Robert (Wed Jan 23 2008 - 18:40:22 CST)
AMBER: collision with surface Z Insepov (Tue Jan 22 2008 - 18:25:55 CST)
AMBER: Re: Systematic drift Francesco Pietra (Wed Jan 23 2008 - 01:23:07 CST)
AMBER: Amber 9: Question regarding Test Failures and Compilers Jan Schulze (Wed Jan 23 2008 - 04:01:04 CST)
- Re: AMBER: Amber 9: Question regarding Test Failures and Compilers David A. Case (Wed Jan 23 2008 - 10:22:04 CST)
AMBER: distorted aromatic rings Marc Lindner (Wed Jan 23 2008 - 04:40:20 CST)
- Re: AMBER: distorted aromatic rings David A. Case (Wed Jan 23 2008 - 10:24:15 CST)
  - Re: AMBER: mmpbsa binding energy Marc Lindner (Thu Jan 24 2008 - 04:16:23 CST)
AMBER: vlimit exceeded error priya priya (Wed Jan 23 2008 - 05:27:37 CST)
- Re: AMBER: vlimit exceeded error David A. Case (Wed Jan 23 2008 - 10:29:18 CST)
AMBER: ptraj: new mask parser Vlad Cojocaru (Wed Jan 23 2008 - 05:59:24 CST)
- Re: AMBER: ptraj: new mask parser Jianyin Shao (Thu Jan 24 2008 - 11:23:53 CST)
  - Re: AMBER: ptraj: new mask parser Vlad Cojocaru (Thu Jan 24 2008 - 12:19:25 CST)
AMBER: regarding :scee jani sahil (Wed Jan 23 2008 - 09:50:45 CST)
- Re: AMBER: regarding :scee David A. Case (Wed Jan 23 2008 - 10:45:07 CST)
  - Re: AMBER: regarding :scee jani sahil (Wed Jan 23 2008 - 22:37:48 CST)
AMBER: tutorial_8_section_6 Urszula Uciechowska (Wed Jan 23 2008 - 11:04:38 CST)
AMBER: antechamber run on charged system san_amber roy (Wed Jan 23 2008 - 12:09:34 CST)
- Re: AMBER: antechamber run on charged system David A. Case (Wed Jan 23 2008 - 12:37:06 CST)
  - Re: AMBER: antechamber run on charged system snoze pa (Wed Jan 23 2008 - 13:34:04 CST)
AMBER: Units of atomicfluct Lili Peng (Wed Jan 23 2008 - 18:27:16 CST)
AMBER: Tough time with antechamber David Cerutti (Thu Jan 24 2008 - 01:29:38 CST)
- AMBER: Tough time with antechamber (UPDATE, still need help) David Cerutti (Thu Jan 24 2008 - 02:09:42 CST)
- Re: AMBER: Tough time with antechamber Junmei Wang (Thu Jan 24 2008 - 09:23:08 CST)
- Re: AMBER: Tough time with antechamber David Mobley (Thu Jan 24 2008 - 12:14:42 CST)
  - Re: AMBER: Tough time with antechamber David A. Case (Thu Jan 24 2008 - 12:42:56 CST)
AMBER: Problems in execution of Replica Exchange calculations Amber 9.0 rebeca_at_mmb.pcb.ub.es (Thu Jan 24 2008 - 10:50:22 CST)
- Re: AMBER: Problems in execution of Replica Exchange calculations Amber 9.0 David A. Case (Thu Jan 24 2008 - 11:25:09 CST)
AMBER: Help needed to analyze DNA Holliday Junction - Drug Binding MD simulations. Subramanian Arun Kumar (Thu Jan 24 2008 - 11:14:56 CST)
AMBER: NMR refinement Seth Lilavivat (Thu Jan 24 2008 - 11:39:08 CST)
- Re: AMBER: NMR refinement David A. Case (Thu Jan 24 2008 - 20:18:48 CST)
AMBER: QM/MM: input conversion error Pankaj R. Daga (Thu Jan 24 2008 - 12:11:36 CST)
- Re: AMBER: QM/MM: input conversion error M. L. Dodson (Thu Jan 24 2008 - 12:31:44 CST)
  - RE: AMBER: QM/MM: input conversion error Pankaj R. Daga (Thu Jan 24 2008 - 13:05:31 CST)
AMBER: Number of Hydrogen Bonds? d90223013_at_ntu.edu.tw (Thu Jan 24 2008 - 19:07:39 CST)
- RE: AMBER: Number of Hydrogen Bonds? Jiapu.Zhang_at_csiro.au (Thu Jan 24 2008 - 19:35:04 CST)
  - Re: AMBER: Number of Hydrogen Bonds? Jack Lei (Fri Jan 25 2008 - 07:20:53 CST)
AMBER: flexible molecule parameterization Zhenwei Lu (Fri Jan 25 2008 - 09:36:46 CST)
- Re: AMBER: flexible molecule parameterization FyD (Sun Jan 27 2008 - 08:09:37 CST)
AMBER: AMBER installation problem Jun Liu (Fri Jan 25 2008 - 12:59:29 CST)
- Re: AMBER: AMBER installation problem Bertrand P. S. Russell (Sat Jan 26 2008 - 09:53:43 CST)
- Re: AMBER: AMBER installation problem Sampath Koppole (Mon Jan 28 2008 - 02:36:27 CST)
  - Re: AMBER: AMBER installation problem David A. Case (Mon Jan 28 2008 - 10:06:54 CST)
AMBER: Reg cysteine protonaitons states in pH constant MD D.Usharani (Sun Jan 27 2008 - 23:15:58 CST)
AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? Jack Lei (Mon Jan 28 2008 - 06:59:38 CST)
- RE: AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? Steve Spronk (Mon Jan 28 2008 - 07:47:39 CST)
  - Re: AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? Jack Lei (Mon Jan 28 2008 - 08:35:06 CST)
  - Re: AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? David A. Case (Mon Jan 28 2008 - 10:11:02 CST)
AMBER: Reference for rmsd Francesco Pietra (Mon Jan 28 2008 - 11:51:02 CST)
AMBER: How to determine the basic parameters of a Replica Exchange Molecular Dynamics(REMD? d90223013_at_ntu.edu.tw (Tue Jan 29 2008 - 01:35:08 CST)
- Re: AMBER: How to determine the basic parameters of a Replica Exchange Molecular Dynamics(REMD? Carlos Simmerling (Tue Jan 29 2008 - 06:21:37 CST)
AMBER: radial distribution function in ptraj Lili Peng (Tue Jan 29 2008 - 03:36:37 CST)
AMBER: Amber parallel version on CPU power of 2 only fatima.chami_at_durham.ac.uk (Tue Jan 29 2008 - 07:38:34 CST)
- RE: AMBER: Amber parallel version on CPU power of 2 only Ross Walker (Tue Jan 29 2008 - 08:39:21 CST)
  - RE: AMBER: Amber parallel version on CPU power of 2 only fatima.chami_at_durham.ac.uk (Tue Jan 29 2008 - 12:19:22 CST)
    - Re: AMBER: Amber parallel version on CPU power of 2 only Robert Duke (Tue Jan 29 2008 - 12:43:03 CST)
    - Re: AMBER: Amber parallel version on CPU power of 2 only fatima.chami_at_durham.ac.uk (Tue Jan 29 2008 - 15:04:56 CST)
AMBER: problem to compile PMEMD? fatima.chami_at_durham.ac.uk (Tue Jan 29 2008 - 16:45:41 CST)
- Re: AMBER: problem to compile PMEMD? Robert Duke (Tue Jan 29 2008 - 17:09:05 CST)
  - Re: AMBER: problem to compile PMEMD? fatima.chami_at_durham.ac.uk (Tue Jan 29 2008 - 18:10:48 CST)
    - Re: AMBER: problem to compile PMEMD? Robert Duke (Tue Jan 29 2008 - 20:11:57 CST)
    - Re: AMBER: problem to compile PMEMD? Robert Duke (Tue Jan 29 2008 - 20:10:49 CST)
AMBER: Reg cysteine protonation states D.Usharani (Tue Jan 29 2008 - 21:58:22 CST)
AMBER: setting periodic box Vijay Manickam Achari (Tue Jan 29 2008 - 22:22:05 CST)
AMBER: Entropy calculation nag raj (Wed Jan 30 2008 - 03:51:26 CST)
AMBER: SANDER BOMB in subroutine nonbond_list Pankaj R. Daga (Wed Jan 30 2008 - 09:13:45 CST)
- RE: AMBER: SANDER BOMB in subroutine nonbond_list Ross Walker (Wed Jan 30 2008 - 10:20:51 CST)
AMBER: Amber9 fails test.parallel Marc Cozzi (Wed Jan 30 2008 - 12:58:41 CST)
- Re: AMBER: Amber9 fails test.parallel Mark Williamson (Wed Jan 30 2008 - 14:04:31 CST)
AMBER: (no subject) Syed Tarique Moin (Wed Jan 30 2008 - 23:31:24 CST)
- Re: AMBER: RESP FyD (Wed Jan 30 2008 - 23:47:38 CST)
AMBER: Entropy calculation nag raj (Thu Jan 31 2008 - 06:47:51 CST)
AMBER: LEAP: solute concentration fatima.chami_at_durham.ac.uk (Thu Jan 31 2008 - 09:12:24 CST)
AMBER: disulfide bridge with ff03ua FF Marcin Krol (Thu Jan 31 2008 - 12:30:56 CST)
- AMBER: disulfide bridge with ff03ua FF Marcin Krol (Thu Feb 07 2008 - 08:50:16 CST)
  - Re: AMBER: disulfide bridge with ff03ua FF raja pandian (Fri Feb 08 2008 - 10:17:50 CST)
AMBER: benchmark walltime to ps/day calculation Andrew Ring (Thu Jan 31 2008 - 14:11:05 CST)
- Re: AMBER: benchmark walltime to ps/day calculation Steven Winfield (Thu Jan 31 2008 - 14:34:49 CST)
  - Re: AMBER: benchmark walltime to ps/day calculation Andrew Ring (Thu Jan 31 2008 - 15:16:22 CST)
AMBER: hbonds in first solvation shells Ignacio J. General (Fri Feb 01 2008 - 13:02:30 CST)
AMBER: silica slab / FF Arturas Ziemys (Fri Feb 01 2008 - 15:42:13 CST)
AMBER: Entropy calculations using NMODE saurabh agrawal (Sat Feb 02 2008 - 01:18:24 CST)
- Re: AMBER: Entropy calculations using NMODE Eddie Mende (Sat Feb 02 2008 - 07:17:06 CST)
  - Re: AMBER: Entropy calculations using NMODE saurabh agrawal (Sat Feb 02 2008 - 07:50:13 CST)
AMBER: twin cut-off radii Sandeep Kaushik (Mon Feb 04 2008 - 03:17:57 CST)
- Re: AMBER: twin cut-off radii David A. Case (Mon Feb 04 2008 - 10:09:51 CST)
  - Re: AMBER: twin cut-off radii Robert Duke (Mon Feb 04 2008 - 10:55:06 CST)
AMBER: principal component analysis rams rams (Mon Feb 04 2008 - 06:26:31 CST)
- Re: AMBER: principal component analysis Mark Williamson (Mon Feb 04 2008 - 06:55:47 CST)
  - Re: AMBER: principal component analysis rams rams (Mon Feb 04 2008 - 09:45:17 CST)
  - RE: AMBER: principal component analysis Marco A. Lopez (Mon Feb 04 2008 - 13:22:36 CST)
AMBER: (no subject) Syed Tarique Moin (Mon Feb 04 2008 - 08:07:26 CST)
AMBER: Re: bad atom type f(fluorine) in MM-PBSA kanazta1_at_yahoo.co.jp (Mon Feb 04 2008 - 11:32:51 CST)
AMBER: time autocorrelation: ?? fatima.chami_at_durham.ac.uk (Mon Feb 04 2008 - 12:05:47 CST)
AMBER: Using antechamber without AMBER program Surasak Chunsrivirot (Mon Feb 04 2008 - 14:58:59 CST)
- Re: AMBER: Using antechamber without AMBER program Scott Brozell (Mon Feb 04 2008 - 15:32:11 CST)
  - Re: AMBER: Using antechamber without AMBER program Surasak Chunsrivirot (Mon Feb 04 2008 - 18:38:07 CST)
    - Re: AMBER: Using antechamber without AMBER program David A. Case (Mon Feb 04 2008 - 19:55:47 CST)
- Re: AMBER: Using antechamber without AMBER program David A. Case (Mon Feb 04 2008 - 15:46:00 CST)
  - Re: AMBER: Using antechamber without AMBER program Surasak Chunsrivirot (Mon Feb 04 2008 - 18:22:38 CST)
- Re: AMBER: Using antechamber without AMBER program Junmei Wang (Fri Feb 08 2008 - 09:10:27 CST)
AMBER: Amber 9 installation Taufik Al-Sarraj (Mon Feb 04 2008 - 15:53:23 CST)
- Re: AMBER: Amber 9 installation Yu Chen (Mon Feb 04 2008 - 16:10:37 CST)
- RE: AMBER: Amber 9 installation Ross Walker (Mon Feb 04 2008 - 16:21:41 CST)
  - AMBER: Amber 9 installation Taufik Al-Sarraj (Tue Feb 05 2008 - 09:14:56 CST)
AMBER: VLIMIT units; TGTFITMASK Hopkins, Robert (Mon Feb 04 2008 - 16:55:03 CST)
- Re: AMBER: VLIMIT units; TGTFITMASK David A. Case (Mon Feb 04 2008 - 17:18:39 CST)
  - RE: AMBER: VLIMIT units; TGTFITMASK Hopkins, Robert (Tue Feb 05 2008 - 09:08:07 CST)
AMBER: mm_pbsa: vertex atom mismatch Marc Lindner (Tue Feb 05 2008 - 04:47:23 CST)
AMBER: infinite polymers in CHARMM David A. Case (Tue Feb 05 2008 - 10:39:45 CST)
AMBER: silica slab Arturas Ziemys (Tue Feb 05 2008 - 11:28:55 CST)
- Re: AMBER: silica slab David A. Case (Tue Feb 05 2008 - 12:00:33 CST)
  - Re: AMBER: silica slab Arturas Ziemys (Tue Feb 05 2008 - 12:35:03 CST)
AMBER: Problem with energy decomposition in MMPBSA alfredoq_at_mail.fcq.unc.edu.ar (Tue Feb 05 2008 - 15:32:05 CST)
AMBER: segmentation fault while generating the covariance matrix rams rams (Tue Feb 05 2008 - 23:12:29 CST)
AMBER: re MD simulations of NMR structures: minimized average structure vs. ensemble member Vidana.Epa_at_csiro.au (Wed Feb 06 2008 - 00:08:19 CST)
Fwd: AMBER: (no subject) Syed Tarique Moin (Wed Feb 06 2008 - 02:00:23 CST)
AMBER: Query related to implicit solvent EXTDIEL S.Sundar Raman (Wed Feb 06 2008 - 06:03:02 CST)
- Re: AMBER: Query related to implicit solvent EXTDIEL David A. Case (Wed Feb 06 2008 - 10:31:08 CST)
AMBER: Binary restart file !! Sampath Koppole (Wed Feb 06 2008 - 08:41:03 CST)
- Re: AMBER: Binary restart file !! David A. Case (Wed Feb 06 2008 - 10:35:42 CST)
  - Re: AMBER: Binary restart file !! Sampath Koppole (Wed Feb 06 2008 - 11:01:43 CST)
AMBER: using NAB to calculate entropy Wang, Xuelin (Wed Feb 06 2008 - 11:52:06 CST)
- Re: AMBER: using NAB to calculate entropy David A. Case (Wed Feb 06 2008 - 14:21:28 CST)
  - RE: AMBER: using NAB to calculate entropy. . Wang, Xuelin (Wed Feb 06 2008 - 15:00:46 CST)
AMBER: Amber compilation with ifort Andrey Semichaevsky (Wed Feb 06 2008 - 15:23:26 CST)
- Re: AMBER: Amber compilation with ifort David A. Case (Wed Feb 06 2008 - 15:47:20 CST)
- RE: AMBER: Amber compilation with ifort Ross Walker (Wed Feb 06 2008 - 16:06:20 CST)
- Re: AMBER: Amber compilation with ifort Mark Williamson (Wed Feb 06 2008 - 16:24:16 CST)
- Re: AMBER: Amber compilation with ifort Atro Tossavainen (Thu Feb 07 2008 - 01:45:09 CST)
AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Mohd Farid Ismail (Wed Feb 06 2008 - 16:07:55 CST)
- RE: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Ross Walker (Wed Feb 06 2008 - 18:35:33 CST)
Re: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Bill Ross (Wed Feb 06 2008 - 18:18:38 CST)
- RE: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Mohd Farid Ismail (Tue Mar 04 2008 - 19:09:52 CST)
AMBER: Problem:neturalization jani sahil (Wed Feb 06 2008 - 23:03:35 CST)
- Re: AMBER: Problem:neturalization David Cerutti (Thu Feb 07 2008 - 01:42:39 CST)
AMBER: A new program for doing RESP David Cerutti (Thu Feb 07 2008 - 00:56:04 CST)
AMBER: Deleting solute from box Kevin Davies (Thu Feb 07 2008 - 14:45:48 CST)
Re: AMBER: Deleting solute from box Bill Ross (Thu Feb 07 2008 - 15:37:27 CST)
- Re: AMBER: Deleting solute from box Kevin Davies (Thu Feb 07 2008 - 16:21:22 CST)
RE: AMBER: QMMM with printcharges Ross Walker (Thu Feb 07 2008 - 16:12:17 CST)
AMBER: Error while compiling Amber Lili Peng (Thu Feb 07 2008 - 19:14:42 CST)
- Re: AMBER: Error while compiling Amber David A. Case (Thu Feb 07 2008 - 19:42:31 CST)
  - Re: AMBER: Error while compiling Amber Lili Peng (Fri Feb 08 2008 - 19:51:55 CST)
AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! rams rams (Thu Feb 07 2008 - 23:36:15 CST)
- RE: AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! Ross Walker (Fri Feb 08 2008 - 10:40:25 CST)
  - Re: AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! rams rams (Sun Feb 10 2008 - 23:32:01 CST)
AMBER: Which install compiler and flags? Sam Kaye (Fri Feb 08 2008 - 04:07:15 CST)
- RE: AMBER: Which install compiler and flags? Ross Walker (Fri Feb 08 2008 - 10:52:24 CST)
- Re: AMBER: Which install compiler and flags? David A. Case (Fri Feb 08 2008 - 11:04:55 CST)
AMBER: PB Bomb in pb_atmlist(): maxnba too short Eddie Mende (Fri Feb 08 2008 - 07:22:07 CST)
- RE: AMBER: PB Bomb in pb_atmlist(): maxnba too short Ross Walker (Fri Feb 08 2008 - 10:53:56 CST)
AMBER: Antechamber/mopac query Lynn F. Ten Eyck (Fri Feb 08 2008 - 19:15:12 CST)
AMBER: Input file for Minimization Campbell, Patrick (Sat Feb 09 2008 - 15:18:51 CST)
- RE: AMBER: Input file for Minimization Ross Walker (Sun Feb 10 2008 - 12:55:34 CST)
  - Re: AMBER: Input file for Minimization Carlos Simmerling (Mon Feb 11 2008 - 11:06:42 CST)
- RE: AMBER: Input file for Minimization Campbell, Patrick (Tue Feb 12 2008 - 11:43:34 CST)
  - Re: AMBER: Input file for Minimization Carlos Simmerling (Tue Feb 12 2008 - 11:55:18 CST)
AMBER: leaprc help snoze pa (Mon Feb 11 2008 - 11:50:30 CST)
- Re: AMBER: leaprc help Carlos Simmerling (Mon Feb 11 2008 - 11:56:38 CST)
  - Re: AMBER: leaprc help snoze pa (Mon Feb 11 2008 - 15:08:14 CST)
    - Re: AMBER: leaprc help Reena ..... (Mon Feb 11 2008 - 22:19:22 CST)
AMBER: mm_pbsa problem Badry Bursulaya (Mon Feb 11 2008 - 16:45:29 CST)
AMBER: Non-polar Parameters For MM_PBSA Calculation Neil Bruce (Tue Feb 12 2008 - 05:54:02 CST)
- RE: AMBER: Non-polar Parameters For MM_PBSA Calculation rluo_at_uci.edu (Tue Feb 12 2008 - 17:23:40 CST)
AMBER: PKa calculation Wang, Xuelin (Tue Feb 12 2008 - 10:45:16 CST)
- Re: AMBER: PKa calculation David A. Case (Tue Feb 12 2008 - 11:15:55 CST)
AMBER: RDCs in AMBER 10 Douglas Kojetin (Tue Feb 12 2008 - 17:39:37 CST)
- Re: AMBER: RDCs in AMBER 10 David A. Case (Tue Feb 12 2008 - 17:56:52 CST)
  - Re: AMBER: RDCs in AMBER 10 Douglas Kojetin (Tue Feb 12 2008 - 19:01:30 CST)
AMBER: (no subject) Syed Tarique Moin (Wed Feb 13 2008 - 04:55:02 CST)
- RE: AMBER: (no subject) Ross Walker (Wed Feb 13 2008 - 09:21:52 CST)
  - RE: AMBER: (no subject) Syed Tarique Moin (Wed Feb 13 2008 - 22:58:56 CST)
AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen (Wed Feb 13 2008 - 07:31:54 CST)
- RE: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Ross Walker (Wed Feb 13 2008 - 09:20:07 CST)
  - Re: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen (Wed Feb 13 2008 - 14:27:29 CST)
    - Re: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen (Wed Feb 13 2008 - 14:49:57 CST)
    - Re: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen (Thu Feb 14 2008 - 01:02:22 CST)
AMBER: Is boiling point a good way to validate solvent paramters? Mike Wykes (Wed Feb 13 2008 - 08:08:25 CST)
- Re: AMBER: Is boiling point a good way to validate solvent paramters? David A. Case (Wed Feb 13 2008 - 14:34:01 CST)
  - RE: AMBER: Is boiling point a good way to validate solvent paramters? Mike Wykes (Fri Feb 15 2008 - 09:27:35 CST)
    - Re: AMBER: Is boiling point a good way to validate solvent paramters? David A. Case (Fri Feb 15 2008 - 20:49:12 CST)
    - RE: AMBER: Is boiling point a good way to validate solvent paramters? FyD (Sat Feb 16 2008 - 01:31:14 CST)
AMBER: sander error on Make test.serial Evan Kelly (Wed Feb 13 2008 - 14:26:25 CST)
- Re: AMBER: sander error on Make test.serial Evan Kelly (Wed Feb 13 2008 - 15:03:58 CST)
- Re: AMBER: sander error on Make test.serial David A. Case (Wed Feb 13 2008 - 23:57:32 CST)
  - Re: AMBER: sander error on Make test.serial Evan Kelly (Thu Feb 14 2008 - 12:36:25 CST)
AMBER: ambmask problem Hopkins, Robert (Wed Feb 13 2008 - 18:42:53 CST)
- Re: AMBER: ambmask problem David A. Case (Fri Feb 15 2008 - 11:32:46 CST)
AMBER: AMBER parameters for Chlorophyll Sreeja Parameswaran (Wed Feb 13 2008 - 19:31:05 CST)
- Re: AMBER: AMBER parameters for Chlorophyll mathew k varghese (Sat Feb 16 2008 - 08:09:30 CST)
  - Re: AMBER: AMBER parameters for Chlorophyll Sreeja Parameswaran (Sat Feb 16 2008 - 08:45:32 CST)
    - Re: AMBER: AMBER parameters for Chlorophyll David LeBard (Sat Feb 16 2008 - 11:25:51 CST)
AMBER: xmgr graphics display program Hopkins, Robert (Wed Feb 13 2008 - 20:02:23 CST)
- Re: AMBER: xmgr graphics display program Gustavo Seabra (Wed Feb 13 2008 - 20:29:26 CST)
- Re: AMBER: xmgr graphics display program David A. Case (Wed Feb 13 2008 - 23:46:40 CST)
  - Re: AMBER: xmgr graphics display program Junmei Wang (Thu Feb 14 2008 - 14:04:16 CST)
- Re: AMBER: xmgr graphics display program Hopkins, Robert (Sun Feb 17 2008 - 14:38:41 CST)
AMBER: mpd error in submitting parallel job Lili Peng (Thu Feb 14 2008 - 03:11:25 CST)
- Re: AMBER: mpd error in submitting parallel job Gustavo Seabra (Thu Feb 14 2008 - 13:45:47 CST)
  - RE: AMBER: mpd error in submitting parallel job Ross Walker (Thu Feb 14 2008 - 22:11:23 CST)
AMBER: Distance restraints between com of two groups of residues Sudha Mani Karra (Thu Feb 14 2008 - 16:20:26 CST)
AMBER: print distance between atoms during simulation within sander itsself Vlad Cojocaru (Fri Feb 15 2008 - 08:06:24 CST)
AMBER: setbox for solvateoct model Wang, Xuelin (Fri Feb 15 2008 - 09:22:07 CST)
- Re: AMBER: setbox for solvateoct model David A. Case (Fri Feb 15 2008 - 20:52:14 CST)
AMBER: problem with ambmask David A. Case (Fri Feb 15 2008 - 12:07:54 CST)
- RE: AMBER: problem with ambmask Hopkins, Robert (Mon Feb 18 2008 - 15:57:07 CST)
AMBER: matrix correl David Beveridge (Sat Feb 16 2008 - 03:09:29 CST)
- Re: AMBER: matrix correl Holger Gohlke (Mon Feb 18 2008 - 06:56:07 CST)
- RE: AMBER: matrix correl Ibrahim Moustafa (Wed Feb 20 2008 - 11:22:53 CST)
- Re: AMBER: matrix correl Lars Skjærven (Wed Feb 20 2008 - 11:35:30 CST)
  - RE: AMBER: matrix correl Ibrahim Moustafa (Wed Feb 20 2008 - 12:19:31 CST)
AMBER: setting perioding box in AMBER Vijay Manickam Achari (Sun Feb 17 2008 - 19:47:17 CST)
- Re: AMBER: setting perioding box in AMBER David A. Case (Sun Feb 17 2008 - 20:14:31 CST)
  - Re: AMBER: setting perioding box in AMBER Vijay Manickam Achari (Tue Feb 19 2008 - 00:00:06 CST)
AMBER: TERs Steve Seibold (Mon Feb 18 2008 - 07:19:39 CST)
- Re: AMBER: TERs David A. Case (Mon Feb 18 2008 - 10:49:55 CST)
- Re: AMBER: TERs Thomas Cheatham (Mon Feb 18 2008 - 11:18:36 CST)
  - RE: AMBER: TERs Steve Seibold (Mon Feb 18 2008 - 11:51:51 CST)
AMBER: parameters of nonbonded potentials Alexander Klenner (Tue Feb 19 2008 - 04:43:27 CST)
- Re: AMBER: parameters of nonbonded potentials David A. Case (Tue Feb 19 2008 - 10:05:07 CST)
AMBER: Generating RESP charges Christopher Illingworth (Tue Feb 19 2008 - 05:39:22 CST)
- Re: AMBER: Generating RESP charges Junmei Wang (Tue Feb 19 2008 - 09:05:39 CST)
  - Re: AMBER: Generating RESP charges Christopher Illingworth (Tue Feb 19 2008 - 10:11:21 CST)
AMBER: united atom force field: antechamber fatima.chami_at_durham.ac.uk (Tue Feb 19 2008 - 15:59:42 CST)
- Re: AMBER: united atom force field: antechamber David A. Case (Tue Feb 19 2008 - 17:33:32 CST)
AMBER: NAB to calcuate entropy Wang, Xuelin (Tue Feb 19 2008 - 17:58:15 CST)
- Re: AMBER: NAB to calcuate entropy David A. Case (Tue Feb 19 2008 - 19:33:59 CST)
  - Re: AMBER: NAB to calcuate entropy Z. Nevin Gerek (Wed Feb 20 2008 - 14:38:28 CST)
AMBER: Regarding:PME and neturalization jani sahil (Tue Feb 19 2008 - 23:12:45 CST)
- Re: AMBER: Regarding:PME and neturalization Lars Skjærven (Wed Feb 20 2008 - 02:39:59 CST)
AMBER: is that possible fix box size in constant pressure MD Vijay Manickam Achari (Tue Feb 19 2008 - 23:39:46 CST)
AMBER: Dimension of the solvated box? abiram abiram (Wed Feb 20 2008 - 07:54:08 CST)
- Re: AMBER: Dimension of the solvated box? David A. Case (Wed Feb 20 2008 - 10:31:36 CST)
AMBER: Problem with "trajout pdb" Yi-Ming Cheng (Wed Feb 20 2008 - 10:53:32 CST)
- Re: AMBER: Problem with "trajout pdb" Yi-Ming Cheng (Sat Feb 23 2008 - 03:36:24 CST)
- Re: AMBER: Problem with "trajout pdb" Yi-Ming Cheng (Sat Feb 23 2008 - 04:15:29 CST)
AMBER: saveAmberPrep in internal coordinates Xu, Huafeng (Wed Feb 20 2008 - 11:02:00 CST)
- Re: AMBER: saveAmberPrep in internal coordinates Junmei Wang (Wed Feb 20 2008 - 11:43:31 CST)
AMBER: XLEaP Anamika Awasthi (Thu Feb 21 2008 - 03:36:20 CST)
- Re: AMBER: XLEaP David A. Case (Thu Feb 21 2008 - 10:45:08 CST)
AMBER: simulated annealing Holly Freedman (Thu Feb 21 2008 - 13:31:48 CST)
- Re: AMBER: simulated annealing David A. Case (Thu Feb 21 2008 - 14:04:26 CST)
- Re: AMBER: simulated annealing Holly Freedman (Thu Feb 21 2008 - 14:52:42 CST)
AMBER: Question: tweaking topology files to add SHAKE-constrained bonds David Cerutti (Thu Feb 21 2008 - 23:37:28 CST)
- AMBER: (no subject) Syed Tarique Moin (Fri Feb 22 2008 - 00:10:36 CST)
- Re: AMBER: Question: tweaking topology files to add SHAKE-constrained bonds David A. Case (Fri Feb 22 2008 - 11:14:59 CST)
AMBER: problem bull linux compiling Yannick Monclin (Fri Feb 22 2008 - 05:22:49 CST)
- Re: AMBER: problem bull linux compiling Gustavo Seabra (Fri Feb 22 2008 - 09:56:25 CST)
  - Re: AMBER: problem bull linux compiling Yannick Monclin (Mon Feb 25 2008 - 07:16:06 CST)
    - Re: AMBER: problem bull linux compiling Gustavo Seabra (Tue Feb 26 2008 - 11:18:27 CST)
AMBER: gaff paramters servaas michielssens (Fri Feb 22 2008 - 11:38:53 CST)
- Re: AMBER: gaff paramters Servaas Michielssens (Fri Feb 22 2008 - 15:15:23 CST)
  - Re: AMBER: gaff paramters Servaas Michielssens (Sat Feb 23 2008 - 01:06:54 CST)
AMBER: More on tweaking a topology file David Cerutti (Fri Feb 22 2008 - 21:15:40 CST)
- Re: AMBER: More on tweaking a topology file Carlos Simmerling (Sat Feb 23 2008 - 06:08:30 CST)
Fwd: Re: AMBER: Problem with "trajout pdb" Yi-Ming Cheng (Sat Feb 23 2008 - 04:21:29 CST)
AMBER: dihedral energy in amber aneesh cna (Sat Feb 23 2008 - 04:32:08 CST)
- Re: AMBER: dihedral energy in amber David A. Case (Sat Feb 23 2008 - 10:37:09 CST)
Re: AMBER: parameters for silicon atom Scott Brozell (Mon Feb 25 2008 - 20:24:03 CST)
- Re: AMBER: parameters for silicon atom Scott Brozell (Fri Feb 29 2008 - 02:31:03 CST)
AMBER: compiling PMEMD with MKL10.0 Alessandro Nascimento (Tue Feb 26 2008 - 04:20:47 CST)
- Re: AMBER: compiling PMEMD with MKL10.0 Francesco Pietra (Tue Feb 26 2008 - 05:00:32 CST)
  - Re: AMBER: compiling PMEMD with MKL10.0 Alessandro Nascimento (Tue Feb 26 2008 - 05:36:40 CST)
    - Re: AMBER: compiling PMEMD with MKL10.0 Gustavo Seabra (Tue Feb 26 2008 - 13:46:24 CST)
- Re: AMBER: compiling PMEMD with MKL10.0 Robert Duke (Tue Feb 26 2008 - 07:22:04 CST)
AMBER: Force fields oguz gurbulak (Tue Feb 26 2008 - 10:12:48 CST)
- Re: AMBER: Force fields David A. Case (Tue Feb 26 2008 - 11:31:19 CST)
AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 10:16:21 CST)
- Re: AMBER: bond breaking in proteins David A. Case (Tue Feb 26 2008 - 11:16:46 CST)
- Re: AMBER: bond breaking in proteins Gustavo Seabra (Tue Feb 26 2008 - 13:58:22 CST)
  - Re: AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 14:49:04 CST)
  - Re: AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 15:04:02 CST)
AMBER: mol2 save snoze pa (Tue Feb 26 2008 - 11:09:18 CST)
- Re: AMBER: mol2 save Steven Winfield (Tue Feb 26 2008 - 11:13:23 CST)
- Re: AMBER: mol2 save FyD (Tue Feb 26 2008 - 11:38:40 CST)
- Re: AMBER: mol2 save David A. Case (Tue Feb 26 2008 - 11:51:19 CST)
AMBER: autodock pdb to obtain parm with tleap Henar Martínez (Tue Feb 26 2008 - 11:23:43 CST)
- Re: AMBER: autodock pdb to obtain parm with tleap David A. Case (Tue Feb 26 2008 - 15:34:07 CST)
  - Re: AMBER: autodock pdb to obtain parm with tleap Henar Martínez (Wed Feb 27 2008 - 04:58:09 CST)
    - Re: AMBER: autodock pdb to obtain parm with tleap David A. Case (Wed Feb 27 2008 - 12:25:02 CST)
    - Re: AMBER: autodock pdb to obtain parm with tleap Henar Martínez (Wed Feb 27 2008 - 12:30:33 CST)
  - Re: AMBER: autodock pdb to obtain parm with tleap Henar Martínez (Wed Feb 27 2008 - 05:14:58 CST)
AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 16:41:22 CST)
- AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 17:40:03 CST)
  - Re: AMBER: bond breaking in proteins David A. Case (Tue Feb 26 2008 - 18:41:26 CST)
- Re: AMBER: bond breaking in proteins Gustavo Seabra (Wed Feb 27 2008 - 10:09:58 CST)
- Re: AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 16:55:20 CST)
AMBER: Using restart files Lili Peng (Tue Feb 26 2008 - 17:36:50 CST)
- Re: AMBER: Using restart files David A. Case (Tue Feb 26 2008 - 18:45:34 CST)
AMBER: charge derivation for modified amino acids Denzil Bernard (Tue Feb 26 2008 - 19:14:44 CST)
- Re: AMBER: charge derivation for modified amino acids FyD (Wed Feb 27 2008 - 00:35:10 CST)
AMBER: "Assuming uniform neutralizing plasma" Evan Kelly (Tue Feb 26 2008 - 20:01:52 CST)
- Re: AMBER: "Assuming uniform neutralizing plasma" Thomas Cheatham (Tue Feb 26 2008 - 21:31:39 CST)
AMBER: stops writing trajectory Swarup Gupta (Wed Feb 27 2008 - 03:55:10 CST)
AMBER: initial command? Anamika Awasthi (Wed Feb 27 2008 - 06:01:51 CST)
- Re: AMBER: initial command? Carlos Simmerling (Wed Feb 27 2008 - 06:10:01 CST)
  - RE: AMBER: initial command? Steve Spronk (Wed Feb 27 2008 - 12:45:43 CST)
- RE: AMBER: initial command? Bill Ross (Wed Feb 27 2008 - 12:56:20 CST)
  - RE: AMBER: initial command? Steve Spronk (Fri Feb 29 2008 - 08:17:38 CST)
AMBER: Amber: shared memory vs cluster Francesco Pietra (Wed Feb 27 2008 - 12:08:19 CST)
- Re: AMBER: Amber: shared memory vs cluster Robert Duke (Wed Feb 27 2008 - 12:37:31 CST)
  - Re: AMBER: Amber: shared memory vs cluster Francesco Pietra (Wed Feb 27 2008 - 15:00:32 CST)
    - Re: AMBER: Amber: shared memory vs cluster Robert Duke (Wed Feb 27 2008 - 15:20:56 CST)
AMBER: Lennard-Jones parameters zhan chen (Thu Feb 28 2008 - 01:41:02 CST)
- Re: AMBER: Lennard-Jones parameters Klenner_at_bioinformatik.uni-frankfurt.de (Wed Feb 27 2008 - 16:11:50 CST)
  - Re: AMBER: Lennard-Jones parameters Bill Ross (Wed Feb 27 2008 - 18:09:10 CST)
    - Re: AMBER: Lennard-Jones parameters Zhan Chen (Wed Feb 27 2008 - 20:59:26 CST)
- Re: AMBER: Lennard-Jones parameters David A. Case (Wed Feb 27 2008 - 16:16:34 CST)
  - AMBER: change in secondary structure during MD Ibrahim Moustafa (Wed Feb 27 2008 - 19:45:21 CST)
- Re: AMBER: Lennard-Jones parameters Bill Ross (Thu Feb 28 2008 - 14:07:31 CST)
AMBER: DFTB/SCC-DFTB Eddie Mende (Wed Feb 27 2008 - 13:21:42 CST)
- Re: AMBER: DFTB/SCC-DFTB David A. Case (Thu Feb 28 2008 - 00:15:48 CST)
AMBER: varying restraint_wt with nmropt=1 Andrew Borgert (Wed Feb 27 2008 - 14:18:28 CST)
- Re: AMBER: varying restraint_wt with nmropt=1 Daniel Cappel (Thu Feb 28 2008 - 01:50:02 CST)
AMBER: problem with antechamber aneesh cna (Wed Feb 27 2008 - 23:55:53 CST)
- Re: AMBER: problem with antechamber Junmei Wang (Thu Feb 28 2008 - 09:06:31 CST)
AMBER: problems with Replica Exchange rebeca_at_mmb.pcb.ub.es (Thu Feb 28 2008 - 06:29:23 CST)
- Re: AMBER: problems with Replica Exchange Carlos Simmerling (Thu Feb 28 2008 - 06:46:57 CST)
  - Re: AMBER: problems with Replica Exchange rebeca_at_mmb.pcb.ub.es (Thu Feb 28 2008 - 09:16:27 CST)
    - Re: AMBER: problems with Replica Exchange Carlos Simmerling (Thu Feb 28 2008 - 10:14:14 CST)
    - AMBER: el w-end en galicia! neva_at_mmb.pcb.ub.es (Wed Mar 05 2008 - 03:05:09 CST)
- Re: AMBER: problems with Replica Exchange Carlos Simmerling (Fri Feb 29 2008 - 12:33:59 CST)
- AMBER: implicit energy calculations rebeca_at_mmb.pcb.ub.es (Thu Mar 13 2008 - 11:26:43 CDT)
  - Re: AMBER: implicit energy calculations Thomas Cheatham III (Thu Mar 13 2008 - 12:47:04 CDT)
AMBER: Plea for REMD tutorial tushar garud (Thu Feb 28 2008 - 07:56:42 CST)
- Re: AMBER: Plea for REMD tutorial Carlos Simmerling (Thu Feb 28 2008 - 08:08:26 CST)
  - AMBER: Molecular dynamics simulation of large-scale domainmovement in a protein Fenghui Fan (Thu Feb 28 2008 - 08:38:23 CST)
AMBER: Liquid/Gas Phase Rita Cassia (Thu Feb 28 2008 - 10:34:00 CST)
AMBER: problems with 10-12 potential in amber8 sander Amie Demmel (Thu Feb 28 2008 - 14:59:27 CST)
- Re: AMBER: problems with 10-12 potential in amber8 sander David A. Case (Thu Feb 28 2008 - 16:27:47 CST)
  - Re: AMBER: problems with 10-12 potential in amber8 sander Amie Demmel (Thu Feb 28 2008 - 16:53:15 CST)
    - Re: AMBER: problems with 10-12 potential in amber8 sander David A. Case (Thu Feb 28 2008 - 17:47:10 CST)
    - Re: AMBER: problems with 10-12 potential in amber8 sander Amie Demmel (Fri Feb 29 2008 - 10:23:15 CST)
  - Re: AMBER: problems with 10-12 potential in amber8 sander Lynn F. Ten Eyck (Thu Feb 28 2008 - 16:54:47 CST)
AMBER: problems with 10-12 potential in amber8 sander Amie Demmel (Thu Feb 28 2008 - 14:59:27 CST)
AMBER: Re: Force field parameter file for CNT Andrey Semichaevsky (Thu Feb 28 2008 - 15:34:01 CST)
- Re: AMBER: Re: Force field parameter file for CNT David A. Case (Fri Feb 29 2008 - 10:19:47 CST)
  - Re: AMBER: Re: Force field parameter file for CNT Andrey Semichaevsky (Fri Feb 29 2008 - 10:38:39 CST)
AMBER: for NMR refinement Wenyong Tong (Thu Feb 28 2008 - 20:20:08 CST)
- Re: AMBER: for NMR refinement David A. Case (Fri Feb 29 2008 - 12:53:59 CST)
AMBER: Visualizing Periodc box Vijay Manickam Achari (Fri Feb 29 2008 - 01:50:13 CST)
AMBER: Plea for REMD tutorial tushar garud (Fri Feb 29 2008 - 08:57:41 CST)
- Re: AMBER: Plea for REMD tutorial Carlos Simmerling (Fri Feb 29 2008 - 11:47:47 CST)
AMBER: Re: Amber Force field for CNT: leaprc.ff23 Andrey Semichaevsky (Fri Feb 29 2008 - 09:35:16 CST)
AMBER: Non aqueous implicit solvation Mike Wykes (Fri Feb 29 2008 - 12:56:01 CST)
AMBER: regarding:calculation of b factor using ptraj jani sahil (Sat Mar 01 2008 - 10:10:10 CST)
- Re: AMBER: regarding:calculation of b factor using ptraj gurpreet singh (Sun Mar 02 2008 - 11:24:29 CST)
AMBER: questions about run MD at different pH Kailee (Mon Mar 03 2008 - 08:51:40 CST)
- Re: AMBER: questions about run MD at different pH David A. Case (Mon Mar 03 2008 - 23:07:00 CST)
  - Re: AMBER: questions about run MD at different pH Kailee (Tue Mar 04 2008 - 05:40:30 CST)
    - Re: AMBER: questions about run MD at different pH David A. Case (Tue Mar 04 2008 - 19:59:49 CST)
  - Re: AMBER: questions about run MD at different pH Taufik Al-Sarraj (Tue Apr 15 2008 - 11:15:28 CDT)
AMBER: Writing pressure in md.out file in NVT simulation Sudha Mani Karra (Mon Mar 03 2008 - 12:58:46 CST)
- Re: AMBER: Writing pressure in md.out file in NVT simulation David A. Case (Mon Mar 03 2008 - 13:24:20 CST)
  - Re: AMBER: Writing pressure in md.out file in NVT simulation Sudha Mani Karra (Mon Mar 03 2008 - 14:56:13 CST)
- Re: AMBER: Writing pressure in md.out file in NVT simulation Vlad Cojocaru (Mon Mar 03 2008 - 13:26:50 CST)
AMBER: xleap screen output Francesco Pietra (Mon Mar 03 2008 - 15:02:54 CST)
- Re: AMBER: xleap screen output David A. Case (Mon Mar 03 2008 - 15:31:17 CST)
  - Re: AMBER: xleap screen output Francesco Pietra (Mon Mar 03 2008 - 15:48:59 CST)
- Re: AMBER: xleap screen output Bill Ross (Mon Mar 03 2008 - 16:08:17 CST)
  - Re: AMBER: xleap screen output Francesco Pietra (Tue Mar 04 2008 - 11:27:00 CST)
AMBER: ACS COMP Division awards- deadline this week Carlos Simmerling (Mon Mar 03 2008 - 18:14:03 CST)
AMBER: Problem running implicit minimization Lili Peng (Mon Mar 03 2008 - 23:10:52 CST)
- Re: AMBER: Problem running implicit minimization David A. Case (Mon Mar 03 2008 - 23:59:00 CST)
  - Re: AMBER: Problem running implicit minimization Lili Peng (Tue Mar 04 2008 - 00:17:27 CST)
AMBER: missing gaff parameters Samuele Giani (Tue Mar 04 2008 - 02:46:38 CST)
- Re: AMBER: missing gaff parameters Junmei Wang (Tue Mar 04 2008 - 08:53:39 CST)
- RE: AMBER: missing gaff parameters Ross Walker (Tue Mar 04 2008 - 09:39:03 CST)
  - Re: AMBER: missing gaff parameters Samuele Giani (Tue Mar 04 2008 - 10:42:03 CST)
Fwd: Re: AMBER: xleap screen output Francesco Pietra (Tue Mar 04 2008 - 11:33:34 CST)
Fwd: Re: AMBER: xleap screen output SOLVED Francesco Pietra (Tue Mar 04 2008 - 14:44:15 CST)
Re: Fwd: Re: AMBER: xleap screen output Bill Ross (Tue Mar 04 2008 - 11:59:58 CST)
AMBER: a question about parameter b in the hyperbolic form of penalty function for RESP fit Ye Mei (Wed Mar 05 2008 - 03:30:50 CST)
AMBER: Atom types/parameters for chromene anna.schrey_at_gmx.de (Wed Mar 05 2008 - 03:34:24 CST)
- Re: AMBER: Atom types/parameters for chromene Junmei Wang (Wed Mar 05 2008 - 10:23:19 CST)
  - Re: AMBER: Atom types/parameters for chromene Francesco Pietra (Wed Mar 05 2008 - 12:07:05 CST)
    - Re: AMBER: Atom types/parameters for chromene David A. Case (Wed Mar 05 2008 - 13:15:25 CST)
  - Re: AMBER: Atom types/parameters for chromene anna.schrey_at_gmx.de (Thu Mar 06 2008 - 07:35:06 CST)
AMBER: setBox command Vijay Manickam Achari (Wed Mar 05 2008 - 23:20:01 CST)
- Re: AMBER: setBox command Thomas Steinbrecher (Thu Mar 06 2008 - 12:06:32 CST)
AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Edyta Malolepsza (Thu Mar 06 2008 - 06:23:06 CST)
- Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? David A. Case (Wed Mar 19 2008 - 10:42:13 CDT)
  - Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Edyta Malolepsza (Wed Mar 19 2008 - 11:49:45 CDT)
AMBER: Steve Seibold (Thu Mar 06 2008 - 12:04:01 CST)
- Re: AMBER: Thomas Steinbrecher (Thu Mar 06 2008 - 12:13:23 CST)
  - RE: AMBER: Steve Seibold (Thu Mar 06 2008 - 12:27:34 CST)
Re: AMBER: XMGRACE on Linux 64 Bit Bill Ross (Thu Mar 06 2008 - 18:12:51 CST)
- Re: AMBER: XMGRACE on Linux 64 Bit dpandit_at_brandeis.edu (Thu Mar 06 2008 - 19:50:55 CST)
  - RE: AMBER: XMGRACE on Linux 64 Bit Ross Walker (Thu Mar 06 2008 - 20:30:44 CST)
    - RE: AMBER: XMGRACE on Linux 64 Bit dpandit_at_brandeis.edu (Fri Mar 07 2008 - 12:40:19 CST)
    - Re: AMBER: XMGRACE on Linux 64 Bit David LeBard (Fri Mar 07 2008 - 12:53:47 CST)
AMBER: Microcannonical MD Reference priya priya (Fri Mar 07 2008 - 07:40:34 CST)
- Re: AMBER: Microcannonical MD Reference David A. Case (Fri Mar 07 2008 - 16:47:02 CST)
AMBER: NVE energy and temperature drift Lars Skjærven (Fri Mar 07 2008 - 09:36:48 CST)
- Re: AMBER: NVE energy and temperature drift David A. Case (Fri Mar 07 2008 - 10:32:51 CST)
  - Re: AMBER: NVE energy and temperature drift Lars Skjærven (Fri Mar 07 2008 - 11:34:33 CST)
AMBER: Fwd: positive potential energy and large 1-4 EEL Mey Khalili (Fri Mar 07 2008 - 10:54:28 CST)
- Re: AMBER: Fwd: positive potential energy and large 1-4 EEL David A. Case (Mon Mar 10 2008 - 19:19:51 CDT)
AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis James Thomas (Fri Mar 07 2008 - 11:30:58 CST)
- Re: AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis David A. Case (Fri Mar 07 2008 - 15:36:33 CST)
AMBER: AMBER install problem Kijeong Kwac (Fri Mar 07 2008 - 12:12:08 CST)
- Re: AMBER: AMBER install problem David A. Case (Mon Mar 10 2008 - 19:50:30 CDT)
  - Re: AMBER: AMBER install problem Atro Tossavainen (Tue Mar 11 2008 - 01:51:18 CDT)
    - Re: AMBER: AMBER install problem David A. Case (Tue Mar 11 2008 - 19:47:58 CDT)
    - AMBER: RE: Re: AMBER: AMBER install problem Kijeong Kwac (Thu Mar 13 2008 - 12:35:10 CDT)
AMBER: RE: Request Ross Walker (Fri Mar 07 2008 - 14:38:25 CST)
AMBER: reg molecular dynamics Uma R (Fri Mar 07 2008 - 21:17:32 CST)
AMBER: Negative ligand (Peroxide) Syed Tarique Moin (Sat Mar 08 2008 - 05:36:56 CST)
AMBER: Compiler issues with Altix450 finke_at_oakland.edu (Sat Mar 08 2008 - 12:37:25 CST)
- Re: AMBER: Compiler issues with Altix450 Atro Tossavainen (Sat Mar 08 2008 - 16:19:36 CST)
- Re: AMBER: Compiler issues with Altix450 finke_at_oakland.edu (Mon Mar 10 2008 - 15:45:37 CDT)
  - Re: AMBER: Compiler issues with Altix450 Atro Tossavainen (Mon Mar 10 2008 - 18:13:45 CDT)
  - Re: AMBER: Compiler issues with Altix450 David A. Case (Mon Mar 10 2008 - 18:29:50 CDT)
AMBER: Clarification on error message Campbell, Patrick (Sat Mar 08 2008 - 14:09:23 CST)
- Re: AMBER: Clarification on error message Thomas Steinbrecher (Sat Mar 08 2008 - 14:17:35 CST)
  - RE: AMBER: Clarification on error message Campbell, Patrick (Sat Mar 08 2008 - 15:15:36 CST)
AMBER: mmpbsa INSTRNG error? Sergio Wong (Sun Mar 09 2008 - 00:06:44 CST)
- Re: AMBER: mmpbsa INSTRNG error? Gohlke_at_bioinformatik.uni-frankfurt.de (Sun Mar 09 2008 - 11:13:05 CDT)
AMBER: Timing analysis on Ranger David LeBard (Sun Mar 09 2008 - 15:06:18 CDT)
AMBER: Antechamber, net molecular charge gurpreet singh (Sun Mar 09 2008 - 23:51:58 CDT)
- Re: AMBER: Antechamber, net molecular charge Junmei Wang (Mon Mar 10 2008 - 09:39:08 CDT)
AMBER: Benchmarks on Fujitsu PrimePower 2500? Craig Gough (Mon Mar 10 2008 - 00:36:28 CDT)
- Re: AMBER: Benchmarks on Fujitsu PrimePower 2500? Atro Tossavainen (Mon Mar 10 2008 - 03:04:20 CDT)
  - Re: AMBER: Benchmarks on Fujitsu PrimePower 2500? Robert Duke (Mon Mar 10 2008 - 08:24:21 CDT)
    - Re: AMBER: Benchmarks on Fujitsu PrimePower 2500? Atro Tossavainen (Mon Mar 10 2008 - 08:24:33 CDT)
Fwd: AMBER: Negative ligand (Peroxide) Syed Tarique Moin (Mon Mar 10 2008 - 00:59:43 CDT)
AMBER: writing out a distance between two atoms in sander Vlad Cojocaru (Mon Mar 10 2008 - 08:33:55 CDT)
- Re: AMBER: writing out a distance between two atoms in sander Thomas Steinbrecher (Mon Mar 10 2008 - 12:17:35 CDT)
  - Re: AMBER: writing out a distance between two atoms in sander Vlad Cojocaru (Mon Mar 10 2008 - 12:35:58 CDT)
AMBER: problem with antech amber Madjid Taghdir (Mon Mar 10 2008 - 10:07:16 CDT)
- Re: AMBER: problem with antech amber David A. Case (Sat Mar 15 2008 - 00:09:00 CDT)
AMBER: output effective Born radii Holly Freedman (Mon Mar 10 2008 - 17:57:06 CDT)
- Re: AMBER: output effective Born radii David A. Case (Mon Mar 10 2008 - 19:07:39 CDT)
- Re: AMBER: output effective Born radii Holly Freedman (Mon Mar 10 2008 - 21:24:32 CDT)
AMBER: Re: Amber: parameters for Silicon Scott Brozell (Mon Mar 10 2008 - 18:57:29 CDT)
AMBER: SMD using amber ChengZhong Zhang (Mon Mar 10 2008 - 20:54:23 CDT)
AMBER: convert AMBER format input files into DL_POLY format input files? Kefa Lu (Tue Mar 11 2008 - 03:27:23 CDT)
AMBER: solvate with methanol san_amber roy (Tue Mar 11 2008 - 04:23:40 CDT)
- Re: AMBER: solvate with methanol Rita Cassia (Tue Mar 11 2008 - 07:33:46 CDT)
AMBER: Adding New Parameters and Modifying Existing Parameters serhanyigen_at_mail.ege.edu.tr (Tue Mar 11 2008 - 06:51:18 CDT)
- Re: AMBER: Adding New Parameters and Modifying Existing Parameters Thomas Steinbrecher (Tue Mar 11 2008 - 11:46:33 CDT)
AMBER: SPARC benchmarks (was re Fujitsu PRIMEPOWER) Atro Tossavainen (Tue Mar 11 2008 - 09:33:33 CDT)
AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 David Rangel (Tue Mar 11 2008 - 22:30:14 CDT)
- Re: AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 David A. Case (Wed Mar 12 2008 - 00:43:26 CDT)
  - Re: AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 David Rangel (Wed Mar 12 2008 - 12:04:18 CDT)
AMBER: lastrst problem san_amber roy (Wed Mar 12 2008 - 10:07:23 CDT)
- Fwd: AMBER: lastrst problem san_amber roy (Wed Mar 12 2008 - 10:19:08 CDT)
  - Re: Fwd: AMBER: lastrst problem David A. Case (Tue Mar 18 2008 - 10:37:48 CDT)
    - Re: Fwd: AMBER: lastrst problem san_amber roy (Wed Mar 19 2008 - 11:07:26 CDT)
AMBER: ptraj and non-bonded contacts Samuel Genheden (a03samge) (Wed Mar 12 2008 - 11:34:44 CDT)
AMBER: study of protein stability in different ion using AMBER Prem Prakash Pathak (Thu Mar 13 2008 - 01:20:31 CDT)
- Re: AMBER: study of protein stability in different ion using AMBER David A. Case (Sat Mar 15 2008 - 00:48:13 CDT)
AMBER: distance restraint gurpreet singh (Thu Mar 13 2008 - 06:28:28 CDT)
- Re: AMBER: distance restraint David A. Case (Thu Mar 13 2008 - 15:40:07 CDT)
AMBER: [success] problem compiling Amber9 on Bull Linux Yannick Monclin (Thu Mar 13 2008 - 06:56:48 CDT)
AMBER: Energy calculation and replica exchange in Amber9 Li Dawei (Thu Mar 13 2008 - 08:50:49 CDT)
AMBER: can't make antechamber work for regular nucleotides Mey Khalili (Thu Mar 13 2008 - 09:03:45 CDT)
- Re: AMBER: can't make antechamber work for regular nucleotides Junmei Wang (Fri Mar 14 2008 - 21:10:41 CDT)
  - Re: AMBER: can't make antechamber work for regular nucleotides Mey Khalili (Mon Mar 17 2008 - 08:59:01 CDT)
    - Re: AMBER: can't make antechamber work for regular nucleotides Junmei Wang (Tue Mar 18 2008 - 16:08:46 CDT)
AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Thu Mar 13 2008 - 09:54:03 CDT)
- Re: AMBER: ptraj, hbond and non-bonded contacts Thomas Cheatham III (Thu Mar 13 2008 - 12:49:14 CDT)
  - SV: AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Mon Mar 17 2008 - 05:43:21 CDT)
- Re: AMBER: ptraj, hbond and non-bonded contacts Jojart Balazs (Fri Mar 14 2008 - 03:19:37 CDT)
  - SV: AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Mon Mar 17 2008 - 06:02:59 CDT)
AMBER: Temperature Range For REMD tushar garud (Thu Mar 13 2008 - 10:20:02 CDT)
- Re: AMBER: Temperature Range For REMD Carlos Simmerling (Thu Mar 13 2008 - 10:26:44 CDT)
AMBER: force field oguz gurbulak (Thu Mar 13 2008 - 17:00:58 CDT)
AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ) Lwin, ThuZar (Thu Mar 13 2008 - 19:13:57 CDT)
AMBER: How to calculate deformability by PTRAJ ? sychen (Thu Mar 13 2008 - 20:44:36 CDT)
AMBER: Torsion potential in GAFF / "statistic value of parm94" Alexander Metz (Fri Mar 14 2008 - 07:53:10 CDT)
- Re: AMBER: Torsion potential in GAFF / "statistic value of parm94" Junmei Wang (Fri Mar 14 2008 - 22:01:20 CDT)
AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ). Lwin, ThuZar (Fri Mar 14 2008 - 10:32:25 CDT)
- RE: AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ). Ross Walker (Fri Mar 14 2008 - 11:30:13 CDT)
  - RE: AMBER: protonated histidine ( charges in parm file versus all_a mino03.lib ). . . Lwin, ThuZar (Tue Mar 18 2008 - 11:45:49 CDT)
AMBER: Heating POL3 Box Troubles Paul Johns (Fri Mar 14 2008 - 13:44:44 CDT)
- Re: AMBER: Heating POL3 Box Troubles Thomas Steinbrecher (Fri Mar 14 2008 - 14:01:06 CDT)
  - Re: AMBER: Heating POL3 Box Troubles Paul Johns (Fri Mar 14 2008 - 14:13:02 CDT)
- Re: AMBER: Heating POL3 Box Troubles David A. Case (Fri Mar 14 2008 - 22:40:35 CDT)
  - Re: AMBER: Heating POL3 Box Troubles David A. Case (Fri Mar 14 2008 - 23:41:09 CDT)
  - Re: AMBER: Heating POL3 Box Troubles Paul Johns (Mon Mar 17 2008 - 15:07:02 CDT)
AMBER: Negative ligand Syed Tarique Moin (Sat Mar 15 2008 - 04:12:09 CDT)
AMBER: mm_pbsa positive ELE Qi Yan (Mon Mar 17 2008 - 13:20:21 CDT)
- Re: AMBER: mm_pbsa positive ELE Ray Luo (Mon Mar 17 2008 - 13:33:11 CDT)
  - RE: AMBER: mm_pbsa positive ELE Qi Yan (Mon Mar 17 2008 - 14:23:52 CDT)
    - Re: AMBER: mm_pbsa positive ELE Ray Luo (Mon Mar 17 2008 - 15:14:57 CDT)
  - AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Qi Yan (Mon Mar 24 2008 - 15:01:35 CDT)
AMBER: compiling AMBER9 with bintraj option on AMD64 Vlad Cojocaru (Fri Mar 14 2008 - 12:44:56 CDT)
- Re: AMBER: compiling AMBER9 with bintraj option on AMD64 David A. Case (Mon Mar 17 2008 - 18:48:00 CDT)
  - Re: AMBER: compiling AMBER9 with bintraj option on AMD64 Vlad Cojocaru (Tue Mar 18 2008 - 04:32:13 CDT)
AMBER: What's making my system lose total energy? David Cerutti (Mon Mar 17 2008 - 19:20:30 CDT)
- RE: AMBER: What's making my system lose total energy? Ross Walker (Mon Mar 17 2008 - 21:54:19 CDT)
- Re: AMBER: What's making my system lose total energy? Thomas Cheatham (Mon Mar 17 2008 - 22:36:30 CDT)
  - Re: AMBER: What's making my system lose total energy? David Cerutti (Mon Mar 17 2008 - 22:52:10 CDT)
    - Re: AMBER: What's making my system lose total energy? David Cerutti (Tue Mar 18 2008 - 13:43:42 CDT)
    - Re: AMBER: What's making my system lose total energy? David A. Case (Wed Mar 19 2008 - 20:46:31 CDT)
AMBER: a minor bug in RESP Ye Mei (Tue Mar 18 2008 - 02:05:34 CDT)
AMBER: problem with distance restrain aneesh cna (Tue Mar 18 2008 - 05:16:09 CDT)
- Re: AMBER: problem with distance restrain David A. Case (Tue Mar 18 2008 - 14:00:11 CDT)
AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 09:09:34 CDT)
- Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Tue Mar 18 2008 - 09:29:38 CDT)
  - Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 10:29:39 CDT)
  - Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 11:21:21 CDT)
AMBER: Problems with neglected restaints anna.schrey_at_gmx.de (Tue Mar 18 2008 - 11:40:20 CDT)
- Re: AMBER: Problems with neglected restaints Carlos Simmerling (Tue Mar 18 2008 - 12:05:11 CDT)
- Re: AMBER: Problems with neglected restaints David A. Case (Tue Mar 18 2008 - 12:15:56 CDT)
  - Re: AMBER: Problems with neglected restaints anna.schrey_at_gmx.de (Thu Mar 20 2008 - 14:43:20 CDT)
AMBER: Inquiry on analyzing the amplitude from nmdout results James Thomas (Wed Mar 19 2008 - 11:09:05 CDT)
- Re: AMBER: Inquiry on analyzing the amplitude from nmdout results David A. Case (Wed Mar 19 2008 - 16:46:10 CDT)
  - Re: AMBER: Inquiry on analyzing the amplitude from nmdout results James Thomas (Wed Mar 19 2008 - 17:00:35 CDT)
    - Re: AMBER: Inquiry on analyzing the amplitude from nmdout results David A. Case (Wed Mar 19 2008 - 17:49:21 CDT)
AMBER: Amber9 Installation Problem trudy_at_uoguelph.ca (Wed Mar 19 2008 - 11:28:35 CDT)
- Re: AMBER: Amber9 Installation Problem Cenk Andac (Wed Mar 19 2008 - 15:25:25 CDT)
  - Re: AMBER: Amber9 Installation Problem Cenk Andac (Wed Mar 19 2008 - 15:43:50 CDT)
    - Re: AMBER: Amber9 Installation Problem Cenk Andac (Wed Mar 19 2008 - 15:55:23 CDT)
    - Re: AMBER: Amber9 Installation Problem trudy_at_uoguelph.ca (Thu Mar 20 2008 - 17:43:48 CDT)
- Re: AMBER: Amber9 Installation Problem David A. Case (Wed Mar 19 2008 - 20:37:57 CDT)
  - Re: AMBER: Amber9 Installation Problem trudy_at_uoguelph.ca (Thu Mar 20 2008 - 17:51:08 CDT)
    - Re: AMBER: Amber9 Installation Problem David A. Case (Thu Mar 20 2008 - 18:23:53 CDT)
AMBER: Amber9 Installation Problem trudy_at_uoguelph.ca (Wed Mar 19 2008 - 11:28:35 CDT)
AMBER: MNDO parameters for Mg+2 E.M. (Wed Mar 19 2008 - 12:28:09 CDT)
- RE: AMBER: MNDO parameters for Mg+2 Ross Walker (Wed Mar 19 2008 - 13:10:18 CDT)
AMBER: standard residues Holly Freedman (Wed Mar 19 2008 - 15:03:02 CDT)
- Re: AMBER: standard residues David A. Case (Sat Mar 22 2008 - 11:30:03 CDT)
- Re: AMBER: standard residues Holly Freedman (Sat Mar 22 2008 - 17:27:07 CDT)
AMBER: Water Topology Ivelin Georgiev (Wed Mar 19 2008 - 23:12:28 CDT)
- RE: AMBER: Water Topology Ross Walker (Wed Mar 19 2008 - 23:49:43 CDT)
  - Re: AMBER: Water Topology Ivelin Georgiev (Thu Mar 20 2008 - 08:44:51 CDT)
AMBER: potential of mean force: Unit of PMF energies and min path Catein Catherine (Thu Mar 20 2008 - 00:26:43 CDT)
AMBER: Happy holi Bertrand P. S. Russell (Thu Mar 20 2008 - 04:03:22 CDT)
AMBER: problem with distance restraints aneesh cna (Thu Mar 20 2008 - 05:13:31 CDT)
- Re: AMBER: problem with distance restraints David A. Case (Fri Mar 21 2008 - 12:56:28 CDT)
AMBER: Charge scheme for simulating protonated adenine prateeksha s (Fri Mar 21 2008 - 01:58:19 CDT)
- Re: AMBER: Charge scheme for simulating protonated adenine FyD (Fri Mar 21 2008 - 02:43:51 CDT)
  - Re: AMBER: Charge scheme for simulating protonated adenine prateeksha s (Fri Mar 21 2008 - 11:32:06 CDT)
    - Re: AMBER: Charge scheme for simulating protonated adenine prateeksha s (Thu Apr 10 2008 - 01:11:35 CDT)
    - Re: AMBER: Charge scheme for simulating protonated adenine prateeksha s (Thu Apr 10 2008 - 01:19:40 CDT)
- Re: AMBER: Charge scheme for simulating protonated adenine rpaduri_at_chem.wayne.edu (Fri Mar 21 2008 - 10:29:18 CDT)
  - Re: AMBER: Charge scheme for simulating protonated adenine prateeksha s (Fri Mar 21 2008 - 11:32:14 CDT)
AMBER: equilibration of peptide tushar garud (Fri Mar 21 2008 - 23:02:25 CDT)
- Re: AMBER: equilibration of peptide David A. Case (Sat Mar 22 2008 - 12:51:47 CDT)
  - AMBER: addions and addions2 dpandit_at_brandeis.edu (Tue Mar 25 2008 - 09:38:22 CDT)
AMBER: cntrl namelist error Campbell, Patrick (Sat Mar 22 2008 - 10:40:16 CDT)
- RE: AMBER: cntrl namelist error Ross Walker (Sat Mar 22 2008 - 11:01:47 CDT)
  - RE: AMBER: cntrl namelist error Campbell, Patrick (Sat Mar 22 2008 - 11:11:39 CDT)
- Re: AMBER: cntrl namelist error David A. Case (Sat Mar 22 2008 - 11:11:52 CDT)
  - RE: AMBER: cntrl namelist error Campbell, Patrick (Sat Mar 22 2008 - 11:22:18 CDT)
AMBER: RE: Force Field Parameterizing Shultz, Jack (Mon Mar 24 2008 - 10:31:32 CDT)
- Re: AMBER: RE: Force Field Parameterizing David A. Case (Tue Mar 25 2008 - 10:23:34 CDT)
  - AMBER: RE: Force Field Parameterizing FyD (Tue Mar 25 2008 - 14:42:03 CDT)
AMBER: hybrid remd imaging Geoff Wood (Mon Mar 24 2008 - 10:51:51 CDT)
- Re: AMBER: hybrid remd imaging Carlos Simmerling (Mon Mar 24 2008 - 10:59:24 CDT)
  - Re: AMBER: hybrid remd imaging Geoff Wood (Mon Mar 24 2008 - 11:21:41 CDT)
    - Re: AMBER: hybrid remd imaging Geoff Wood (Thu Mar 27 2008 - 07:56:30 CDT)
  - Re: AMBER: hybrid remd imaging Geoff Wood (Mon Mar 24 2008 - 11:16:25 CDT)
AMBER: Nmode segmentation fault James Thomas (Tue Mar 25 2008 - 06:53:21 CDT)
- Re: AMBER: Nmode segmentation fault David A. Case (Tue Mar 25 2008 - 11:34:37 CDT)
  - Re: AMBER: Nmode segmentation fault James Thomas (Tue Mar 25 2008 - 12:22:43 CDT)
AMBER: anion and cation simulaton gurpreet singh (Tue Mar 25 2008 - 11:22:29 CDT)
- Re: AMBER: anion and cation simulaton FyD (Tue Mar 25 2008 - 14:54:56 CDT)
AMBER: help regarding warning message snoze pa (Tue Mar 25 2008 - 11:17:43 CDT)
- Re: AMBER: help regarding warning message David A. Case (Tue Mar 25 2008 - 13:51:07 CDT)
  - Re: AMBER: help regarding warning message snoze pa (Tue Mar 25 2008 - 15:23:55 CDT)
Re: AMBER: addions and addions2 Bill Ross (Tue Mar 25 2008 - 12:34:52 CDT)
AMBER: Convert dcd to mdcrd Seth Lilavivat (Tue Mar 25 2008 - 13:13:22 CDT)
- Re: AMBER: Convert dcd to mdcrd Vlad Cojocaru (Wed Mar 26 2008 - 04:02:38 CDT)
  - AMBER: FAD and NAD parameters Thomas Leonard (Wed Mar 26 2008 - 04:26:52 CDT)
    - Re: AMBER: FAD and NAD parameters FyD (Wed Mar 26 2008 - 05:57:27 CDT)
    - Re: AMBER: FAD and NAD parameters Thomas Leonard (Thu Apr 10 2008 - 01:43:47 CDT)
AMBER: umbrella sampling for proton transfer cniu_at_ualberta.ca (Tue Mar 25 2008 - 19:30:33 CDT)
- Re: AMBER: umbrella sampling for proton transfer Thomas Steinbrecher (Tue Mar 25 2008 - 20:11:58 CDT)
AMBER: NTR Restraints Daniel Smith (Tue Mar 25 2008 - 20:17:27 CDT)
- Re: AMBER: NTR Restraints David A. Case (Thu Mar 27 2008 - 15:17:31 CDT)
AMBER: OPLS force field aneesh cna (Wed Mar 26 2008 - 10:48:19 CDT)
- Re: AMBER: OPLS force field David A. Case (Wed Mar 26 2008 - 11:08:57 CDT)
AMBER: mm-pbsa multiple trajectory approach? Seth Lilavivat (Wed Mar 26 2008 - 12:32:54 CDT)
- Re: AMBER: mm-pbsa multiple trajectory approach? Chris Moth (Wed Mar 26 2008 - 17:21:25 CDT)
  - Re: AMBER: mm-pbsa multiple trajectory approach? Seth Lilavivat (Fri Mar 28 2008 - 10:28:31 CDT)
    - Re: AMBER: mm-pbsa multiple trajectory approach? Chris Moth (Wed Apr 02 2008 - 16:18:06 CDT)
AMBER: residual dipolar couplings - alignment tensor energy Douglas Kojetin (Wed Mar 26 2008 - 14:46:48 CDT)
- Re: AMBER: residual dipolar couplings - alignment tensor energy Douglas Kojetin (Tue Apr 01 2008 - 10:23:59 CDT)
  - Re: AMBER: residual dipolar couplings - alignment tensor energy Douglas Kojetin (Tue Apr 01 2008 - 10:53:55 CDT)
  - AMBER: Electric field on atoms in equallibrium Lishan Yao (Tue Apr 01 2008 - 11:55:39 CDT)
- Re: AMBER: residual dipolar couplings - alignment tensor energy David A. Case (Wed Apr 02 2008 - 12:53:38 CDT)
AMBER: RMSD of two different molecules JunJun Liu (Wed Mar 26 2008 - 15:35:32 CDT)
- Re: AMBER: RMSD of two different molecules Da-Wei Li (Wed Mar 26 2008 - 15:39:19 CDT)
  - Re: AMBER: RMSD of two different molecules JunJun Liu (Wed Mar 26 2008 - 16:54:11 CDT)
AMBER: how to link two different atoms in xLeap snoze pa (Wed Mar 26 2008 - 15:56:12 CDT)
- Re: AMBER: how to link two different atoms in xLeap David A. Case (Wed Mar 26 2008 - 23:52:18 CDT)
AMBER: Error with a binary restart file Kijeong Kwac (Wed Mar 26 2008 - 18:07:51 CDT)
- Re: AMBER: Error with a binary restart file David A. Case (Wed Mar 26 2008 - 20:11:58 CDT)
AMBER: PF6 parameters aneesh cna (Wed Mar 26 2008 - 23:43:58 CDT)
- RE: AMBER: PF6 parameters caoch (Thu Mar 27 2008 - 23:28:03 CDT)
AMBER: Error- MM_PBSA calculation vikky 99 (Thu Mar 27 2008 - 03:47:53 CDT)
AMBER: FW: MD run time inquiry Campbell, Patrick (Thu Mar 27 2008 - 05:13:00 CDT)
- Re: AMBER: FW: MD run time inquiry Carlos Simmerling (Thu Mar 27 2008 - 05:41:02 CDT)
- FW: AMBER: FW: MD run time inquiry Campbell, Patrick (Thu Mar 27 2008 - 07:14:16 CDT)
  - Re: FW: AMBER: FW: MD run time inquiry Carlos Simmerling (Thu Mar 27 2008 - 08:15:09 CDT)
- FW: FW: AMBER: FW: MD run time inquiry Campbell, Patrick (Thu Mar 27 2008 - 08:55:28 CDT)
AMBER: Protein rotating out of box Lars Skjærven (Thu Mar 27 2008 - 16:34:48 CDT)
- RE: AMBER: Protein rotating out of box Steve Spronk (Tue Apr 01 2008 - 09:55:20 CDT)
  - Re: AMBER: Protein rotating out of box Lars Skjærven (Wed Apr 02 2008 - 07:36:20 CDT)
    - RE: AMBER: Protein rotating out of box Steve Spronk (Wed Apr 02 2008 - 08:13:12 CDT)
    - Re: AMBER: Protein rotating out of box Thomas Cheatham III (Wed Apr 02 2008 - 11:54:46 CDT)
- Re: AMBER: Protein rotating out of box Qiang Li (Wed Apr 02 2008 - 12:35:04 CDT)
  - Re: AMBER: Protein rotating out of box Lars Skjærven (Wed Apr 02 2008 - 14:17:23 CDT)
    - Re: AMBER: Protein rotating out of box Lars Skjærven (Wed Apr 02 2008 - 16:01:54 CDT)
    - Re: AMBER: Protein rotating out of box David A. Case (Tue Apr 08 2008 - 20:54:29 CDT)
AMBER: measuring contacts: error "glibc detected" rebeca_at_mmb.pcb.ub.es (Fri Mar 28 2008 - 07:26:42 CDT)
AMBER: GAFF Eric Germaneau (Fri Mar 28 2008 - 07:38:41 CDT)
AMBER: REMD simulation error Guillaume Renvez (Fri Mar 28 2008 - 09:01:20 CDT)
AMBER: problem with nmod yuri pomè (Fri Mar 28 2008 - 11:42:54 CDT)
- Re: AMBER: problem with nmod David A. Case (Fri Mar 28 2008 - 19:19:40 CDT)
AMBER: meet problem in adding ions and waterbox Qiang Li (Sun Mar 30 2008 - 00:43:54 CDT)
- Re: AMBER: meet problem in adding ions and waterbox Emilio Xavier Esposito (Sun Mar 30 2008 - 12:26:45 CDT)
AMBER: Regarding SHAKE gurpreet singh (Sun Mar 30 2008 - 05:38:48 CDT)
- Re: AMBER: Regarding SHAKE David A. Case (Wed Apr 02 2008 - 12:54:59 CDT)
AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water Markus Kaukonen (Mon Mar 31 2008 - 01:34:48 CDT)
- Re: AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water David A. Case (Mon Apr 07 2008 - 15:40:27 CDT)
  - AMBER: how to change the force field parameters inside the prmtop file? Chih-Ying Lin (Mon Apr 07 2008 - 16:24:17 CDT)
AMBER: Free energy landscape? HOWTO? Yi-Ming Cheng (Mon Mar 31 2008 - 03:12:05 CDT)
AMBER: TI: perturbation method fatima.chami_at_durham.ac.uk (Mon Mar 31 2008 - 03:40:40 CDT)
- Re: AMBER: TI: perturbation method Thomas Steinbrecher (Mon Mar 31 2008 - 11:32:21 CDT)
AMBER: energy problems in simulation with restraints Daniel Cappel (Mon Mar 31 2008 - 04:39:13 CDT)
- Re: AMBER: energy problems in simulation with restraints David A. Case (Mon Mar 31 2008 - 10:35:58 CDT)
AMBER: Select specific residues (leap) Marta Rossini (Mon Mar 31 2008 - 04:28:31 CDT)
- Re: AMBER: Select specific residues (leap) FyD (Mon Mar 31 2008 - 05:31:39 CDT)
  - RE: AMBER: Select specific residues (leap) Marta Rossini (Mon Mar 31 2008 - 06:00:52 CDT)
AMBER: installation amber9 Geoff Wood (Mon Mar 31 2008 - 06:02:01 CDT)
- Re: AMBER: installation amber9 David A. Case (Mon Mar 31 2008 - 12:51:45 CDT)
AMBER: multiple dihedral restraints using group mkseo (Mon Mar 31 2008 - 12:11:30 CDT)
- Re: AMBER: multiple dihedral restraints using group David A. Case (Wed Apr 02 2008 - 15:44:20 CDT)
AMBER: memory limitation of Amber 9 yavuzturkm_at_prc.boun.edu.tr (Mon Mar 31 2008 - 13:49:40 CDT)
- Re: AMBER: memory limitation of Amber 9 David A. Case (Tue Apr 01 2008 - 00:50:41 CDT)
AMBER: nmode James Thomas (Mon Mar 31 2008 - 13:48:43 CDT)
- Re: AMBER: nmode David A. Case (Mon Mar 31 2008 - 14:25:52 CDT)
AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Mon Mar 31 2008 - 14:45:20 CDT)
- Re: AMBER: running minimisation on cis-azobenzene Thomas Steinbrecher (Mon Mar 31 2008 - 15:14:17 CDT)
AMBER: Amber 8 on Redhat 4 X86_64 yavuzturkm_at_prc.boun.edu.tr (Tue Apr 01 2008 - 00:30:32 CDT)
AMBER: TIP5P water simulation with AMBER7 Biman Jana (Tue Apr 01 2008 - 02:14:54 CDT)
AMBER: hybrid remd imaging Geoff Wood (Tue Apr 01 2008 - 02:47:18 CDT)
AMBER: working with unformatted restart files in AMBER9 Vlad Cojocaru (Tue Apr 01 2008 - 08:35:57 CDT)
- Re: AMBER: working with unformatted restart files in AMBER9 Thomas Cheatham III (Wed Apr 02 2008 - 12:26:00 CDT)
AMBER: atomic posiltional fluctuation Furia Gargano (Tue Apr 01 2008 - 09:11:12 CDT)
- Re: AMBER: atomic posiltional fluctuation Thomas Cheatham III (Tue Apr 01 2008 - 11:50:43 CDT)
AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
- Re: AMBER: B-factor Thomas Cheatham III (Wed Apr 02 2008 - 12:18:18 CDT)
AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
- Re: AMBER: Simulating DNA Backbone in NAB David A. Case (Wed Apr 02 2008 - 15:24:25 CDT)
  - AMBER: PMF calculation for rate constant or binding constant? Catein Catherine (Tue Apr 15 2008 - 21:28:43 CDT)
AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
AMBER: LEap error message for parmBSC0 force field Cenk Andac (Tue Apr 01 2008 - 18:31:17 CDT)
- Re: AMBER: LEap error message for parmBSC0 force field Thomas Cheatham III (Tue Apr 01 2008 - 18:55:38 CDT)
  - Re: AMBER: LEap error message for parmBSC0 force field Cenk Andac (Thu Apr 03 2008 - 07:52:37 CDT)
    - Re: AMBER: LEap error message for parmBSC0 force field Alberto Perez (Thu Apr 03 2008 - 09:00:09 CDT)
- Re: AMBER: LEap error message for parmBSC0 force field Bill Ross (Thu Apr 03 2008 - 12:28:51 CDT)
  - Re: AMBER: LEap error message for parmBSC0 force field Cenk Andac (Thu Apr 03 2008 - 13:08:58 CDT)
- Re: AMBER: LEap error message for parmBSC0 force field Bill Ross (Thu Apr 03 2008 - 15:12:12 CDT)
- Re: AMBER: LEap error message for parmBSC0 force field Bill Ross (Thu Apr 03 2008 - 15:16:27 CDT)
AMBER: meet problems in adding ions and waterbox Qiang Li (Wed Apr 02 2008 - 00:12:31 CDT)
- Re: AMBER: meet problems in adding ions and waterbox David A. Case (Wed Apr 02 2008 - 00:22:52 CDT)
- Re: AMBER: meet problems in adding ions and waterbox Qiang Li (Wed Apr 02 2008 - 01:12:13 CDT)
  - Re: AMBER: meet problems in adding ions and waterbox David A. Case (Wed Apr 02 2008 - 11:37:05 CDT)
AMBER: LJ parameters aneesh cna (Wed Apr 02 2008 - 06:46:22 CDT)
- Re: AMBER: LJ parameters Thomas Steinbrecher (Wed Apr 02 2008 - 12:31:57 CDT)
  - Re: AMBER: LJ parameters aneesh cna (Thu Apr 03 2008 - 06:30:39 CDT)
AMBER: REMD simulation error Guillaume Renvez (Wed Apr 02 2008 - 07:47:20 CDT)
AMBER: ANNOUNCE: Release of AmberTools, version 1.0 David A. Case (Wed Apr 02 2008 - 11:49:20 CDT)
AMBER: ptraj / covariance / quasiharmonic approximation / entropy Seth Lilavivat (Wed Apr 02 2008 - 14:18:55 CDT)
- Re: AMBER: ptraj / covariance / quasiharmonic approximation / entropy Chris Moth (Wed Apr 02 2008 - 16:09:14 CDT)
AMBER: NAD parameters Urszula Uciechowska (Thu Apr 03 2008 - 09:30:05 CDT)
- Re: AMBER: NAD parameters David A. Case (Thu Apr 03 2008 - 10:01:46 CDT)
- RE: AMBER: NAD parameters Ross Walker (Thu Apr 03 2008 - 09:56:45 CDT)
AMBER: dockmolecules in examples directory of AmberTools-1.0 M. L. Dodson (Thu Apr 03 2008 - 10:54:50 CDT)
AMBER: MPI run problem Qi Yan (Thu Apr 03 2008 - 11:33:19 CDT)
- AMBER: Simple Minimization - Error dpandit_at_brandeis.edu (Thu Apr 03 2008 - 14:55:08 CDT)
  - Re: AMBER: Simple Minimization - Error Daniel Smith (Thu Apr 03 2008 - 15:10:28 CDT)
  - Re: AMBER: Simple Minimization - Error David A. Case (Thu Apr 03 2008 - 15:11:13 CDT)
- Re: AMBER: MPI run problem David A. Case (Thu Apr 03 2008 - 15:38:38 CDT)
  - Re: AMBER: MPI run problem Robert Duke (Thu Apr 03 2008 - 15:57:33 CDT)
    - RE: AMBER: MPI run problem Qi Yan (Thu Apr 03 2008 - 16:59:27 CDT)
AMBER: problem with Mg2+ during MD Zhenwei Lu (Thu Apr 03 2008 - 11:48:13 CDT)
AMBER: mm_pbsa error rams rams (Thu Apr 03 2008 - 11:28:56 CDT)
- Re: AMBER: mm_pbsa error stephane acoca (Thu Apr 03 2008 - 15:21:29 CDT)
  - Re: AMBER: mm_pbsa error Scott Pendley (Fri Apr 04 2008 - 11:29:16 CDT)
AMBER: Using mdcrd files to look at minor charge changes Cooper, Matthew (Thu Apr 03 2008 - 13:45:12 CDT)
- Re: AMBER: Using mdcrd files to look at minor charge changes David A. Case (Thu Apr 03 2008 - 14:46:46 CDT)
AMBER: imem keyword using mmpbsa Sergio Wong (Thu Apr 03 2008 - 15:43:01 CDT)
- Re: AMBER: imem keyword using mmpbsa Sergio Wong (Thu Apr 03 2008 - 20:18:10 CDT)
- Re: AMBER: imem keyword using mmpbsa David A. Case (Thu Apr 03 2008 - 23:04:11 CDT)
  - AMBER: Restraintmask and Restraint_WT : Question dpandit_at_brandeis.edu (Fri Apr 04 2008 - 10:24:32 CDT)
    - Re: AMBER: Restraintmask and Restraint_WT : Question Thomas Steinbrecher (Fri Apr 04 2008 - 11:18:17 CDT)
AMBER: ligand slips out of pocket Hannes Wallnoefer (Fri Apr 04 2008 - 02:58:29 CDT)
AMBER: solvateOct produces strange residues compared to solvateCap Markus Kaukonen (Fri Apr 04 2008 - 03:08:53 CDT)
- Re: AMBER: solvateOct produces strange residues compared to solvateCap David A. Case (Thu Apr 10 2008 - 14:29:52 CDT)
AMBER: GAFF Eric Germaneau (Fri Apr 04 2008 - 03:18:03 CDT)
- Re: AMBER: GAFF Vlad Cojocaru (Fri Apr 04 2008 - 03:22:30 CDT)
  - Re: AMBER: GAFF Eric Germaneau (Fri Apr 04 2008 - 03:27:07 CDT)
AMBER: sander.MPI setup with SGE Sasha Buzko (Fri Apr 04 2008 - 11:59:34 CDT)
- RE: AMBER: sander.MPI setup with SGE Ross Walker (Sat Apr 05 2008 - 11:18:45 CDT)
  - Re: AMBER: sander.MPI setup with SGE Sasha Buzko (Mon Apr 07 2008 - 15:51:20 CDT)
AMBER: artifacts in ptraj avg output stephane acoca (Sat Apr 05 2008 - 03:46:55 CDT)
- Re: AMBER: artifacts in ptraj avg output Barbault Florent (Sat Apr 05 2008 - 04:11:37 CDT)
  - Re: AMBER: artifacts in ptraj avg output stephane acoca (Sat Apr 05 2008 - 04:52:26 CDT)
AMBER: RE: amber help Ross Walker (Sat Apr 05 2008 - 22:25:19 CDT)
AMBER: NAB examples Hu, Shaowen (JSC-SK)[USRA] (Mon Apr 07 2008 - 09:32:07 CDT)
- Re: AMBER: NAB examples David A. Case (Mon Apr 07 2008 - 10:33:26 CDT)
  - RE: AMBER: NAB examples Hu, Shaowen (JSC-SK)[USRA] (Mon Apr 07 2008 - 11:09:44 CDT)
- Re: AMBER: NAB examples Andreas Svrcek-Seiler (Mon Apr 07 2008 - 11:46:34 CDT)
AMBER: restraint box dimension aneesh cna (Tue Apr 08 2008 - 05:45:20 CDT)
- Re: AMBER: restraint box dimension David A. Case (Tue Apr 08 2008 - 19:34:05 CDT)
  - Re: AMBER: restraint box dimension aneesh cna (Fri Apr 11 2008 - 04:56:17 CDT)
    - Re: AMBER: restraint box dimension Carlos Simmerling (Fri Apr 11 2008 - 05:22:38 CDT)
AMBER: Should the two phenyl rings of the trans-azobenzene on the same plane after minimisation? Chih-Ying Lin (Tue Apr 08 2008 - 20:09:24 CDT)
AMBER: converting from CNS file format Sally Pias (Wed Apr 09 2008 - 00:32:11 CDT)
- Re: AMBER: converting from CNS file format Sally Pias (Fri Apr 11 2008 - 00:04:55 CDT)
AMBER: Estimating dielectric constant Marcelo Puiatti (Wed Apr 09 2008 - 09:42:40 CDT)
AMBER: Collect dihedral angles Chih-Ying Lin (Wed Apr 09 2008 - 16:35:09 CDT)
- AMBER: Tutorial B3- Section6 Chih-Ying Lin (Wed Apr 09 2008 - 20:30:27 CDT)
  - Re: AMBER: Tutorial B3- Section6 David A. Case (Wed Apr 09 2008 - 20:46:16 CDT)
AMBER: Force field Parameters Chih-Ying Lin (Wed Apr 09 2008 - 21:17:51 CDT)
AMBER: tempi in Replica Exchange rebeca_at_mmb.pcb.ub.es (Thu Apr 10 2008 - 04:23:00 CDT)
- Re: AMBER: tempi in Replica Exchange Carlos Simmerling (Thu Apr 10 2008 - 10:37:46 CDT)
AMBER: WHAM: how frequently do I need data on the system coordinates? David Cerutti (Thu Apr 10 2008 - 11:14:23 CDT)
- Re: AMBER: WHAM: how frequently do I need data on the system coordinates? John Chodera (Thu Apr 10 2008 - 12:47:57 CDT)
AMBER: protein-ligand complex problem Lynn (Thu Apr 10 2008 - 17:51:32 CDT)
- RE: AMBER: protein-ligand complex problem Ross Walker (Thu Apr 10 2008 - 18:50:19 CDT)
- Re: AMBER: protein-ligand complex problem David A. Case (Thu Apr 10 2008 - 18:51:55 CDT)
AMBER: trans-azobenzene under minimisation Chih-Ying Lin (Thu Apr 10 2008 - 19:29:37 CDT)
AMBER: query about Generalized Born simulation gurvisha_at_leadinvent.com (Fri Apr 11 2008 - 08:42:23 CDT)
- Re: AMBER: query about Generalized Born simulation Carlos Simmerling (Fri Apr 11 2008 - 09:15:53 CDT)
- Re: AMBER: query about Generalized Born simulation rpaduri_at_chem.wayne.edu (Fri Apr 11 2008 - 09:31:21 CDT)
AMBER: Amber installation jacopo.sgrignani_at_unifi.it (Fri Apr 11 2008 - 08:23:24 CDT)
- RE: AMBER: Amber installation Ross Walker (Fri Apr 11 2008 - 13:09:14 CDT)
- Re: AMBER: Amber installation Mengjuei Hsieh (Fri Apr 11 2008 - 16:39:48 CDT)
- RE: AMBER: Amber installation Ross Walker (Fri Apr 11 2008 - 17:45:42 CDT)
AMBER: Imaging before HBond analysis? Evan Kelly (Fri Apr 11 2008 - 15:34:41 CDT)
- Re: AMBER: Imaging before HBond analysis? Thomas Cheatham III (Fri Apr 11 2008 - 17:24:29 CDT)
  - Re: AMBER: Imaging before HBond analysis? Evan Kelly (Fri Apr 11 2008 - 17:41:51 CDT)
    - Re: AMBER: Imaging before HBond analysis? Thomas Cheatham III (Fri Apr 11 2008 - 17:52:04 CDT)
    - Re: AMBER: Imaging before HBond analysis? Evan Kelly (Fri Apr 11 2008 - 18:09:32 CDT)
AMBER: installing pmemd with fftw YangMingjun (Sun Apr 13 2008 - 08:07:44 CDT)
- Re: AMBER: installing pmemd with fftw Robert Duke (Sun Apr 13 2008 - 08:57:36 CDT)
  - Re: Re: AMBER: installing pmemd with fftw YangMingjun (Sun Apr 13 2008 - 20:08:16 CDT)
AMBER: topology file Giuseppe De Marco (Mon Apr 14 2008 - 04:38:37 CDT)
- Re: AMBER: topology file David A. Case (Wed Apr 16 2008 - 12:45:52 CDT)
AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits Ted Fischer (Mon Apr 14 2008 - 07:53:42 CDT)
- Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits David A. Case (Tue Apr 15 2008 - 00:26:45 CDT)
- Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits Ted Fischer (Tue Apr 15 2008 - 04:09:47 CDT)
  - Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits David A. Case (Fri Apr 18 2008 - 17:00:23 CDT)
AMBER: error in compilation elsize.cc snoze pa (Mon Apr 14 2008 - 11:38:07 CDT)
- Re: AMBER: error in compilation elsize.cc David A. Case (Mon Apr 14 2008 - 12:11:33 CDT)
  - Re: AMBER: error in compilation elsize.cc snoze pa (Mon Apr 14 2008 - 13:20:40 CDT)
- Re: AMBER: error in compilation elsize.cc Scott Brozell (Mon May 05 2008 - 13:55:49 CDT)
AMBER: ANNOUNCEMENT: release of Amber 10 David A. Case (Mon Apr 14 2008 - 12:18:40 CDT)
- AMBER: Prepgen does not give correct result? Rajendra P. OJHA (Fri May 09 2008 - 11:13:58 CDT)
AMBER: loadPdb returns extra atoms Seth Lilavivat (Mon Apr 14 2008 - 13:50:32 CDT)
- Re: AMBER: loadPdb returns extra atoms Thomas Cheatham III (Mon Apr 14 2008 - 14:19:03 CDT)
AMBER: Problems compiling Amber with MKL Sasha Buzko (Mon Apr 14 2008 - 14:13:23 CDT)
- RE: AMBER: Problems compiling Amber with MKL Ross Walker (Mon Apr 14 2008 - 16:32:49 CDT)
  - RE: AMBER: Problems compiling Amber with MKL Sasha Buzko (Mon Apr 14 2008 - 17:25:43 CDT)
    - RE: AMBER: Problems compiling Amber with MKL Sasha Buzko (Mon Apr 14 2008 - 18:24:05 CDT)
AMBER: JavaGenes Shultz, Jack (Mon Apr 14 2008 - 14:26:25 CDT)
- AMBER: Whole System Equilibration & Pressure dpandit_at_brandeis.edu (Mon Apr 14 2008 - 15:57:54 CDT)
  - RE: AMBER: Whole System Equilibration & Pressure Ross Walker (Mon Apr 14 2008 - 16:37:51 CDT)
    - RE: AMBER: Whole System Equilibration & Pressure dpandit_at_brandeis.edu (Tue Apr 15 2008 - 09:16:35 CDT)
AMBER: energy decomposition vs ala scan Sergio Wong (Mon Apr 14 2008 - 21:05:41 CDT)
AMBER: imaging problem Marcin Krol (Tue Apr 15 2008 - 06:54:30 CDT)
- Re: AMBER: imaging problem Carlos Simmerling (Tue Apr 15 2008 - 07:22:18 CDT)
  - Re: AMBER: imaging problem Marcin Krol (Tue Apr 15 2008 - 08:16:01 CDT)
    - Re: AMBER: imaging problem David Smith (Tue Apr 15 2008 - 08:30:48 CDT)
    - Re: AMBER: imaging problem Marcin Krol (Tue Apr 15 2008 - 08:38:07 CDT)
AMBER: mmpbsa with gromacs trajectory jacopo.sgrignani_at_unifi.it (Tue Apr 15 2008 - 09:10:21 CDT)
AMBER: loading pdb in leap to create parameter files Cristina Sisu (Tue Apr 15 2008 - 08:43:57 CDT)
- Re: AMBER: loading pdb in leap to create parameter files Da-Wei Li (Tue Apr 15 2008 - 08:53:06 CDT)
  - Re: AMBER: loading pdb in leap to create parameter files Cristina Sisu (Tue Apr 15 2008 - 09:50:12 CDT)
    - RE: AMBER: loading pdb in leap to create parameter files Steve Spronk (Mon Apr 21 2008 - 12:04:34 CDT)
AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? cgji (Tue Apr 15 2008 - 10:27:08 CDT)
- RE: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? Ross Walker (Tue Apr 15 2008 - 10:47:53 CDT)
- Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? David A. Case (Tue Apr 15 2008 - 16:01:15 CDT)
- Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? cgji (Sat Sep 20 2008 - 11:22:07 CDT)
  - Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? David A. Case (Mon Sep 22 2008 - 06:25:38 CDT)
AMBER: xleap segmentation fault on SaveAmberParm Brendan Duggan (Tue Apr 15 2008 - 14:15:46 CDT)
- Re: AMBER: xleap segmentation fault on SaveAmberParm Wei Zhang (Tue Apr 15 2008 - 14:32:32 CDT)
- Re: AMBER: xleap segmentation fault on SaveAmberParm David A. Case (Tue Apr 15 2008 - 16:00:47 CDT)
AMBER: Extracting the electric field (and its gradient) on particular solute atoms John Chodera (Tue Apr 15 2008 - 19:36:01 CDT)
- Re: AMBER: Extracting the electric field (and its gradient) on particular solute atoms Tom Darden (Wed Apr 16 2008 - 16:30:53 CDT)
  - Re: AMBER: Extracting the electric field (and its gradient) on particular solute atoms John Chodera (Wed Apr 16 2008 - 17:15:19 CDT)
AMBER: PMF calculation for binding constant or rate constant? Catein Catherine (Tue Apr 15 2008 - 21:26:46 CDT)
- Re: AMBER: PMF calculation for binding constant or rate constant? David A. Case (Wed Apr 16 2008 - 16:26:13 CDT)
AMBER: leap - using default radius 1.500000 for HO3 Nina Fischer (Wed Apr 16 2008 - 04:08:59 CDT)
- AMBER: vlimit-problems after image and restart Anselm Horn (Tue Apr 22 2008 - 04:04:46 CDT)
  - RE: AMBER: vlimit-problems after image and restart Ross Walker (Tue Apr 22 2008 - 23:45:29 CDT)
AMBER: Protonation states in Constant pH Simulations Neil Bruce (Wed Apr 16 2008 - 07:54:44 CDT)
AMBER: Distance in z dimension Age.Skjevik_at_student.uib.no (Wed Apr 16 2008 - 09:50:55 CDT)
AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko (Wed Apr 16 2008 - 16:43:07 CDT)
- RE: AMBER: Amber9 with MPICH2 failure at runtime Ross Walker (Wed Apr 16 2008 - 17:05:26 CDT)
  - RE: AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko (Wed Apr 16 2008 - 17:43:12 CDT)
AMBER: xLeap unit editor "seg fault" inonshar_at_post.tau.ac.il (Thu Apr 17 2008 - 00:49:01 CDT)
- AMBER: Accessing Equilibration Results dpandit_at_brandeis.edu (Thu Apr 17 2008 - 08:29:35 CDT)
- Re: AMBER: xLeap unit editor "seg fault" David A. Case (Thu Apr 17 2008 - 19:53:29 CDT)
AMBER: Scale LJ parameters fatima.chami_at_durham.ac.uk (Thu Apr 17 2008 - 06:20:40 CDT)
- Re: AMBER: Scale LJ parameters David A. Case (Thu Apr 17 2008 - 19:54:43 CDT)
AMBER: uccabke_at_ucl.ac.uk (Thu Apr 17 2008 - 10:02:06 CDT)
- AMBER: H atom names in Amber David A. Case (Thu Apr 17 2008 - 10:16:19 CDT)
  - Re: AMBER: H atom names in Amber uccabke_at_ucl.ac.uk (Thu Apr 17 2008 - 10:49:57 CDT)
- Re: AMBER: Da-Wei Li (Thu Apr 17 2008 - 10:18:04 CDT)
- Re: AMBER: Florian Haberl (Thu Apr 17 2008 - 10:17:24 CDT)
AMBER: Performance issues on Ethernet clusters Sasha Buzko (Thu Apr 17 2008 - 13:20:52 CDT)
- Re: AMBER: Performance issues on Ethernet clusters David A. Case (Thu Apr 17 2008 - 14:02:45 CDT)
- Re: AMBER: Performance issues on Ethernet clusters Robert Duke (Thu Apr 17 2008 - 15:14:32 CDT)
  - Re: AMBER: Performance issues on Ethernet clusters Sasha Buzko (Thu Apr 17 2008 - 16:18:44 CDT)
    - AMBER: SiCortex as an alternative to Ethernet and infiniband clusters Kevin Abbey (Thu Apr 17 2008 - 16:37:23 CDT)
    - Re: AMBER: SiCortex as an alternative to Ethernet and infiniband clusters Sasha Buzko (Thu Apr 17 2008 - 17:39:46 CDT)
AMBER: Conformation search... Anthony Cruz (Thu Apr 17 2008 - 14:32:52 CDT)
AMBER: Short trajectory segments / frequent restarts causes explosion David Cerutti (Thu Apr 17 2008 - 16:04:14 CDT)
- Re: AMBER: Short trajectory segments / frequent restarts causes explosion Robert Duke (Thu Apr 17 2008 - 16:52:55 CDT)
AMBER: compile Amber9 on 64bit AMD Opteron Jeffrey (Fri Apr 18 2008 - 02:02:24 CDT)
- Re: AMBER: compile Amber9 on 64bit AMD Opteron David A. Case (Fri Apr 18 2008 - 10:23:48 CDT)
AMBER: nmode problem Hannes Wallnoefer (Fri Apr 18 2008 - 04:01:27 CDT)
- Re: AMBER: nmode problem Hannes Wallnoefer (Fri Apr 18 2008 - 04:44:38 CDT)
AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen (Fri Apr 18 2008 - 14:17:37 CDT)
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers David A. Case (Fri Apr 18 2008 - 15:44:36 CDT)
  - Re: AMBER: AmberTools on OS X Leopard with Intel compilers David A. Case (Fri Apr 18 2008 - 16:17:32 CDT)
  - Re: AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen (Mon Apr 21 2008 - 09:30:10 CDT)
AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai (Fri Apr 18 2008 - 18:43:01 CDT)
- Re: AMBER: hydrogens are flying in replica exchange simulations Carlos Simmerling (Fri Apr 18 2008 - 19:02:39 CDT)
  - Re: AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai (Fri Apr 18 2008 - 19:18:32 CDT)
AMBER: How to add radius of an atom saurabh agrawal (Mon Apr 21 2008 - 00:45:43 CDT)
AMBER: Average structure James Thomas (Mon Apr 21 2008 - 05:21:26 CDT)
- Re: AMBER: Average structure David Cerutti (Mon Apr 21 2008 - 11:12:30 CDT)
  - RE: AMBER: Average structure Ross Walker (Mon Apr 21 2008 - 21:27:08 CDT)
    - RE: AMBER: Average structure Francesco Pietra (Tue Apr 22 2008 - 02:02:23 CDT)
AMBER: nmode jacopo.sgrignani_at_unifi.it (Mon Apr 21 2008 - 12:38:44 CDT)
- Re: AMBER: nmode David A. Case (Mon Apr 21 2008 - 16:05:20 CDT)
AMBER: aromatic residues lost planarity during MD simulation cniu_at_ualberta.ca (Mon Apr 21 2008 - 15:18:26 CDT)
- Re: AMBER: aromatic residues lost planarity during MD simulation Carlos Simmerling (Mon Apr 21 2008 - 15:25:19 CDT)
AMBER: Can sander provide ESP with PBC? Khatcharin Siriwong (Mon Apr 21 2008 - 20:36:17 CDT)
- Re: AMBER: Can sander provide ESP with PBC? John Chodera (Mon Apr 21 2008 - 21:24:25 CDT)
  - Re: AMBER: Can sander provide ESP with PBC? Thomas Steinbrecher (Wed Apr 23 2008 - 13:39:10 CDT)
    - Re: AMBER: Can sander provide ESP with PBC? Khatcharin Siriwong (Wed Apr 23 2008 - 20:43:12 CDT)
AMBER: How to change default radius assigned to an atom saurabh agrawal (Mon Apr 21 2008 - 23:47:14 CDT)
- Re: AMBER: How to change default radius assigned to an atom David A. Case (Tue Apr 22 2008 - 00:36:16 CDT)
  - Re: AMBER: How to change default radius assigned to an atom Wei Zhang (Wed Apr 23 2008 - 10:29:03 CDT)
AMBER: pressure varies in constant pressure membrane simulation Vijay Manickam Achari (Tue Apr 22 2008 - 00:58:29 CDT)
- Re: AMBER: pressure varies in constant pressure membrane simulation David A. Case (Tue Apr 22 2008 - 13:31:53 CDT)
  - Re: AMBER: pressure varies in constant pressure membrane simulation Vijay Manickam Achari (Tue Apr 22 2008 - 23:10:54 CDT)
AMBER: matrxi dist command priya priya (Tue Apr 22 2008 - 06:37:50 CDT)
AMBER: minimization san_amber roy (Tue Apr 22 2008 - 09:01:52 CDT)
AMBER: refine cyana structures! Hongyan Li (Tue Apr 22 2008 - 20:33:08 CDT)
AMBER: RE: amber tutorial A3 Ross Walker (Tue Apr 22 2008 - 23:45:29 CDT)
AMBER: Topology file format for Amber9 Xioling Chuang (Wed Apr 23 2008 - 00:41:32 CDT)
- Re: AMBER: Topology file format for Amber9 David A. Case (Wed Apr 23 2008 - 11:01:13 CDT)
AMBER: cross time correlation function fatima.chami_at_durham.ac.uk (Wed Apr 23 2008 - 07:55:28 CDT)
- Re: AMBER: cross time correlation function David A. Case (Wed Apr 23 2008 - 10:55:07 CDT)
  - Re: AMBER: cross time correlation function fatima.chami_at_durham.ac.uk (Wed Apr 23 2008 - 12:00:43 CDT)
    - Re: AMBER: cross time correlation function David A. Case (Wed Apr 23 2008 - 12:10:46 CDT)
AMBER: ESP on atoms (2) Khatcharin Siriwong (Wed Apr 23 2008 - 09:29:04 CDT)
AMBER: 2D-RMSD Tom McGrory (Wed Apr 23 2008 - 10:00:57 CDT)
AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error Yu Chen (Wed Apr 23 2008 - 13:03:13 CDT)
- Re: AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error David A. Case (Wed Apr 23 2008 - 13:34:30 CDT)
  - Re: AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error Yu Chen (Wed Apr 23 2008 - 13:50:54 CDT)
  - AMBER: Tutorial B5 Chih-Ying Lin (Wed Apr 23 2008 - 17:13:56 CDT)
AMBER: saveamberparm taufik.alsarraj_at_utoronto.ca (Wed Apr 23 2008 - 19:34:02 CDT)
- Re: AMBER: saveamberparm David A. Case (Thu Apr 24 2008 - 09:58:20 CDT)
  - AMBER: Si parameters for MD (AMBER9) Taufik Al-Sarraj (Fri Apr 25 2008 - 17:08:44 CDT)
AMBER: saveamberparm taufik.alsarraj_at_utoronto.ca (Wed Apr 23 2008 - 19:38:16 CDT)
AMBER: sander & imin=5 Xioling Chuang (Thu Apr 24 2008 - 02:03:09 CDT)
- Re: AMBER: sander & imin=5 David A. Case (Fri Apr 25 2008 - 13:38:25 CDT)
AMBER: water in the binding site MMPBSA jacopo.sgrignani_at_unifi.it (Thu Apr 24 2008 - 08:51:43 CDT)
AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Lachele Foley (Lists) (Thu Apr 24 2008 - 09:22:42 CDT)
- Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Robert Duke (Thu Apr 24 2008 - 10:04:31 CDT)
  - Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Gustavo Seabra (Thu Apr 24 2008 - 12:51:10 CDT)
    - Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Lachele Foley (Lists) (Thu Apr 24 2008 - 14:16:50 CDT)
    - Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Robert Duke (Thu Apr 24 2008 - 14:45:31 CDT)
AMBER: double strand DNA break up (imaging) Seth Lilavivat (Thu Apr 24 2008 - 13:53:44 CDT)
- Re: AMBER: double strand DNA break up (imaging) Thomas Cheatham III (Thu Apr 24 2008 - 14:43:36 CDT)
AMBER: nmode output jacopo.sgrignani_at_unifi.it (Fri Apr 25 2008 - 03:36:35 CDT)
- Re: AMBER: nmode output Lachele Foley (Lists) (Fri Apr 25 2008 - 09:09:37 CDT)
AMBER: query regarding loadpadb Anamika Awasthi (Fri Apr 25 2008 - 03:33:19 CDT)
- Re: AMBER: query regarding loadpadb Reena ..... (Fri Apr 25 2008 - 06:07:21 CDT)
AMBER: parallel error : undefined reference to `MAIN_' Arturas Ziemys (Fri Apr 25 2008 - 16:14:59 CDT)
AMBER: AMD Opteron: compiler recommendations? Sasha Buzko (Fri Apr 25 2008 - 16:54:57 CDT)
- Re: AMBER: AMD Opteron: compiler recommendations? Robert Duke (Fri Apr 25 2008 - 17:04:58 CDT)
  - Re: AMBER: AMD Opteron: compiler recommendations? Sasha Buzko (Fri Apr 25 2008 - 17:14:19 CDT)
  - Re: AMBER: AMD Opteron: compiler recommendations? Francesco Pietra (Sat Apr 26 2008 - 02:01:46 CDT)
AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... saurabh agrawal (Sat Apr 26 2008 - 06:36:13 CDT)
- Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... Barbault Florent (Sat Apr 26 2008 - 08:13:47 CDT)
  - AMBER: Azobenzene: dihedral angle CCNN force field parameter Chih-Ying Lin (Sat Apr 26 2008 - 14:09:03 CDT)
    - Re: AMBER: Azobenzene: dihedral angle CCNN force field parameter Adrian Roitberg (Sat Apr 26 2008 - 16:10:25 CDT)
  - Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... saurabh agrawal (Sat Apr 26 2008 - 09:15:38 CDT)
    - Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... Barbault Florent (Tue Apr 29 2008 - 15:56:09 CDT)
    - RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... Ross Walker (Tue Apr 29 2008 - 15:57:21 CDT)
- RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... Ross Walker (Sun Apr 27 2008 - 00:59:57 CDT)
  - RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... saurabh agrawal (Mon Apr 28 2008 - 00:18:50 CDT)
AMBER: memory usage Ye Mei (Sat Apr 26 2008 - 08:57:44 CDT)
- RE: AMBER: memory usage Ross Walker (Sun Apr 27 2008 - 01:07:04 CDT)
- Re: RE: AMBER: memory usage Ye Mei (Sun Apr 27 2008 - 09:52:42 CDT)
  - RE: RE: AMBER: memory usage Ross Walker (Sun Apr 27 2008 - 11:45:16 CDT)
  - Re: RE: RE: AMBER: memory usage Ye Mei (Mon Apr 28 2008 - 09:06:20 CDT)
    - Re: RE: RE: AMBER: memory usage David A. Case (Mon Apr 28 2008 - 12:26:22 CDT)
AMBER: NMR restraints Ilyas Yildirim (Mon Apr 28 2008 - 01:53:51 CDT)
- Re: AMBER: NMR restraints David A. Case (Mon Apr 28 2008 - 10:20:53 CDT)
AMBER: Read trajectories generated by CHARMM Jeffrey (Mon Apr 28 2008 - 08:06:17 CDT)
- Re: AMBER: Read trajectories generated by CHARMM David A. Case (Mon Apr 28 2008 - 10:25:13 CDT)
  - AMBER: Parrallel computing Chih-Ying Lin (Mon Apr 28 2008 - 19:14:10 CDT)
    - RE: AMBER: Parrallel computing Ross Walker (Tue Apr 29 2008 - 01:09:44 CDT)
  - Re: Re: AMBER: Read trajectories generated by CHARMM Jeffrey (Mon Apr 28 2008 - 19:58:36 CDT)
AMBER: query regarding energy minimization Anamika Awasthi (Mon Apr 28 2008 - 08:22:24 CDT)
- Re: AMBER: query regarding energy minimization rpaduri_at_chem.wayne.edu (Mon Apr 28 2008 - 09:26:25 CDT)
- Re: AMBER: query regarding energy minimization Deepangi Pandit (Mon Apr 28 2008 - 09:39:39 CDT)
- Re: AMBER: query regarding energy minimization D.Usharani (Tue Apr 29 2008 - 00:20:29 CDT)
- RE: AMBER: query regarding energy minimization Ross Walker (Tue Apr 29 2008 - 01:16:11 CDT)
AMBER: Charge derivation: RESP vs. antechamber Catein Catherine (Tue Apr 29 2008 - 05:21:54 CDT)
AMBER: Charge derivation: RESP vs. antechamber Catein Catherine (Tue Apr 29 2008 - 05:21:55 CDT)
- Re: AMBER: Charge derivation: RESP vs. antechamber David A. Case (Tue Apr 29 2008 - 18:40:40 CDT)
AMBER: segmentation fault in SANDER Anamika Awasthi (Tue Apr 29 2008 - 06:44:29 CDT)
- RE: AMBER: segmentation fault in SANDER Ross Walker (Tue Apr 29 2008 - 09:15:08 CDT)
AMBER: prmtop spec trivia Lachele Foley (Lists) (Tue Apr 29 2008 - 10:07:29 CDT)
- RE: AMBER: prmtop spec trivia Ross Walker (Tue Apr 29 2008 - 10:34:04 CDT)
  - Re: AMBER: prmtop spec trivia Lachele Foley (Lists) (Tue Apr 29 2008 - 11:13:41 CDT)
AMBER: regarding segfault during energy minimization Anamika Awasthi (Wed Apr 30 2008 - 00:13:21 CDT)
- RE: AMBER: regarding segfault during energy minimization Ross Walker (Wed Apr 30 2008 - 00:40:21 CDT)
  - Re: AMBER: regarding segfault during energy minimization Anamika Awasthi (Thu May 01 2008 - 00:57:35 CDT)
AMBER: distance matrix command priya priya (Wed Apr 30 2008 - 04:01:24 CDT)
AMBER: Constat area simulation gurpreet singh (Wed Apr 30 2008 - 06:23:35 CDT)
AMBER: Dose AMBER 10 pmemd support openmpi? Hu, Shaowen (JSC-SK)[USRA] (Wed Apr 30 2008 - 08:04:28 CDT)
- Re: AMBER: Dose AMBER 10 pmemd support openmpi? Robert Duke (Wed Apr 30 2008 - 10:16:58 CDT)
- Re: AMBER: Dose AMBER 10 pmemd support openmpi? David A. Case (Wed Apr 30 2008 - 10:22:48 CDT)
  - Re: AMBER: Dose AMBER 10 pmemd support openmpi? Robert Duke (Wed Apr 30 2008 - 10:40:44 CDT)
    - RE: AMBER: Dose AMBER 10 pmemd support openmpi? Hu, Shaowen (JSC-SK)[USRA] (Wed Apr 30 2008 - 11:07:39 CDT)
AMBER: amber 9 compilation problem on IBM SP5 Andrew Emerson (Wed Apr 30 2008 - 07:44:38 CDT)
- Re: AMBER: amber 9 compilation problem on IBM SP5 David A. Case (Wed Apr 30 2008 - 13:37:11 CDT)
  - AMBER: Re: amber 9 compilation problem on IBM SP5 Andrew Emerson (Mon May 05 2008 - 02:57:53 CDT)
AMBER: about glycam06 WANG,YING (Wed Apr 30 2008 - 11:00:12 CDT)
- Re: AMBER: about glycam06 Austin B. Yongye (Wed Apr 30 2008 - 12:26:44 CDT)
AMBER: calibration of constant pH simulations Lillian Chong (Wed Apr 30 2008 - 12:17:47 CDT)
- Re: AMBER: calibration of constant pH simulations Adrian Roitberg (Wed Apr 30 2008 - 13:05:33 CDT)
- Re: AMBER: calibration of constant pH simulations Pradipta Bandyopadhyay (Wed Apr 30 2008 - 23:02:55 CDT)
AMBER: Cysteine sulphonic acid parameters Rima Chaudhuri (Wed Apr 30 2008 - 17:48:42 CDT)
- Re: AMBER: Cysteine sulphonic acid parameters David A. Case (Wed Apr 30 2008 - 19:06:02 CDT)
- Re: AMBER: Cysteine sulphonic acid parameters FyD (Thu May 01 2008 - 07:03:19 CDT)
  - Re: AMBER: Cysteine sulphonic acid parameters Rima Chaudhuri (Thu May 01 2008 - 10:43:48 CDT)
AMBER: Discontinuous Constant pH Restarts Neil Bruce (Thu May 01 2008 - 08:41:21 CDT)
- Re: AMBER: Discontinuous Constant pH Restarts David A. Case (Fri May 02 2008 - 14:44:31 CDT)
  - Re: AMBER: Discontinuous Constant pH Restarts Neil Bruce (Wed May 07 2008 - 15:21:28 CDT)
AMBER: Water residue tracking Steve Seibold (Thu May 01 2008 - 11:19:42 CDT)
AMBER: Installation problem of AMBER on cluster sudipta sinha (Thu May 01 2008 - 13:16:44 CDT)
- Re: AMBER: Installation problem of AMBER on cluster David A. Case (Thu May 01 2008 - 13:55:17 CDT)
  - Re: AMBER: Installation problem of AMBER on cluster sudipta sinha (Fri May 02 2008 - 02:39:09 CDT)
AMBER: Amber10 installation error juyong Lee (Thu May 01 2008 - 21:28:07 CDT)
- RE: AMBER: Amber10 installation error Ross Walker (Thu May 01 2008 - 23:01:02 CDT)
  - Re: AMBER: Amber10 installation error juyong Lee (Thu May 01 2008 - 23:52:10 CDT)
    - RE: AMBER: Amber10 installation error Ross Walker (Fri May 02 2008 - 10:33:43 CDT)
    - Re: AMBER: Amber10 installation error David A. Case (Fri May 02 2008 - 11:07:50 CDT)
AMBER: test.parallel.QMMM problem Carra, Claudio (JSC-SK)[USRA] (Fri May 02 2008 - 08:37:28 CDT)
- RE: AMBER: test.parallel.QMMM problem Ross Walker (Fri May 02 2008 - 10:50:31 CDT)
AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 sychen (Fri May 02 2008 - 09:22:50 CDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Fri May 09 2008 - 15:05:39 CDT)
  - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Mon May 12 2008 - 23:09:11 CDT)
    - RE: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Ross Walker (Tue May 13 2008 - 10:08:08 CDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Tue May 27 2008 - 10:37:57 CDT)
  - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Tue May 27 2008 - 11:03:54 CDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Tue May 27 2008 - 13:20:09 CDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Tue May 27 2008 - 14:29:43 CDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Wed May 28 2008 - 10:51:12 CDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Wed May 28 2008 - 23:07:18 CDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Thu May 29 2008 - 13:15:15 CDT)
  - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Thu May 29 2008 - 14:19:53 CDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Thu May 29 2008 - 16:47:43 CDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Fri May 30 2008 - 12:11:24 CDT)
  - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Fri Jul 04 2008 - 01:28:44 CDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Sat Aug 02 2008 - 21:23:53 CDT)
AMBER: Water tracking Steve Seibold (Fri May 02 2008 - 10:09:35 CDT)
- Re: AMBER: Water tracking Thomas Cheatham III (Fri May 02 2008 - 11:14:21 CDT)
AMBER: Help with NMODE Seth Lilavivat (Fri May 02 2008 - 10:24:25 CDT)
- Re: AMBER: Help with NMODE David A. Case (Fri May 02 2008 - 11:23:34 CDT)
  - Re: AMBER: Help with NMODE Seth Lilavivat (Fri May 02 2008 - 11:50:35 CDT)
AMBER: cfortran.h error with xlf90 compiler juyong Lee (Fri May 02 2008 - 11:35:32 CDT)
- RE: AMBER: cfortran.h error with xlf90 compiler Ross Walker (Fri May 02 2008 - 11:58:27 CDT)
- Re: AMBER: cfortran.h error with xlf90 compiler David A. Case (Fri May 02 2008 - 12:10:54 CDT)
AMBER: Compiling amber10 with xlf90 fortran compiler juyong Lee (Fri May 02 2008 - 13:27:10 CDT)
AMBER: Mn2+ parameters in AMBER jitrayut jitonnom (Fri May 02 2008 - 13:46:25 CDT)
- Re: AMBER: Mn2+ parameters in AMBER Guillermo Mulliert Carlín (Fri May 23 2008 - 01:26:51 CDT)
  - Re: AMBER: Mn2+ parameters in AMBER jitrayut jitonnom (Fri May 23 2008 - 03:58:10 CDT)
AMBER: Inquiry on B-factor of NMR James Thomas (Fri May 02 2008 - 14:31:09 CDT)
AMBER: printing dipoles in Amber10 (and earlier) Piotr Cieplak (Fri May 02 2008 - 15:29:49 CDT)
- AMBER: point charges Chih-Ying Lin (Fri May 02 2008 - 15:53:50 CDT)
  - RE: AMBER: point charges Ross Walker (Fri May 02 2008 - 16:32:43 CDT)
- RE: AMBER: printing dipoles in Amber10 (and earlier) Ross Walker (Fri May 02 2008 - 16:16:08 CDT)
AMBER: Example .prepi file for nonstandard amino acids finke_at_oakland.edu (Fri May 02 2008 - 17:00:45 CDT)
- Re: AMBER: Example .prepi file for nonstandard amino acids David A. Case (Fri May 02 2008 - 17:54:03 CDT)
- Re: AMBER: Example .prepi file for nonstandard amino acids finke_at_oakland.edu (Fri May 02 2008 - 20:06:30 CDT)
AMBER: about glycam06 WANG,YING (Sat May 03 2008 - 18:22:18 CDT)
- Re: AMBER: about glycam06 WANG,YING (Wed Apr 30 2008 - 14:49:46 CDT)
  - Re: AMBER: about glycam06 Austin B. Yongye (Wed Apr 30 2008 - 16:47:32 CDT)
- Re: AMBER: about glycam06 David A. Case (Sat May 03 2008 - 18:49:27 CDT)
- Re: AMBER: about glycam06 WANG,YING (Sat May 03 2008 - 18:55:11 CDT)
  - Re: AMBER: about glycam06 Austin B. Yongye (Sat May 03 2008 - 20:59:47 CDT)
- Re: AMBER: about glycam06 WANG,YING (Sat May 03 2008 - 18:57:35 CDT)
  - Re: AMBER: about glycam06 David A. Case (Sat May 03 2008 - 19:32:10 CDT)
- Re: AMBER: about glycam06 WANG,YING (Sat May 03 2008 - 21:35:05 CDT)
- Re: AMBER: about glycam06 WANG,YING (Sat May 03 2008 - 21:40:14 CDT)
- Re: AMBER: about glycam06 Bill Ross (Sun May 04 2008 - 17:46:05 CDT)
- Re: AMBER: about glycam06 WANG,YING (Mon May 05 2008 - 09:30:19 CDT)
AMBER: Amber10 Installation error - incorrect file suffix juyong Lee (Sun May 04 2008 - 07:46:10 CDT)
- Re: AMBER: Amber10 Installation error - incorrect file suffix David A. Case (Sun May 04 2008 - 20:20:55 CDT)
  - Re: AMBER: Amber10 Installation error - incorrect file suffix juyong Lee (Sun May 04 2008 - 21:01:02 CDT)
AMBER: Deriving Force Field Parameters Shultz, Jack (Sun May 04 2008 - 16:32:03 CDT)
- AMBER: GAFF Schema Shultz, Jack (Sun May 04 2008 - 17:11:37 CDT)
  - Re: AMBER: GAFF Schema David A. Case (Sun May 04 2008 - 20:21:59 CDT)
- Re: AMBER: Deriving Force Field Parameters FyD (Mon May 05 2008 - 09:14:22 CDT)
AMBER: Jarzinsky relationship E.M. (Sun May 04 2008 - 21:39:51 CDT)
- Re: AMBER: Jarzinsky relationship Adrian Roitberg (Mon May 05 2008 - 09:46:53 CDT)
  - Re: AMBER: Jarzinsky relationship E.M. (Mon May 05 2008 - 10:02:49 CDT)
AMBER: Torsion angle restrains and Jarzinsky E.M. (Mon May 05 2008 - 02:06:56 CDT)
AMBER: Installation error on IBM cluster juyong Lee (Mon May 05 2008 - 03:40:59 CDT)
- RE: AMBER: Installation error on IBM cluster Ross Walker (Mon May 05 2008 - 10:06:11 CDT)
AMBER: unable to compile AmberTools 1.0 Rabin (Mon May 05 2008 - 12:07:00 CDT)
- Re: AMBER: unable to compile AmberTools 1.0 David A. Case (Mon May 05 2008 - 13:14:44 CDT)
  - Re: AMBER: unable to compile AmberTools 1.0 Yu Chen (Mon May 05 2008 - 14:06:26 CDT)
AMBER: About reading in heme and CO molecule together with myoglobin Yang, Lee-Wei (Mon May 05 2008 - 13:08:53 CDT)
- Re: AMBER: About reading in heme and CO molecule together with myoglobin David A. Case (Mon May 05 2008 - 18:51:44 CDT)
AMBER: AMBER Parallel test error jitrayut jitonnom (Mon May 05 2008 - 13:37:39 CDT)
- RE: AMBER: AMBER Parallel test error Ross Walker (Mon May 05 2008 - 14:42:09 CDT)
  - Re: AMBER: AMBER Parallel test error jitrayut jitonnom (Tue May 06 2008 - 08:09:10 CDT)
AMBER: DCCM correlation analysis Ibrahim Moustafa (Mon May 05 2008 - 15:21:37 CDT)
AMBER: Units, units units E.M. (Mon May 05 2008 - 17:18:37 CDT)
- Re: AMBER: Units, units units David A. Case (Mon May 05 2008 - 18:02:57 CDT)
AMBER: Minimization in Octahedric Box guardiani_at_fi.infn.it (Tue May 06 2008 - 06:31:50 CDT)
- Re: AMBER: Minimization in Octahedric Box David A. Case (Tue May 06 2008 - 12:28:20 CDT)
- RE: AMBER: Minimization in Octahedric Box Ross Walker (Tue May 06 2008 - 12:22:39 CDT)
AMBER: rmsd per residue Furia Gargano (Tue May 06 2008 - 09:28:59 CDT)
AMBER: steered MD initial state M. L. Dodson (Tue May 06 2008 - 11:04:09 CDT)
- Re: AMBER: steered MD initial state Gustavo Seabra (Tue May 06 2008 - 11:37:54 CDT)
  - Re: AMBER: steered MD initial state Adrian Roitberg (Tue May 06 2008 - 12:16:52 CDT)
    - Re: AMBER: steered MD initial state M. L. Dodson (Tue May 06 2008 - 12:39:04 CDT)
  - Re: AMBER: steered MD initial state M. L. Dodson (Tue May 06 2008 - 12:27:03 CDT)
AMBER: mm_pbsa.pl not reading parameters for nmode Seth Lilavivat (Tue May 06 2008 - 12:50:18 CDT)
- Re: AMBER: mm_pbsa.pl not reading parameters for nmode David A. Case (Tue May 06 2008 - 13:13:54 CDT)
  - AMBER: Improper dihedral parameters Chih-Ying Lin (Tue May 06 2008 - 14:00:36 CDT)
  - AMBER: single stranded DNA Taufik Al-Sarraj (Tue May 06 2008 - 17:37:41 CDT)
    - Re: AMBER: single stranded DNA David A. Case (Tue May 06 2008 - 17:41:29 CDT)
    - Re: AMBER: single stranded DNA Taufik Al-Sarraj (Tue May 06 2008 - 19:11:07 CDT)
Re: AMBER: Improper dihedral parameters Bill Ross (Tue May 06 2008 - 14:23:55 CDT)
- Re: AMBER: Improper dihedral parameters Da-Wei Li (Tue May 06 2008 - 14:30:29 CDT)
AMBER: DFTB parameters for O-P Carra, Claudio (JSC-SK)[USRA] (Tue May 06 2008 - 15:01:55 CDT)
- Re: AMBER: DFTB parameters for O-P Gustavo Seabra (Wed May 07 2008 - 14:19:50 CDT)
AMBER: Ewald error estimate æ¬§é˜³å¾·æ–¹ (Wed May 07 2008 - 03:25:22 CDT)
- Re: AMBER: Ewald error estimate David A. Case (Wed May 07 2008 - 10:57:03 CDT)
  - RE: AMBER: Ewald error estimate Å·ÑôµÂ·½ (Wed May 07 2008 - 22:38:18 CDT)
- AMBER: to unsubscribe email Rabin (Mon May 12 2008 - 10:47:43 CDT)
  - Re: AMBER: to unsubscribe email Bill Ross (Mon May 12 2008 - 12:46:24 CDT)
    - Re: AMBER: to unsubscribe email Rabin (Mon May 12 2008 - 16:29:56 CDT)
AMBER: molsurf jacopo.sgrignani_at_unifi.it (Wed May 07 2008 - 06:11:34 CDT)
AMBER: uninstall of AMBER sudipta sinha (Wed May 07 2008 - 10:50:37 CDT)
- Re: AMBER: uninstall of AMBER David A. Case (Wed May 07 2008 - 11:07:25 CDT)
- RE: AMBER: uninstall of AMBER Ross Walker (Wed May 07 2008 - 12:05:20 CDT)
AMBER: nmode: number of atoms limitation Qi Yan (Wed May 07 2008 - 13:25:58 CDT)
- RE: AMBER: nmode: number of atoms limitation Ross Walker (Wed May 07 2008 - 16:39:44 CDT)
- AMBER: Azobenzene: AMBER+Gromos Force Field parameters Chih-Ying Lin (Wed May 07 2008 - 16:43:17 CDT)
AMBER: GBSA SA calculation Titus, Jamie $bairdje$ (Wed May 07 2008 - 13:32:43 CDT)
- Re: AMBER: GBSA SA calculation Carlos Simmerling (Wed May 07 2008 - 14:05:44 CDT)
- Re: AMBER: GBSA SA calculation David A. Case (Wed May 07 2008 - 16:17:07 CDT)
  - Re: AMBER: GBSA SA calculation Carlos Simmerling (Wed May 07 2008 - 17:05:26 CDT)
- Re: AMBER: GBSA SA calculation Carlos Simmerling (Tue May 13 2008 - 12:46:30 CDT)
AMBER: Hydroxyprolines!!! Titus, Jamie $bairdje$ (Wed May 07 2008 - 13:54:03 CDT)
- Re: AMBER: Hydroxyprolines!!! David A. Case (Wed May 07 2008 - 20:26:16 CDT)
AMBER: Harmonic Force Constant Shultz, Jack (Wed May 07 2008 - 14:32:18 CDT)
- RE: AMBER: Harmonic Force Constant Shultz, Jack (Thu May 08 2008 - 15:21:00 CDT)
AMBER: How to transfer unformatted coordinates into formatted ones Qi Yan (Wed May 07 2008 - 14:44:10 CDT)
- Re: AMBER: How to transfer unformatted coordinates into formatted ones David A. Case (Wed May 07 2008 - 20:14:04 CDT)
  - RE: AMBER: How to transfer unformatted coordinates into formatted ones Qi Yan (Wed May 07 2008 - 21:55:18 CDT)
    - Re: AMBER: How to transfer unformatted coordinates into formatted ones David A. Case (Thu May 08 2008 - 12:13:59 CDT)
AMBER: nmode: number of atoms limitation Qi Yan (Wed May 07 2008 - 13:10:48 CDT)
AMBER: Compilation of PMEMD sudipta sinha (Thu May 08 2008 - 06:07:28 CDT)
- Re: AMBER: Compilation of PMEMD Robert Duke (Thu May 08 2008 - 07:17:43 CDT)
AMBER: mm_pbsa problem: bad atom type: IP mori_at_cerm.unifi.it (Thu May 08 2008 - 06:59:12 CDT)
- Re: AMBER: mm_pbsa problem: bad atom type: IP David A. Case (Thu May 08 2008 - 12:27:22 CDT)
AMBER: nmode "Atom out of bounds" for min of multiple ligands Seth Lilavivat (Thu May 08 2008 - 09:30:24 CDT)
- RE: AMBER: nmode "Atom out of bounds" for min of multiple ligands Ross Walker (Thu May 08 2008 - 12:19:34 CDT)
  - Re: AMBER: nmode "Atom out of bounds" for min of multiple ligands Seth Lilavivat (Thu May 08 2008 - 15:01:45 CDT)
    - Re: AMBER: nmode "Atom out of bounds" for min of multiple ligands David A. Case (Thu May 08 2008 - 15:49:31 CDT)
AMBER: can amber read .xyz files? WANG,YING (Thu May 08 2008 - 10:29:57 CDT)
- RE: AMBER: can amber read .xyz files? Ross Walker (Thu May 08 2008 - 12:23:16 CDT)
AMBER: velocity autocorrelation function for SPC felxible water model Rahaman, Asif (Thu May 08 2008 - 12:07:41 CDT)
- Re: AMBER: velocity autocorrelation function for SPC felxible water model David A. Case (Thu May 08 2008 - 13:00:28 CDT)
  - RE: AMBER: velocity autocorrelation function for SPC felxible water model Rahaman, Asif (Thu May 08 2008 - 15:42:22 CDT)
AMBER: AmberTools on OS X fails tests Hans Martin Senn (Thu May 08 2008 - 13:59:12 CDT)
- Re: AMBER: AmberTools on OS X fails tests Wei Zhang (Thu May 08 2008 - 14:15:46 CDT)
- Re: AMBER: AmberTools on OS X fails tests David A. Case (Thu May 08 2008 - 14:30:53 CDT)
AMBER: QM/MM Syed Tarique Moin (Fri May 09 2008 - 03:28:06 CDT)
- Re: AMBER: QM/MM Gustavo Seabra (Fri May 09 2008 - 09:18:21 CDT)
AMBER: distance Urszula Uciechowska (Fri May 09 2008 - 09:36:18 CDT)
- Re: AMBER: distance E.M. (Fri May 09 2008 - 09:43:12 CDT)
- Re: AMBER: distance Ibrahim Moustafa (Fri May 09 2008 - 09:49:37 CDT)
AMBER: help to install AMBER9 Jeffrey (Fri May 09 2008 - 09:47:16 CDT)
- Re: AMBER: help to install AMBER9 Ye Mei (Fri May 09 2008 - 09:55:56 CDT)
- Re: AMBER: help to install AMBER9 Gustavo Seabra (Fri May 09 2008 - 10:01:04 CDT)
  - AMBER: MM_PBSA output file Qi Yan (Fri May 09 2008 - 11:03:38 CDT)
    - Re: AMBER: MM_PBSA output file Navnit Kumar Mishra (Fri May 09 2008 - 11:21:17 CDT)
    - Re: AMBER: MM_PBSA output file Alessandro Nascimento (Fri May 09 2008 - 11:22:35 CDT)
- RE: AMBER: help to install AMBER9 Ross Walker (Fri May 09 2008 - 11:12:53 CDT)
- Re: AMBER: help to install AMBER9 Jeffrey (Sun May 11 2008 - 04:12:18 CDT)
  - Re: AMBER: help to install AMBER9 Gustavo Seabra (Mon May 12 2008 - 09:56:41 CDT)
    - Re: Re: AMBER: help to install AMBER9 Jeffrey (Mon May 12 2008 - 19:51:46 CDT)
AMBER: neutral C-terminus and N-terminus parameters for amber Lisa Perez (Fri May 09 2008 - 12:32:13 CDT)
- Re: AMBER: neutral C-terminus and N-terminus parameters for amber FyD (Sat May 10 2008 - 02:52:10 CDT)
AMBER: cannot read big .pdb files WANG,YING (Fri May 09 2008 - 21:00:29 CDT)
- Re: AMBER: cannot read big .pdb files David A. Case (Sat May 10 2008 - 10:24:41 CDT)
- Re: AMBER: cannot read big .pdb files Lynn F. Ten Eyck (Sat May 10 2008 - 11:37:02 CDT)
- Re: AMBER: cannot read big .pdb files WANG,YING (Sun May 11 2008 - 08:38:41 CDT)
- Re: AMBER: cannot read big .pdb files WANG,YING (Sun May 11 2008 - 08:36:48 CDT)
  - Re: AMBER: cannot read big .pdb files Wei Zhang (Mon May 12 2008 - 09:34:40 CDT)
- Re: AMBER: cannot read big .pdb files WANG,YING (Mon May 12 2008 - 09:37:24 CDT)
- Re: AMBER: cannot read big .pdb files WANG,YING (Mon May 12 2008 - 14:42:27 CDT)
  - Re: AMBER: cannot read big .pdb files David Watson (Mon May 12 2008 - 18:32:49 CDT)
- Re: AMBER: cannot read big .pdb files WANG,YING (Tue May 13 2008 - 08:40:34 CDT)
AMBER: parmbsc0 parameters for RNA.DNA systems Cenk $Jenk$ Andac (Sat May 10 2008 - 08:47:50 CDT)
- Re: AMBER: parmbsc0 parameters for RNA.DNA systems David A. Case (Sat May 10 2008 - 10:27:36 CDT)
AMBER: Calculate number of ions Dong Xu (Sat May 10 2008 - 13:32:01 CDT)
- Re: AMBER: Calculate number of ions Mathy Froeyen (Tue May 13 2008 - 02:50:29 CDT)
  - Re: AMBER: Calculate number of ions Ruchi Sachdeva (Wed May 14 2008 - 02:24:08 CDT)
    - AMBER: Weighting factors in RESP charge fitting Anselm Horn (Fri May 16 2008 - 07:32:22 CDT)
    - Re: AMBER: Weighting factors in RESP charge fitting Piotr Cieplak (Fri May 16 2008 - 13:46:51 CDT)
AMBER: Solvent mixture box Francesco Pietra (Sun May 11 2008 - 12:04:52 CDT)
AMBER: Ewald PARAMETER RANGE WRONG WANG,YING (Sun May 11 2008 - 13:01:09 CDT)
- Re: AMBER: Ewald PARAMETER RANGE WRONG David A. Case (Mon May 12 2008 - 11:00:44 CDT)
- Re: AMBER: Ewald PARAMETER RANGE WRONG WANG,YING (Mon May 12 2008 - 12:06:03 CDT)
AMBER: rms Urszula Uciechowska (Mon May 12 2008 - 06:19:41 CDT)
- Re: AMBER: rms Vlad Cojocaru (Mon May 12 2008 - 07:40:46 CDT)
  - Re: AMBER: rms Urszula Uciechowska (Mon May 12 2008 - 08:41:06 CDT)
    - Re: AMBER: rms Cenk $Jenk$ Andac (Mon May 12 2008 - 08:51:56 CDT)
    - Re: AMBER: rms Vlad Cojocaru (Wed May 14 2008 - 09:01:17 CDT)
AMBER: About Hydrophobic Interactions. cgji (Mon May 12 2008 - 11:14:00 CDT)
AMBER: Problems installing Amber Tools for Amber 10 Sam Danziger (Mon May 12 2008 - 13:20:23 CDT)
- Re: AMBER: Problems installing Amber Tools for Amber 10 David A. Case (Thu May 15 2008 - 23:47:19 CDT)
AMBER: Ligand energy minimization Dong Xu (Mon May 12 2008 - 17:07:31 CDT)
- RE: AMBER: Ligand energy minimization Ross Walker (Tue May 13 2008 - 10:14:53 CDT)
  - AMBER: Prepgen Rajendra P. OJHA (Wed May 14 2008 - 04:45:47 CDT)
AMBER: nab Rabin (Mon May 12 2008 - 19:40:54 CDT)
- Re: AMBER: nab Alessandro Nascimento (Mon May 12 2008 - 19:59:27 CDT)
- Re: AMBER: nab Andreas Svrcek-Seiler (Tue May 13 2008 - 04:39:19 CDT)
  - Re: AMBER: nab Rabin (Tue May 13 2008 - 08:17:51 CDT)
AMBER: from Gromax to AMBER Cristina Sisu (Tue May 13 2008 - 05:00:24 CDT)
- RE: AMBER: from Gromax to AMBER jacopo.sgrignani_at_unifi.it (Tue May 13 2008 - 08:19:19 CDT)
  - AMBER: building quadruplex with nab Rabin (Tue May 13 2008 - 08:38:15 CDT)
    - Re: AMBER: building quadruplex with nab Rabin (Tue May 20 2008 - 17:30:17 CDT)
    - Re: AMBER: building quadruplex with nab David A. Case (Wed May 21 2008 - 00:08:10 CDT)
  - Re: AMBER: from Gromax to AMBER Cristina Sisu (Tue May 13 2008 - 08:49:12 CDT)
AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222- Catein Catherine (Tue May 13 2008 - 05:17:29 CDT)
- Re: AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222- David A. Case (Sun May 18 2008 - 15:09:00 CDT)
AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params Marcin Krol (Tue May 13 2008 - 08:44:48 CDT)
- RE: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params Ray Luo (Thu May 22 2008 - 15:37:04 CDT)
  - Re: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params ke dong (Sat May 24 2008 - 09:46:19 CDT)
AMBER: periodic boundary condition WANG,YING (Tue May 13 2008 - 08:55:00 CDT)
- Re: AMBER: periodic boundary condition David A. Case (Wed May 14 2008 - 08:50:40 CDT)
- RE: AMBER: periodic boundary condition WANG,YING (Sun May 25 2008 - 08:58:20 CDT)
AMBER: Free Energy Calculations - parameters for MM Seth Lilavivat (Tue May 13 2008 - 11:29:23 CDT)
- AMBER: initial velocities of MD Jena M (Tue May 13 2008 - 11:37:31 CDT)
  - Re: AMBER: initial velocities of MD Carlos Simmerling (Tue May 13 2008 - 11:59:26 CDT)
  - RE: AMBER: initial velocities of MD Ross Walker (Tue May 13 2008 - 12:05:05 CDT)
AMBER: divcon E.M. (Tue May 13 2008 - 11:58:49 CDT)
- Re: AMBER: divcon Gustavo Seabra (Tue May 13 2008 - 12:43:35 CDT)
AMBER: Amber10 testing problem Cenk $Jenk$ Andac (Tue May 13 2008 - 14:46:02 CDT)
- RE: AMBER: Amber10 testing problem Ross Walker (Tue May 13 2008 - 16:20:53 CDT)
  - RE: AMBER: Amber10 testing problem Cenk $Jenk$ Andac (Wed May 14 2008 - 04:13:13 CDT)
    - AMBER: AMBER PBSA Thomas Leonard (Wed May 14 2008 - 04:35:54 CDT)
AMBER: simulating the pull out of Carbon Nanotube from polymer with AMBER yuan li (Tue May 13 2008 - 21:53:10 CDT)
AMBER: MM_PBSA problem in binding_energy mori_at_cerm.unifi.it (Wed May 14 2008 - 09:17:40 CDT)
- Re: AMBER: MM_PBSA problem in binding_energy jacopo sgrignani (Wed May 14 2008 - 13:43:55 CDT)
AMBER: about addles:¡°forrtl: severe (71): integer divide by zero¡±. ³ÉÈ« (Wed May 14 2008 - 09:57:25 CDT)
- AMBER: RE: AMBER: about addles:¡°forrtl: severe (71): integer divide by zero¡±. Ross Walker (Wed May 14 2008 - 11:30:51 CDT)
  - AMBER: RE: AMBER: RE: AMBER: about addles:¡°forrtl: severe (71): integer divide by zero¡±. ³ÉÈ« (Wed May 14 2008 - 19:18:05 CDT)
AMBER: subscribe amber wangluohuaxue (Wed May 14 2008 - 09:40:04 CDT)
AMBER: simulate dipole moment Qiuting Hong (Wed May 14 2008 - 15:52:33 CDT)
- Re: AMBER: simulate dipole moment Neelanjana Sengupta (Wed May 14 2008 - 16:14:54 CDT)
- RE: AMBER: simulate dipole moment Ross Walker (Wed May 14 2008 - 16:25:33 CDT)
AMBER: AMBER entropy calculation Thomas Leonard (Wed May 14 2008 - 18:00:45 CDT)
- Re: AMBER: AMBER entropy calculation Dong Xu (Wed May 14 2008 - 19:37:27 CDT)
- Re: AMBER: AMBER entropy calculation Swarup Gupta (Wed May 14 2008 - 21:20:07 CDT)
  - AMBER: how to calculate delta G from IC50 Thomas Leonard (Tue May 20 2008 - 00:12:04 CDT)
    - Re: AMBER: how to calculate delta G from IC50 Chris Moth (Tue May 20 2008 - 07:30:29 CDT)
AMBER: Amber10:Compiling with gcc 2.4.1 yongleli (Thu May 15 2008 - 10:36:29 CDT)
- Re: AMBER: Amber10:Compiling with gcc 2.4.1 Gustavo Seabra (Thu May 15 2008 - 17:58:05 CDT)
  - Re: Re: AMBER: Amber10:Compiling with gcc 2.4.1 yongleli (Thu May 15 2008 - 21:40:51 CDT)
    - Re: Re: AMBER: Amber10:Compiling with gcc 2.4.1 David A. Case (Fri May 16 2008 - 15:16:56 CDT)
- Re: AMBER: Amber10:Compiling with gcc 2.4.1 David A. Case (Thu May 15 2008 - 22:42:31 CDT)
  - Re: Re: AMBER: Amber10:Compiling with gcc 2.4.1 yongleli (Thu May 15 2008 - 23:03:41 CDT)
AMBER: Points on a Sphere Justine Condo (Thu May 15 2008 - 11:27:06 CDT)
AMBER: MKL libraries/Amber10 Francesco Pietra (Thu May 15 2008 - 13:01:34 CDT)
- Re: AMBER: MKL libraries/Amber10 Gustavo Seabra (Thu May 15 2008 - 18:02:42 CDT)
- Re: AMBER: MKL libraries/Amber10 yongleli (Thu May 15 2008 - 21:03:57 CDT)
  - RE: AMBER: MKL libraries/Amber10 Ross Walker (Thu May 15 2008 - 21:59:16 CDT)
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Wed May 21 2008 - 08:33:35 CDT)
  - RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker (Wed May 21 2008 - 13:05:20 CDT)
AMBER: RESP and Jaguar Seth Lilavivat (Thu May 15 2008 - 15:52:35 CDT)
AMBER: solvatebox error WANG,YING (Thu May 15 2008 - 16:47:06 CDT)
- RE: AMBER: solvatebox error Ross Walker (Thu May 15 2008 - 16:54:08 CDT)
- RE: AMBER: solvatebox error WANG,YING (Thu May 15 2008 - 17:16:17 CDT)
AMBER: reading PDB trajectory Mark Abraham (Thu May 15 2008 - 22:49:55 CDT)
AMBER: PGI amber9 problems Lorenzo Gontrani (Fri May 16 2008 - 04:52:21 CDT)
- Re: AMBER: PGI amber9 problems David A. Case (Fri May 16 2008 - 06:29:06 CDT)
  - Re: AMBER: PGI amber9 problems Lorenzo Gontrani (Fri May 16 2008 - 07:02:53 CDT)
    - RE: AMBER: PGI amber9 problems Ross Walker (Fri May 16 2008 - 13:06:14 CDT)
AMBER: RESP charges of an unusual substrate Jiayun Pang (Fri May 16 2008 - 05:45:54 CDT)
- Re: AMBER: RESP charges of an unusual substrate FyD (Mon May 19 2008 - 01:46:40 CDT)
AMBER: STEERED MD fatima.chami_at_durham.ac.uk (Fri May 16 2008 - 11:25:55 CDT)
- Re: AMBER: STEERED MD Robert Duke (Fri May 16 2008 - 12:15:40 CDT)
  - Re: AMBER: STEERED MD Robert Duke (Fri May 16 2008 - 12:29:29 CDT)
    - Re: AMBER: STEERED MD fatima.chami_at_durham.ac.uk (Sat May 17 2008 - 05:26:28 CDT)
    - Re: AMBER: STEERED MD Robert Duke (Sat May 17 2008 - 08:21:10 CDT)
AMBER: build proline Qiuting Hong (Fri May 16 2008 - 16:32:47 CDT)
AMBER: Amber 10 ambpdb bug? Sam Danziger (Sat May 17 2008 - 21:17:44 CDT)
- Re: AMBER: Amber 10 ambpdb bug? David A. Case (Sat May 17 2008 - 23:37:09 CDT)
  - Re: AMBER: Amber 10 ambpdb bug? Sam Danziger (Sun May 18 2008 - 22:41:43 CDT)
AMBER: ambertools: static linking of user binaries is not supported on Mac OS X Alan (Mon May 19 2008 - 04:39:32 CDT)
- Re: AMBER: ambertools: static linking of user binaries is not supported on Mac OS X Hans Martin Senn (Mon May 19 2008 - 05:35:24 CDT)
AMBER: parameters in ff03 and ff99 Peter Kiss (Mon May 19 2008 - 06:21:21 CDT)
AMBER: Hybrid REMD amber10 Geoff Wood (Mon May 19 2008 - 07:41:54 CDT)
- RE: AMBER: Hybrid REMD amber10 Ross Walker (Mon May 19 2008 - 10:51:13 CDT)
  - Re: AMBER: Hybrid REMD amber10 Carlos Simmerling (Tue May 20 2008 - 01:55:06 CDT)
    - Re: AMBER: Hybrid REMD amber10 Geoff Wood (Tue May 20 2008 - 09:24:11 CDT)
AMBER: anal Marina Grabar (Mon May 19 2008 - 08:30:13 CDT)
- Re: AMBER: anal David A. Case (Tue May 20 2008 - 03:25:13 CDT)
  - Re: AMBER: anal Marina Grabar (Tue May 20 2008 - 04:20:04 CDT)
AMBER: nfft1-3 too large WANG,YING (Mon May 19 2008 - 09:46:51 CDT)
AMBER: gasteiger is not working with ambertools 1.0 Alan (Mon May 19 2008 - 09:51:05 CDT)
- Re: AMBER: gasteiger is not working with ambertools 1.0 David A. Case (Mon Jun 02 2008 - 19:12:55 CDT)
  - Re: AMBER: gasteiger is not working with ambertools 1.0 Alan (Tue Jun 03 2008 - 09:44:07 CDT)
AMBER: nfft1-3 too large WANG,YING (Mon May 19 2008 - 09:46:51 CDT)
AMBER: atom type in glycam06 tinni sona (Mon May 19 2008 - 12:06:57 CDT)
- Re: AMBER: atom type in glycam06 Lachele Foley (Lists) (Wed May 21 2008 - 08:37:51 CDT)
AMBER: bye frustrated modeller (Mon May 19 2008 - 13:29:40 CDT)
- Re: AMBER: bye Sara Alexandra Moura (Tue May 20 2008 - 09:14:51 CDT)
AMBER: analysis REMD rebeca (Mon May 19 2008 - 13:41:15 CDT)
- Re: AMBER: analysis REMD Carlos Simmerling (Tue May 20 2008 - 01:51:22 CDT)
  - Re: AMBER: analysis REMD rebeca_at_mmb.pcb.ub.es (Tue May 20 2008 - 05:49:00 CDT)
- Re: AMBER: analysis REMD Carlos Simmerling (Tue May 20 2008 - 07:11:29 CDT)
  - Re: AMBER: analysis REMD rebeca_at_mmb.pcb.ub.es (Tue May 20 2008 - 13:31:30 CDT)
AMBER: 3rd Annual CMM Workshop on QM/MM Simulations Ross Walker (Mon May 19 2008 - 18:33:55 CDT)
- AMBER: parallel test / libmpi_f90.so.0 Arturas Ziemys (Wed May 28 2008 - 10:10:36 CDT)
  - Re: AMBER: parallel test / libmpi_f90.so.0 Arturas Ziemys (Wed May 28 2008 - 10:24:14 CDT)
AMBER: MM-PBSA for carbohydrates Neha Gandhi (Mon May 19 2008 - 21:07:24 CDT)
- Re: AMBER: MM-PBSA for carbohydrates Navnit Kumar Mishra (Tue May 20 2008 - 06:25:20 CDT)
AMBER: massively parallel computation Mingfeng Yang (Tue May 20 2008 - 02:03:51 CDT)
- Re: AMBER: massively parallel computation Adrian Roitberg (Tue May 20 2008 - 09:11:46 CDT)
  - Re: AMBER: massively parallel computation Lars Skjærven (Tue May 20 2008 - 09:28:24 CDT)
  - Re: AMBER: massively parallel computation Robert Duke (Tue May 20 2008 - 09:32:22 CDT)
- Re: AMBER: massively parallel computation Robert Duke (Tue May 20 2008 - 09:22:56 CDT)
  - Re: AMBER: massively parallel computation Mingfeng Yang (Tue May 20 2008 - 11:58:56 CDT)
AMBER: xLeap compilation issues Sasha Buzko (Tue May 20 2008 - 18:41:49 CDT)
- Re: AMBER: xLeap compilation issues David A. Case (Wed May 21 2008 - 00:27:53 CDT)
  - Re: AMBER: xLeap compilation issues Sasha Buzko (Wed May 21 2008 - 10:52:00 CDT)
AMBER: How to set a ZN atom radius for PB calculations Sam Danziger (Tue May 20 2008 - 19:23:30 CDT)
- RE: AMBER: How to set a ZN atom radius for PB calculations Ray Luo (Thu May 22 2008 - 15:41:36 CDT)
AMBER: Regarding binding free energy calculation using MM_PBSA method nag raj (Wed May 21 2008 - 02:01:14 CDT)
- RE: AMBER: Regarding binding free energy calculation using MM_PBSA method nag raj (Thu May 22 2008 - 07:18:59 CDT)
AMBER: $AMBERHOME/dat/slko Francesco Pietra (Wed May 21 2008 - 07:47:59 CDT)
- Re: AMBER: $AMBERHOME/dat/slko Gustavo Seabra (Wed May 21 2008 - 09:29:35 CDT)
  - Re: AMBER: $AMBERHOME/dat/slko Francesco Pietra (Thu May 22 2008 - 04:14:55 CDT)
AMBER: ptraj analyze matrix Seth Lilavivat (Wed May 21 2008 - 09:53:28 CDT)
AMBER: amber tools installation vijayaraj_at_clri.info (Wed May 21 2008 - 10:22:37 CDT)
- Re: AMBER: amber tools installation David A. Case (Wed May 21 2008 - 10:30:32 CDT)
  - Re: AMBER: amber tools installation vijayaraj_at_clri.info (Thu May 22 2008 - 03:55:00 CDT)
AMBER: pressure regulation methods Vlad Cojocaru (Wed May 21 2008 - 11:25:08 CDT)
AMBER: ff99 and ff03 forcefield parameters Peter Kiss (Wed May 21 2008 - 16:01:47 CDT)
- Re: AMBER: ff99 and ff03 forcefield parameters Vlad Cojocaru (Fri May 23 2008 - 04:31:47 CDT)
  - Re: AMBER: ff99 and ff03 forcefield parameters Vlad Cojocaru (Fri May 23 2008 - 04:43:38 CDT)
AMBER: Parallel Self-guided Langevin simulation Dirar Homouz (Wed May 21 2008 - 17:23:27 CDT)
- Re: AMBER: Parallel Self-guided Langevin simulation David A. Case (Thu May 22 2008 - 05:16:23 CDT)
  - RE: AMBER: Parallel Self-guided Langevin simulation Dirar Homouz (Thu May 22 2008 - 10:58:27 CDT)
AMBER: about hydrogen bond in amber force field WANG,YING (Wed May 21 2008 - 21:24:47 CDT)
- RE: AMBER: about hydrogen bond in amber force field Ross Walker (Wed May 21 2008 - 22:32:06 CDT)
- Re: AMBER: about hydrogen bond in amber force field Carlos Simmerling (Thu May 22 2008 - 02:08:08 CDT)
AMBER: COM RESTRAINT fatima.chami_at_durham.ac.uk (Thu May 22 2008 - 07:17:09 CDT)
- Re: AMBER: COM RESTRAINT David A. Case (Fri May 23 2008 - 00:19:24 CDT)
AMBER: potassium ion Lars Skjærven (Thu May 22 2008 - 08:09:59 CDT)
- Re: AMBER: potassium ion Bill Ross (Sat Jun 14 2008 - 15:04:31 CDT)
AMBER: amber10 installation vijayaraj_at_clri.info (Thu May 22 2008 - 09:22:47 CDT)
- Re: AMBER: amber10 installation Ibrahim Moustafa (Thu May 22 2008 - 10:03:15 CDT)
  - AMBER: Force field in water and in vacuum ?? Chih-Ying Lin (Thu May 22 2008 - 10:46:15 CDT)
    - RE: AMBER: Force field in water and in vacuum ?? Ross Walker (Thu May 22 2008 - 11:06:36 CDT)
- RE: AMBER: amber10 installation Ross Walker (Thu May 22 2008 - 10:40:20 CDT)
AMBER: AMBER file preparation for protein-carbohydrate complex Neha Gandhi (Thu May 22 2008 - 09:31:50 CDT)
- Re: AMBER: AMBER file preparation for protein-carbohydrate complex Lachele Foley (Lists) (Thu May 22 2008 - 16:39:44 CDT)
  - Re: AMBER: AMBER file preparation for protein-carbohydrate complex n.gandhiau_at_gmail.com (Sun May 25 2008 - 02:17:55 CDT)
    - Re: AMBER: AMBER file preparation for protein-carbohydrate complex Karl Kirschner (Sun May 25 2008 - 04:25:35 CDT)
AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system Pavan G (Thu May 22 2008 - 10:37:56 CDT)
- RE: AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system Ross Walker (Thu May 22 2008 - 10:54:51 CDT)
Re: AMBER: potassium ion Bill Ross (Thu May 22 2008 - 13:27:21 CDT)
- Re: AMBER: potassium ion Lars Skjærven (Thu Jun 12 2008 - 12:46:36 CDT)
AMBER: Calculate the RESP charge Fe3+ of heme (p450) chen bents (Thu May 22 2008 - 21:16:12 CDT)
- Re: AMBER: Calculate the RESP charge Fe3+ of heme (p450) David A. Case (Fri May 23 2008 - 00:35:29 CDT)
AMBER: self-diffusion coefficient and Berendsen Jennifer.Thomas_at_cbt.uhp-nancy.fr (Fri May 23 2008 - 03:03:49 CDT)
- Re: AMBER: self-diffusion coefficient and Berendsen Andreas Svrcek-Seiler (Fri May 23 2008 - 04:22:57 CDT)
- Re: AMBER: self-diffusion coefficient and Berendsen David A. Case (Sat May 24 2008 - 15:20:27 CDT)
  - Re: AMBER: self-diffusion coefficient and Berendsen Jennifer.Thomas_at_cbt.uhp-nancy.fr (Sun May 25 2008 - 05:47:22 CDT)
    - Re: AMBER: self-diffusion coefficient and Berendsen David A. Case (Sun May 25 2008 - 23:09:32 CDT)
AMBER: help MD running error Qiuting Hong (Fri May 23 2008 - 03:40:12 CDT)
- RE: AMBER: help MD running error Ross Walker (Fri May 23 2008 - 10:30:03 CDT)
AMBER: PBC in 2D fatima.chami_at_durham.ac.uk (Fri May 23 2008 - 08:13:39 CDT)
AMBER: how generate the final output file using mmpbsa luzhenw1_at_msu.edu (Fri May 23 2008 - 15:49:33 CDT)
- Re: AMBER: how generate the final output file using mmpbsa Miguel Ortiz-Lombardía (Sat May 24 2008 - 01:40:40 CDT)
AMBER: how to extract energy WANG,YING (Fri May 23 2008 - 20:08:13 CDT)
- RE: AMBER: how to extract energy Ross Walker (Fri May 23 2008 - 22:07:41 CDT)
  - RE: AMBER: how to extract energy Francesco Pietra (Sat May 24 2008 - 02:24:13 CDT)
  - Re: AMBER: how to extract energy David A. Case (Sat May 24 2008 - 15:21:22 CDT)
- RE: AMBER: how to extract energy WANG,YING (Sun May 25 2008 - 08:57:20 CDT)
AMBER: periodic bondary condition WANG,YING (Fri May 23 2008 - 20:16:34 CDT)
- RE: AMBER: periodic boundary condition Ross Walker (Fri May 23 2008 - 22:09:39 CDT)
AMBER: ptraj mask not working with psf file Dong Xu (Fri May 23 2008 - 21:53:27 CDT)
AMBER: Amber9 vs Amber10+MKL benchmark Francesco Pietra (Sat May 24 2008 - 08:48:12 CDT)
AMBER: Fw: Amber9 vs Amber10+MKL benchmark Francesco Pietra (Sat May 24 2008 - 08:51:53 CDT)
AMBER: calculating the energy from the restart file priya priya (Sat May 24 2008 - 09:03:46 CDT)
AMBER: Fw: Amber9 vs Amber10+MKL benchmark Francesco Pietra (Sat May 24 2008 - 09:50:45 CDT)
AMBER: caculating nonpolar solvation energies ke dong (Sat May 24 2008 - 09:53:17 CDT)
AMBER: trajectories into trajectory Hakkim Boy (Sun May 25 2008 - 06:30:22 CDT)
- Re: AMBER: trajectories into trajectory Florian Haberl (Sun May 25 2008 - 07:10:41 CDT)
AMBER: mass weighted rms fit Dong Xu (Sun May 25 2008 - 11:11:43 CDT)
- Re: AMBER: mass weighted rms fit Adrian Roitberg (Sun May 25 2008 - 11:26:11 CDT)
  - AMBER: using amber ports in Gromacs Cristina Sisu (Sun May 25 2008 - 13:28:26 CDT)
    - Re: AMBER: using amber ports in Gromacs Carlos Simmerling (Sun May 25 2008 - 14:32:05 CDT)
AMBER: using amber ports in gromacs Cristina Sisu (Sun May 25 2008 - 13:22:58 CDT)
AMBER: is in vacuo simulation neccessary? Anamika Awasthi (Mon May 26 2008 - 00:18:58 CDT)
- Re: AMBER: is in vacuo simulation neccessary? Mark Abraham (Mon May 26 2008 - 00:44:20 CDT)
AMBER: Umbrella Sampling for proteins German Erlenkamp (Mon May 26 2008 - 04:23:56 CDT)
AMBER: peptide at the box center during NVT-MD Darek Czapiewski (Mon May 26 2008 - 05:01:45 CDT)
- Re: AMBER: peptide at the box center during NVT-MD David A. Case (Mon May 26 2008 - 11:09:51 CDT)
AMBER: B-factor calculation from data with different write frequencies Sally Pias (Mon May 26 2008 - 23:19:42 CDT)
- Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross (Wed May 28 2008 - 12:47:28 CDT)
  - Re: AMBER: B-factor calculation from data with different write frequencies Adrian Roitberg (Wed May 28 2008 - 12:54:09 CDT)
- Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross (Wed May 28 2008 - 13:11:30 CDT)
  - Re: AMBER: B-factor calculation from data with different write frequencies Adrian Roitberg (Wed May 28 2008 - 13:58:53 CDT)
- Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross (Wed May 28 2008 - 13:18:06 CDT)
AMBER: Which is best temperature controlling method sudipta sinha (Tue May 27 2008 - 05:25:02 CDT)
- Re: AMBER: Which is best temperature controlling method David A. Case (Tue May 27 2008 - 23:59:23 CDT)
  - Re: AMBER: Which is best temperature controlling method Reena ..... (Wed May 28 2008 - 00:34:39 CDT)
Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross (Tue May 27 2008 - 11:44:23 CDT)
- Re: AMBER: B-factor calculation from data with different write frequencies Sally Pias (Tue May 27 2008 - 22:42:13 CDT)
AMBER: error when read inpcrd WANG,YING (Tue May 27 2008 - 15:32:02 CDT)
- RE: AMBER: error when read inpcrd Ross Walker (Tue May 27 2008 - 15:50:23 CDT)
- RE: AMBER: error when read inpcrd WANG,YING (Tue May 27 2008 - 16:14:02 CDT)
AMBER: bugfix (imin=5) in amber9 Xioling Chuang (Tue May 27 2008 - 23:23:09 CDT)
- Re: AMBER: bugfix (imin=5) in amber9 David A. Case (Wed May 28 2008 - 00:16:40 CDT)
AMBER: compilation problem with AMBER10 bhargav patel (Wed May 28 2008 - 00:56:15 CDT)
- Re: AMBER: compilation problem with AMBER10 Atro Tossavainen (Wed May 28 2008 - 03:04:09 CDT)
AMBER: Hydration free energies of charged ions using PME Markus Kaukonen (Wed May 28 2008 - 01:51:26 CDT)
- Re: AMBER: Hydration free energies of charged ions using PME David A. Case (Wed May 28 2008 - 11:51:26 CDT)
AMBER: install amber tools Alejandro Valbuena (Wed May 28 2008 - 05:14:35 CDT)
- AMBER: energy pairwise decomposition in GB/SA simulation wfli_at_biophy.nju.edu.cn (Wed May 28 2008 - 05:29:42 CDT)
- Re: AMBER: install amber tools David A. Case (Wed May 28 2008 - 11:56:30 CDT)
AMBER: Segmentation faults trying to run sander mpi Idan Gabdank (Wed May 28 2008 - 05:59:09 CDT)
- Re: AMBER: Segmentation faults trying to run sander mpi David A. Case (Wed May 28 2008 - 12:00:34 CDT)
- Re: AMBER: Segmentation faults trying to run sander mpi Idan Gabdank (Thu May 29 2008 - 09:57:07 CDT)
  - Re: AMBER: Segmentation faults trying to run sander mpi David A. Case (Thu May 29 2008 - 10:20:08 CDT)
AMBER: restarting molecular dynamics Germain Vallverdu (Wed May 28 2008 - 08:18:16 CDT)
- Re: AMBER: restarting molecular dynamics Adrian Roitberg (Wed May 28 2008 - 08:34:17 CDT)
  - Re: AMBER: restarting molecular dynamics Germain Vallverdu (Wed May 28 2008 - 09:25:23 CDT)
    - Re: AMBER: restarting molecular dynamics Adrian Roitberg (Wed May 28 2008 - 10:48:45 CDT)
AMBER: mbondi radii for gaff atom types Sara J (Wed May 28 2008 - 10:03:52 CDT)
- Re: AMBER: mbondi radii for gaff atom types David A. Case (Wed May 28 2008 - 12:31:30 CDT)
AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error Kateryna Miroshnychenko (Wed May 28 2008 - 10:08:19 CDT)
- Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error David A. Case (Wed May 28 2008 - 12:27:31 CDT)
  - Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error Kateryna Miroshnychenko (Thu May 29 2008 - 02:22:17 CDT)
    - Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error David A. Case (Mon Jun 02 2008 - 18:23:46 CDT)
    - Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error Kateryna Miroshnychenko (Tue Jun 03 2008 - 02:05:51 CDT)
AMBER: protonate in Amber10 Benjamin Juhl (Wed May 28 2008 - 09:55:06 CDT)
- Re: AMBER: protonate in Amber10 David A. Case (Thu May 29 2008 - 16:10:34 CDT)
AMBER: rmsd vs frame Francesco Pietra (Wed May 28 2008 - 17:56:24 CDT)
AMBER: Fw: rmsd vs frame Francesco Pietra (Wed May 28 2008 - 18:19:11 CDT)
AMBER: VMD Movie Campbell, Patrick (Wed May 28 2008 - 18:33:39 CDT)
- Re: AMBER: VMD Movie Carlos Simmerling (Wed May 28 2008 - 19:10:03 CDT)
AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Thu May 29 2008 - 00:56:48 CDT)
AMBER: ligand unit charge is not zero amor san juan (Thu May 29 2008 - 03:44:58 CDT)
- Re: AMBER: ligand unit charge is not zero mori_at_cerm.unifi.it (Thu May 29 2008 - 04:17:55 CDT)
  - Re: AMBER: ligand unit charge is not zero amor san juan (Thu May 29 2008 - 07:32:57 CDT)
    - Re: AMBER: ligand unit charge is not zero Swarup Gupta (Thu May 29 2008 - 07:48:13 CDT)
- AMBER: how to overcome theunusual bonds formation Thomas Leonard (Thu May 29 2008 - 06:03:29 CDT)
  - Re: AMBER: how to overcome theunusual bonds formation Florian Haberl (Thu May 29 2008 - 06:54:20 CDT)
AMBER: solvatebox fatima.chami_at_durham.ac.uk (Thu May 29 2008 - 06:46:42 CDT)
- RE: AMBER: solvatebox Ross Walker (Thu May 29 2008 - 10:22:53 CDT)
AMBER: Installing PMEMD with Amber10 Justin A. Lemkul (Thu May 29 2008 - 08:23:05 CDT)
- Re: AMBER: Installing PMEMD with Amber10 Robert Duke (Thu May 29 2008 - 09:44:38 CDT)
  - Re: AMBER: Installing PMEMD with Amber10 Justin A. Lemkul (Thu May 29 2008 - 14:12:26 CDT)
    - Re: AMBER: Installing PMEMD with Amber10 Robert Duke (Thu May 29 2008 - 15:16:39 CDT)
    - Re: AMBER: Installing PMEMD with Amber10 Justin A. Lemkul (Thu May 29 2008 - 15:41:30 CDT)
- Re: AMBER: Installing PMEMD with Amber10 Atro Tossavainen (Fri May 30 2008 - 01:42:02 CDT)
  - Re: AMBER: Installing PMEMD with Amber10 Justin A. Lemkul (Fri May 30 2008 - 05:42:53 CDT)
    - Re: AMBER: Installing PMEMD with Amber10 Atro Tossavainen (Sat May 31 2008 - 06:23:31 CDT)
    - Re: AMBER: Installing PMEMD with Amber10 Justin A. Lemkul (Sat May 31 2008 - 07:24:30 CDT)
AMBER: VMD Movie 2 Campbell, Patrick (Thu May 29 2008 - 12:39:20 CDT)
- Re: AMBER: VMD Movie 2 Carlos Simmerling (Thu May 29 2008 - 12:48:10 CDT)
AMBER: ptraj rmsd calculation Pavan G (Thu May 29 2008 - 13:08:36 CDT)
AMBER: VMD Movie 3 Campbell, Patrick (Thu May 29 2008 - 13:12:20 CDT)
- RE: AMBER: VMD Movie 3 Ross Walker (Thu May 29 2008 - 13:47:52 CDT)
  - AMBER: NTC and NTF dpandit_at_brandeis.edu (Thu May 29 2008 - 14:18:14 CDT)
    - RE: AMBER: NTC and NTF Ross Walker (Thu May 29 2008 - 14:30:28 CDT)
    - RE: AMBER: NTC and NTF dpandit_at_brandeis.edu (Thu May 29 2008 - 14:39:33 CDT)
  - Re: AMBER: VMD Movie 3 Ibrahim Moustafa (Thu May 29 2008 - 16:03:16 CDT)
AMBER: VMD Movie 4 Campbell, Patrick (Thu May 29 2008 - 14:37:43 CDT)
AMBER: ptraj has trouble with x-plor psf file from VMD Dong Xu (Thu May 29 2008 - 15:23:56 CDT)
- Re: AMBER: ptraj has trouble with x-plor psf file from VMD Jufang Shan (Mon Jun 02 2008 - 10:52:28 CDT)
AMBER: Ptraj | Multiple trajout commands? Ian (Fri May 30 2008 - 03:39:23 CDT)
- Re: AMBER: Ptraj | Multiple trajout commands? Jianyin Shao (Sat May 31 2008 - 19:02:17 CDT)
AMBER: Iron-Sulfur Cluster Joachim Reichelt (Fri May 30 2008 - 04:46:30 CDT)
- Re: AMBER: Iron-Sulfur Cluster Justine Condo (Fri May 30 2008 - 12:52:24 CDT)
- Re: AMBER: Iron-Sulfur Cluster FyD (Sat May 31 2008 - 07:35:31 CDT)
AMBER: nab Joachim Reichelt (Fri May 30 2008 - 04:48:56 CDT)
- Re: AMBER: nab David A. Case (Fri May 30 2008 - 09:55:10 CDT)
AMBER: Jarzynski fatima.chami_at_durham.ac.uk (Fri May 30 2008 - 06:44:41 CDT)
- Re: AMBER: Jarzynski David Mobley (Fri May 30 2008 - 11:02:28 CDT)
  - Re: AMBER: Jarzynski fatima.chami_at_durham.ac.uk (Sat May 31 2008 - 06:50:24 CDT)
AMBER: Sander instead of PMEMD Cristina Sisu (Fri May 30 2008 - 08:47:13 CDT)
- Re: AMBER: Sander instead of PMEMD Robert Duke (Fri May 30 2008 - 09:13:20 CDT)
  - Re: AMBER: Sander instead of PMEMD Cristina Sisu (Fri May 30 2008 - 09:32:27 CDT)
AMBER: VMD Movie 3 Campbell, Patrick (Fri May 30 2008 - 09:56:41 CDT)
AMBER: tleap error message Wang,Ying (Fri May 30 2008 - 11:08:14 CDT)
AMBER: igb and ibelly Holly Freedman (Fri May 30 2008 - 14:23:21 CDT)
- RE: AMBER: igb and ibelly Ross Walker (Fri May 30 2008 - 15:16:11 CDT)
- Re: AMBER: igb and ibelly David A. Case (Fri May 30 2008 - 15:20:52 CDT)
- RE: AMBER: igb and ibelly Holly Freedman (Fri May 30 2008 - 15:21:06 CDT)
- Re: AMBER: igb and ibelly Holly Freedman (Fri May 30 2008 - 17:36:03 CDT)
AMBER: SANDER and PMEMD with openmpi Ross Walker (Fri May 30 2008 - 17:18:04 CDT)
AMBER: MMPBSA error Cristina Sisu (Sat May 31 2008 - 09:00:08 CDT)
- Re: AMBER: MMPBSA error Peter Gannett (Sat May 31 2008 - 09:15:40 CDT)
  - Re: AMBER: MMPBSA error Cristina Sisu (Sat May 31 2008 - 09:53:32 CDT)
AMBER: ptraj analyze modes from nmode Miguel Ortiz-Lombardía (Sat May 31 2008 - 10:40:50 CDT)
Re: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Francesco Pietra (Sat May 31 2008 - 13:31:04 CDT)
- RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Ross Walker (Sat May 31 2008 - 15:57:48 CDT)
  - RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Francesco Pietra (Sun Jun 01 2008 - 02:12:12 CDT)
    - RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Ross Walker (Mon Jun 02 2008 - 12:52:33 CDT)
AMBER: amber9 , ptraj vector commad issue Vijay Singh (Sat May 31 2008 - 18:34:23 CDT)
AMBER: PCA - analysis Ibrahim Moustafa (Sun Jun 01 2008 - 13:00:35 CDT)
Fw: RE: AMBER: SANDER and PMEMD with openmpi. NO MORE failure 'make test.pmemd' Francesco Pietra (Mon Jun 02 2008 - 05:22:38 CDT)
AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 Jarrod Smith (Mon Jun 02 2008 - 11:43:24 CDT)
- Re: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 David A. Case (Mon Jun 02 2008 - 12:56:16 CDT)
  - Re: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 Jarrod Smith (Tue Jun 03 2008 - 14:29:31 CDT)
    - RE: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 Ross Walker (Tue Jun 03 2008 - 15:43:43 CDT)
AMBER: VMD file generation 4 - mdcrd ptraj analysis Campbell, Patrick (Mon Jun 02 2008 - 13:26:15 CDT)
- Re: AMBER: VMD file generation 4 - mdcrd ptraj analysis Carlos Simmerling (Mon Jun 02 2008 - 14:11:24 CDT)
  - AMBER: MAXAT can not be changed for AMBERTool 1.0 Hu, Shaowen (JSC-SK)[USRA] (Mon Jun 02 2008 - 14:41:54 CDT)
    - Re: AMBER: MAXAT can not be changed for AMBERTool 1.0 David A. Case (Mon Jun 02 2008 - 18:15:38 CDT)
- RE:AMBER: VMD file generation 4 - mdcrd ptraj analysis Campbell, Patrick (Mon Jun 02 2008 - 14:54:06 CDT)
  - Re: AMBER: VMD file generation 4 - mdcrd ptraj analysis Carlos Simmerling (Mon Jun 02 2008 - 15:06:39 CDT)
AMBER: VMD file generation 4 - mdcrd analysis Campbell, Patrick (Mon Jun 02 2008 - 15:21:00 CDT)
AMBER: PCA analysis Ibrahim Moustafa (Mon Jun 02 2008 - 16:09:17 CDT)
AMBER: Missing gaff angle parameters for dimethyl esters Lin, Pohan (Mon Jun 02 2008 - 16:20:24 CDT)
- AMBER: Error message: Install Amber9 on fedora 9 Chih-Ying Lin (Mon Jun 02 2008 - 17:33:42 CDT)
  - Re: AMBER: Error message: Install Amber9 on fedora 9 David A. Case (Mon Jun 02 2008 - 18:04:48 CDT)
- Re: AMBER: Missing gaff angle parameters for dimethyl esters Junmei Wang (Tue Jun 03 2008 - 08:19:25 CDT)
  - AMBER: Trajectory in "Sietraj" Alfredo Quevedo (Tue Jun 03 2008 - 08:35:20 CDT)
  - RE: AMBER: Missing gaff angle parameters for dimethyl esters Lin, Pohan (Tue Jun 03 2008 - 14:56:32 CDT)
AMBER: corrupted restart file yavuzturkm_at_prc.boun.edu.tr (Tue Jun 03 2008 - 04:18:25 CDT)
- Re: AMBER: corrupted restart file Cenk $Jenk$ Andac (Tue Jun 03 2008 - 05:13:29 CDT)
- Re: AMBER: corrupted restart file Carlos Simmerling (Tue Jun 03 2008 - 05:15:21 CDT)
AMBER: Temperature controlling method in AMBER tinni sona (Tue Jun 03 2008 - 04:43:11 CDT)
- Re: AMBER: Temperature controlling method in AMBER David A. Case (Tue Jun 03 2008 - 09:56:51 CDT)
AMBER: solvate box : buffer list fatima.chami_at_durham.ac.uk (Tue Jun 03 2008 - 12:51:55 CDT)
- Re: AMBER: solvate box : buffer list David A. Case (Tue Jun 03 2008 - 13:22:16 CDT)
  - Re: AMBER: solvate box : buffer list fatima.chami_at_durham.ac.uk (Wed Jun 04 2008 - 05:07:06 CDT)
AMBER: How to calculate RMSIP after PCA analysis by PTRAJ? sychen (Wed Jun 04 2008 - 07:27:45 CDT)
AMBER: problems with sleap Alan (Wed Jun 04 2008 - 10:40:04 CDT)
- Re: AMBER: problems with sleap David A. Case (Wed Jun 04 2008 - 18:52:00 CDT)
  - Re: AMBER: problems with sleap Alan (Thu Jun 05 2008 - 01:48:03 CDT)
AMBER: NMODE units and hrmax value for Langevine modes Yang, Lee-Wei (Wed Jun 04 2008 - 11:27:00 CDT)
- Re: AMBER: NMODE units and hrmax value for Langevine modes David A. Case (Wed Jun 04 2008 - 12:30:36 CDT)
  - RE: AMBER: NMODE units and hrmax value for Langevine modes Yang, Lee-Wei (Wed Jun 04 2008 - 22:55:45 CDT)
    - Re: AMBER: NMODE units and hrmax value for Langevine modes David A. Case (Thu Jun 05 2008 - 13:12:24 CDT)
AMBER: amber installation on cluster Pankaj R. Daga (Wed Jun 04 2008 - 12:27:57 CDT)
- RE: AMBER: amber installation on cluster Ross Walker (Wed Jun 04 2008 - 12:54:36 CDT)
- Re: AMBER: amber installation on cluster David A. Case (Wed Jun 04 2008 - 12:55:39 CDT)
AMBER: NAB documentation for programmers ramu_at_vt.edu (Wed Jun 04 2008 - 13:59:27 CDT)
AMBER: ptraj imaging issue Vlad Cojocaru (Wed Jun 04 2008 - 14:07:44 CDT)
- AMBER: syn and anti conformation Rabin (Wed Jun 04 2008 - 14:29:58 CDT)
  - Re: AMBER: syn and anti conformation Carlos Simmerling (Wed Jun 04 2008 - 14:34:31 CDT)
- Re: AMBER: ptraj imaging issue Jianyin Shao (Wed Jun 04 2008 - 16:25:27 CDT)
  - Re: AMBER: ptraj imaging issue Vlad Cojocaru (Thu Jun 05 2008 - 03:48:43 CDT)
    - Re: AMBER: ptraj imaging issue Vlad Cojocaru (Thu Jun 05 2008 - 09:30:42 CDT)
    - Re: AMBER: ptraj imaging issue Jianyin Shao (Thu Jun 05 2008 - 11:23:52 CDT)
AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Thu Jun 05 2008 - 00:27:39 CDT)
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Thu Jun 05 2008 - 22:52:12 CDT)
AMBER: problem of install amber9 Xioling Chuang (Thu Jun 05 2008 - 03:37:27 CDT)
- RE: AMBER: problem of install amber9 Xioling Chuang (Thu Jun 05 2008 - 04:09:27 CDT)
AMBER: Free energy of dissociation fatima.chami_at_durham.ac.uk (Thu Jun 05 2008 - 07:02:43 CDT)
- Re: AMBER: Free energy of dissociation Gustavo Seabra (Thu Jun 05 2008 - 08:41:03 CDT)
  - Re: AMBER: Free energy of dissociation fatima.chami_at_durham.ac.uk (Thu Jun 05 2008 - 10:13:03 CDT)
- Re: AMBER: Free energy of dissociation David Mobley (Thu Jun 05 2008 - 11:22:24 CDT)
AMBER: NAN errors in Etot, EPtot, EKtot and EELEC Praveena Gopal (Thu Jun 05 2008 - 07:04:00 CDT)
- Re: AMBER: NAN errors in Etot, EPtot, EKtot and EELEC Carlos Simmerling (Thu Jun 05 2008 - 07:16:22 CDT)
  - Re: AMBER: NAN errors in Etot, EPtot, EKtot and EELEC Praveena Gopal (Fri Jun 06 2008 - 01:16:40 CDT)
  - AMBER: NAN errors still exist Praveena Gopal (Fri Jun 06 2008 - 04:56:58 CDT)
    - Re: AMBER: NAN errors still exist Carlos Simmerling (Fri Jun 06 2008 - 05:57:49 CDT)
AMBER: netcdf configure returned 1 Jens Lattig (Thu Jun 05 2008 - 08:46:45 CDT)
AMBER: netcdf configure returned 1 - PROBLEM SOLVED Jens Lattig (Thu Jun 05 2008 - 09:42:03 CDT)
AMBER: A problem of installing Amber10 Yicun Ni (Thu Jun 05 2008 - 10:55:53 CDT)
- Re: AMBER: A problem of installing Amber10 David A. Case (Thu Jun 05 2008 - 12:49:58 CDT)
  - Re: AMBER: A problem of installing Amber10 Harry Ni (Thu Jun 05 2008 - 13:27:23 CDT)
AMBER: Nmode - entropy calculation of receptor - should I apply restraint? Seth Lilavivat (Thu Jun 05 2008 - 12:03:08 CDT)
- Re: AMBER: Nmode - entropy calculation of receptor - should I apply restraint? David A. Case (Thu Jun 05 2008 - 13:50:16 CDT)
AMBER: RE: solvating RNA in 8M urea box Ross Walker (Thu Jun 05 2008 - 19:12:42 CDT)
AMBER: Query on MM-PBSA Neha Gandhi (Fri Jun 06 2008 - 00:46:32 CDT)
AMBER: PROBLEM: AmberTools Installation using Ubuntu Jens Lattig (Fri Jun 06 2008 - 03:13:06 CDT)
- Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu David Case (Fri Jun 06 2008 - 11:25:45 CDT)
  - Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu Jens Lattig (Tue Jun 10 2008 - 03:00:08 CDT)
AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Ian (Fri Jun 06 2008 - 04:19:58 CDT)
- Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Vlad Cojocaru (Fri Jun 06 2008 - 04:59:54 CDT)
- Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory David Case (Fri Jun 06 2008 - 11:27:06 CDT)
  - AMBER: Problems simulating a protein-ligand complex Sasha Buzko (Fri Jun 06 2008 - 12:55:05 CDT)
  - Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Vlad Cojocaru (Fri Jun 06 2008 - 13:50:55 CDT)
    - Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Ian (Wed Jun 11 2008 - 05:53:42 CDT)
    - Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Jianyin Shao (Wed Jun 11 2008 - 10:55:12 CDT)
AMBER: Problem While Installing Amber Ranga Swamy (Fri Jun 06 2008 - 04:34:17 CDT)
- RE: AMBER: Problem While Installing Amber Ross Walker (Fri Jun 06 2008 - 10:30:26 CDT)
AMBER: VMD Movie .mdcrd file ptraj Campbell, Patrick (Fri Jun 06 2008 - 08:22:50 CDT)
- Re: AMBER: VMD Movie .mdcrd file ptraj David Watson (Fri Jun 06 2008 - 09:57:16 CDT)
AMBER: NAB documentation David Case (Fri Jun 06 2008 - 11:24:44 CDT)
- Re: AMBER: NAB documentation Ramu Anandakrishnan (Fri Jun 06 2008 - 23:08:51 CDT)
  - Re: AMBER: NAB documentation David A. Case (Sun Jun 08 2008 - 20:38:05 CDT)
Re:AMBER:VMD Movie.mdcrd Campbell, Patrick (Fri Jun 06 2008 - 13:56:52 CDT)
AMBER: 100 short MD runs within a single Sander script? Sebastian Stolzenberg (Fri Jun 06 2008 - 23:55:37 CDT)
- RE: AMBER: 100 short MD runs within a single Sander script? Ross Walker (Sat Jun 07 2008 - 00:22:36 CDT)
AMBER: Combine mdcrd while stripping WAT problem Francesco Pietra (Sun Jun 08 2008 - 10:40:07 CDT)
- Re: AMBER: Combine mdcrd while stripping WAT problem Gustavo Seabra (Sun Jun 08 2008 - 13:58:34 CDT)
  - Re: AMBER: Combine mdcrd while stripping WAT problem Carlos Simmerling (Sun Jun 08 2008 - 14:33:47 CDT)
AMBER: problem in starting sander Qiuting Hong (Sun Jun 08 2008 - 13:25:43 CDT)
- Re: AMBER: problem in starting sander Carlos Simmerling (Sun Jun 08 2008 - 14:53:33 CDT)
  - Re: AMBER: problem in starting sander Qiuting Hong (Sun Jun 08 2008 - 16:52:34 CDT)
- RE: AMBER: problem in starting sander Ross Walker (Sun Jun 08 2008 - 17:30:17 CDT)
  - Re: AMBER: problem in starting sander Qiuting Hong (Sun Jun 08 2008 - 21:40:52 CDT)
    - Re: AMBER: problem in starting sander Carlos Simmerling (Sun Jun 08 2008 - 23:36:32 CDT)
AMBER: MM-PBSA and delphi Neha Gandhi (Mon Jun 09 2008 - 00:49:54 CDT)
- Re: AMBER: MM-PBSA and delphi Neha Gandhi (Mon Jun 09 2008 - 00:56:00 CDT)
  - Re: AMBER: MM-PBSA and delphi Navnit Kumar Mishra (Mon Jun 09 2008 - 04:05:38 CDT)
AMBER: Calcium and Magnesium LJ parameters Daniel Smith (Mon Jun 09 2008 - 18:02:28 CDT)
AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating xiaonan zhang (Tue Jun 10 2008 - 07:24:02 CDT)
- Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating David A. Case (Tue Jun 10 2008 - 07:50:27 CDT)
  - Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating xiaonan zhang (Tue Jun 10 2008 - 09:23:15 CDT)
    - Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating David A. Case (Wed Jun 11 2008 - 12:53:20 CDT)
AMBER: SMD pulling velocity fatima.chami_at_durham.ac.uk (Tue Jun 10 2008 - 09:06:38 CDT)
- Re: AMBER: SMD pulling velocity Gustavo Seabra (Tue Jun 10 2008 - 09:22:48 CDT)
AMBER: how to calculate the interaction energy Wang,Ying (Tue Jun 10 2008 - 09:52:10 CDT)
- Re: AMBER: how to calculate the interaction energy Thomas Steinbrecher (Tue Jun 10 2008 - 11:45:16 CDT)
  - AMBER: amber10 installation problem Ed Pate (Tue Jun 10 2008 - 15:59:47 CDT)
- Re: AMBER: how to calculate the interaction energy Wang,Ying (Tue Jun 10 2008 - 14:12:17 CDT)
AMBER: Simulating complexes with magnesium atoms Sasha Buzko (Tue Jun 10 2008 - 16:32:13 CDT)
AMBER: box shape changed at NVT fatima.chami_at_durham.ac.uk (Wed Jun 11 2008 - 09:25:09 CDT)
- Re: AMBER: box shape changed at NVT David A. Case (Wed Jun 11 2008 - 10:18:46 CDT)
AMBER: sander.MPI / openmpi on PBS Arturas Ziemys (Wed Jun 11 2008 - 13:59:52 CDT)
AMBER: 2D RMS plot Steve Spronk (Wed Jun 11 2008 - 14:18:32 CDT)
- Re: AMBER: 2D RMS plot Jianyin Shao (Wed Jun 11 2008 - 17:17:43 CDT)
  - RE: AMBER: 2D RMS plot Steve Spronk (Thu Jun 12 2008 - 07:42:41 CDT)
AMBER: Coordinated Zinc Khaled Barakat (Wed Jun 11 2008 - 14:29:18 CDT)
- Re: AMBER: Coordinated Zinc David A. Case (Thu Jun 12 2008 - 10:59:42 CDT)
  - Re: AMBER: Coordinated Zinc FyD (Fri Jun 13 2008 - 02:56:08 CDT)
  - AMBER: Simulating protein conformational changes? Sasha Buzko (Fri Aug 01 2008 - 17:42:07 CDT)
AMBER: Antechamber and topology file TAEJIN KIM (Wed Jun 11 2008 - 18:05:14 CDT)
- Re: AMBER: Antechamber and topology file David A. Case (Thu Jun 12 2008 - 11:03:50 CDT)
AMBER: updating documentation Alan (Thu Jun 12 2008 - 04:52:40 CDT)
- Re: AMBER: updating documentation David A. Case (Thu Jun 12 2008 - 10:10:36 CDT)
  - Re: AMBER: updating documentation Alan (Thu Jun 12 2008 - 18:09:24 CDT)
    - Re: AMBER: updating documentation David A. Case (Fri Jun 13 2008 - 11:52:14 CDT)
AMBER: using Velocity-Verlet algorithm oguz gurbulak (Thu Jun 12 2008 - 07:07:20 CDT)
- Re: AMBER: using Velocity-Verlet algorithm David A. Case (Thu Jun 12 2008 - 11:09:49 CDT)
AMBER: anisotropic pressure scaling ntp=2 fatima.chami_at_durham.ac.uk (Thu Jun 12 2008 - 08:18:13 CDT)
- Re: AMBER: anisotropic pressure scaling ntp=2 David A. Case (Thu Jun 12 2008 - 10:13:52 CDT)
AMBER: SMD RESTRAINTS fatima.chami_at_durham.ac.uk (Thu Jun 12 2008 - 11:23:00 CDT)
- Re: AMBER: SMD RESTRAINTS Adrian Roitberg (Thu Jun 12 2008 - 11:51:56 CDT)
  - Re: AMBER: SMD RESTRAINTS fatima.chami_at_durham.ac.uk (Thu Jun 12 2008 - 12:07:49 CDT)
    - Re: AMBER: SMD RESTRAINTS Adrian Roitberg (Thu Jun 12 2008 - 14:23:26 CDT)
AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell (Thu Jun 12 2008 - 11:31:03 CDT)
- RE: AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell (Thu Jun 12 2008 - 12:32:13 CDT)
  - Re: AMBER: Compile amber10 parallel with suppied LAM Gustavo Seabra (Thu Jun 12 2008 - 12:39:34 CDT)
  - AMBER: How to get all eigenvalues by "analyze matrix" Qi Yan (Thu Jun 12 2008 - 12:39:52 CDT)
AMBER: Sander crashes >99999 atoms plmallip_at_mail.uh.edu (Thu Jun 12 2008 - 18:26:57 CDT)
- Re: AMBER: Sander crashes >99999 atoms David A. Case (Thu Jun 12 2008 - 20:25:31 CDT)
  - Re: AMBER: Sander crashes >99999 atoms plmallip_at_mail.uh.edu (Thu Jun 12 2008 - 23:47:47 CDT)
    - Re: AMBER: Sander crashes >99999 atoms David A. Case (Fri Jun 13 2008 - 11:59:32 CDT)
  - AMBER: MM-GBSA with very positive GB value Catein Catherine (Fri Jun 13 2008 - 02:05:02 CDT)
    - Re: AMBER: MM-GBSA with very positive GB value Carlos Simmerling (Fri Jun 13 2008 - 02:46:55 CDT)
    - RE: AMBER: MM-GBSA with very positive GB value Catein Catherine (Fri Jun 13 2008 - 20:49:53 CDT)
AMBER: PCAL and polar contribution in the output file Neha Gandhi (Fri Jun 13 2008 - 00:42:54 CDT)
- Re: AMBER: PCAL and polar contribution in the output file Hannes Kopitz (Sun Jun 15 2008 - 08:30:23 CDT)
  - Re: AMBER: PCAL and polar contribution in the output file Neha Gandhi (Sun Jun 15 2008 - 08:56:20 CDT)
AMBER: amber10 make fails for static/parallel James W. Caldwell (Fri Jun 13 2008 - 17:50:19 CDT)
AMBER: Ewald error estimate Pavan G (Sun Jun 15 2008 - 09:22:48 CDT)
AMBER: Problem with running refinement of NMR structures with RDCs Qi Zhang (Sun Jun 15 2008 - 15:20:21 CDT)
- Re: AMBER: Problem with running refinement of NMR structures with RDCs David A. Case (Sun Jun 15 2008 - 20:50:53 CDT)
AMBER: Eigenmode dynamics in Ptraj fatima.chami_at_durham.ac.uk (Mon Jun 16 2008 - 07:59:42 CDT)
AMBER: the SPCFW water model Vlad Cojocaru (Mon Jun 16 2008 - 11:19:34 CDT)
AMBER: sander.MPI / parallel Arturas Ziemys (Mon Jun 16 2008 - 12:00:34 CDT)
- Re: AMBER: sander.MPI / parallel Carlos Simmerling (Mon Jun 16 2008 - 12:43:39 CDT)
  - Re: AMBER: sander.MPI / parallel Arturas Ziemys (Mon Jun 16 2008 - 12:56:57 CDT)
AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez (Mon Jun 16 2008 - 09:31:12 CDT)
- Re: AMBER: [Fwd: segmentation fault in nmode] David A. Case (Mon Jun 16 2008 - 18:42:47 CDT)
  - Re: AMBER: [Fwd: segmentation fault in nmode] JAMES W CALDWELL (Mon Jun 16 2008 - 19:53:03 CDT)
  - Re: AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez (Tue Jun 17 2008 - 02:48:34 CDT)
- Re: AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez (Tue Jun 17 2008 - 02:50:33 CDT)
  - Re: AMBER: [Fwd: segmentation fault in nmode] David A. Case (Thu Jun 19 2008 - 19:22:34 CDT)
    - Re: AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez (Mon Jun 23 2008 - 03:27:27 CDT)
AMBER: about resp charges WanJ Ding (Mon Jun 16 2008 - 14:44:55 CDT)
- Re: AMBER: about resp charges FyD (Tue Jun 17 2008 - 07:58:03 CDT)
  - Re: AMBER: about resp charges wanjian ding (Wed Jun 18 2008 - 15:43:35 CDT)
AMBER: IRED to time correlation fatima.chami_at_durham.ac.uk (Mon Jun 16 2008 - 15:25:22 CDT)
AMBER: program to calculate rmsd rams rams (Mon Jun 16 2008 - 21:28:24 CDT)
- RE: AMBER: program to calculate rmsd Ross Walker (Tue Jun 17 2008 - 03:26:53 CDT)
AMBER: How to solve - Missing BELE for MM in 1 in amber. Thomas Leonard (Mon Jun 16 2008 - 22:05:59 CDT)
AMBER: How to solve - Missing BELE for MM in 1 in amber. Thomas Leonard (Mon Jun 16 2008 - 22:06:01 CDT)
- Re: AMBER: How to solve - Missing BELE for MM in 1 in amber. Hannes Kopitz (Tue Jun 17 2008 - 03:32:31 CDT)
AMBER: improving GAFF sulfonamide parameters Floris Buelens (Tue Jun 17 2008 - 04:57:46 CDT)
- Re: AMBER: improving GAFF sulfonamide parameters Junmei Wang (Tue Jun 24 2008 - 09:34:28 CDT)
  - Re: AMBER: improving GAFF sulfonamide parameters David Mobley (Thu Jun 26 2008 - 15:50:03 CDT)
AMBER: ligand complexed simulation Siddharth Rastogi (Tue Jun 17 2008 - 05:56:15 CDT)
- Re: AMBER: ligand complexed simulation mori_at_cerm.unifi.it (Tue Jun 17 2008 - 06:15:11 CDT)
AMBER: suggestion for next amberTools 1.1 Alan (Tue Jun 17 2008 - 06:01:06 CDT)
- Re: AMBER: suggestion for next amberTools 1.1 David A. Case (Tue Jun 17 2008 - 10:42:14 CDT)
  - libpdb, ptraj, and nab Was: Re: AMBER: suggestion for next amberTools 1.1 M. L. Dodson (Wed Jun 18 2008 - 10:43:44 CDT)
    - Re: libpdb, ptraj, and nab Was: Re: AMBER: suggestion for next amberTools 1.1 David A. Case (Wed Jun 18 2008 - 19:32:36 CDT)
AMBER: "Dumping RAW 2D RMS data is not yet implemented"? Steve Spronk (Tue Jun 17 2008 - 09:00:08 CDT)
- Re: AMBER: "Dumping RAW 2D RMS data is not yet implemented"? David A. Case (Tue Jun 17 2008 - 10:18:08 CDT)
  - RE: AMBER: "Dumping RAW 2D RMS data is not yet implemented"? Steve Spronk (Tue Jun 17 2008 - 10:54:04 CDT)
- Re: AMBER: "Dumping RAW 2D RMS data is not yet implemented"? Jianyin Shao (Tue Jun 17 2008 - 10:36:01 CDT)
AMBER: to understand GAFF: about A and B coefficients Alan (Tue Jun 17 2008 - 11:42:34 CDT)
- Re: AMBER: to understand GAFF: about A and B coefficients David A. Case (Tue Jun 17 2008 - 11:52:41 CDT)
AMBER: multiple dihedral restraints using group (in Amber 10) mkseo (Tue Jun 17 2008 - 16:00:50 CDT)
- Re: AMBER: multiple dihedral restraints using group (in Amber 10) fatima.chami_at_durham.ac.uk (Wed Jun 18 2008 - 05:05:40 CDT)
AMBER: MM-PBSA Neha Gandhi (Wed Jun 18 2008 - 02:37:33 CDT)
- AW: AMBER: MM-PBSA Alexander Metz (Wed Jun 18 2008 - 05:43:18 CDT)
  - Re: AMBER: MM-PBSA Miguel Ortiz-Lombardía (Wed Jun 18 2008 - 09:41:12 CDT)
AMBER: Eigenmode dynamics - imaging traj fatima.chami_at_durham.ac.uk (Wed Jun 18 2008 - 05:09:26 CDT)
- Re: AMBER: Eigenmode dynamics - imaging traj E.M. (Wed Jun 18 2008 - 06:16:49 CDT)
  - Re: AMBER: Eigenmode dynamics - imaging traj Myunggi Yi (Wed Jun 18 2008 - 08:33:07 CDT)
AMBER: about gaff.dat in ambeTools 1.0 Alan (Wed Jun 18 2008 - 09:44:02 CDT)
- Re: AMBER: about gaff.dat in ambeTools 1.0 Junmei Wang (Tue Jun 24 2008 - 08:37:09 CDT)
AMBER: ptraj fatima.chami_at_durham.ac.uk (Wed Jun 18 2008 - 10:21:50 CDT)
AMBER: cross correlation function using iRED matrix fatima.chami_at_durham.ac.uk (Wed Jun 18 2008 - 12:07:25 CDT)
- Re: AMBER: cross correlation function using iRED matrix Myunggi Yi (Wed Jun 18 2008 - 13:07:03 CDT)
AMBER: tip3p water and shake Wang,Ying (Wed Jun 18 2008 - 15:07:13 CDT)
- RE: AMBER: tip3p water and shake Ross Walker (Wed Jun 18 2008 - 16:35:30 CDT)
- RE: AMBER: tip3p water and shake Wang,Ying (Wed Jun 18 2008 - 20:03:55 CDT)
- RE: AMBER: tip3p water and shake Wang,Ying (Wed Jun 18 2008 - 22:44:27 CDT)
  - Re: AMBER: tip3p water and shake David A. Case (Thu Jun 19 2008 - 00:15:48 CDT)
AMBER: sp carbon notation? Laura Benton (Wed Jun 18 2008 - 18:16:35 CDT)
- Re: AMBER: sp carbon notation? David A. Case (Wed Jun 18 2008 - 19:22:14 CDT)
AMBER: questions about gaff yzhao (Wed Jun 18 2008 - 21:01:45 CDT)
- Re: AMBER: questions about gaff Mark Williamson (Wed Jun 18 2008 - 21:35:42 CDT)
  - Re: Re: AMBER: questions about gaff Steven (Fri Jun 20 2008 - 09:11:08 CDT)
AMBER: [Fwd: failure to load box parameters] Daniel Smith (Wed Jun 18 2008 - 22:58:10 CDT)
- Re: AMBER: [Fwd: failure to load box parameters] David A. Case (Thu Jun 19 2008 - 00:35:53 CDT)
  - Re: AMBER: [Fwd: failure to load box parameters] Daniel Smith (Mon Jun 23 2008 - 16:26:22 CDT)
AMBER: How to create average structure? Shen, Lingling (Wed Jun 18 2008 - 23:44:03 CDT)
- Re: AMBER: How to create average structure? Carlos Simmerling (Wed Jun 18 2008 - 23:52:35 CDT)
AMBER: how to extract x,y,z of a set of atoms from an MD trajectories fatima.chami_at_durham.ac.uk (Thu Jun 19 2008 - 04:16:52 CDT)
AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge) (Thu Jun 19 2008 - 05:22:53 CDT)
- Re: AMBER: Correlation functions from iRED analysis Myunggi Yi (Thu Jun 19 2008 - 07:52:55 CDT)
  - RE: AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge) (Thu Jun 19 2008 - 08:10:51 CDT)
AMBER: Installation Problem of AMBER10 bhargav patel (Thu Jun 19 2008 - 05:57:26 CDT)
- Re: AMBER: Installation Problem of AMBER10 Carlos Simmerling (Thu Jun 19 2008 - 06:05:21 CDT)
- Re: AMBER: Installation Problem of AMBER10 David A. Case (Thu Jun 19 2008 - 09:53:03 CDT)
  - Re: AMBER: Installation Problem of AMBER10 bhargav patel (Fri Jun 20 2008 - 04:07:12 CDT)
- Re: AMBER: Installation Problem of AMBER10 Bill Ross (Thu Jun 19 2008 - 12:31:42 CDT)
- Re: AMBER: Installation Problem of AMBER10 Bill Ross (Fri Jun 20 2008 - 15:46:35 CDT)
AMBER: How to extract solvent box information from .rst or .mdcrd files? Panwang Zhou (Thu Jun 19 2008 - 09:13:18 CDT)
- Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? fatima.chami_at_durham.ac.uk (Thu Jun 19 2008 - 09:47:50 CDT)
- Re: Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? Panwang Zhou (Thu Jun 19 2008 - 10:34:02 CDT)
  - Re: Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? fatima.chami_at_durham.ac.uk (Thu Jun 19 2008 - 11:00:32 CDT)
- Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? David A. Case (Sat Jun 28 2008 - 11:37:45 CDT)
AMBER: simple sander James W. Caldwell (Thu Jun 19 2008 - 18:30:39 CDT)
- Re: AMBER: simple sander David A. Case (Thu Jun 19 2008 - 20:40:46 CDT)
  - Re: AMBER: simple sander JAMES W CALDWELL (Thu Jun 19 2008 - 20:47:32 CDT)
AMBER: ligand complexed simulation Siddharth Rastogi (Fri Jun 20 2008 - 02:14:18 CDT)
AMBER: GAFF for organic crystals Rabone, Jeremy (Fri Jun 20 2008 - 03:05:18 CDT)
- Re: AMBER: GAFF for organic crystals Junmei Wang (Mon Jun 23 2008 - 10:16:50 CDT)
AMBER: rdparm help Alan (Fri Jun 20 2008 - 06:12:17 CDT)
- Re: AMBER: rdparm help Thomas Cheatham (Fri Jun 20 2008 - 09:35:36 CDT)
  - Re: AMBER: rdparm help Alan (Mon Jun 23 2008 - 10:23:50 CDT)
AMBER: AmberTools 1.0 installation error: x86_64 Matthew Danielson (Fri Jun 20 2008 - 10:44:21 CDT)
- Re: AMBER: AmberTools 1.0 installation error: x86_64 David A. Case (Fri Jun 20 2008 - 11:17:35 CDT)
AMBER: Amber 10 timing Ed Pate (Fri Jun 20 2008 - 12:08:37 CDT)
- Re: AMBER: Amber 10 timing Robert Duke (Fri Jun 20 2008 - 16:29:00 CDT)
AMBER: SIZE.h problems Å·ÑôµÂ·½ (Sat Jun 21 2008 - 07:33:49 CDT)
- Re: AMBER: SIZE.h problems Mark Williamson (Sat Jun 21 2008 - 16:22:37 CDT)
AMBER: (no subject) Daniel B. Kaplan (Sun Jun 22 2008 - 18:46:17 CDT)
- Re: AMBER: (no subject) Junmei Wang (Mon Jun 23 2008 - 10:01:39 CDT)
AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Mon Jun 23 2008 - 00:07:34 CDT)
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Mon Jun 23 2008 - 20:32:24 CDT)
  - Re: AMBER: MM-PBSA in AMBER 10 David A. Case (Mon Jun 23 2008 - 20:47:44 CDT)
AMBER: How to adjust the problem of "Vlimit exceeded" Biman Jana (Mon Jun 23 2008 - 02:28:27 CDT)
- Re: AMBER: How to adjust the problem of "Vlimit exceeded" David A. Case (Mon Jun 23 2008 - 10:16:05 CDT)
AMBER: How to confirm atom types of small molecule perceived by antechamber xiaonan zhang (Mon Jun 23 2008 - 03:39:30 CDT)
- Re: AMBER: How to confirm atom types of small molecule perceived by antechamber David A. Case (Mon Jun 23 2008 - 09:56:17 CDT)
- Re: AMBER: How to confirm atom types of small molecule perceived by antechamber Junmei Wang (Mon Jun 23 2008 - 09:57:18 CDT)
AMBER: source of AMBER9 Germain Vallverdu (Mon Jun 23 2008 - 09:09:29 CDT)
AMBER: amber10/dat/leap/cmd/README need update Alan (Mon Jun 23 2008 - 09:59:21 CDT)
- Re: AMBER: amber10/dat/leap/cmd/README need update Vlad Cojocaru (Mon Jun 23 2008 - 10:12:29 CDT)
AMBER: Antechamber Question Daniel B. Kaplan (Mon Jun 23 2008 - 11:51:28 CDT)
- Re: AMBER: Antechamber Question Junmei Wang (Tue Jun 24 2008 - 08:33:58 CDT)
AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- Re: AMBER: problems form the pdb to the mol2 David A. Case (Mon Jun 23 2008 - 20:51:46 CDT)
- Re: AMBER: problems form the pdb to the mol2 Junmei Wang (Tue Jun 24 2008 - 08:47:24 CDT)
  - AMBER: Further request answers from Dr. Junmei Wang Rilei Yu (Tue Jun 24 2008 - 10:59:05 CDT)
    - Re: AMBER: Further request answers from Dr. Junmei Wang Junmei Wang (Tue Jun 24 2008 - 11:58:49 CDT)
- Re: AMBER: problems form the pdb to the mol2 Cyril Bauvais (Tue Jun 24 2008 - 09:05:36 CDT)
  - £º Re: AMBER: problems form the pdb to the mol2 Rilei Yu (Tue Jun 24 2008 - 11:14:15 CDT)
    - AMBER: Re: £º Re: AMBER: problems form the pdb to the mol2 Cyril Bauvais (Wed Jun 25 2008 - 08:00:54 CDT)
    - AMBER: Re: AMBER: Re: £º Re: AMBER: problems form the pdb to the mol2 Junmei Wang (Wed Jun 25 2008 - 11:29:44 CDT)
AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
AMBER: dihedral energy calculation inconsistent with gaussian's result Q733 (Mon Jun 23 2008 - 21:43:36 CDT)
- Re: AMBER: dihedral energy calculation inconsistent with gaussian's result Jerome.GOLEBIOWSKI_at_unice.fr (Tue Jun 24 2008 - 03:01:35 CDT)
AMBER: unsubscribe amber sanket.deshmukh_at_ucd.ie (Tue Jun 24 2008 - 06:07:42 CDT)
- AMBER: unsubscribe amber Rabin (Wed Jun 25 2008 - 19:48:51 CDT)
AMBER: A-prime RNA input file Å·ÑôµÂ·½ (Tue Jun 24 2008 - 06:16:27 CDT)
AMBER: qmmm_DFTB problem Dr. Xiaofeng (Frank) Duan (Tue Jun 24 2008 - 08:58:46 CDT)
- Re: AMBER: qmmm_DFTB problem Gustavo Seabra (Tue Jun 24 2008 - 09:31:15 CDT)
AMBER: Compilation of amber8 patched with ramd Francesco Pietra (Tue Jun 24 2008 - 09:32:54 CDT)
- Re: AMBER: Compilation of amber8 patched with ramd David A. Case (Tue Jun 24 2008 - 09:55:10 CDT)
- Re: AMBER: Compilation of amber8 patched with ramd Vlad Cojocaru (Tue Jun 24 2008 - 10:07:03 CDT)
  - Re: AMBER: Compilation of amber8 patched with ramd Francesco Pietra (Tue Jun 24 2008 - 11:28:18 CDT)
AMBER: dihedral potential with odd periodicity Germain Vallverdu (Tue Jun 24 2008 - 09:43:26 CDT)
AMBER: Using AMBER forces Steven Winfield (Tue Jun 24 2008 - 10:44:41 CDT)
- RE: AMBER: Using AMBER forces Ross Walker (Tue Jun 24 2008 - 11:22:25 CDT)
  - Re: AMBER: Using AMBER forces Steven Winfield (Tue Jun 24 2008 - 11:54:49 CDT)
    - RE: AMBER: Using AMBER forces Ross Walker (Tue Jun 24 2008 - 13:19:13 CDT)
    - Re: AMBER: Using AMBER forces Germain Vallverdu (Tue Sep 09 2008 - 08:48:32 CDT)
AMBER: rdparm Segmentation fault on Ubuntu Alan (Tue Jun 24 2008 - 10:50:12 CDT)
AMBER: how to derive torsional angle parameters in gaff Junmei Wang (Tue Jun 24 2008 - 20:45:42 CDT)
- AMBER: local coordinate system question caoch (Wed Jun 25 2008 - 04:33:15 CDT)
  - Re: AMBER: local coordinate system question David A. Case (Wed Jun 25 2008 - 09:32:16 CDT)
- Re: AMBER: how to derive torsional angle parameters in gaff Balazs JOJART (Thu Jun 26 2008 - 03:53:40 CDT)
AMBER: Debugf AMBER9 John Palmeri (Wed Jun 25 2008 - 02:38:53 CDT)
AMBER: TI calculations in Amber10 Samuel Genheden (a03samge) (Wed Jun 25 2008 - 06:58:28 CDT)
- Re: AMBER: TI calculations in Amber10 Thomas Steinbrecher (Wed Jun 25 2008 - 11:15:47 CDT)
AMBER: A problem of dihedral angle Harry (Yicun) Ni (Wed Jun 25 2008 - 10:31:24 CDT)
- RE: AMBER: A problem of dihedral angle Ross Walker (Wed Jun 25 2008 - 10:48:56 CDT)
  - Re: AMBER: A problem of dihedral angle Harry (Yicun) Ni (Wed Jun 25 2008 - 14:42:09 CDT)
- Re: AMBER: A problem of dihedral angle Carlos Simmerling (Wed Jun 25 2008 - 10:53:16 CDT)
AMBER: amber10 compile gfortran question James W. Caldwell (Wed Jun 25 2008 - 13:10:58 CDT)
- Re: AMBER: amber10 compile gfortran question David A. Case (Wed Jun 25 2008 - 14:03:54 CDT)
  - RE: AMBER: amber10 compile gfortran question James W. Caldwell (Wed Jun 25 2008 - 14:11:58 CDT)
AMBER: sleap - TER-card In Hee Park (Wed Jun 25 2008 - 14:14:39 CDT)
- Re: AMBER: sleap - TER-card David A. Case (Wed Jun 25 2008 - 17:05:59 CDT)
  - Re: AMBER: sleap - TER-card In Hee Park (Thu Jun 26 2008 - 19:31:40 CDT)
    - Re: AMBER: sleap - TER-card David A. Case (Thu Jun 26 2008 - 20:19:01 CDT)
AMBER: rdparm Segmentation fault Alan (Wed Jun 25 2008 - 16:24:34 CDT)
- Re: AMBER: rdparm Segmentation fault David A. Case (Wed Jun 25 2008 - 19:07:20 CDT)
AMBER: Antechamber/mopac am1-bcc charge Dong Xu (Wed Jun 25 2008 - 17:09:39 CDT)
- Re: AMBER: Antechamber/mopac am1-bcc charge Junmei Wang (Wed Jun 25 2008 - 17:44:07 CDT)
  - Re: AMBER: Antechamber/mopac am1-bcc charge Dong Xu (Thu Jun 26 2008 - 01:21:03 CDT)
AMBER: (no subject) Daniel B. Kaplan (Wed Jun 25 2008 - 21:23:43 CDT)
AMBER: Amber:unsubscribe amber sanket.deshmukh_at_ucd.ie (Thu Jun 26 2008 - 06:53:22 CDT)
AMBER: concerning force fields Adrien Delmont (Thu Jun 26 2008 - 10:14:15 CDT)
- Re: AMBER: concerning force fields Carlos Simmerling (Thu Jun 26 2008 - 11:16:48 CDT)
- Re: AMBER: concerning force fields Adrien Delmont (Thu Jun 26 2008 - 13:29:39 CDT)
  - Re: AMBER: concerning force fields Carlos Simmerling (Thu Jun 26 2008 - 14:25:04 CDT)
- Re: AMBER: concerning force fields Adrien Delmont (Fri Jun 27 2008 - 07:22:08 CDT)
  - Re: AMBER: concerning force fields Carlos Simmerling (Fri Jun 27 2008 - 07:34:21 CDT)
  - Re: AMBER: concerning force fields Karl Kirschner (kkirschn) (Fri Jun 27 2008 - 08:02:03 CDT)
- Re: AMBER: concerning force fields Adrien Delmont (Sat Jun 28 2008 - 11:10:05 CDT)
AMBER: Peseckis, Steven M. (Thu Jun 26 2008 - 10:54:05 CDT)
- Re: AMBER: David A. Case (Fri Jun 27 2008 - 13:55:04 CDT)
  - AMBER: RE: AMBER 10 failure to run in UBUNTU Peseckis, Steven M. (Sun Jun 29 2008 - 19:13:38 CDT)
AMBER: ligand partial charge and conformation question Dong Xu (Thu Jun 26 2008 - 13:01:31 CDT)
AMBER: output file AMBER9_MPI Vijay Manickam Achari (Thu Jun 26 2008 - 14:06:19 CDT)
AMBER: Dihedral Angle Parameters Ilyas Yildirim (Thu Jun 26 2008 - 16:07:16 CDT)
- Re: AMBER: Dihedral Angle Parameters Carlos Simmerling (Thu Jun 26 2008 - 16:30:53 CDT)
  - Re: AMBER: Dihedral Angle Parameters Ilyas Yildirim (Thu Jun 26 2008 - 17:07:55 CDT)
    - RE: AMBER: Dihedral Angle Parameters Ross Walker (Thu Jun 26 2008 - 17:18:52 CDT)
    - Re: AMBER: Dihedral Angle Parameters Carlos Simmerling (Thu Jun 26 2008 - 17:20:41 CDT)
AMBER: REMD Amber10 : error in reading namelist cntrl rebeca (Fri Jun 27 2008 - 04:01:26 CDT)
- Re: AMBER: REMD Amber10 : error in reading namelist cntrl Carlos Simmerling (Fri Jun 27 2008 - 09:47:42 CDT)
AMBER: Group specification problem fatima.chami_at_durham.ac.uk (Fri Jun 27 2008 - 07:59:09 CDT)
AMBER: pmemd 10 output Vlad Cojocaru (Fri Jun 27 2008 - 10:48:35 CDT)
- RE: AMBER: pmemd 10 output Ross Walker (Fri Jun 27 2008 - 11:16:44 CDT)
  - Re: AMBER: pmemd 10 output Vlad Cojocaru (Fri Jun 27 2008 - 11:24:58 CDT)
  - Re: AMBER: pmemd 10 output Vlad Cojocaru (Fri Jun 27 2008 - 11:34:37 CDT)
AMBER: Test scripts James W. Caldwell (Fri Jun 27 2008 - 11:35:26 CDT)
- Re: AMBER: Test scripts David A. Case (Fri Jun 27 2008 - 11:44:25 CDT)
  - RE: AMBER: Test scripts James W. Caldwell (Fri Jun 27 2008 - 11:54:56 CDT)
AMBER: ptraj - read in part of trajectory Seth Lilavivat (Fri Jun 27 2008 - 11:41:51 CDT)
- Re: AMBER: ptraj - read in part of trajectory Vlad Cojocaru (Fri Jun 27 2008 - 11:59:14 CDT)
- Re: AMBER: ptraj - read in part of trajectory Carlos Simmerling (Fri Jun 27 2008 - 12:00:32 CDT)
- Re: AMBER: ptraj - read in part of trajectory Seth Lilavivat (Fri Jun 27 2008 - 12:01:03 CDT)
AMBER: question about the charge Harry (Yicun) Ni (Fri Jun 27 2008 - 15:37:55 CDT)
- Re: AMBER: question about the charge Carlos Simmerling (Fri Jun 27 2008 - 15:52:22 CDT)
  - Re: AMBER: question about the charge Harry (Yicun) Ni (Fri Jun 27 2008 - 18:57:37 CDT)
AMBER: Seed for random number generator Francesco Pietra (Sun Jun 29 2008 - 03:22:12 CDT)
AMBER: Constrained group fatima.chami_at_durham.ac.uk (Mon Jun 30 2008 - 04:54:02 CDT)
- Re: AMBER: Constrained group Robert Duke (Mon Jun 30 2008 - 11:03:15 CDT)
AMBER: NMR refinement teresa.ierano_at_unina.it (Mon Jun 30 2008 - 05:37:48 CDT)
- Re: AMBER: NMR refinement David A. Case (Mon Jun 30 2008 - 09:44:51 CDT)
AMBER: nmode analysis Joachim Reichelt (Mon Jun 30 2008 - 06:53:21 CDT)
- Re: AMBER: nmode analysis Mark Williamson (Mon Jun 30 2008 - 07:12:09 CDT)
  - Re: AMBER: nmode analysis Joachim Reichelt (Mon Jun 30 2008 - 07:36:32 CDT)
AMBER: hold atoms fixed Boutheina Kerkeni (Mon Jun 30 2008 - 07:51:17 CDT)
- Re: AMBER: hold atoms fixed Carlos Simmerling (Mon Jun 30 2008 - 08:02:19 CDT)
  - Re: AMBER: hold atoms fixed Boutheina Kerkeni (Mon Jun 30 2008 - 08:12:33 CDT)
  - Re: AMBER: hold atoms fixed Boutheina Kerkeni (Mon Jun 30 2008 - 08:12:33 CDT)
- Re: AMBER: hold atoms fixed fatima.chami_at_durham.ac.uk (Mon Jun 30 2008 - 08:16:09 CDT)
- Re: AMBER: hold atoms fixed Gustavo Seabra (Mon Jun 30 2008 - 09:10:53 CDT)
AMBER: wrapping a restart file fatima.chami_at_durham.ac.uk (Mon Jun 30 2008 - 09:40:58 CDT)
- Re: AMBER: wrapping a restart file Gustavo Seabra (Mon Jun 30 2008 - 10:31:53 CDT)
- Re: AMBER: wrapping a restart file Robert Duke (Mon Jun 30 2008 - 11:34:54 CDT)
AMBER: (no subject) fatima.chami_at_durham.ac.uk (Mon Jun 30 2008 - 11:26:23 CDT)
- Re: AMBER: (no subject) Robert Duke (Mon Jun 30 2008 - 11:43:11 CDT)
AMBER: watershell cero? rebeca (Mon Jun 30 2008 - 11:22:11 CDT)
AMBER: MM-PBSA calculation problem Wei Huang (Mon Jun 30 2008 - 11:41:16 CDT)
AMBER: error in reading namelist cntrl Maria Frushicheva (Mon Jun 30 2008 - 15:02:50 CDT)
- Re: AMBER: error in reading namelist cntrl David A. Case (Mon Jun 30 2008 - 15:28:36 CDT)
- RE: AMBER: error in reading namelist cntrl Ross Walker (Mon Jun 30 2008 - 15:26:38 CDT)
AMBER: Regarding force field ff02 and ion library Abhishek Singh (Mon Jun 30 2008 - 15:54:52 CDT)
- Re: AMBER: Regarding force field ff02 and ion library David A. Case (Mon Jun 30 2008 - 16:14:37 CDT)
  - Re: AMBER: Regarding force field ff02 and ion library Thomas Cheatham III (Mon Jun 30 2008 - 16:30:05 CDT)
    - Re: AMBER: Regarding force field ff02 and ion library Abhishek Singh (Tue Jul 01 2008 - 14:02:28 CDT)
AMBER: missing torsion parameters John Bennett (Mon Jun 30 2008 - 16:06:07 CDT)
- RE: AMBER: missing torsion parameters Ross Walker (Mon Jun 30 2008 - 17:46:45 CDT)
AMBER: concerning force fields ( to Karl Kirschner ) Adrien Delmont (Tue Jul 01 2008 - 03:04:45 CDT)
- Re: AMBER: concerning force fields ( to Karl Kirschner ) Karl Kirschner (kkirschn) (Tue Jul 01 2008 - 10:06:29 CDT)
AMBER: Anna Reymer (Tue Jul 01 2008 - 03:36:12 CDT)
- Re: AMBER: Carlos Simmerling (Tue Jul 01 2008 - 07:15:15 CDT)
  - Re: AMBER: Anna Reymer (Tue Jul 01 2008 - 07:46:24 CDT)
AMBER: AMBER10: ambpdb problems Anna Reymer (Tue Jul 01 2008 - 03:37:38 CDT)
AMBER: RDF in ptraj fatima.chami_at_durham.ac.uk (Tue Jul 01 2008 - 08:34:35 CDT)
AMBER: "radius = 0.000" Arturas Ziemys (Tue Jul 01 2008 - 11:08:45 CDT)
- Re: AMBER: "radius = 0.000" Carlos Simmerling (Tue Jul 01 2008 - 11:16:38 CDT)
  - Re: AMBER: "radius = 0.000" Arturas Ziemys (Tue Jul 01 2008 - 12:17:54 CDT)
- Re: AMBER: "radius = 0.000" Robert Duke (Tue Jul 01 2008 - 11:24:10 CDT)
- Re: AMBER: "radius = 0.000" Thomas Steinbrecher (Tue Jul 01 2008 - 11:39:30 CDT)
AMBER: Protonated Phosphate Problem Kliman, Michal (Tue Jul 01 2008 - 12:20:14 CDT)
- Re: AMBER: Protonated Phosphate Problem Thomas Steinbrecher (Tue Jul 01 2008 - 12:41:55 CDT)
AMBER: compile amber10 on Mac Junmei Wang (Tue Jul 01 2008 - 16:45:31 CDT)
- Re: AMBER: compile amber10 on Mac Scott Brozell (Thu Jul 03 2008 - 20:38:19 CDT)
AMBER: parameters for Fe coordinated to four CYS ? Jose Borreguero (Tue Jul 01 2008 - 19:12:37 CDT)
AMBER: NMR refinement teresa.ierano_at_unina.it (Wed Jul 02 2008 - 03:38:57 CDT)
- Re: AMBER: NMR refinement Wenyong Tong (Fri Jan 18 2008 - 22:18:18 CST)
  - Re: AMBER: NMR refinement David A. Case (Sat Jan 19 2008 - 12:39:08 CST)
- Re: AMBER: NMR refinement Ilyas Yildirim (Wed Jul 02 2008 - 04:58:05 CDT)
  - Re: AMBER: NMR refinement teresa.ierano_at_unina.it (Thu Jul 03 2008 - 04:37:02 CDT)
- Re: AMBER: NMR refinement David A. Case (Wed Jul 02 2008 - 19:21:54 CDT)
AMBER: NONBONDED_PARM_INDEX Max (Wed Jul 02 2008 - 03:54:35 CDT)
- Re: AMBER: NONBONDED_PARM_INDEX David A. Case (Wed Jul 02 2008 - 10:04:26 CDT)
AMBER: ptraj problem with imaging fatima.chami_at_durham.ac.uk (Wed Jul 02 2008 - 11:52:32 CDT)
- RE: AMBER: ptraj problem with imaging Ross Walker (Wed Jul 02 2008 - 15:06:42 CDT)
  - RE: AMBER: ptraj problem with imaging fatima.chami_at_durham.ac.uk (Thu Jul 03 2008 - 11:11:19 CDT)
AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential yongleli (Wed Jul 02 2008 - 13:19:03 CDT)
- Re: AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential Thomas Steinbrecher (Wed Jul 02 2008 - 14:08:40 CDT)
AMBER: RED III execution problem ben rodriguez (Wed Jul 02 2008 - 20:24:19 CDT)
- Re: AMBER: RED III execution problem FyD (Thu Jul 03 2008 - 04:25:24 CDT)
  - RE: AMBER: RED III execution problem ben rodriguez (Mon Jul 07 2008 - 14:21:11 CDT)
    - RE: AMBER: RED III execution problem FyD (Mon Jul 07 2008 - 15:54:30 CDT)
AMBER: How to obtain the oriented trajectories? Panwang Zhou (Thu Jul 03 2008 - 09:06:58 CDT)
- Re: AMBER: How to obtain the oriented trajectories? Carlos Simmerling (Thu Jul 03 2008 - 09:22:03 CDT)
AMBER: PMEMD and polarized force field ff 02 Abhishek Singh (Thu Jul 03 2008 - 09:50:00 CDT)
AMBER: PMEMD and polarized force field ff 02 Abhishek Singh (Thu Jul 03 2008 - 09:53:36 CDT)
- RE: AMBER: PMEMD and polarized force field ff 02 Ross Walker (Thu Jul 03 2008 - 10:02:17 CDT)
- Re: AMBER: PMEMD and polarized force field ff 02 David A. Case (Thu Jul 03 2008 - 10:10:06 CDT)
  - AMBER: Force Field parameters : A new chemical compound Chih-Ying Lin (Thu Jul 03 2008 - 12:52:17 CDT)
AMBER: bellymask for DNA backbone doesn't seem to work Seth Lilavivat (Thu Jul 03 2008 - 15:13:40 CDT)
- Re: AMBER: bellymask for DNA backbone doesn't seem to work Thomas Cheatham III (Thu Jul 03 2008 - 15:40:47 CDT)
AMBER: about QMMM output linfu (Thu Jul 03 2008 - 21:40:33 CDT)
- Re: AMBER: about QMMM output Gustavo Seabra (Fri Jul 04 2008 - 10:33:06 CDT)
  - RE: AMBER: about QMMM output Ross Walker (Fri Jul 04 2008 - 11:30:09 CDT)
AMBER: RESP calculation on Copper containing molecule Vidana.Epa_at_csiro.au (Fri Jul 04 2008 - 02:16:24 CDT)
- Re: AMBER: RESP calculation on Copper containing molecule FyD (Fri Jul 04 2008 - 05:25:42 CDT)
AMBER: Boutheina Kerkeni (Fri Jul 04 2008 - 05:34:55 CDT)
- Re: AMBER: Carlos Simmerling (Fri Jul 04 2008 - 05:42:27 CDT)
  - Re: AMBER: Boutheina Kerkeni (Fri Jul 04 2008 - 06:02:10 CDT)
AMBER: trouble interpreting <P2> time correlation function data Sally Pias (Sun Jul 06 2008 - 01:59:57 CDT)
- Re: AMBER: trouble interpreting <P2> time correlation function data David A. Case (Sun Jul 06 2008 - 10:04:30 CDT)
  - Re: AMBER: trouble interpreting <P2> time correlation function data Sally Pias (Sun Jul 06 2008 - 12:08:18 CDT)
AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10 yongleli (Mon Jul 07 2008 - 17:04:53 CDT)
- Re: AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10 Thomas Steinbrecher (Mon Jul 07 2008 - 17:56:49 CDT)
AMBER: Constant pH with new parameters (amber10) Markus Kaukonen (Tue Jul 08 2008 - 02:39:57 CDT)
- Re: AMBER: Constant pH with new parameters (amber10) David A. Case (Fri Jul 11 2008 - 13:41:09 CDT)
  - Re: AMBER: Constant pH with new parameters (amber10) Markus Kaukonen (Sat Jul 12 2008 - 14:24:05 CDT)
    - Re: AMBER: Constant pH with new parameters (amber10) Adrian Roitberg (Sat Jul 12 2008 - 18:47:41 CDT)
    - Re: AMBER: Constant pH with new parameters (amber10) Markus Kaukonen (Sun Jul 20 2008 - 03:08:35 CDT)
AMBER: [amber/glycam] dealing with fucose... Waqas Nasir (Tue Jul 08 2008 - 09:56:31 CDT)
- Re: AMBER: [amber/glycam] dealing with fucose... Lachele Foley (Lists) (Tue Jul 08 2008 - 11:08:52 CDT)
- Re: AMBER: [amber/glycam] dealing with fucose... Waqas Nasir (Thu Jul 10 2008 - 07:59:34 CDT)
  - Re: AMBER: [amber/glycam] dealing with fucose... Lachele Foley (Lists) (Thu Jul 10 2008 - 12:24:41 CDT)
    - Re: AMBER: [amber/glycam] dealing with fucose... Waqas Nasir (Fri Jul 11 2008 - 04:47:36 CDT)
    - Re: AMBER: [amber/glycam] dealing with fucose... Lachele Foley (Lists) (Fri Jul 11 2008 - 09:19:17 CDT)
- Re: AMBER: [amber/glycam] dealing with fucose... Waqas Nasir (Sat Jul 12 2008 - 14:44:13 CDT)
  - Re: AMBER: [amber/glycam] dealing with fucose... Lachele Foley (Lists) (Tue Jul 15 2008 - 09:45:19 CDT)
AMBER: Force fields for REMD with GB solvent guardiani_at_fi.infn.it (Tue Jul 08 2008 - 11:24:27 CDT)
- Re: AMBER: Force fields for REMD with GB solvent Carlos Simmerling (Tue Jul 08 2008 - 17:03:31 CDT)
  - Re: AMBER: Force fields for REMD with GB solvent guardiani_at_fi.infn.it (Wed Jul 09 2008 - 04:37:43 CDT)
    - Re: AMBER: Force fields for REMD with GB solvent Carlos Simmerling (Wed Jul 09 2008 - 08:37:36 CDT)
AMBER: analysing normal modes Vahdati N. (Tue Jul 08 2008 - 13:03:39 CDT)
- AMBER: analysing normal modes Chris Moth (Wed Jul 09 2008 - 14:45:57 CDT)
  - RE: AMBER: analysing normal modes Vahdati N. (Thu Jul 10 2008 - 07:49:15 CDT)
AMBER: Distance diagnolization matrix plot Siddharth Rastogi (Wed Jul 09 2008 - 02:04:08 CDT)
AMBER: REMD temperature profile guardiani_at_fi.infn.it (Wed Jul 09 2008 - 08:47:13 CDT)
- Re: AMBER: REMD temperature profile Carlos Simmerling (Wed Jul 09 2008 - 10:28:59 CDT)
AMBER: XLeap Problems Schwehm, Jeffrey M. (Wed Jul 09 2008 - 11:26:14 CDT)
- Re: AMBER: XLeap Problems Mark Williamson (Wed Jul 09 2008 - 11:41:51 CDT)
- RE: AMBER: XLeap Problems Ross Walker (Wed Jul 09 2008 - 13:08:50 CDT)
AMBER: amber9 / difference of igb=0 and igb=6 Arturas Ziemys (Wed Jul 09 2008 - 14:45:32 CDT)
- RE: AMBER: amber9 / difference of igb=0 and igb=6 Ross Walker (Wed Jul 09 2008 - 15:54:54 CDT)
  - Re: AMBER: amber9 / difference of igb=0 and igb=6 Arturas Ziemys (Wed Jul 09 2008 - 16:03:32 CDT)
AMBER: Question about loading frcmod.ionsjc_tip3p in xleap Jeff Schwinefus (Wed Jul 09 2008 - 16:27:46 CDT)
- Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap Thomas Cheatham III (Thu Jul 10 2008 - 17:20:04 CDT)
  - Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap David A. Case (Thu Jul 10 2008 - 23:42:28 CDT)
    - Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap Jeff Schwinefus (Fri Jul 11 2008 - 11:41:21 CDT)
    - Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap Scott Brozell (Thu Jul 31 2008 - 17:40:43 CDT)
AMBER: ptraj selection Ilyas Yildirim (Wed Jul 09 2008 - 20:07:39 CDT)
- Re: AMBER: ptraj selection David Watson (Wed Jul 09 2008 - 21:11:16 CDT)
  - Re: AMBER: ptraj selection Ilyas Yildirim (Wed Jul 09 2008 - 22:13:22 CDT)
  - Re: AMBER: ptraj selection Ilyas Yildirim (Wed Jul 09 2008 - 22:13:22 CDT)
- Re: AMBER: ptraj selection Jianyin Shao (Thu Jul 10 2008 - 10:56:55 CDT)
  - Re: AMBER: ptraj selection Ilyas Yildirim (Thu Jul 10 2008 - 19:58:08 CDT)
AMBER: mm_pbsa incorrect complex prmtop file xiaonan zhang (Thu Jul 10 2008 - 02:44:58 CDT)
- Re: AMBER: mm_pbsa incorrect complex prmtop file Neha Gandhi (Thu Jul 10 2008 - 03:02:27 CDT)
- Re: AMBER: mm_pbsa incorrect complex prmtop file Neha Gandhi (Thu Jul 10 2008 - 03:02:27 CDT)
AMBER: replicas trapped in a few low temperatures Ye Mei (Thu Jul 10 2008 - 04:13:25 CDT)
- Re: AMBER: replicas trapped in a few low temperatures Carlos Simmerling (Thu Jul 10 2008 - 05:59:03 CDT)
  - Re: Re: AMBER: replicas trapped in a few low temperatures Ye Mei (Thu Jul 10 2008 - 06:16:59 CDT)
AMBER: antechamber and charmm Alan (Thu Jul 10 2008 - 04:43:58 CDT)
- Re: AMBER: antechamber and charmm Junmei Wang (Thu Jul 17 2008 - 09:33:23 CDT)
  - Re: AMBER: antechamber and charmm Alan (Thu Jul 17 2008 - 11:05:40 CDT)
    - Re: AMBER: antechamber and charmm David A. Case (Thu Jul 17 2008 - 11:16:02 CDT)
AMBER: bond command Boutheina Kerkeni (Thu Jul 10 2008 - 12:30:46 CDT)
- Re: AMBER: bond command Wang,Ying (Thu Jul 10 2008 - 12:56:01 CDT)
- Re: AMBER: bond command M. L. Dodson (Thu Jul 10 2008 - 13:34:33 CDT)
- RE: AMBER: bond command Ross Walker (Thu Jul 10 2008 - 14:15:53 CDT)
  - Re: AMBER: bond command Boutheina Kerkeni (Fri Jul 11 2008 - 07:00:48 CDT)
AMBER: problem with restraints Barbault Florent (Thu Jul 10 2008 - 13:59:15 CDT)
AMBER: difference between sander and NAB Hu, Shaowen (JSC-SK)[USRA] (Thu Jul 10 2008 - 14:44:41 CDT)
- Re: AMBER: difference between sander and NAB David A. Case (Thu Jul 10 2008 - 17:22:49 CDT)
  - RE: AMBER: difference between sander and NAB Hu, Shaowen (JSC-SK)[USRA] (Fri Jul 11 2008 - 08:02:51 CDT)
AMBER: problem with rdparm Harry (Yicun) Ni (Thu Jul 10 2008 - 17:05:41 CDT)
- Re: AMBER: problem with rdparm Thomas Cheatham III (Thu Jul 10 2008 - 17:13:35 CDT)
AMBER: timing info output from pmemd Vlad Cojocaru (Fri Jul 11 2008 - 03:49:28 CDT)
- Re: AMBER: timing info output from pmemd Robert Duke (Fri Jul 11 2008 - 07:14:29 CDT)
  - Re: AMBER: timing info output from pmemd Vlad Cojocaru (Fri Jul 11 2008 - 07:33:31 CDT)
    - Re: AMBER: timing info output from pmemd Robert Duke (Fri Jul 11 2008 - 08:41:21 CDT)
    - Re: AMBER: timing info output from pmemd Vlad Cojocaru (Fri Jul 11 2008 - 08:54:02 CDT)
AMBER: configure_amber (10) for pg compilers Vlad Cojocaru (Fri Jul 11 2008 - 06:51:47 CDT)
- Re: AMBER: configure_amber (10) for pg compilers Robert Duke (Fri Jul 11 2008 - 07:27:02 CDT)
AMBER: size of pdb Boutheina Kerkeni (Fri Jul 11 2008 - 10:13:57 CDT)
- Re: AMBER: size of pdb David A. Case (Sat Jul 12 2008 - 09:45:51 CDT)
AMBER: question about the improper torsion Harry (Yicun) Ni (Fri Jul 11 2008 - 11:34:17 CDT)
- Re: AMBER: question about the improper torsion David A. Case (Sat Jul 12 2008 - 09:43:46 CDT)
  - Re: AMBER: question about the improper torsion Harry (Yicun) Ni (Mon Jul 14 2008 - 23:12:57 CDT)
- Re: AMBER: question about the improper torsion Bill Ross (Tue Jul 15 2008 - 11:48:24 CDT)
AMBER: NMA Steve Seibold (Fri Jul 11 2008 - 11:34:00 CDT)
- Re: AMBER: NMA David A. Case (Fri Jul 11 2008 - 13:19:06 CDT)
AMBER: Installation on Mac OSX G5 dual processor George Tzotzos (Fri Jul 11 2008 - 15:30:21 CDT)
AMBER: Installation of Amber 10 on Dual-Core Intel Mac George Tzotzos (Fri Jul 11 2008 - 15:33:55 CDT)
AMBER: empty output Boutheina Kerkeni (Sat Jul 12 2008 - 10:29:47 CDT)
- RE: AMBER: empty output Ross Walker (Sat Jul 12 2008 - 11:54:01 CDT)
  - RE: AMBER: empty output Boutheina Kerkeni (Tue Jul 15 2008 - 12:31:50 CDT)
AMBER: Atom type with 10-12 and 6-12 interactions in Amber9 Brad Lambeth (Sat Jul 12 2008 - 19:20:09 CDT)
AMBER: Nmode entropy calcs Sergio Wong (Sat Jul 12 2008 - 20:09:51 CDT)
- Re: AMBER: Nmode entropy calcs David A. Case (Sun Jul 13 2008 - 10:45:56 CDT)
AMBER: Model of deoxyadenosine in Cornell 95 paper Ilyas Yildirim (Sun Jul 13 2008 - 18:14:48 CDT)
- Re: AMBER: Model of deoxyadenosine in Cornell 95 paper Piotr Cieplak (Wed Jul 16 2008 - 01:32:08 CDT)
AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Grange Hermitage (Sun Jul 13 2008 - 20:06:33 CDT)
- RE: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Ross Walker (Sun Jul 13 2008 - 23:35:42 CDT)
  - Re: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Grange Hermitage (Mon Jul 14 2008 - 02:41:40 CDT)
    - RE: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Ross Walker (Tue Jul 15 2008 - 10:50:20 CDT)
  - Re: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Grange Hermitage (Mon Jul 14 2008 - 19:18:40 CDT)
    - RE: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Ross Walker (Tue Jul 15 2008 - 11:01:55 CDT)
AMBER: POL3 with gaff and ff02EP Grange Hermitage (Sun Jul 13 2008 - 20:15:43 CDT)
- RE: AMBER: POL3 with gaff and ff02EP Ross Walker (Sun Jul 13 2008 - 23:40:02 CDT)
AMBER: Alanine scanning Khaled Barakat (Sun Jul 13 2008 - 20:50:47 CDT)
AMBER: querry dipti lele (Mon Jul 14 2008 - 03:05:15 CDT)
- Re: AMBER: querry Sandeep Kaushik (Tue Jul 22 2008 - 07:09:08 CDT)
  - Re: AMBER: querry Lachele Foley (Lists) (Tue Jul 22 2008 - 08:55:08 CDT)
AMBER: Tutorial 6 Beale, John (Mon Jul 14 2008 - 11:48:21 CDT)
- RE: AMBER: Tutorial 6 Ross Walker (Mon Jul 14 2008 - 13:48:05 CDT)
AMBER: bad nonbon in nmode (amber9) Enghui Yap (Mon Jul 14 2008 - 11:25:29 CDT)
- AMBER: Res minimization Thomas Leonard (Tue Jul 15 2008 - 02:34:47 CDT)
  - RE: AMBER: Res minimization Ross Walker (Tue Jul 15 2008 - 10:53:46 CDT)
  - Re: AMBER: Res minimization gurpreet singh (Tue Jul 15 2008 - 23:25:54 CDT)
AMBER: Error when performing Alanine scanning Khaled Barakat (Mon Jul 14 2008 - 20:41:26 CDT)
AMBER: files in Amber directory ( to Junmei Wang ) John Bennett (Tue Jul 15 2008 - 06:10:40 CDT)
- Re: AMBER: files in Amber directory ( to Junmei Wang ) David A. Case (Tue Jul 15 2008 - 13:55:41 CDT)
- Re: AMBER: files in Amber directory ( to Junmei Wang ) Junmei Wang (Thu Jul 17 2008 - 09:56:06 CDT)
  - Re: AMBER: files in Amber directory ( to Junmei Wang ) John Bennett (Fri Jul 18 2008 - 06:25:38 CDT)
AMBER: ptraj: projection command missing in dispatch.c (AMBER 10) Vlad Cojocaru (Tue Jul 15 2008 - 08:45:11 CDT)
- Re: AMBER: ptraj: projection command missing in dispatch.c (AMBER 10) David A. Case (Tue Jul 15 2008 - 13:57:52 CDT)
AMBER: sleap test failures Vlad Cojocaru (Tue Jul 15 2008 - 09:14:23 CDT)
- Re: AMBER: sleap test failures David A. Case (Tue Jul 15 2008 - 17:46:00 CDT)
  - Re: AMBER: sleap test failures Vlad Cojocaru (Wed Jul 16 2008 - 03:07:48 CDT)
  - Re: AMBER: sleap test failures Vlad Cojocaru (Wed Jul 16 2008 - 07:40:12 CDT)
AMBER: test of parallel sander 10 fail Vlad Cojocaru (Tue Jul 15 2008 - 12:05:51 CDT)
- Re: AMBER: test of parallel sander 10 fail Thomas Cheatham III (Tue Jul 15 2008 - 12:41:12 CDT)
AMBER: RMSD per residue luzhenw1_at_msu.edu (Tue Jul 15 2008 - 15:28:08 CDT)
- Re: AMBER: RMSD per residue gurpreet singh (Tue Jul 15 2008 - 23:13:59 CDT)
AMBER: Ligand force field generation, and its consistency with the force field of the protein. SeungPyo Hong (Wed Jul 16 2008 - 07:15:48 CDT)
- Re: AMBER: Ligand force field generation, and its consistency with the force field of the protein. Alan (Wed Jul 16 2008 - 07:46:15 CDT)
- AMBER:Some questions about replica exchan ge huzehan19870731_at_126.com (Wed Jul 16 2008 - 08:07:46 CDT)
  - RE: AMBER:Some questions about replica exchan ge Ross Walker (Wed Jul 16 2008 - 09:45:38 CDT)
    - Re: AMBER:Some questions about replica exchan ge Carlos Simmerling (Wed Jul 16 2008 - 10:04:25 CDT)
- Re: AMBER: Ligand force field generation, and its consistency with the force field of the protein. Gustavo Seabra (Wed Jul 16 2008 - 09:08:45 CDT)
  - Re: AMBER: Ligand force field generation, and its consistency with the force field of the protein. SeungPyo Hong (Wed Jul 16 2008 - 20:50:31 CDT)
AMBER: about RMSD per residue luzhenw1_at_msu.edu (Wed Jul 16 2008 - 08:48:05 CDT)
- Re: AMBER: about RMSD per residue Wei Huang (Wed Jul 16 2008 - 09:20:03 CDT)
  - RE: AMBER: about RMSD per residue Ross Walker (Wed Jul 16 2008 - 09:52:38 CDT)
- RE: AMBER: about RMSD per residue Ross Walker (Wed Jul 16 2008 - 11:40:42 CDT)
AMBER: free energy Boutheina Kerkeni (Wed Jul 16 2008 - 10:54:39 CDT)
- Re: AMBER: free energy Christopher Gaughan (Wed Jul 16 2008 - 11:03:26 CDT)
  - Re: AMBER: free energy Adrian Roitberg (Wed Jul 16 2008 - 09:10:41 CDT)
    - Re: AMBER: free energy Boutheina Kerkeni (Wed Jul 16 2008 - 11:30:44 CDT)
- Re: AMBER: free energy Thomas Steinbrecher (Wed Jul 16 2008 - 11:22:45 CDT)
AMBER: amber 10 and mpich2 (got eof on console error message from mpich2) Vlad Cojocaru (Thu Jul 17 2008 - 08:30:24 CDT)
- AMBER: Re: amber 10 and mpich2 (got eof on console error message from mpich2) Vlad Cojocaru (Thu Jul 17 2008 - 08:33:04 CDT)
- AMBER: entropy of released water Swarup Gupta (Thu Aug 07 2008 - 07:36:32 CDT)
AMBER: SCC-DFTB for Zinc atom Jifeng Wang (Thu Jul 17 2008 - 10:33:15 CDT)
- Re: AMBER: SCC-DFTB for Zinc atom Gustavo Seabra (Thu Jul 17 2008 - 10:48:33 CDT)
  - Re: AMBER: SCC-DFTB for Zinc atom Jifeng Wang (Fri Jul 18 2008 - 12:10:17 CDT)
    - Re: AMBER: SCC-DFTB for Zinc atom Gustavo Seabra (Fri Jul 18 2008 - 18:21:45 CDT)
AMBER: paricular atom coordinates? Vijay Singh (Thu Jul 17 2008 - 11:13:30 CDT)
AMBER: The list-directed or NAMELIST READ statement cannot be completed rebeca (Thu Jul 17 2008 - 11:42:25 CDT)
- Re: AMBER: The list-directed or NAMELIST READ statement cannot be completed Carlos Simmerling (Thu Jul 17 2008 - 11:47:24 CDT)
- RE: AMBER: The list-directed or NAMELIST READ statement cannot be completed Ross Walker (Thu Jul 17 2008 - 11:55:22 CDT)
AMBER: AmberTools-1.1 port for FreeBSD M. L. Dodson (Thu Jul 17 2008 - 12:59:05 CDT)
AMBER: the plot of the groove width versus time for RNA Å·ÑôµÂ·½ (Thu Jul 17 2008 - 18:35:31 CDT)
AMBER: how to generate psf file using the AMBER topology file tinni sona (Fri Jul 18 2008 - 05:41:11 CDT)
- Re: AMBER: how to generate psf file using the AMBER topology file Balazs JOJART (Fri Jul 18 2008 - 06:09:21 CDT)
  - Re: AMBER: how to generate psf file using the AMBER topology file tinni sona (Fri Jul 18 2008 - 07:08:48 CDT)
    - RE: AMBER: how to generate psf file using the AMBER topology file Ross Walker (Fri Jul 18 2008 - 11:57:14 CDT)
    - Re: AMBER: how to generate psf file using the AMBER topology file tinni sona (Sun Jul 20 2008 - 00:38:10 CDT)
AMBER: Restarting Problem in MD Simulation khuram sb (Fri Jul 18 2008 - 05:37:07 CDT)
- RE: AMBER: Restarting Problem in MD Simulation Ross Walker (Fri Jul 18 2008 - 12:08:46 CDT)
AMBER: Problems with Frozen atoms julliane Yoneda (Fri Jul 18 2008 - 15:06:54 CDT)
AMBER: a link for Amber ff ported to Charmm Alan (Sat Jul 19 2008 - 04:07:27 CDT)
- Re: AMBER: a link for Amber ff ported to Charmm David A. Case (Sat Jul 19 2008 - 13:29:18 CDT)
  - Re: AMBER: a link for Amber ff ported to Charmm Alan (Sat Jul 19 2008 - 16:50:25 CDT)
AMBER: parmbsc0 Dr. Suzie Byun (Sat Jul 19 2008 - 10:40:05 CDT)
AMBER: antechamber generated input for gaussian error Grange Hermitage (Sat Jul 19 2008 - 19:53:49 CDT)
- Re: AMBER: antechamber generated input for gaussian error Junmei Wang (Wed Jul 23 2008 - 10:29:21 CDT)
AMBER: Trans proline dipti lele (Sun Jul 20 2008 - 00:53:00 CDT)
- Re: AMBER: Trans proline Barbault Florent (Sun Jul 20 2008 - 01:27:37 CDT)
- Re: AMBER: Trans proline Carlos Simmerling (Sun Jul 20 2008 - 06:50:39 CDT)
  - Re: AMBER: Trans proline Adrian Roitberg (Sun Jul 20 2008 - 07:27:45 CDT)
    - Re: AMBER: Trans proline Brent Krueger (Sat Aug 02 2008 - 22:47:16 CDT)
AMBER: Release of version 1.2 of AmberTools David A. Case (Mon Jul 21 2008 - 12:01:29 CDT)
AMBER: Where is ICO read from the ix array? Brad Lambeth (Mon Jul 21 2008 - 14:49:44 CDT)
- Re: AMBER: Where is ICO read from the ix array? David A. Case (Mon Jul 21 2008 - 18:54:18 CDT)
AMBER: Amber tools 1.2 test failure (installation) Myunggi Yi (Mon Jul 21 2008 - 17:17:05 CDT)
- Re: AMBER: Amber tools 1.2 test failure (installation) David A. Case (Mon Jul 21 2008 - 18:36:16 CDT)
  - Re: AMBER: Amber tools 1.2 test failure (installation) Myunggi Yi (Thu Jul 24 2008 - 12:09:11 CDT)
AMBER: Problem with box dimension in AmberTools ptraj Steve Spronk (Tue Jul 22 2008 - 01:35:47 CDT)
- Re: AMBER: Problem with box dimension in AmberTools ptraj Thomas Cheatham (Tue Jul 22 2008 - 11:47:42 CDT)
AMBER: amber ff and how it deals with out-plane chiral C Alan (Tue Jul 22 2008 - 02:59:05 CDT)
- Re: AMBER: amber ff and how it deals with out-plane chiral C Carlos Simmerling (Tue Jul 22 2008 - 06:57:04 CDT)
  - Re: AMBER: amber ff and how it deals with out-plane chiral C Alan (Tue Jul 22 2008 - 09:41:27 CDT)
    - Re: AMBER: amber ff and how it deals with out-plane chiral C Carlos Simmerling (Tue Jul 22 2008 - 10:15:56 CDT)
- Re: AMBER: amber ff and how it deals with out-plane chiral C Bill Ross (Tue Jul 22 2008 - 16:44:36 CDT)
AMBER: targeted MD Germain Vallverdu (Tue Jul 22 2008 - 05:08:04 CDT)
- Re: AMBER: targeted MD Carlos Simmerling (Tue Jul 22 2008 - 06:48:15 CDT)
- AMBER: Indentifying cluster center structures in trajectory Anselm Horn (Wed Jul 23 2008 - 02:14:41 CDT)
  - RE: AMBER: Indentifying cluster center structures in trajectory Ross Walker (Wed Jul 23 2008 - 04:14:27 CDT)
AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj? Hannes Loeffler (Tue Jul 22 2008 - 09:08:36 CDT)
- Re: AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj? Thomas Cheatham (Tue Jul 22 2008 - 11:45:12 CDT)
  - Re: AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj? Hannes Loeffler (Wed Jul 23 2008 - 06:11:57 CDT)
AMBER: FreeBSD "port" for AmberTools-1.2 M. L. Dodson (Tue Jul 22 2008 - 14:15:48 CDT)
- Re: AMBER: FreeBSD "port" for AmberTools-1.2 M. L. Dodson (Tue Jul 22 2008 - 14:30:27 CDT)
- AMBER: Re: FreeBSD "port" for AmberTools-1.2 M. L. Dodson (Wed Jul 23 2008 - 09:17:56 CDT)
AMBER: SHIFTS compile error IN SUK JOUNG (Tue Jul 22 2008 - 15:25:43 CDT)
- Re: AMBER: SHIFTS compile error David A. Case (Wed Jul 23 2008 - 12:22:32 CDT)
AMBER: protonated guanine, cytosine parameters Kliman, Michal (Tue Jul 22 2008 - 17:22:19 CDT)
AMBER: improper dihedral in ff03 united atom forcefield ÇØæ©æ© (Tue Jul 22 2008 - 20:49:28 CDT)
AMBER: improper dihedrals in 03 united atom force field Q733 (Tue Jul 22 2008 - 21:00:03 CDT)
Re: AMBER: improper dihedral in ff03 united atom forcefield Bill Ross (Tue Jul 22 2008 - 23:28:07 CDT)
- Re: Re: AMBER: improper dihedral in ff03 united atom forcefield ÇØæ©æ© (Wed Jul 23 2008 - 00:14:11 CDT)
- Re: Re: AMBER: improper dihedral in ff03 united atom forcefield Bill Ross (Wed Jul 23 2008 - 13:19:31 CDT)
AMBER: 1.5ns rst file to PDB file Conversion Error khuram sb (Wed Jul 23 2008 - 00:07:24 CDT)
- RE: AMBER: 1.5ns rst file to PDB file Conversion Error Ross Walker (Wed Jul 23 2008 - 04:08:46 CDT)
AMBER: High force constant for MD ??? Waqas Nasir (Wed Jul 23 2008 - 04:49:46 CDT)
- Re: AMBER: High force constant for MD ??? Carlos Simmerling (Wed Jul 23 2008 - 06:02:13 CDT)
- Re: AMBER: High force constant for MD ??? Waqas Nasir (Thu Jul 24 2008 - 05:42:13 CDT)
AMBER: Trans proline dipti lele (Wed Jul 23 2008 - 06:01:28 CDT)
AMBER: Polarizable force field for divalent ions? Yi-Ming Cheng (Wed Jul 23 2008 - 05:59:08 CDT)
AMBER: Problems in restrained minimization julliane Yoneda (Wed Jul 23 2008 - 08:08:32 CDT)
AMBER: Hydroxyproline in AMBER Michael Entz (Wed Jul 23 2008 - 10:40:05 CDT)
- Re: AMBER: Hydroxyproline in AMBER Carlos Simmerling (Wed Jul 23 2008 - 11:03:01 CDT)
- Re: AMBER: Hydroxyproline in AMBER Adrian Roitberg (Wed Jul 23 2008 - 11:14:06 CDT)
AMBER: Query about the charge of atoms in the parmtop file tinni sona (Wed Jul 23 2008 - 11:48:19 CDT)
- Re: AMBER: Query about the charge of atoms in the parmtop file Carlos Simmerling (Wed Jul 23 2008 - 12:16:09 CDT)
  - Re: AMBER: Query about the charge of atoms in the parmtop file tinni sona (Thu Jul 24 2008 - 02:19:26 CDT)
AMBER: Which CO2 potential? Jones de Andrade (Wed Jul 23 2008 - 19:27:58 CDT)
- Re: AMBER: Which CO2 potential? gustavo.seabra_at_gmail.com (Wed Jul 23 2008 - 22:32:58 CDT)
  - Re: AMBER: Which CO2 potential? Jones de Andrade (Wed Jul 23 2008 - 22:45:00 CDT)
    - Re: AMBER: Which CO2 potential? Gustavo Seabra (Thu Jul 24 2008 - 08:08:53 CDT)
AMBER: amber9 install problem hklwatergod (Thu Jul 24 2008 - 01:11:33 CDT)
- Re: AMBER: amber9 install problem David A. Case (Thu Jul 24 2008 - 10:08:21 CDT)
  - AMBER: AMBER 10: Fortran Runtime Error George Tzotzos (Fri Jul 25 2008 - 09:38:32 CDT)
AMBER: EVB tests failure Vlad Cojocaru (Thu Jul 24 2008 - 03:34:52 CDT)
AMBER: solvate dna in TIP3PBOX 10.0 Collins Nganou (Thu Jul 24 2008 - 04:28:44 CDT)
- RE: AMBER: solvate dna in TIP3PBOX 10.0 Ross Walker (Thu Jul 24 2008 - 07:29:51 CDT)
AMBER: adding missing residues soumick (Thu Jul 24 2008 - 06:09:16 CDT)
- RE: AMBER: adding missing residues Ross Walker (Thu Jul 24 2008 - 07:35:41 CDT)
- Re: AMBER: adding missing residues David A. Case (Thu Jul 24 2008 - 10:37:36 CDT)
AMBER: calculating the enthalpy of evaporation jessica stolee (Thu Jul 24 2008 - 14:24:40 CDT)
- Re: AMBER: calculating the enthalpy of evaporation David A. Case (Thu Jul 24 2008 - 15:31:01 CDT)
AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 Mike Hanby (Thu Jul 24 2008 - 16:47:34 CDT)
- Re: AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 David A. Case (Thu Jul 24 2008 - 18:37:32 CDT)
  - RE: AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 Mike Hanby (Fri Jul 25 2008 - 11:16:37 CDT)
    - RE: AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 Scott Brozell (Thu Jul 31 2008 - 17:04:55 CDT)
AMBER: big molecule numbers Adrien Delmont (Thu Jul 24 2008 - 17:27:22 CDT)
- Re: AMBER: big molecule numbers David A. Case (Thu Jul 24 2008 - 20:43:26 CDT)
  - AMBER: AMBER10: Fortran Runtime Error George Tzotzos (Fri Jul 25 2008 - 10:19:03 CDT)
    - RE: AMBER: AMBER10: Fortran Runtime Error Ross Walker (Fri Jul 25 2008 - 16:22:16 CDT)
- RE: AMBER: big molecule numbers Ross Walker (Fri Jul 25 2008 - 03:10:05 CDT)
AMBER: solvate dna in TIP3PBOX 10.0 Collins Nganou (Fri Jul 25 2008 - 01:51:54 CDT)
- RE: AMBER: solvate dna in TIP3PBOX 10.0 Ross Walker (Fri Jul 25 2008 - 03:14:26 CDT)
AMBER: Regarding ff03 forcefield Reena ..... (Fri Jul 25 2008 - 02:24:41 CDT)
- RE: AMBER: Regarding ff03 forcefield Ross Walker (Fri Jul 25 2008 - 03:16:57 CDT)
- RE: AMBER: Regarding ff03 forcefield Yong Duan (Fri Jul 25 2008 - 11:24:19 CDT)
- RE: AMBER: Regarding ff03 forcefield Bill Ross (Fri Jul 25 2008 - 15:32:02 CDT)
  - Re: AMBER: Regarding ff03 forcefield David A. Case (Fri Jul 25 2008 - 15:46:26 CDT)
AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Sandeep Kaushik (Fri Jul 25 2008 - 05:04:11 CDT)
- Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Lachele Foley (Lists) (Fri Jul 25 2008 - 09:47:54 CDT)
  - Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Sandeep Kaushik (Mon Jul 28 2008 - 07:30:16 CDT)
- Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Bill Ross (Mon Jul 28 2008 - 19:26:35 CDT)
AMBER: amber 10: sander and pmemd performance Vlad Cojocaru (Fri Jul 25 2008 - 04:57:45 CDT)
- Re: AMBER: amber 10: sander and pmemd performance Robert Duke (Fri Jul 25 2008 - 09:31:30 CDT)
  - Re: AMBER: amber 10: sander and pmemd performance Vlad Cojocaru (Fri Jul 25 2008 - 10:14:08 CDT)
    - Re: AMBER: amber 10: sander and pmemd performance Robert Duke (Fri Jul 25 2008 - 11:06:41 CDT)
AMBER: simulation with many formamide molecules Adrien Delmont (Fri Jul 25 2008 - 05:44:23 CDT)
- AMBER: the pmemd problem hklwatergod (Fri Jul 25 2008 - 06:51:32 CDT)
  - Re: AMBER: the pmemd problem Robert Duke (Fri Jul 25 2008 - 08:46:24 CDT)
AMBER: # of ligands and receptors in mmpbsa Christopher Gaughan (Fri Jul 25 2008 - 09:57:03 CDT)
- Re: AMBER: # of ligands and receptors in mmpbsa Scott Brozell (Thu Jul 31 2008 - 21:14:50 CDT)
AMBER: Energy analysis aneesh cna (Fri Jul 25 2008 - 10:12:10 CDT)
AMBER: amber10: pmemd gfortran James W. Caldwell (Fri Jul 25 2008 - 13:23:06 CDT)
- Re: AMBER: amber10: pmemd gfortran Robert Duke (Fri Jul 25 2008 - 14:01:27 CDT)
- Re: AMBER: amber10: pmemd gfortran David A. Case (Fri Jul 25 2008 - 14:05:23 CDT)
  - RE: AMBER: amber10: pmemd gfortran James W. Caldwell (Fri Jul 25 2008 - 17:06:01 CDT)
    - RE: AMBER: amber10: pmemd gfortran Scott Brozell (Thu Jul 31 2008 - 22:16:45 CDT)
AMBER: Does clustering involve fitting? Steve Spronk (Fri Jul 25 2008 - 15:02:09 CDT)
- Re: AMBER: Does clustering involve fitting? Jianyin Shao (Wed Jul 30 2008 - 16:29:57 CDT)
Re: AMBER: solvate dna in TIP3PBOX 10.0 Bill Ross (Fri Jul 25 2008 - 15:28:46 CDT)
- Re: AMBER: solvate dna in TIP3PBOX 10.0 Bill Ross (Sat Jul 26 2008 - 13:11:44 CDT)
Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Bill Ross (Fri Jul 25 2008 - 15:40:27 CDT)
AMBER: fortran runtime error in "make test.serial" with gfortran Jaber Jahanbin Sardroodi (Fri Jul 25 2008 - 17:23:25 CDT)
- Re: AMBER: fortran runtime error in "make test.serial" with gfortran David A. Case (Fri Jul 25 2008 - 18:03:57 CDT)
AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? Alan (Sat Jul 26 2008 - 03:33:46 CDT)
- Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? Alan (Mon Jul 28 2008 - 05:54:31 CDT)
  - Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? FyD (Mon Jul 28 2008 - 07:28:50 CDT)
AMBER: big molecule numbers ( simulation with many formamide molecules ) Adrien Delmont (Sat Jul 26 2008 - 04:04:08 CDT)
- RE: AMBER: big molecule numbers ( simulation with many formamide molecules ) Ross Walker (Sat Jul 26 2008 - 08:58:34 CDT)
- Re: AMBER: big molecule numbers ( simulation with many formamide molecules ) Adrien Delmont (Sat Jul 26 2008 - 10:55:11 CDT)
  - RE: AMBER: big molecule numbers ( simulation with many formamide molecules ) Ross Walker (Sun Jul 27 2008 - 04:19:41 CDT)
AMBER: solvate dna in TIP3PBOX 10.0 Collins Nganou (Sat Jul 26 2008 - 04:08:26 CDT)
AMBER: RE: AMBER Question Ross Walker (Sat Jul 26 2008 - 08:53:25 CDT)
AMBER: interaction energies in Amber and VMD/NAMD Alessandro Nascimento (Sat Jul 26 2008 - 11:09:38 CDT)
- Re: AMBER: interaction energies in Amber and VMD/NAMD Carlos Simmerling (Sat Jul 26 2008 - 12:20:11 CDT)
- Re: AMBER: interaction energies in Amber and VMD/NAMD David A. Case (Sat Jul 26 2008 - 19:36:46 CDT)
  - Re: AMBER: interaction energies in Amber and VMD/NAMD Carlos Simmerling (Sat Jul 26 2008 - 19:46:58 CDT)
AMBER: Query dipti lele (Sun Jul 27 2008 - 01:40:54 CDT)
- RE: AMBER: Query Ross Walker (Sun Jul 27 2008 - 04:04:57 CDT)
AMBER: radius of calcium ion in MM_PBSA Hannes Wallnoefer (Mon Jul 28 2008 - 03:18:22 CDT)
- Re: AMBER: radius of calcium ion in MM_PBSA Neha Gandhi (Mon Jul 28 2008 - 03:46:50 CDT)
  - Re: AMBER: radius of calcium ion in MM_PBSA Hannes Wallnoefer (Mon Jul 28 2008 - 04:28:01 CDT)
    - Re: AMBER: radius of calcium ion in MM_PBSA Navnit Kumar Mishra (Mon Jul 28 2008 - 04:55:33 CDT)
AMBER: Problem in .parmtop file sudipta sinha (Mon Jul 28 2008 - 10:30:09 CDT)
AMBER: Amber 10 on the BlueGene Mike Hanby (Mon Jul 28 2008 - 11:15:58 CDT)
- Re: AMBER: Amber 10 on the BlueGene Robert Duke (Mon Jul 28 2008 - 12:17:18 CDT)
  - Re: AMBER: Amber 10 on the BlueGene Carlos Simmerling (Mon Jul 28 2008 - 13:37:59 CDT)
  - Re: AMBER: Amber 10 on the BlueGene Carlos Simmerling (Mon Jul 28 2008 - 13:37:59 CDT)
Re: AMBER: interaction energies in Amber Alessandro Nascimento (Mon Jul 28 2008 - 19:51:01 CDT)
AMBER: Energy minimization of protein-ligand complex Dong Xu (Tue Jul 29 2008 - 02:18:57 CDT)
AMBER: PMEND 9 compilation problems Nick Holway (Tue Jul 29 2008 - 11:04:36 CDT)
- Re: AMBER: PMEND 9 compilation problems Robert Duke (Tue Jul 29 2008 - 12:41:54 CDT)
  - Re: AMBER: PMEND 9 compilation problems Nick Holway (Wed Jul 30 2008 - 08:50:42 CDT)
    - Re: AMBER: PMEND 9 compilation problems Robert Duke (Wed Jul 30 2008 - 09:40:00 CDT)
AMBER: for mask in rms Wenyong Tong (Tue Jul 29 2008 - 22:35:23 CDT)
AMBER: Volume of ucell too big baohua zhang (Tue Jul 29 2008 - 22:30:43 CDT)
- Re: AMBER: Volume of ucell too big David A. Case (Wed Jul 30 2008 - 00:19:31 CDT)
AMBER: DMSOBOX jacopo.sgrignani_at_unifi.it (Wed Jul 30 2008 - 02:05:00 CDT)
- Re: AMBER: DMSOBOX Panwang Zhou (Wed Jul 30 2008 - 02:31:53 CDT)
Re: AMBER: interaction energies in Amber and VMD/NAMD (SOLVED) Alessandro Nascimento (Wed Jul 30 2008 - 10:29:47 CDT)
AMBER: mask for oligosaccharide Wenyong Tong (Wed Jul 30 2008 - 13:23:58 CDT)
- Re: AMBER: mask for oligosaccharide Jianyin Shao (Wed Jul 30 2008 - 17:26:31 CDT)
  - Re: AMBER: mask for oligosaccharide Wenyong Tong (Wed Jul 30 2008 - 23:13:08 CDT)
AMBER: Q: ntc = 3 parallel runnable not compiled in Amber 9? Qicun Shi (Wed Jul 30 2008 - 22:51:17 CDT)
- Re: AMBER: Q: ntc = 3 parallel runnable not compiled in Amber 9? Carlos Simmerling (Thu Jul 31 2008 - 07:07:21 CDT)
AMBER: how to get the potential energy of a protein from the system TaoPaul (Thu Jul 31 2008 - 03:29:08 CDT)
- Re: AMBER: how to get the potential energy of a protein from the system David A. Case (Thu Jul 31 2008 - 09:45:47 CDT)
  - AMBER: addles Urszula Uciechowska (Tue Aug 05 2008 - 03:30:20 CDT)
    - Re: AMBER: addles Carlos Simmerling (Tue Aug 05 2008 - 06:02:47 CDT)
  - AMBER: linear interaction energy Urszula Uciechowska (Thu Aug 07 2008 - 08:55:18 CDT)
AMBER: opls/aa in Amber status Alan (Thu Jul 31 2008 - 03:41:58 CDT)
AMBER: amb2gmx for big systems rebeca_at_mmb.pcb.ub.es (Thu Jul 31 2008 - 05:40:39 CDT)
AMBER: ACPYPI announcement Alan (Thu Jul 31 2008 - 06:17:02 CDT)
AMBER: imin = 5 and PBC sai kumar ramadugu (Thu Jul 31 2008 - 09:51:21 CDT)
AMBER: prepare an initial structure in Amber oguz gurbulak (Thu Jul 31 2008 - 11:58:24 CDT)
- Fwd: AMBER: prepare an initial structure in Amber Lachele Foley (Lists) (Fri Aug 01 2008 - 09:52:50 CDT)
AMBER: Compailation problum in Amber 10 srinivas sudani (Fri Aug 01 2008 - 01:59:00 CDT)
- Re: AMBER: Compailation problum in Amber 10 David A. Case (Fri Aug 01 2008 - 14:48:55 CDT)
  - Re: AMBER: Compailation problum in Amber 10 srinivas sudani (Mon Aug 04 2008 - 00:41:13 CDT)
AMBER: bacteriochlorophyll ff Anna Karawajczyk (Fri Aug 01 2008 - 05:04:44 CDT)
AMBER: Bonds getting shorter in sander Peter Gannett (Fri Aug 01 2008 - 07:47:02 CDT)
- Re: AMBER: Bonds getting shorter in sander Carlos Simmerling (Fri Aug 01 2008 - 08:18:36 CDT)
AMBER: respgen -a charge groups function ineffective unless Grange Hermitage (Sat Aug 02 2008 - 00:00:29 CDT)
- Re: AMBER: respgen -a charge groups function ineffective unless Junmei Wang (Wed Aug 27 2008 - 15:55:47 CDT)
AMBER: PDB files in Amber10 Francesco Pietra (Sat Aug 02 2008 - 02:21:58 CDT)
- Re: AMBER: PDB files in Amber10 Scott Brozell (Mon Aug 25 2008 - 16:32:16 CDT)
AMBER: error in parallel amber 9 test Jaber Jahanbin Sardroodi (Sat Aug 02 2008 - 16:12:07 CDT)
- Re: AMBER: error in parallel amber 9 test David A. Case (Sat Aug 02 2008 - 20:37:10 CDT)
  - Re: AMBER: error in parallel amber 9 test Jaber Jahanbin Sardroodi (Sun Aug 03 2008 - 03:15:19 CDT)
    - Re: AMBER: error in parallel amber 9 test David A. Case (Sun Aug 03 2008 - 23:28:45 CDT)
AMBER: Problem with setting the NMR restraints Alex Spasic (Mon Aug 04 2008 - 09:15:25 CDT)
- Re: AMBER: Problem with setting the NMR restraints David A. Case (Mon Aug 04 2008 - 10:26:51 CDT)
  - Re: AMBER: Problem with setting the NMR restraints Alex Spasic (Mon Aug 04 2008 - 11:58:17 CDT)
    - Re: AMBER: Problem with setting the NMR restraints Carlos Simmerling (Mon Aug 04 2008 - 13:28:36 CDT)
    - Re: AMBER: Problem with setting the NMR restraints Alex Spasic (Mon Aug 04 2008 - 14:35:20 CDT)
AMBER: Set 251 is corrupted, ptraj error... Waqas Nasir (Mon Aug 04 2008 - 09:54:09 CDT)
- Re: AMBER: Set 251 is corrupted, ptraj error... David A. Case (Mon Aug 04 2008 - 10:31:28 CDT)
- Re: AMBER: Set 251 is corrupted, ptraj error... Waqas Nasir (Tue Aug 05 2008 - 06:23:47 CDT)
AMBER: Biased MD with Amber 10 Francesco Pietra (Mon Aug 04 2008 - 13:35:31 CDT)
AMBER: divcon.rst ?? IN SUK JOUNG (Mon Aug 04 2008 - 19:06:43 CDT)
AMBER: help me for filling a nanotube with water?? Jaber Jahanbin Sardroodi (Mon Aug 04 2008 - 20:39:05 CDT)
- Re: AMBER: help me for filling a nanotube with water?? Markus Kaukonen (Wed Aug 13 2008 - 01:29:48 CDT)
  - Re: AMBER: help me for filling a nanotube with water?? Thomas Steinbrecher (Wed Aug 13 2008 - 11:40:22 CDT)
AMBER: NMR structure as initial structure Siddharth Rastogi (Tue Aug 05 2008 - 01:40:54 CDT)
- Re: AMBER: NMR structure as initial structure David A. Case (Tue Aug 05 2008 - 19:09:25 CDT)
AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) dipti lele (Tue Aug 05 2008 - 05:03:10 CDT)
- Re: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) Wenyong Tong (Tue Aug 05 2008 - 09:51:31 CDT)
  - RE: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) Matthew Tessier (Tue Aug 05 2008 - 10:07:22 CDT)
- Re: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) Wenyong Tong (Tue Aug 05 2008 - 14:32:31 CDT)
AMBER: MM_PBSA snapshot statistic calc problem Hannes Wallnoefer (Tue Aug 05 2008 - 07:45:48 CDT)
- Re: AMBER: MM_PBSA snapshot statistic calc problem haixiao jin (Sat Sep 27 2008 - 01:40:20 CDT)
  - Re: AMBER: MM_PBSA snapshot statistic calc problem Vasu Chandrasekaran (Mon Sep 29 2008 - 14:08:15 CDT)
    - RE: AMBER: MM_PBSA snapshot statistic calc problem Peterson, Matthew W. (Mon Sep 29 2008 - 16:25:57 CDT)
AMBER: NAB: getseq_from_pdb() IN SUK JOUNG (Tue Aug 05 2008 - 19:00:21 CDT)
AMBER: Problems with the charge (membrane simulation) rebeca_at_mmb.pcb.ub.es (Wed Aug 06 2008 - 13:20:30 CDT)
- AMBER: Not integral charge increasing with number of lipids rebeca_at_mmb.pcb.ub.es (Thu Aug 07 2008 - 05:18:01 CDT)
  - RE: AMBER: Not integral charge increasing with number of lipids Ross Walker (Thu Aug 07 2008 - 10:24:28 CDT)
- RE: AMBER: Problems with the charge (membrane simulation) Ross Walker (Thu Aug 07 2008 - 10:18:12 CDT)
AMBER: Re: entropy of released water Swarup Gupta (Thu Aug 07 2008 - 07:40:26 CDT)
AMBER: aggregation or cluster detection fatima.chami_at_durham.ac.uk (Thu Aug 07 2008 - 08:41:24 CDT)
- RE: AMBER: aggregation or cluster detection Ross Walker (Thu Aug 07 2008 - 10:29:28 CDT)
  - Re: AMBER: aggregation or cluster detection Carlos Simmerling (Thu Aug 07 2008 - 10:38:52 CDT)
- Re: AMBER: aggregation or cluster detection Lachele Foley (Lists) (Thu Aug 07 2008 - 10:44:07 CDT)
AMBER: NAB conjgrad returns error? Carra, Claudio (JSC-SK)[USRA] (Thu Aug 07 2008 - 10:04:38 CDT)
- Re: AMBER: NAB conjgrad returns error? Andreas Svrcek-Seiler (Thu Aug 07 2008 - 10:33:28 CDT)
  - RE: AMBER: NAB conjgrad returns error? Carra, Claudio (JSC-SK)[USRA] (Thu Aug 07 2008 - 11:19:52 CDT)
- RE: AMBER: NAB conjgrad returns error? NIEL MICHAEL HENRIKSEN (Fri Aug 08 2008 - 08:50:05 CDT)
  - RE: AMBER: NAB conjgrad returns error? Andreas Svrcek-Seiler (Fri Aug 08 2008 - 10:48:28 CDT)
  - RE: AMBER: NAB conjgrad returns error? Carra, Claudio (JSC-SK)[USRA] (Mon Aug 11 2008 - 16:14:12 CDT)
    - Re: AMBER: NAB conjgrad returns error? David A. Case (Mon Aug 11 2008 - 16:40:49 CDT)
    - RE: AMBER: NAB conjgrad returns error? Carra, Claudio (JSC-SK)[USRA] (Mon Aug 11 2008 - 17:44:09 CDT)
- RE: AMBER: NAB conjgrad returns error? NIEL MICHAEL HENRIKSEN (Fri Aug 08 2008 - 14:31:13 CDT)
- RE: AMBER: NAB conjgrad returns error? NIEL MICHAEL HENRIKSEN (Mon Aug 11 2008 - 18:07:27 CDT)
AMBER: problem with minimization luzhenw1_at_msu.edu (Thu Aug 07 2008 - 10:13:17 CDT)
- Re: AMBER: problem with minimization Carlos Simmerling (Thu Aug 07 2008 - 10:29:10 CDT)
- RE: AMBER: problem with minimization Ross Walker (Thu Aug 07 2008 - 10:40:46 CDT)
  - AMBER: parameters Thomas Leonard (Fri Aug 08 2008 - 00:45:09 CDT)
AMBER: value of Pi in Amber Alan (Fri Aug 08 2008 - 05:36:06 CDT)
- AMBER: LES Urszula Uciechowska (Fri Aug 08 2008 - 07:31:56 CDT)
- Re: AMBER: value of Pi in Amber Scott Brozell (Tue Aug 26 2008 - 17:07:49 CDT)
  - AMBER: molecular structure Chih-Ying Lin (Tue Aug 26 2008 - 17:24:29 CDT)
    - Re: AMBER: molecular structure Carlos Simmerling (Tue Aug 26 2008 - 17:32:51 CDT)
AMBER: PBCAL in MM_PBSA Hannes Wallnoefer (Fri Aug 08 2008 - 09:19:30 CDT)
- RE: AMBER: PBCAL in MM_PBSA Ray Luo (Fri Aug 08 2008 - 13:27:17 CDT)
  - AMBER: PBCAL in MM_PBSA Thomas Leonard (Mon Aug 11 2008 - 03:12:51 CDT)
    - AMBER: mmpbsa Urszula Uciechowska (Mon Aug 11 2008 - 03:43:17 CDT)
AMBER: Is G_disp calculated in MM_PBSA now? cgji (Sat Aug 09 2008 - 07:51:55 CDT)
- RE: AMBER: Is G_disp calculated in MM_PBSA now? Ray Luo (Mon Aug 11 2008 - 14:33:14 CDT)
AMBER: Minimization methods teresa.ierano_at_unina.it (Mon Aug 11 2008 - 07:11:23 CDT)
- Re: AMBER: Minimization methods E.M. (Mon Aug 11 2008 - 07:22:25 CDT)
  - Re: AMBER: Minimization methods M. L. Dodson (Mon Aug 11 2008 - 10:34:05 CDT)
    - Re: AMBER: Minimization methods teresa.ierano_at_unina.it (Mon Aug 11 2008 - 11:39:30 CDT)
- RE: AMBER: Minimization methods Ross Walker (Mon Aug 11 2008 - 09:43:47 CDT)
  - RE: AMBER: Minimization methods teresa.ierano_at_unina.it (Mon Aug 11 2008 - 11:30:50 CDT)
AMBER: GPCR membrane simulation, setting surface tension Fiona McRobb (Mon Aug 11 2008 - 20:42:47 CDT)
- Re: AMBER: GPCR membrane simulation, setting surface tension Vlad Cojocaru (Tue Aug 12 2008 - 03:45:08 CDT)
  - RE: [!!!] - Re: AMBER: GPCR membrane simulation, setting surface tension - Message is from an unknown sender Fiona McRobb (Wed Aug 13 2008 - 00:09:49 CDT)
AMBER: questions about previous posts Naser Alijabbari (Mon Aug 11 2008 - 23:17:40 CDT)
- RE: AMBER: questions about previous posts Ross Walker (Tue Aug 12 2008 - 01:18:49 CDT)
- Re: AMBER: questions about previous posts David A. Case (Sat Aug 16 2008 - 10:00:38 CDT)
AMBER: Using RDCs for structure refinement David Witte (Tue Aug 12 2008 - 02:52:53 CDT)
- Re: AMBER: Using RDCs for structure refinement David A. Case (Tue Aug 12 2008 - 11:36:24 CDT)
AMBER: Querry about simulating a glycopeptide dipti lele (Tue Aug 12 2008 - 05:23:24 CDT)
- Re: AMBER: Querry about simulating a glycopeptide Lachele Foley (Lists) (Tue Aug 12 2008 - 09:03:14 CDT)
AMBER: MM-PBSA Issue in Amber 10 Peterson, Matthew W. (Tue Aug 12 2008 - 12:44:29 CDT)
AMBER: empty frcmod file but missing parameters moitrayee_at_mbu.iisc.ernet.in (Tue Aug 12 2008 - 16:20:19 CDT)
- Re: AMBER: empty frcmod file but missing parameters Alessandro Nascimento (Tue Aug 12 2008 - 17:02:01 CDT)
  - Re: AMBER: empty frcmod file but missing parameters moitrayee_at_mbu.iisc.ernet.in (Tue Aug 12 2008 - 17:10:03 CDT)
AMBER: frcmod:attn needs revision moitrayee_at_mbu.iisc.ernet.in (Tue Aug 12 2008 - 17:18:02 CDT)
- Re: AMBER: frcmod:attn needs revision Junmei Wang (Wed Aug 13 2008 - 11:45:11 CDT)
  - Re: AMBER: frcmod:attn needs revision moitrayee_at_mbu.iisc.ernet.in (Wed Aug 13 2008 - 11:55:40 CDT)
    - Re: AMBER: frcmod:attn needs revision Junmei Wang (Wed Aug 13 2008 - 14:34:50 CDT)
    - Re: AMBER: frcmod:attn needs revision moitrayee_at_mbu.iisc.ernet.in (Wed Aug 13 2008 - 23:51:50 CDT)
AMBER: glycoprotein setup Arturas Ziemys (Tue Aug 12 2008 - 22:35:35 CDT)
AMBER: general question Gigil Toton (Wed Aug 13 2008 - 01:49:12 CDT)
AMBER: amber 9 on Intel Harpertown Geoff Wood (Wed Aug 13 2008 - 04:45:36 CDT)
- RE: AMBER: amber 9 on Intel Harpertown Ross Walker (Wed Aug 13 2008 - 09:24:47 CDT)
AMBER: problem with prep file generation aneesh cna (Wed Aug 13 2008 - 07:05:58 CDT)
- Re: AMBER: problem with prep file generation Junmei Wang (Wed Aug 13 2008 - 11:59:49 CDT)
AMBER: modified parmtop file from ptraj? Hannes Wallnoefer (Wed Aug 13 2008 - 07:14:34 CDT)
- Re: AMBER: modified parmtop file from ptraj? Florian Haberl (Wed Aug 13 2008 - 07:47:21 CDT)
- Re: AMBER: modified parmtop file from ptraj? Daniel Cappel (Wed Aug 13 2008 - 08:37:19 CDT)
- Re: AMBER: modified parmtop file from ptraj? Thomas Cheatham (Wed Aug 13 2008 - 12:43:24 CDT)
AMBER: Querry dipti lele (Wed Aug 13 2008 - 07:15:11 CDT)
- RE: AMBER: Querry Ross Walker (Wed Aug 13 2008 - 09:48:19 CDT)
  - Re: AMBER: Querry Lachele Foley (Lists) (Wed Aug 13 2008 - 10:03:49 CDT)
AMBER: Compile AMBER 9 on TACC Ranger super computer jialei (Wed Aug 13 2008 - 17:26:07 CDT)
- RE: AMBER: Compile AMBER 9 on TACC Ranger super computer Ross Walker (Wed Aug 13 2008 - 22:39:47 CDT)
- Re:AMBER: Compile AMBER 9 on TACC Ranger super computer ÕÅÓÂ (Thu Aug 14 2008 - 08:32:30 CDT)
  - RE: AMBER: Compile AMBER 9 on TACC Ranger super computer Ross Walker (Thu Aug 14 2008 - 11:00:02 CDT)
- Re:AMBER: Compile AMBER 9 on TACC Ranger super computer ÕÅÓÂ (Thu Aug 14 2008 - 08:32:30 CDT)
AMBER: mm-pbsa / sander.MPI ? Arturas Ziemys (Wed Aug 13 2008 - 17:26:56 CDT)
- Re: AMBER: mm-pbsa / sander.MPI ? Miguel Ortiz-Lombardía (Thu Aug 14 2008 - 02:58:54 CDT)
  - Re: AMBER: mm-pbsa / sander.MPI ? Arturas Ziemys (Thu Aug 14 2008 - 09:42:02 CDT)
AMBER: how to choose the appropriate ensemble for a given problem Ruchi Sachdeva (Wed Aug 13 2008 - 23:09:28 CDT)
AMBER: MD with NMR restraints Sally Pias (Wed Aug 13 2008 - 23:25:56 CDT)
- Re: AMBER: MD with NMR restraints David A. Case (Wed Aug 20 2008 - 12:07:15 CDT)
AMBER: amber9 hangas after job submission Vijay Manickam Achari (Thu Aug 14 2008 - 01:40:03 CDT)
- Re: AMBER: amber9 hangas after job submission Carlos Simmerling (Thu Aug 14 2008 - 05:45:14 CDT)
- Re: AMBER: amber9 hangas after job submission Robert Duke (Thu Aug 14 2008 - 07:54:43 CDT)
AMBER: minimization stops or does not write anything rebeca_at_mmb.pcb.ub.es (Thu Aug 14 2008 - 04:01:17 CDT)
- Re: AMBER: minimization stops or does not write anything Robert Duke (Thu Aug 14 2008 - 07:39:01 CDT)
AMBER: Glycoprotein once again.......... dipti lele (Thu Aug 14 2008 - 07:10:10 CDT)
- Re: AMBER: Glycoprotein once again.......... Lachele Foley (Lists) (Thu Aug 14 2008 - 08:28:30 CDT)
AMBER: constph shubhra srivastava (Thu Aug 14 2008 - 06:54:57 CDT)
AMBER: interaction energies Arturas Ziemys (Thu Aug 14 2008 - 10:21:34 CDT)
- Re: AMBER: interaction energies Alessandro Nascimento (Fri Aug 15 2008 - 11:18:05 CDT)
AMBER: Help compiling Nab programs for AMBER tools Ragnarok sdf (Thu Aug 14 2008 - 14:36:04 CDT)
- Re: AMBER: Help compiling Nab programs for AMBER tools M. L. Dodson (Thu Aug 14 2008 - 14:50:51 CDT)
AMBER: generate topology file for alanine scanning (mmpbsa) luzhenw1_at_msu.edu (Thu Aug 14 2008 - 14:32:56 CDT)
AMBER: Proton Parameters Shultz, Jack (Thu Aug 14 2008 - 15:34:54 CDT)
- Re: AMBER: Proton Parameters David A. Case (Wed Aug 20 2008 - 12:12:02 CDT)
AMBER: impropers over bonds between sidechains Grange Hermitage (Thu Aug 14 2008 - 20:12:05 CDT)
- Re: AMBER: impropers over bonds between sidechains M. L. Dodson (Thu Aug 14 2008 - 21:29:54 CDT)
  - Re: AMBER: impropers over bonds between sidechains Grange Hermitage (Thu Aug 14 2008 - 22:08:49 CDT)
    - Re: AMBER: impropers over bonds between sidechains David A. Case (Wed Aug 20 2008 - 12:14:03 CDT)
AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro Grange Hermitage (Sun Aug 17 2008 - 21:28:17 CDT)
- Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro Grange Hermitage (Mon Aug 18 2008 - 00:04:18 CDT)
  - Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro Alan (Mon Aug 18 2008 - 02:42:35 CDT)
AMBER: Negative dihedral coefficients in amber99 - Possible? Ilyas Yildirim (Sun Aug 17 2008 - 21:33:16 CDT)
- RE: AMBER: Negative dihedral coefficients in amber99 - Possible? Ross Walker (Mon Aug 18 2008 - 00:15:45 CDT)
AMBER: trying ff99SP Grange Hermitage (Mon Aug 18 2008 - 01:12:33 CDT)
- Re: AMBER: trying ff99SP David A. Case (Wed Aug 20 2008 - 13:31:22 CDT)
AMBER: unsubscribe khuram sb (Mon Aug 18 2008 - 03:56:36 CDT)
AMBER: RDF output file format aneesh cna (Mon Aug 18 2008 - 04:48:45 CDT)
- Re: AMBER: RDF output file format Bertrand P. S. Russell (Mon Aug 18 2008 - 05:26:08 CDT)
AMBER: Initial structure from NMR structures Siddharth Rastogi (Tue Aug 19 2008 - 01:15:44 CDT)
- RE: AMBER: Initial structure from NMR structures Ross Walker (Tue Aug 19 2008 - 09:05:43 CDT)
AMBER: How to convert a CHARMM trajectory to AMBER format? Jeffrey (Tue Aug 19 2008 - 06:30:35 CDT)
- Re: AMBER: How to convert a CHARMM trajectory to AMBER format? Wei Huang (Tue Aug 19 2008 - 09:02:22 CDT)
  - RE: AMBER: How to convert a CHARMM trajectory to AMBER format? Ross Walker (Tue Aug 19 2008 - 09:26:25 CDT)
    - Re: RE: AMBER: How to convert a CHARMM trajectory to AMBER format? Jeffrey (Tue Aug 19 2008 - 19:43:58 CDT)
    - Re: Re: RE: AMBER: How to convert a CHARMM trajectory to AMBER format? Jeffrey (Thu Aug 21 2008 - 02:11:55 CDT)
AMBER: Compile Error Shultz, Jack (Tue Aug 19 2008 - 10:44:25 CDT)
AMBER: Amber compile Shultz, Jack (Tue Aug 19 2008 - 13:21:18 CDT)
- RE: AMBER: Amber compile Shultz, Jack (Tue Aug 19 2008 - 14:25:56 CDT)
AMBER: IGB=10 in Amber10 In Hee Park (Tue Aug 19 2008 - 13:55:05 CDT)
AMBER: Problem loading the leaprc.amoeba force field file in Amber 10. Zhao, Zhen (zhaozh) (Tue Aug 19 2008 - 15:20:00 CDT)
- Re: AMBER: Problem loading the leaprc.amoeba force field file in Amber 10. David A. Case (Wed Aug 20 2008 - 12:24:17 CDT)
AMBER: Problems with sleap and amoeba Neil J. Henson (Tue Aug 19 2008 - 18:16:17 CDT)
- AMBER: Force field equation Chih-Ying Lin (Wed Aug 20 2008 - 11:05:39 CDT)
  - Re: AMBER: Force field equation Carlos Simmerling (Wed Aug 20 2008 - 12:53:03 CDT)
Re: AMBER: Problems with sleap and amoeba Bill Ross (Tue Aug 19 2008 - 18:51:18 CDT)
- Re: AMBER: Problems with sleap and amoeba Neil J. Henson (Tue Aug 19 2008 - 19:03:52 CDT)
AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange xiaonan zhang (Wed Aug 20 2008 - 02:25:43 CDT)
- Re: AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange Carlos Simmerling (Wed Aug 20 2008 - 12:47:12 CDT)
AMBER: Trouble installing Amber 9 Sampath Koppole (Wed Aug 20 2008 - 05:28:58 CDT)
AMBER: Silicon parameters Abdul Hameed, MohamedDiwanMo (Wed Aug 20 2008 - 11:15:56 CDT)
- Re: AMBER: Silicon parameters Junmei Wang (Fri Aug 22 2008 - 15:29:05 CDT)
AMBER: Using Na+ ions as input to leap? Pablo Englebienne (Wed Aug 20 2008 - 12:40:11 CDT)
AMBER: NMR average structure Gigil Toton (Wed Aug 20 2008 - 12:42:08 CDT)
- Re: AMBER: NMR average structure Carlos Simmerling (Wed Aug 20 2008 - 12:50:28 CDT)
Re: AMBER: Using Na+ ions as input to leap? - solved Pablo Englebienne (Wed Aug 20 2008 - 14:25:25 CDT)
AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! Piyush Wanjari (Wed Aug 20 2008 - 23:36:20 CDT)
- Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! David A. Case (Fri Aug 22 2008 - 22:11:14 CDT)
  - Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! Piyush Wanjari (Mon Aug 25 2008 - 14:52:37 CDT)
    - Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! Piyush Wanjari (Mon Aug 25 2008 - 17:00:33 CDT)
AMBER: new residues in AMOEBA Grange Hermitage (Thu Aug 21 2008 - 02:14:59 CDT)
AMBER: Fwd: Welcome to amber Maicon Sartin (Thu Aug 21 2008 - 07:33:08 CDT)
AMBER: SANDER Parallel Maicon Sartin (Thu Aug 21 2008 - 07:36:56 CDT)
AMBER: Gohlke in-house iRED Simulated Order Parameter Script Titus, Jamie (bairdje) (Thu Aug 21 2008 - 07:53:09 CDT)
AMBER: DFTB QMMM parameters ambiguity in AMBER10 docs M. L. Dodson (Thu Aug 21 2008 - 12:56:38 CDT)
AMBER: Error when compiling and testing AmberTools Ben Roberts (Thu Aug 21 2008 - 16:46:43 CDT)
- Re: AMBER: Error when compiling and testing AmberTools Andreas Svrcek-Seiler (Fri Aug 22 2008 - 04:11:14 CDT)
AMBER: all & united atoms force field fatima.chami_at_durham.ac.uk (Thu Aug 21 2008 - 17:05:12 CDT)
- Re: AMBER: all & united atoms force field cgji (Thu Aug 21 2008 - 17:28:49 CDT)
  - Re: AMBER: all & united atoms force field fatima.chami_at_durham.ac.uk (Fri Aug 22 2008 - 08:31:34 CDT)
AMBER: Error runing Addles Shultz, Jack (Thu Aug 21 2008 - 22:25:17 CDT)
- Re: AMBER: Error runing Addles Carlos Simmerling (Fri Aug 22 2008 - 07:48:07 CDT)
AMBER: united atom force field Adrien Delmont (Fri Aug 22 2008 - 07:35:06 CDT)
- Re: AMBER: united atom force field Ray Luo (Fri Aug 22 2008 - 12:37:38 CDT)
- Re: AMBER: united atom force field Adrien Delmont (Fri Aug 22 2008 - 14:17:10 CDT)
  - RE: AMBER: united atom force field Ray Luo (Tue Aug 26 2008 - 18:11:47 CDT)
AMBER: vdw 6-9 potential fatima.chami_at_durham.ac.uk (Fri Aug 22 2008 - 15:56:57 CDT)
- Re: AMBER: vdw 6-9 potential Carlos Simmerling (Fri Aug 22 2008 - 16:02:48 CDT)
  - Re: AMBER: vdw 6-9 potential fatima.chami_at_durham.ac.uk (Sat Aug 23 2008 - 05:34:57 CDT)
    - Re: AMBER: vdw 6-9 potential Carlos Simmerling (Sat Aug 23 2008 - 05:51:24 CDT)
    - Re: AMBER: vdw 6-9 potential fatima.chami_at_durham.ac.uk (Tue Aug 26 2008 - 11:03:55 CDT)
AMBER: Dell 2 Quad Core System Performance Ilyas Yildirim (Fri Aug 22 2008 - 20:16:49 CDT)
- AMBER: Re: Dell 2 Quad Core System Performance Ilyas Yildirim (Wed Aug 27 2008 - 16:04:14 CDT)
  - Re: AMBER: Re: Dell 2 Quad Core System Performance Carlos Simmerling (Wed Aug 27 2008 - 17:15:42 CDT)
  - RE: AMBER: Re: Dell 2 Quad Core System Performance Ross Walker (Wed Aug 27 2008 - 18:01:59 CDT)
AMBER: LES trajectories Urszula Uciechowska (Mon Aug 25 2008 - 03:12:23 CDT)
- AMBER: Is there a way to cluster frames of a trajectory? Sasha Buzko (Wed Aug 27 2008 - 19:45:01 CDT)
  - Re: AMBER: Is there a way to cluster frames of a trajectory? Carlos Simmerling (Wed Aug 27 2008 - 19:58:27 CDT)
  - Re: AMBER: Is there a way to cluster frames of a trajectory? Adrian Roitberg (Wed Aug 27 2008 - 19:56:08 CDT)
    - Re: AMBER: Is there a way to cluster frames of a trajectory? Sasha Buzko (Wed Aug 27 2008 - 19:57:07 CDT)
AMBER: pmemd iwrap trouble Lars Skjærven (Mon Aug 25 2008 - 05:25:09 CDT)
- Re: AMBER: pmemd iwrap trouble Robert Duke (Mon Aug 25 2008 - 07:40:03 CDT)
  - Re: AMBER: pmemd iwrap trouble Lars Skjærven (Mon Aug 25 2008 - 08:32:26 CDT)
Re: AMBER: xleap fails to savemol2 FyD (Thu Sep 04 2008 - 14:45:49 CDT)
- Re: AMBER: xleap fails to savemol2 alsarraj (Thu Sep 18 2008 - 15:15:20 CDT)
  - Re: AMBER: xleap fails to savemol2 alsarraj (Fri Sep 19 2008 - 15:59:44 CDT)
  - Re: AMBER: xleap fails to savemol2 Mark Williamson (Mon Sep 22 2008 - 13:43:35 CDT)
Re: AMBER: pmemd iwrap trouble Lars Skjærven (Mon Aug 25 2008 - 17:03:14 CDT)
- Re: AMBER: pmemd iwrap trouble Robert Duke (Mon Aug 25 2008 - 23:22:44 CDT)
AMBER: mol2, xleap, Segmentation fault Anna Karawajczyk (Mon Aug 25 2008 - 08:01:31 CDT)
- Re: AMBER: mol2, xleap, Segmentation fault Cenk $Jenk$ Andac (Mon Aug 25 2008 - 09:38:28 CDT)
AMBER: Parameters for chloride ion in contact with a protein Francesco Pietra (Mon Aug 25 2008 - 09:25:13 CDT)
AMBER: Problem with the prmtop file generated by sleap and leaprc.amoeba in Amber 10. Zhao, Zhen (zhaozh) (Mon Aug 25 2008 - 10:04:34 CDT)
AMBER: tan luo radii Jacopo Sgrignani (Tue Aug 26 2008 - 04:06:39 CDT)
- RE: AMBER: tan luo radii Ray Luo (Tue Aug 26 2008 - 14:12:57 CDT)
AMBER: installation amber on suse11.0 selami ercan (Tue Aug 26 2008 - 05:57:12 CDT)
- RE: AMBER: installation amber on suse11.0 Ross Walker (Tue Aug 26 2008 - 09:39:31 CDT)
  - Re: AMBER: installation amber on suse11.0 selami ercan (Wed Aug 27 2008 - 13:50:13 CDT)
- Re: AMBER: installation amber on suse11.0 Cenk $Jenk$ Andac (Tue Aug 26 2008 - 09:40:30 CDT)
- Re: AMBER: installation amber on suse11.0 Maicon Sartin (Tue Aug 26 2008 - 09:52:01 CDT)
AMBER: Querry dipti lele (Tue Aug 26 2008 - 06:50:32 CDT)
- Re: AMBER: Querry Carlos Simmerling (Tue Aug 26 2008 - 09:09:25 CDT)
  - Re: AMBER: Querry dipti lele (Wed Aug 27 2008 - 04:00:46 CDT)
    - Re: AMBER: Querry Carlos Simmerling (Wed Aug 27 2008 - 08:20:55 CDT)
    - Re: AMBER: Querry dipti lele (Wed Aug 27 2008 - 08:33:45 CDT)
AMBER: Bennett acceptance ratio with Amber10 Samuel Genheden (a03samge) (Tue Aug 26 2008 - 06:58:13 CDT)
- Re: AMBER: Bennett acceptance ratio with Amber10 steinbrt_at_scripps.edu (Tue Aug 26 2008 - 08:45:55 CDT)
  - RE: AMBER: Bennett acceptance ratio with Amber10 Samuel Genheden (a03samge) (Wed Aug 27 2008 - 01:04:28 CDT)
    - RE: AMBER: Bennett acceptance ratio with Amber10 steinbrt_at_scripps.edu (Wed Aug 27 2008 - 11:28:13 CDT)
AMBER: latest update on residuegen Junmei Wang (Tue Aug 26 2008 - 08:55:09 CDT)
AMBER: Source FIles of SANDER Maicon Sartin (Tue Aug 26 2008 - 14:17:39 CDT)
- Re: AMBER: Source FIles of SANDER Carlos Simmerling (Tue Aug 26 2008 - 14:20:40 CDT)
AMBER: Source FIles of SANDER Maicon Sartin (Tue Aug 26 2008 - 14:17:39 CDT)
Re: AMBER: Source FIles of SANDER Bill Ross (Tue Aug 26 2008 - 14:28:34 CDT)
- Re: AMBER: Source FIles of SANDER Maicon Sartin (Tue Aug 26 2008 - 18:18:49 CDT)
  - Re: AMBER: Source FIles of SANDER Carlos Simmerling (Tue Aug 26 2008 - 18:21:31 CDT)
    - RE: AMBER: Source FIles of SANDER Ross Walker (Tue Aug 26 2008 - 18:57:55 CDT)
    - Re: AMBER: Source FIles of SANDER Maicon Sartin (Wed Aug 27 2008 - 07:47:47 CDT)
AMBER: net charge Gigil Toton (Wed Aug 27 2008 - 00:03:19 CDT)
AMBER: coordinate change of pdb structure using xleap Henrik Öberg (Wed Aug 27 2008 - 01:26:42 CDT)
- Re: AMBER: coordinate change of pdb structure using xleap saurabh agrawal (Wed Aug 27 2008 - 02:23:09 CDT)
AMBER: constant ph (cpinutil file) shubhra srivastava (Wed Aug 27 2008 - 01:46:36 CDT)
AMBER: querry dipti lele (Wed Aug 27 2008 - 04:07:52 CDT)
AMBER: MM-PBSA multiple trajectory problem Carra, Claudio (JSC-SK)[USRA] (Wed Aug 27 2008 - 09:16:38 CDT)
AMBER: solvent interaction in active site Hakkim Boy (Wed Aug 27 2008 - 21:41:24 CDT)
- Re: AMBER: solvent interaction in active site Carlos Simmerling (Mon Sep 01 2008 - 08:49:20 CDT)
  - Re: AMBER: solvent interaction in active site S.Sundar Raman (Mon Sep 01 2008 - 09:28:10 CDT)
AMBER: Membrane simulations priya priya (Thu Aug 28 2008 - 03:31:57 CDT)
AMBER: to understand how frcmod.ff99SB works Alan (Thu Aug 28 2008 - 05:29:18 CDT)
- Re: AMBER: to understand how frcmod.ff99SB works Melinda Layten (Thu Aug 28 2008 - 09:55:40 CDT)
- RE: AMBER: to understand how frcmod.ff99SB works Ross Walker (Thu Aug 28 2008 - 11:59:09 CDT)
  - Re: AMBER: to understand how frcmod.ff99SB works Alan (Thu Aug 28 2008 - 13:36:55 CDT)
  - RE: AMBER: to understand how frcmod.ff99SB works Ilyas Yildirim (Thu Aug 28 2008 - 16:58:03 CDT)
    - Re: AMBER: to understand how frcmod.ff99SB works Alan (Fri Aug 29 2008 - 04:00:01 CDT)
    - RE: AMBER: to understand how frcmod.ff99SB works Ross Walker (Fri Aug 29 2008 - 10:17:27 CDT)
AMBER: output file format in SANDER.MPI & PMEMD fatima.chami_at_durham.ac.uk (Thu Aug 28 2008 - 05:47:17 CDT)
- Re: AMBER: output file format in SANDER.MPI & PMEMD Robert Duke (Thu Aug 28 2008 - 07:34:44 CDT)
  - Re: AMBER: output file format in SANDER.MPI & PMEMD fatima.chami_at_durham.ac.uk (Thu Aug 28 2008 - 07:53:42 CDT)
- RE: AMBER: output file format in SANDER.MPI & PMEMD Ross Walker (Thu Aug 28 2008 - 12:09:38 CDT)
AMBER: Critical patch for pmemd 10 extra points code Robert Duke (Thu Aug 28 2008 - 10:20:59 CDT)
- Re: AMBER: Critical patch for pmemd 10 extra points code Carlos Simmerling (Sun Aug 31 2008 - 08:54:33 CDT)
  - Re: AMBER: Critical patch for pmemd 10 extra points code Robert Duke (Sun Aug 31 2008 - 11:48:56 CDT)
AMBER: RE: Personal favor Ross Walker (Thu Aug 28 2008 - 11:39:59 CDT)
- Re: AMBER: RE: Personal favor fatima.chami_at_durham.ac.uk (Mon Sep 01 2008 - 06:29:46 CDT)
AMBER: conversion from crd to netcdf returns almost identical file! Jose Borreguero (Thu Aug 28 2008 - 15:38:50 CDT)
AMBER: Problem in calculation of resp charges using RED III moitrayee_at_mbu.iisc.ernet.in (Fri Aug 29 2008 - 01:56:24 CDT)
- Re: AMBER: Problem in calculation of resp charges using RED III FyD (Fri Aug 29 2008 - 02:50:42 CDT)
  - Re: AMBER: Problem in calculation of resp charges using RED III moitrayee_at_mbu.iisc.ernet.in (Fri Aug 29 2008 - 06:41:21 CDT)
    - Re: AMBER: Problem in calculation of resp charges using RED III FyD (Fri Aug 29 2008 - 10:19:23 CDT)
AMBER: Solvent Accesible Surface Area (SASA) - Confused Deepangi Pandit (Fri Aug 29 2008 - 13:45:19 CDT)
AMBER: wrapping w/ ptraj Arturas Ziemys (Fri Aug 29 2008 - 16:57:52 CDT)
AMBER: compilation problem john smith (Sat Aug 30 2008 - 06:51:07 CDT)
- RE: AMBER: compilation problem Ross Walker (Sat Aug 30 2008 - 13:33:13 CDT)
  - Re: AMBER: compilation problem john smith (Tue Sep 02 2008 - 05:03:14 CDT)
- Re: AMBER: compilation problem Manikandan Chandrasekaran (Fri Sep 26 2008 - 22:51:50 CDT)
  - Re: AMBER: compilation problem David A. Case (Sat Sep 27 2008 - 07:29:53 CDT)
AMBER: vlimit exceeded Wang,Ying (Sat Aug 30 2008 - 10:49:03 CDT)
- RE: AMBER: vlimit exceeded Ross Walker (Sat Aug 30 2008 - 13:41:02 CDT)
- RE: AMBER: vlimit exceeded Wang,Ying (Sat Aug 30 2008 - 18:14:21 CDT)
AMBER: RESP charges fitting for polarizable force fields Grange Hermitage (Sat Aug 30 2008 - 23:48:37 CDT)
AMBER: AMBER under cygwin on 64 bit Vista Charles Letner, Ph.D. (Sun Aug 31 2008 - 16:30:08 CDT)
AMBER: tleap and Zn parameter Aust, Susanne (Mon Sep 01 2008 - 03:14:53 CDT)
- Re: AMBER: tleap and Zn parameter David A. Case (Mon Sep 01 2008 - 08:53:26 CDT)
AMBER: ptraj and netcdf with AmberTools1.2 ? Lars Skjærven (Mon Sep 01 2008 - 04:11:23 CDT)
- Re: AMBER: ptraj and netcdf with AmberTools1.2 ? Dave Rogers (Wed Nov 05 2008 - 15:34:21 CST)
  - Re: AMBER: ptraj and netcdf with AmberTools1.2 ? David A. Case (Thu Nov 06 2008 - 06:08:00 CST)
AW: AMBER: tleap and Zn parameter Aust, Susanne (Tue Sep 02 2008 - 01:46:23 CDT)
- Re: AMBER: tleap and Zn parameter David A. Case (Tue Sep 02 2008 - 15:41:21 CDT)
AMBER: mmpbsa Henrik Öberg (Tue Sep 02 2008 - 06:36:55 CDT)
- Re: AMBER: mmpbsa Neha Gandhi (Tue Sep 02 2008 - 07:49:33 CDT)
- Re: AMBER: mmpbsa Matthew Peterson (Tue Sep 02 2008 - 08:57:24 CDT)
  - RE: AMBER: mmpbsa Henrik Öberg (Tue Sep 02 2008 - 09:18:56 CDT)
AMBER: AMBER9 installation problen with open mpi saurabh agrawal (Tue Sep 02 2008 - 06:41:55 CDT)
- Re: AMBER: AMBER9 installation problen with open mpi Vlad Cojocaru (Tue Sep 02 2008 - 07:00:33 CDT)
  - Re: AMBER: AMBER9 installation problen with open mpi saurabh agrawal (Wed Sep 03 2008 - 09:55:31 CDT)
    - RE: AMBER: AMBER9 installation problen with open mpi Ross Walker (Wed Sep 03 2008 - 10:35:43 CDT)
AMBER: ptraj & imaging of velocities FyD (Tue Sep 02 2008 - 08:06:08 CDT)
- Re: AMBER: ptraj & imaging of velocities Lars Skjærven (Tue Sep 02 2008 - 08:15:49 CDT)
AMBER: a question about matrix command? TaoPaul (Tue Sep 02 2008 - 20:01:04 CDT)
AMBER: MM_PBSA - SASA - Question Deepangi Pandit (Tue Sep 02 2008 - 21:10:13 CDT)
AW: AMBER: tleap and Zn parameter Aust, Susanne (Wed Sep 03 2008 - 02:18:28 CDT)
- RE: AMBER: tleap and Zn parameter Ross Walker (Wed Sep 03 2008 - 10:31:26 CDT)
AMBER: Need help... High energies for complex... Waqas Nasir (Wed Sep 03 2008 - 06:20:01 CDT)
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Wed Sep 03 2008 - 06:27:06 CDT)
AMBER: help...ptraj does not output bounding box info Jose Borreguero (Wed Sep 03 2008 - 10:39:41 CDT)
- Re: AMBER: help...ptraj does not output bounding box info Carlos Simmerling (Wed Sep 03 2008 - 10:41:48 CDT)
  - Re: AMBER: help...ptraj does not output bounding box info Jose Borreguero (Wed Sep 03 2008 - 11:12:30 CDT)
- Re: AMBER: help...ptraj does not output bounding box info Bill Ross (Wed Sep 03 2008 - 11:22:18 CDT)
AMBER: Marisa Frechero (Wed Sep 03 2008 - 13:38:06 CDT)
- RE: AMBER: Ross Walker (Wed Sep 03 2008 - 16:14:21 CDT)
  - RE: AMBER: Install problems Marisa Frechero (Mon Sep 08 2008 - 13:35:08 CDT)
AMBER: matrix correl Steve Seibold (Wed Sep 03 2008 - 13:40:28 CDT)
AMBER: nmode units Arturas Ziemys (Wed Sep 03 2008 - 17:28:44 CDT)
- Re: AMBER: nmode units Chris Moth (Wed Sep 03 2008 - 18:10:19 CDT)
  - Re: AMBER: nmode units Arturas Ziemys (Thu Sep 04 2008 - 09:26:57 CDT)
    - Re: AMBER: nmode units David A. Case (Thu Sep 04 2008 - 09:58:22 CDT)
    - Re: AMBER: nmode units Arturas Ziemys (Thu Sep 04 2008 - 10:22:41 CDT)
AMBER: mmpbsa molsurf.c error Ilyas Yildirim (Wed Sep 03 2008 - 18:56:59 CDT)
- Re: AMBER: mmpbsa molsurf.c error Ilyas Yildirim (Thu Sep 04 2008 - 19:45:58 CDT)
  - Re: AMBER: mmpbsa molsurf.c error David A. Case (Wed Sep 17 2008 - 07:10:40 CDT)
    - Re: AMBER: mmpbsa molsurf.c error parvesh singh (Mon Sep 22 2008 - 04:26:29 CDT)
AMBER: No bond and angle parameters for - -????? Waqas Nasir (Thu Sep 04 2008 - 05:15:37 CDT)
- Re: AMBER: No bond and angle parameters for - -????? Lachele Foley (Lists) (Thu Sep 04 2008 - 09:03:08 CDT)
AMBER: Need help... High energies for complex... Waqas Nasir (Thu Sep 04 2008 - 05:38:53 CDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Wed Sep 03 2008 - 06:45:20 CDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Wed Sep 03 2008 - 07:04:07 CDT)
    - Re: AMBER: Need help... High energies for complex... Neha Gandhi (Wed Sep 03 2008 - 07:41:16 CDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Thu Sep 04 2008 - 05:08:49 CDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Thu Sep 04 2008 - 05:39:48 CDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Thu Sep 04 2008 - 09:12:21 CDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Thu Sep 04 2008 - 09:33:32 CDT)
    - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Thu Sep 04 2008 - 09:35:02 CDT)
  - Re: AMBER: Need help... High energies for complex... David A. Case (Thu Sep 04 2008 - 09:36:37 CDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Thu Sep 04 2008 - 10:22:55 CDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Thu Sep 04 2008 - 10:41:38 CDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Thu Sep 04 2008 - 11:14:35 CDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Thu Sep 04 2008 - 11:21:42 CDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Fri Sep 05 2008 - 04:15:59 CDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Fri Sep 05 2008 - 05:07:01 CDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Mon Sep 08 2008 - 11:06:26 CDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Mon Sep 08 2008 - 11:45:51 CDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Tue Sep 09 2008 - 08:16:29 CDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Tue Sep 09 2008 - 09:06:18 CDT)
AMBER: antechamber cannot generate prep files moitrayee_at_mbu.iisc.ernet.in (Thu Sep 04 2008 - 06:47:17 CDT)
AMBER: help... structure factors from amber trajectories? Jose Borreguero (Thu Sep 04 2008 - 12:35:57 CDT)
AMBER: resp and 99999 Markus Kaukonen (Fri Sep 05 2008 - 01:13:10 CDT)
- RE: AMBER: resp and 99999 Ross Walker (Fri Sep 05 2008 - 09:31:51 CDT)
AMBER: ESURF - SASA - isolate residues Deepangi Pandit (Fri Sep 05 2008 - 09:23:23 CDT)
AMBER: help...sander "segmentation fault" after 2hours of minimization Jose Borreguero (Fri Sep 05 2008 - 10:06:42 CDT)
- Re: AMBER: help...sander "segmentation fault" after 2hours of minimization David A. Case (Fri Sep 05 2008 - 10:20:40 CDT)
  - Re: AMBER: help...sander "segmentation fault" after 2hours of minimization Jose Borreguero (Fri Sep 05 2008 - 10:43:39 CDT)
    - RE: AMBER: help...sander "segmentation fault" after 2hours of minimization Ross Walker (Fri Sep 05 2008 - 11:07:27 CDT)
- RE: AMBER: help...sander "segmentation fault" after 2hours of minimization Ross Walker (Fri Sep 05 2008 - 10:23:42 CDT)
  - Re: AMBER: help...sander "segmentation fault" after 2hours of minimization Jose Borreguero (Fri Sep 05 2008 - 11:26:23 CDT)
    - RE: AMBER: help...sander "segmentation fault" after 2hours of minimization Ross Walker (Fri Sep 05 2008 - 12:02:30 CDT)
AMBER: error when using tleap with leaprc.ff02EP Yongmei Pan (Fri Sep 05 2008 - 10:49:38 CDT)
- RE: AMBER: error when using tleap with leaprc.ff02EP Ross Walker (Fri Sep 05 2008 - 11:06:13 CDT)
AMBER: RE: reference paper - pls help Ross Walker (Fri Sep 05 2008 - 11:37:24 CDT)
- AMBER: Question: GAFF Chih-Ying Lin (Fri Sep 05 2008 - 16:33:14 CDT)
  - AMBER: QM/MM Chih-Ying Lin (Fri Sep 05 2008 - 17:33:23 CDT)
AMBER: mm_pbsa error : Scale paremeter for PBSA CHAMI F. (Fri Sep 05 2008 - 12:26:46 CDT)
- RE: AMBER: mm_pbsa error : Scale paremeter for PBSA Ray Luo (Fri Sep 05 2008 - 12:45:12 CDT)
AMBER: Problem in EVB and Trajectory analysis sai kumar ramadugu (Fri Sep 05 2008 - 16:20:17 CDT)
AMBER: Explanation of the energy unit ? Marek Malý (Sat Sep 06 2008 - 09:29:06 CDT)
- Re: AMBER: Explanation of the energy unit ? David A. Case (Sun Sep 07 2008 - 17:12:22 CDT)
  - Re: AMBER: Explanation of the energy unit ? Marek Malý (Mon Sep 08 2008 - 10:01:10 CDT)
AMBER: Test error in installing amber 10 using four threads on a single-cpu machine haixiao jin (Sun Sep 07 2008 - 04:42:10 CDT)
- Re: AMBER: Test error in installing amber 10 using four threads on a single-cpu machine David A. Case (Sun Sep 07 2008 - 07:50:57 CDT)
  - Re: AMBER: Test error in installing amber 10 using four threads on a single-cpu machine haixiao jin (Sun Sep 07 2008 - 08:26:31 CDT)
    - Re: AMBER: Test error in installing amber 10 using four threads on a single-cpu machine David A. Case (Sun Sep 07 2008 - 17:07:14 CDT)
AMBER: PMEMD installation problem. Cenk $Jenk$ Andac (Mon Sep 08 2008 - 01:58:42 CDT)
- RE: AMBER: PMEMD installation problem. Ross Walker (Mon Sep 08 2008 - 03:21:17 CDT)
  - RE: AMBER: PMEMD installation problem. Cenk $Jenk$ Andac (Mon Sep 08 2008 - 04:16:38 CDT)
    - Re: AMBER: PMEMD installation problem. Robert Duke (Mon Sep 08 2008 - 07:20:15 CDT)
    - Re: AMBER: PMEMD installation problem. Cenk $Jenk$ Andac (Mon Sep 08 2008 - 07:46:19 CDT)
AMBER: amber minimisation Majeed Shaik (Mon Sep 08 2008 - 07:32:17 CDT)
- Re: AMBER: amber minimisation Carlos Simmerling (Mon Sep 08 2008 - 07:40:44 CDT)
- Re: AMBER: amber minimisation David A. Case (Mon Sep 08 2008 - 07:59:26 CDT)
AMBER: Changes in the Amber web site David A. Case (Mon Sep 08 2008 - 08:25:41 CDT)
- RE: AMBER: Changes in the Amber web site Majeed Shaik (Mon Sep 08 2008 - 10:07:21 CDT)
  - Re: AMBER: Changes in the Amber web site Carlos Simmerling (Mon Sep 08 2008 - 10:14:33 CDT)
AMBER: problem when running energy minimization with polarizable potential Yongmei Pan (Mon Sep 08 2008 - 10:32:30 CDT)
- Re: AMBER: problem when running energy minimization with polarizable potential David A. Case (Tue Sep 09 2008 - 13:32:27 CDT)
  - Re: AMBER: problem when running energy minimization with polarizable potential Yongmei Pan (Tue Sep 09 2008 - 15:36:33 CDT)
AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors Ben Roberts (Mon Sep 08 2008 - 10:43:47 CDT)
- Re: AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors David A. Case (Mon Sep 08 2008 - 16:09:53 CDT)
  - Re: AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors Ben Roberts (Mon Sep 08 2008 - 16:24:30 CDT)
    - Re: AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors Ben Roberts (Tue Sep 09 2008 - 12:38:56 CDT)
AMBER: Another problem when trying to compile Sander in debug mode Ben Roberts (Mon Sep 08 2008 - 10:49:52 CDT)
AMBER: who can give a sample input file regarding the energy decomposition with sander? Yongmei Pan (Mon Sep 08 2008 - 15:41:37 CDT)
- Re: AMBER: who can give a sample input file regarding the energy decomposition with sander? David A. Case (Mon Sep 08 2008 - 16:31:50 CDT)
AMBER: NAB parameter: wcons ramu_at_vt.edu (Mon Sep 08 2008 - 16:06:54 CDT)
- Re: AMBER: NAB parameter: wcons David A. Case (Wed Sep 10 2008 - 07:19:32 CDT)
AMBER: energy decomposition with sander? Yongmei Pan (Mon Sep 08 2008 - 16:32:32 CDT)
AMBER: PMEMD and sander.MPI Germain Vallverdu (Tue Sep 09 2008 - 08:50:40 CDT)
- Re: AMBER: PMEMD and sander.MPI Robert Duke (Tue Sep 09 2008 - 09:14:52 CDT)
AMBER: Amber10 Compilation Anthony Cruz (Tue Sep 09 2008 - 09:26:04 CDT)
- AMBER: D2O Chih-Ying Lin (Tue Sep 09 2008 - 12:00:59 CDT)
  - Re: AMBER: D2O Carlos Simmerling (Tue Sep 09 2008 - 13:08:37 CDT)
  - Re: AMBER: D2O David A. Case (Tue Sep 09 2008 - 13:21:37 CDT)
- RE: AMBER: Amber10 Compilation Ross Walker (Wed Sep 10 2008 - 07:31:47 CDT)
AMBER: about NMR refinement in explicit solvent Rogelio Hernández (Tue Sep 09 2008 - 14:15:19 CDT)
- Re: AMBER: about NMR refinement in explicit solvent David A. Case (Thu Sep 11 2008 - 12:24:37 CDT)
AMBER: Emperical Valence Bond sai kumar ramadugu (Tue Sep 09 2008 - 16:46:25 CDT)
AMBER: Preparing peptides with D-amino acids David Watson (Tue Sep 09 2008 - 19:06:58 CDT)
- Re: AMBER: Preparing peptides with D-amino acids Carlos Simmerling (Tue Sep 09 2008 - 19:26:20 CDT)
  - Re: AMBER: Preparing peptides with D-amino acids Carlos Simmerling (Tue Sep 09 2008 - 19:28:08 CDT)
    - Re: AMBER: Preparing peptides with D-amino acids David Watson (Tue Sep 09 2008 - 20:04:44 CDT)
    - Re: AMBER: Preparing peptides with D-amino acids Carlos Simmerling (Tue Sep 09 2008 - 20:14:34 CDT)
AMBER: RDF: Segmentation fault Sergey Samsonov (Wed Sep 10 2008 - 03:13:29 CDT)
AMBER: steered MD Germain Vallverdu (Wed Sep 10 2008 - 05:26:31 CDT)
- Re: AMBER: steered MD Carlos Simmerling (Wed Sep 10 2008 - 05:32:02 CDT)
  - Re: AMBER: steered MD Germain Vallverdu (Wed Sep 10 2008 - 06:17:10 CDT)
- Re: AMBER: steered MD David A. Case (Wed Sep 10 2008 - 06:30:27 CDT)
AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik (Wed Sep 10 2008 - 09:54:58 CDT)
- RE: AMBER: Cutoff list exceeds largest sphere in unit cell Ross Walker (Wed Sep 10 2008 - 11:01:18 CDT)
  - RE: AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik (Wed Sep 10 2008 - 12:42:58 CDT)
    - RE: AMBER: Cutoff list exceeds largest sphere in unit cell Ross Walker (Wed Sep 10 2008 - 15:08:53 CDT)
    - RE: AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik (Thu Sep 11 2008 - 06:49:09 CDT)
  - RE: AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik (Wed Sep 10 2008 - 12:44:52 CDT)
AMBER: Nonbonded FE parameter missing in frcmod. moitrayee_at_mbu.iisc.ernet.in (Thu Sep 11 2008 - 07:22:58 CDT)
- Re: AMBER: Nonbonded FE parameter missing in frcmod. David A. Case (Thu Sep 11 2008 - 12:19:53 CDT)
  - Re: AMBER: Nonbonded FE parameter missing in frcmod. moitrayee_at_mbu.iisc.ernet.in (Thu Sep 11 2008 - 12:16:34 CDT)
AMBER: Help...which commands in ptraj does clustering by RMSD? Jose Borreguero (Thu Sep 11 2008 - 15:28:49 CDT)
- Re: AMBER: Help...which commands in ptraj does clustering by RMSD? Sasha Buzko (Thu Sep 11 2008 - 15:39:44 CDT)
  - Re: AMBER: Help...which commands in ptraj does clustering by RMSD? Jose Borreguero (Thu Sep 11 2008 - 16:12:00 CDT)
AMBER: EVB allocation problem sai kumar ramadugu (Fri Sep 12 2008 - 11:08:41 CDT)
AMBER: Comment: constant pH, non-integer charge -> weird error Markus Kaukonen (Sun Sep 14 2008 - 02:51:58 CDT)
AMBER: mulliken charges in QM/MM calculation Barbault Florent (Sun Sep 14 2008 - 03:26:25 CDT)
- RE: AMBER: mulliken charges in QM/MM calculation Ross Walker (Sun Sep 14 2008 - 03:44:00 CDT)
AMBER: Failure of antechamber in amber10 Francesco Pietra (Sun Sep 14 2008 - 09:18:49 CDT)
AMBER: problem in installing parallel version of amber10 with lam Shibasish Chowdhury (Sun Sep 14 2008 - 23:20:12 CDT)
- RE: AMBER: problem in installing parallel version of amber10 with lam Ross Walker (Mon Sep 15 2008 - 21:02:48 CDT)
- RE: AMBER: problem in installing parallel version of amber10 with lam Shibasish Chowdhury (Tue Sep 16 2008 - 05:37:06 CDT)
AMBER: 3fe-4s cluster parameter file generation moitrayee_at_mbu.iisc.ernet.in (Mon Sep 15 2008 - 01:35:39 CDT)
- Re: AMBER: 3fe-4s cluster parameter file generation David A. Case (Mon Sep 15 2008 - 06:15:52 CDT)
  - Re: AMBER: 3fe-4s cluster parameter file generation moitrayee_at_mbu.iisc.ernet.in (Mon Sep 15 2008 - 06:20:19 CDT)
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross (Mon Sep 15 2008 - 13:51:29 CDT)
  - Re: AMBER: 3fe-4s cluster parameter file generation moitrayee_at_mbu.iisc.ernet.in (Tue Sep 16 2008 - 06:39:25 CDT)
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross (Tue Sep 16 2008 - 12:47:00 CDT)
  - Re: AMBER: 3fe-4s cluster parameter file generation moitrayee_at_mbu.iisc.ernet.in (Tue Sep 16 2008 - 13:01:59 CDT)
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross (Tue Sep 16 2008 - 14:15:52 CDT)
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross (Tue Sep 16 2008 - 14:36:24 CDT)
  - Re: AMBER: 3fe-4s cluster parameter file generation moitrayee_at_mbu.iisc.ernet.in (Wed Sep 17 2008 - 01:43:49 CDT)
    - Re: AMBER: 3fe-4s cluster parameter file generation David A. Case (Wed Sep 17 2008 - 06:26:07 CDT)
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross (Wed Sep 17 2008 - 12:41:28 CDT)
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross (Wed Sep 17 2008 - 13:04:32 CDT)
AMBER: question about dihedral angles Harry (Yicun) Ni (Mon Sep 15 2008 - 09:41:31 CDT)
- Re: AMBER: question about dihedral angles Ilyas Yildirim (Mon Sep 15 2008 - 10:10:55 CDT)
AMBER: Hydrogen bond energies in explicit solvent. Waqas Nasir (Mon Sep 15 2008 - 09:56:34 CDT)
- Re: AMBER: Hydrogen bond energies in explicit solvent. Carlos Simmerling (Mon Sep 15 2008 - 10:01:41 CDT)
- Re: AMBER: Hydrogen bond energies in explicit solvent. Waqas Nasir (Mon Sep 15 2008 - 10:47:00 CDT)
  - Re: AMBER: Hydrogen bond energies in explicit solvent. Carlos Simmerling (Mon Sep 15 2008 - 10:54:25 CDT)
- Re: AMBER: Hydrogen bond energies in explicit solvent. Waqas Nasir (Mon Sep 15 2008 - 11:17:04 CDT)
  - Re: AMBER: Hydrogen bond energies in explicit solvent. Carlos Simmerling (Mon Sep 15 2008 - 11:24:07 CDT)
AMBER: Minimizaton stops after Ncyc steps only mon_sharma_at_research.iiit.ac.in (Mon Sep 15 2008 - 11:34:22 CDT)
- Re: AMBER: Minimizaton stops after Ncyc steps only Carlos Simmerling (Mon Sep 15 2008 - 12:23:00 CDT)
AMBER: Announcement of ACS COMP Division CCG and HP award deadlines for Spring 2009 meeting Carlos Simmerling (Mon Sep 15 2008 - 11:39:58 CDT)
AMBER: parallel amber 10 sander.MPI (low cpu utilization) meandme meandme (Mon Sep 15 2008 - 12:27:06 CDT)
AMBER: amber 10 parallel cpu utlization meandme meandme (Mon Sep 15 2008 - 12:30:49 CDT)
- RE: AMBER: amber 10 parallel cpu utlization Ross Walker (Mon Sep 15 2008 - 21:09:37 CDT)
AMBER: AMBER10 Compilation (SGI Altix) Anthony Cruz (Mon Sep 15 2008 - 13:21:49 CDT)
- RE: AMBER: AMBER10 Compilation (SGI Altix) Ross Walker (Mon Sep 15 2008 - 21:15:54 CDT)
  - Re: AMBER: AMBER10 Compilation (SGI Altix) Anthony Cruz (Tue Sep 16 2008 - 11:56:45 CDT)
AMBER: MM-PBSA/NMODE in Amber 10 Peterson, Matthew W. (MPETERSON) (Mon Sep 15 2008 - 15:37:41 CDT)
- Re: AMBER: MM-PBSA/NMODE in Amber 10 Daniel Oehme (Mon Sep 15 2008 - 20:23:26 CDT)
- Re: AMBER: MM-PBSA/NMODE in Amber 10 Daniel Oehme (Mon Sep 22 2008 - 02:13:55 CDT)
AMBER: Temperature regulation julliane Yoneda (Mon Sep 15 2008 - 19:48:50 CDT)
- Re: AMBER: Temperature regulation Carlos Simmerling (Mon Sep 15 2008 - 20:07:57 CDT)
  - Re: AMBER: Temperature regulation julliane Yoneda (Tue Sep 16 2008 - 13:05:27 CDT)
  - Re: AMBER: Temperature regulation julliane Yoneda (Wed Oct 01 2008 - 12:22:06 CDT)
AMBER: top and crd files without hydrogen Waqas Nasir (Tue Sep 16 2008 - 04:18:08 CDT)
- Re: AMBER: top and crd files without hydrogen Carlos Simmerling (Tue Sep 16 2008 - 05:04:36 CDT)
- Re: AMBER: top and crd files without hydrogen Waqas Nasir (Tue Sep 16 2008 - 05:32:42 CDT)
- Re: AMBER: top and crd files without hydrogen Waqas Nasir (Tue Sep 16 2008 - 05:32:42 CDT)
AMBER: nmode/nab entropy calculations memory issues chaitanya koppisetty (Tue Sep 16 2008 - 09:58:01 CDT)
- Re: AMBER: nmode/nab entropy calculations memory issues Andreas Svrcek-Seiler (Tue Sep 16 2008 - 10:50:11 CDT)
  - AMBER: nmode/nab entropy calculations without hydrogens chaitanya koppisetty (Wed Sep 17 2008 - 02:47:58 CDT)
AMBER: problem with editing with xleap moitrayee_at_mbu.iisc.ernet.in (Tue Sep 16 2008 - 10:50:38 CDT)
- Re: AMBER: problem with editing with xleap David A. Case (Wed Sep 17 2008 - 06:30:55 CDT)
AMBER: AMBER9 Compilation chen bents (Tue Sep 16 2008 - 20:25:59 CDT)
AMBER: amber 9 install chen bents (Tue Sep 16 2008 - 22:14:47 CDT)
- Re: AMBER: amber 9 install Ye Mei (Tue Sep 16 2008 - 22:26:07 CDT)
  - Re: AMBER: amber 9 install chen bents (Wed Sep 17 2008 - 02:44:46 CDT)
AMBER: acetone box parvesh singh (Wed Sep 17 2008 - 06:09:01 CDT)
AMBER: Question Beale, John (Wed Sep 17 2008 - 06:14:15 CDT)
- Re: AMBER: Question Carlos Simmerling (Wed Sep 17 2008 - 06:18:19 CDT)
AMBER: MD simulation crashed Aust, Susanne (Wed Sep 17 2008 - 08:10:17 CDT)
- Re: AMBER: MD simulation crashed Carlos Simmerling (Wed Sep 17 2008 - 08:27:59 CDT)
AMBER: adding new potential function Harianto Tjong (Wed Sep 17 2008 - 14:12:34 CDT)
AMBER: Some Problems With the Installation of Ambertools Manikandan Chandrasekaran (Wed Sep 17 2008 - 18:21:06 CDT)
- Re: AMBER: Some Problems With the Installation of Ambertools Atro Tossavainen (Thu Sep 18 2008 - 03:06:57 CDT)
- Re: AMBER: Some Problems With the Installation of Ambertools David A. Case (Thu Sep 18 2008 - 06:10:12 CDT)
  - Re: AMBER: Some Problems With the Installation of Ambertools Manikandan Chandrasekaran (Thu Sep 18 2008 - 11:43:39 CDT)
AMBER: Dihedral: ptraj waqasuddin.khan_at_iccs.edu (Thu Sep 18 2008 - 01:39:33 CDT)
- Re: AMBER: Dihedral: ptraj Carlos Simmerling (Thu Sep 18 2008 - 04:04:24 CDT)
  - Re: AMBER: Dihedral: ptraj waqasuddin.khan_at_iccs.edu (Thu Sep 18 2008 - 04:14:50 CDT)
    - Re: AMBER: Dihedral: ptraj Carlos Simmerling (Thu Sep 18 2008 - 04:32:38 CDT)
AMBER: Single point energy calculations with explicit solvent. Waqas Nasir (Thu Sep 18 2008 - 07:48:47 CDT)
- Re: AMBER: Single point energy calculations with explicit solvent. Carlos Simmerling (Thu Sep 18 2008 - 07:55:00 CDT)
AMBER: problem with traj and strip waters Steve Seibold (Thu Sep 18 2008 - 08:08:21 CDT)
- Re: AMBER: problem with traj and strip waters Carlos Simmerling (Thu Sep 18 2008 - 08:19:17 CDT)
- Re: AMBER: problem with traj and strip waters David A. Case (Thu Sep 18 2008 - 08:34:18 CDT)
AMBER: problem with traj and strip waters Steve Seibold (Thu Sep 18 2008 - 09:13:38 CDT)
- Re: AMBER: problem with traj and strip waters Carlos Simmerling (Thu Sep 18 2008 - 09:22:30 CDT)
AMBER: Error: PB bomb in pb_reslist(): maxnbr too small Rajendra P. OJHA (Thu Sep 18 2008 - 09:34:15 CDT)
AMBER: RMSD restraint in umbrella sampling nurith_at_rice.edu (Thu Sep 18 2008 - 15:36:24 CDT)
- Re: AMBER: RMSD restraint in umbrella sampling Carlos Simmerling (Thu Sep 18 2008 - 16:23:01 CDT)
AMBER: help can amber couple part of the system to different heat bath? Jose Borreguero (Thu Sep 18 2008 - 16:09:27 CDT)
AMBER: problems with ptraj and strip waters Steve Seibold (Thu Sep 18 2008 - 16:19:25 CDT)
- Re: AMBER: problems with ptraj and strip waters Carlos Simmerling (Thu Sep 18 2008 - 16:29:56 CDT)
- Re: AMBER: problems with ptraj and strip waters Gustavo Seabra (Thu Sep 18 2008 - 18:18:44 CDT)
AMBER: help can amber couple part of the system to different heat bath? Jose Borreguero (Thu Sep 18 2008 - 16:09:23 CDT)
AMBER: increasing temperature smoothly Germain Vallverdu (Fri Sep 19 2008 - 10:17:56 CDT)
- Re: AMBER: increasing temperature smoothly David A. Case (Fri Sep 19 2008 - 11:49:46 CDT)
- RE: AMBER: increasing temperature smoothly Ross Walker (Fri Sep 19 2008 - 13:29:31 CDT)
  - Re: AMBER: increasing temperature smoothly Germain Vallverdu (Mon Sep 22 2008 - 04:00:19 CDT)
- Re: AMBER: increasing temperature smoothly Germain Vallverdu (Mon Sep 22 2008 - 06:31:56 CDT)
  - Re: AMBER: increasing temperature smoothly David A. Case (Mon Sep 22 2008 - 06:44:02 CDT)
AMBER: molecule drift out of water box? Qiuting Hong (Fri Sep 19 2008 - 18:39:42 CDT)
- Re: AMBER: molecule drift out of water box? Ilyas Yildirim (Fri Sep 19 2008 - 19:00:03 CDT)
  - Re: AMBER: molecule drift out of water box? Qiuting Hong (Sun Sep 21 2008 - 15:22:19 CDT)
AMBER: Dihedral Drive Hashem Taha (Sat Sep 20 2008 - 02:31:13 CDT)
- Re: AMBER: Dihedral Drive Ilyas Yildirim (Sat Sep 20 2008 - 03:07:07 CDT)
AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber? Zhao, Zhen (zhaozh) (Sat Sep 20 2008 - 15:01:59 CDT)
- Re: AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber? Barbault Florent (Sat Sep 20 2008 - 15:40:34 CDT)
AMBER: bis(trifluoromethylsulfonyl)imide (Tf2N) babak minoofar (Sun Sep 21 2008 - 09:34:39 CDT)
- Re: AMBER: bis(trifluoromethylsulfonyl)imide (Tf2N) David Watson (Sun Sep 21 2008 - 11:01:04 CDT)
AMBER: multiple heat baths in a single simulation? Jose Borreguero (Sun Sep 21 2008 - 18:09:41 CDT)
AMBER: fix for POL3 heating problem? Grange Hermitage (Mon Sep 22 2008 - 04:35:02 CDT)
AMBER: Re: reaction coordinate in umbrella sampling Sudha Mani Karra (Mon Sep 22 2008 - 10:00:42 CDT)
- Re: AMBER: Re: reaction coordinate in umbrella sampling Jerome.GOLEBIOWSKI_at_unice.fr (Tue Sep 23 2008 - 02:33:43 CDT)
AMBER: Position: Postdoctoral Fellow Willy Valdivia-Granda (Mon Sep 22 2008 - 10:50:48 CDT)
AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. Zhao, Zhen (zhaozh) (Mon Sep 22 2008 - 14:02:27 CDT)
- Re: AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. Tom Darden (Mon Sep 22 2008 - 15:51:53 CDT)
  - RE: AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. Zhao, Zhen (zhaozh) (Tue Sep 23 2008 - 09:11:23 CDT)
AMBER: MMPBSA error Cristina Sisu (Tue Sep 23 2008 - 05:30:38 CDT)
AMBER: replica exchange with amber9 greddy1_at_umd.edu (Tue Sep 23 2008 - 17:44:24 CDT)
- Re: AMBER: replica exchange with amber9 Carlos Simmerling (Tue Sep 23 2008 - 17:52:04 CDT)
AMBER: MD goes wrong baohua zhang (Tue Sep 23 2008 - 21:17:57 CDT)
- Re: AMBER: MD goes wrong Adrian Roitberg (Tue Sep 23 2008 - 22:19:19 CDT)
- RE: AMBER: MD goes wrong Ross Walker (Tue Sep 23 2008 - 23:33:43 CDT)
AMBER: to prepare pdb file fro unusual amino acid. priya priya (Wed Sep 24 2008 - 03:03:06 CDT)
- Re: AMBER: to prepare pdb file fro unusual amino acid. Hakkim Boy (Wed Sep 24 2008 - 09:41:33 CDT)
- Re: AMBER: to prepare pdb file fro unusual amino acid. FyD (Wed Sep 24 2008 - 13:36:03 CDT)
- Re: AMBER: to prepare pdb file fro unusual amino acid. waqasuddin.khan_at_iccs.edu (Thu Sep 25 2008 - 00:55:51 CDT)
- RE: AMBER: to prepare pdb file fro unusual amino acid. Ross Walker (Thu Sep 25 2008 - 01:36:08 CDT)
- RE: AMBER: to prepare pdb file fro unusual amino acid. Ross Walker (Thu Sep 25 2008 - 09:55:21 CDT)
- Re: AMBER: to prepare pdb file fro unusual amino acid. priya priya (Thu Sep 25 2008 - 11:40:07 CDT)
AMBER: error while running REMD in amber9 priya priya (Wed Sep 24 2008 - 12:53:09 CDT)
- Re: AMBER: error while running REMD in amber9 Carlos Simmerling (Wed Sep 24 2008 - 13:27:22 CDT)
- Re: AMBER: error while running REMD in amber9 priya priya (Thu Sep 25 2008 - 11:49:28 CDT)
  - Re: AMBER: error while running REMD in amber9 Carlos Simmerling (Thu Sep 25 2008 - 11:55:35 CDT)
- Re: AMBER: error while running REMD in amber9 priya priya (Thu Sep 25 2008 - 12:44:13 CDT)
  - Re: AMBER: error while running REMD in amber9 Carlos Simmerling (Thu Sep 25 2008 - 12:51:58 CDT)
- Re: AMBER: error while running REMD in amber9 priya priya (Thu Sep 25 2008 - 12:44:13 CDT)
- Re: AMBER: error while running REMD in amber9 priya priya (Thu Sep 25 2008 - 13:04:26 CDT)
  - Re: AMBER: error while running REMD in amber9 Carlos Simmerling (Thu Sep 25 2008 - 13:28:17 CDT)
AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support Pablo Englebienne (Wed Sep 24 2008 - 14:04:46 CDT)
- Re: AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support Robert Duke (Wed Sep 24 2008 - 14:39:30 CDT)
  - Re: AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support Pablo Englebienne (Thu Sep 25 2008 - 14:07:48 CDT)
AMBER: solvate without translating Anuradha Mittal (Wed Sep 24 2008 - 14:38:31 CDT)
- RE: AMBER: solvate without translating Ross Walker (Thu Sep 25 2008 - 01:46:52 CDT)
- RE: AMBER: solvate without translating Ross Walker (Thu Sep 25 2008 - 09:55:53 CDT)
AMBER: how to enlarge the TIP3PBOX size Qiuting Hong (Wed Sep 24 2008 - 17:56:10 CDT)
- Re: AMBER: how to enlarge the TIP3PBOX size Carlos Simmerling (Wed Sep 24 2008 - 18:01:44 CDT)
  - AMBER: Amber on Infiniband clusters: SDR vs DDR cables? Sasha Buzko (Thu Sep 25 2008 - 18:06:44 CDT)
- Re: AMBER: how to enlarge the TIP3PBOX size waqasuddin.khan_at_iccs.edu (Thu Sep 25 2008 - 01:01:57 CDT)
- RE: AMBER: how to enlarge the TIP3PBOX size Ross Walker (Thu Sep 25 2008 - 01:40:21 CDT)
  - Re: AMBER: how to enlarge the TIP3PBOX size Qiuting Hong (Fri Sep 26 2008 - 02:28:53 CDT)
    - Re: AMBER: how to enlarge the TIP3PBOX size David A. Case (Fri Sep 26 2008 - 11:06:37 CDT)
- RE: AMBER: how to enlarge the TIP3PBOX size Ross Walker (Thu Sep 25 2008 - 09:55:38 CDT)
AMBER: Amber GB problems on PMEMD !! Sampath Koppole (Thu Sep 25 2008 - 04:09:30 CDT)
- Re: AMBER: Amber GB problems on PMEMD !! Robert Duke (Thu Sep 25 2008 - 07:22:06 CDT)
  - Re: AMBER: Amber GB problems on PMEMD !! Sampath Koppole (Thu Sep 25 2008 - 08:02:42 CDT)
    - Re: AMBER: Amber GB problems on PMEMD !! Andreas Svrcek-Seiler (Thu Sep 25 2008 - 10:12:59 CDT)
- RE: AMBER: Amber GB problems on PMEMD !! Ross Walker (Thu Sep 25 2008 - 10:23:44 CDT)
AMBER: Problem In Paralklel Amber Ranga Swamy (Fri Sep 26 2008 - 06:10:13 CDT)
- Re: AMBER: Problem In Paralklel Amber Carlos Simmerling (Fri Sep 26 2008 - 06:52:00 CDT)
  - Re: AMBER: Problem In Paralklel Amber Ranga Swamy (Mon Sep 29 2008 - 00:23:57 CDT)
    - RE: AMBER: Problem In Paralklel Amber Ross Walker (Mon Sep 29 2008 - 09:35:50 CDT)
AMBER: MD at a given pH Beale, John (Fri Sep 26 2008 - 11:44:32 CDT)
- Re: AMBER: MD at a given pH David A. Case (Sat Sep 27 2008 - 06:53:56 CDT)
AMBER: Harmonic restraint between two atoms greddy1_at_umd.edu (Fri Sep 26 2008 - 13:37:34 CDT)
- Re: AMBER: Harmonic restraint between two atoms Adrian Roitberg (Fri Sep 26 2008 - 13:42:55 CDT)
AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Sat Sep 27 2008 - 08:46:10 CDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type David A. Case (Sat Sep 27 2008 - 09:12:40 CDT)
  - Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Sat Sep 27 2008 - 10:36:47 CDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Carlos Simmerling (Sat Sep 27 2008 - 08:56:22 CDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross (Mon Sep 29 2008 - 13:38:46 CDT)
  - Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Mon Sep 29 2008 - 15:13:05 CDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross (Mon Sep 29 2008 - 17:03:28 CDT)
  - Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Tue Sep 30 2008 - 05:05:13 CDT)
  - Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Thu Oct 02 2008 - 10:47:31 CDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross (Tue Sep 30 2008 - 13:11:12 CDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross (Thu Oct 02 2008 - 12:36:58 CDT)
  - Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Thu Oct 02 2008 - 14:15:54 CDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross (Thu Oct 02 2008 - 15:09:53 CDT)
AMBER: Constant pH simulation force field Soonmin Jang (Sat Sep 27 2008 - 04:13:51 CDT)
- Re: AMBER: Constant pH simulation force field David A. Case (Sat Sep 27 2008 - 07:10:39 CDT)
AMBER: mmpbsa errors in redoing the tutorial A3:MMPBSA haixiao jin (Sat Sep 27 2008 - 02:45:06 CDT)
AMBER: unsubscribe amber steinbrt_at_scripps.edu (Mon Sep 29 2008 - 09:57:50 CDT)
AMBER: Location of vdw radii and partial charges for ff99SB Charles Letner, Ph.D. (Mon Sep 29 2008 - 08:08:27 CDT)
- RE: AMBER: Location of vdw radii and partial charges for ff99SB Ross Walker (Mon Sep 29 2008 - 09:51:44 CDT)
- Re: AMBER: Location of vdw radii and partial charges for ff99SB Carlos Simmerling (Mon Sep 29 2008 - 09:58:45 CDT)
AMBER: energy terms in hybrid REMD calculation Ye Mei (Mon Sep 29 2008 - 04:28:13 CDT)
AMBER: a question Adrien Delmont (Sun Sep 28 2008 - 17:08:00 CDT)
- Re: AMBER: a question Adrien Delmont (Mon Sep 29 2008 - 07:53:51 CDT)
- RE: AMBER: a question Ross Walker (Sun Sep 28 2008 - 23:56:00 CDT)
  - RE: AMBER: a question oguz gurbulak (Mon Sep 29 2008 - 04:55:29 CDT)
    - RE: AMBER: a question Ross Walker (Mon Sep 29 2008 - 09:41:54 CDT)
  - RE: AMBER: a question oguz gurbulak (Mon Sep 29 2008 - 05:23:09 CDT)
- Re: AMBER: a question Adrien Delmont (Mon Sep 29 2008 - 07:53:51 CDT)
AMBER: coordinate file question Robert Hanson (Mon Sep 29 2008 - 22:16:25 CDT)
- RE: AMBER: coordinate file question Ross Walker (Mon Sep 29 2008 - 22:33:10 CDT)
  - Re: AMBER: coordinate file question Robert Hanson (Tue Sep 30 2008 - 08:30:21 CDT)
    - RE: AMBER: coordinate file question Ross Walker (Tue Sep 30 2008 - 08:55:57 CDT)
    - Re: AMBER: coordinate file question Robert Hanson (Tue Sep 30 2008 - 12:24:47 CDT)
AMBER: Ac-Co Parameters for Amber suhaib sh (Tue Sep 30 2008 - 06:49:41 CDT)
- Re: AMBER: Ac-Co Parameters for Amber suhaib sh (Tue Sep 30 2008 - 17:18:48 CDT)
  - Re: AMBER: Ac-Co Parameters for Amber FyD (Wed Oct 01 2008 - 01:14:39 CDT)
AMBER: Ca ions not recognized Cristina Sisu (Tue Sep 30 2008 - 09:00:24 CDT)
- RE: AMBER: Ca ions not recognized Peterson, Matthew W. (Tue Sep 30 2008 - 09:08:16 CDT)
AMBER: Buckingham potential Diddo Diddens (Tue Sep 30 2008 - 09:16:47 CDT)
- Re: AMBER: Buckingham potential Andreas Svrcek-Seiler (Tue Sep 30 2008 - 09:47:27 CDT)
  - Re: AMBER: Buckingham potential Diddo Diddens (Tue Sep 30 2008 - 10:01:57 CDT)
    - Re: AMBER: Buckingham potential Adrian Roitberg (Tue Sep 30 2008 - 10:14:53 CDT)
AMBER: cluster for running amber10 Guillermo Mulliert Carlín (Tue Sep 30 2008 - 10:14:07 CDT)
- RE: AMBER: cluster for running amber10 Ross Walker (Tue Sep 30 2008 - 10:25:09 CDT)
  - AMBER: MM-PBSA problem : Missing PBCAV for PB Carra, Claudio (JSC-SK)[USRA] (Tue Sep 30 2008 - 11:49:26 CDT)
  - AMBER: MM-PBSA problem : Use of uninitialized value in multiplicatiom with Amber10 Carra, Claudio (JSC-SK)[USRA] (Wed Oct 01 2008 - 12:05:55 CDT)
AMBER: problem with parmchck aneesh cna (Tue Sep 30 2008 - 12:10:28 CDT)
AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE liu junjun (Tue Sep 30 2008 - 13:07:09 CDT)
- RE: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE Ross Walker (Tue Sep 30 2008 - 13:18:44 CDT)
  - Re: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE liu junjun (Tue Sep 30 2008 - 13:48:11 CDT)
- Re: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE Jed W Pitera (Tue Sep 30 2008 - 13:56:18 CDT)
  - Re: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE liu junjun (Tue Sep 30 2008 - 14:17:26 CDT)
AMBER: FW: Amber 9 mhamed_at_birzeit.edu (Tue Sep 30 2008 - 12:22:07 CDT)
- Re: AMBER: FW: Amber 9 Gustavo Seabra (Tue Sep 30 2008 - 14:12:19 CDT)
AMBER: problem of use MPICHI2 to run RMED on amber10 xwu_at_purdue.edu (Tue Sep 30 2008 - 15:31:24 CDT)
- Re: AMBER: problem of use MPICHI2 to run RMED on amber10 Carlos Simmerling (Tue Sep 30 2008 - 15:45:58 CDT)
  - Re: AMBER: problem of use MPICHI2 to run RMED on amber10 xwu_at_purdue.edu (Tue Sep 30 2008 - 16:03:08 CDT)
AMBER: How to set up a water slab in Amber? Zhao, Zhen (zhaozh) (Tue Sep 30 2008 - 16:23:06 CDT)
- Re: AMBER: How to set up a water slab in Amber? David A. Case (Wed Oct 01 2008 - 06:51:17 CDT)
AMBER: F modified RNA is split in two parts when running sander simulated annealing Peter Podbev¹ek (Wed Oct 01 2008 - 04:01:52 CDT)
- Re: AMBER: F modified RNA is split in two parts when running sander simulated annealing Andreas Svrcek-Seiler (Wed Oct 01 2008 - 04:56:38 CDT)
  - RE: AMBER: F modified RNA is split in two parts when running sander simulated annealing Peter Podbev¹ek (Thu Oct 02 2008 - 08:08:51 CDT)
AMBER: Sources of disruption during NVE Naser Alijabbari (Wed Oct 01 2008 - 10:59:29 CDT)
- Re: AMBER: Sources of disruption during NVE Gustavo Seabra (Wed Oct 01 2008 - 14:32:06 CDT)
  - Re: AMBER: Sources of disruption during NVE Naser Alijabbari (Wed Oct 01 2008 - 20:10:43 CDT)
    - Re: AMBER: Sources of disruption during NVE Gustavo Seabra (Fri Oct 03 2008 - 08:39:05 CDT)
- Re: AMBER: Sources of disruption during NVE Bill Ross (Fri Oct 03 2008 - 10:27:37 CDT)
AMBER: amber10 installation on sgi_mips Rima Chaudhuri (Wed Oct 01 2008 - 14:05:06 CDT)
- Re: AMBER: amber10 installation on sgi_mips David A. Case (Wed Oct 01 2008 - 14:24:56 CDT)
  - Re: AMBER: amber10 installation on sgi_mips Rima Chaudhuri (Wed Oct 01 2008 - 15:47:14 CDT)
  - Re: AMBER: amber10 installation on sgi_mips Atro Tossavainen (Thu Oct 02 2008 - 04:59:34 CDT)
    - Re: AMBER: amber10 installation on sgi_mips Rima Chaudhuri (Thu Oct 02 2008 - 11:42:25 CDT)
    - Re: AMBER: amber10 installation on sgi_mips Atro Tossavainen (Thu Oct 02 2008 - 14:39:33 CDT)
- Re: AMBER: amber10 installation on sgi_mips Bill Ross (Wed Oct 01 2008 - 17:11:08 CDT)
  - Re: AMBER: amber10 installation on sgi_mips Rima Chaudhuri (Wed Oct 01 2008 - 21:31:06 CDT)
- Re: AMBER: amber10 installation on sgi_mips Bill Ross (Thu Oct 02 2008 - 12:05:17 CDT)
AMBER: thermodynamic integration with Amber9 Sadhna Rana (Thu Oct 02 2008 - 10:12:47 CDT)
- RE: AMBER: thermodynamic integration with Amber9 Ross Walker (Thu Oct 02 2008 - 10:24:01 CDT)
- RE: AMBER: thermodynamic integration with Amber9 Sadhna Rana (Thu Oct 02 2008 - 11:08:27 CDT)
  - RE: AMBER: thermodynamic integration with Amber9 Ross Walker (Thu Oct 02 2008 - 12:10:57 CDT)
AMBER: Oct 6 deadline for ACS computational chemistry awards Carlos Simmerling (Thu Oct 02 2008 - 12:45:35 CDT)
AMBER: Support for intel mpi in pmemd 10; better support for intel MKL Robert Duke (Thu Oct 02 2008 - 15:56:07 CDT)
- Re: AMBER: Support for intel mpi in pmemd 10; better support for intel MKL Francesco Pietra (Thu Oct 02 2008 - 16:35:45 CDT)
  - Re: AMBER: Support for intel mpi in pmemd 10; better support for intel MKL Robert Duke (Thu Oct 02 2008 - 17:39:28 CDT)
- Re: AMBER: Support for intel mpi in pmemd 10; better support for intel MKL Robert Duke (Fri Oct 03 2008 - 10:43:22 CDT)
AMBER: shake the molecule amit jain (Fri Oct 03 2008 - 00:26:33 CDT)
- Re: AMBER: shake the molecule David A. Case (Fri Oct 03 2008 - 11:28:32 CDT)
AMBER: amber10 on SiCortex hardware Peter Varnai (Fri Oct 03 2008 - 11:27:21 CDT)
AMBER: ptraj average structure Yunierkis Perez Castillo (Sat Oct 04 2008 - 08:25:42 CDT)
- Re: AMBER: ptraj average structure Carlos Simmerling (Sat Oct 04 2008 - 08:55:31 CDT)
- RE: AMBER: ptraj average structure Ross Walker (Sat Oct 04 2008 - 09:55:51 CDT)
AMBER: Parameters for alkali cations and halogen anions Francesco Pietra (Sun Oct 05 2008 - 02:29:45 CDT)
AMBER: MM_PBSA problems in AMBER9 Å·ÑôµÂ·½ (Sun Oct 05 2008 - 16:30:12 CDT)
- Re: AMBER: MM_PBSA problems in AMBER9 Ray Luo (Sun Oct 05 2008 - 22:20:01 CDT)
  - Re: AMBER: MM_PBSA problems in AMBER9 Alessandro Nascimento (Mon Oct 06 2008 - 08:04:37 CDT)
    - RE: AMBER: MM_PBSA problems in AMBER9 Å·ÑôµÂ·½ (Tue Oct 07 2008 - 00:19:54 CDT)
    - RE: AMBER: MM_PBSA problems in AMBER9 Å·ÑôµÂ·½ (Tue Oct 07 2008 - 00:19:54 CDT)
AMBER: internal energy INT is not zero from MM_GBSA Fan Yanping (Tue Oct 07 2008 - 01:08:14 CDT)
AMBER: internal energy INT is not zero from MM_GBSA flyanping (Tue Oct 07 2008 - 01:18:49 CDT)
- Re: AMBER: internal energy INT is not zero from MM_GBSA sobereva (Tue Oct 07 2008 - 09:22:57 CDT)
AMBER: Amber heme parameters Shaikh Abdul R S Ramaju (Tue Oct 07 2008 - 01:31:34 CDT)
- Re: AMBER: Amber heme parameters sobereva (Tue Oct 07 2008 - 09:02:12 CDT)
  - RE: AMBER: Amber heme parameters Shaikh Abdul R S Ramaju (Wed Oct 08 2008 - 01:38:59 CDT)
AMBER: Zn2+ Bondi radius value Sergey Samsonov (Tue Oct 07 2008 - 03:50:10 CDT)
- Re: AMBER: Zn2+ Bondi radius value Enguerran Vanquelef (Wed Oct 08 2008 - 06:55:21 CDT)
AMBER: Once again, with feeling --- Support for intel mpi in pmemd 10; better support for intel MKL Robert Duke (Tue Oct 07 2008 - 12:02:51 CDT)
- Re: AMBER: Once again, with feeling --- Support for intel mpi in pmemd 10; better support for intel MKL David A. Case (Tue Oct 07 2008 - 16:05:07 CDT)
AMBER: Question on Urea box Antonios Samiotakis (Tue Oct 07 2008 - 14:31:44 CDT)
AMBER: saveamberparm error Shaikh Abdul R S Ramaju (Wed Oct 08 2008 - 06:33:31 CDT)
- RE: AMBER: saveamberparm error Ross Walker (Wed Oct 08 2008 - 10:23:12 CDT)
  - RE: AMBER: saveamberparm error Shaikh Abdul R S Ramaju (Wed Oct 08 2008 - 21:24:58 CDT)
    - Re: AMBER: saveamberparm error Wei Zhang (Thu Oct 09 2008 - 05:22:45 CDT)
    - RE: AMBER: saveamberparm error Shaikh Abdul R S Ramaju (Thu Oct 09 2008 - 05:53:35 CDT)
AMBER: AMBER force field for glycolipid Stephane Abel (Wed Oct 08 2008 - 07:25:12 CDT)
- RE: AMBER: AMBER force field for glycolipid Matthew Tessier (Thu Oct 09 2008 - 08:57:59 CDT)
  - Re: AMBER: AMBER force field for glycolipid Stephane Abel (Thu Oct 09 2008 - 09:08:49 CDT)
AMBER: ptraj - closest command Ryan Pavlovicz (Wed Oct 08 2008 - 12:36:17 CDT)
- Re: AMBER: ptraj - closest command Jianyin Shao (Wed Oct 08 2008 - 14:50:29 CDT)
  - Re: AMBER: ptraj - closest command Ryan Pavlovicz (Wed Oct 08 2008 - 15:49:08 CDT)
    - Re: AMBER: ptraj - closest command sobereva (Wed Oct 08 2008 - 21:49:46 CDT)
AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files Robert Hanson (Wed Oct 08 2008 - 13:16:55 CDT)
- Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files FyD (Wed Oct 08 2008 - 14:00:33 CDT)
  - Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files Robert Hanson (Wed Oct 08 2008 - 15:55:26 CDT)
    - Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files Robert Hanson (Thu Oct 09 2008 - 11:30:32 CDT)
- Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files Robert Hanson (Thu Oct 09 2008 - 08:59:20 CDT)
AMBER: velocity-verlet algorithm and ensembles oguz gurbulak (Wed Oct 08 2008 - 13:59:46 CDT)
- Re: AMBER: velocity-verlet algorithm and ensembles David A. Case (Thu Oct 09 2008 - 07:46:08 CDT)
Fwd: Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files FyD (Thu Oct 09 2008 - 11:57:07 CDT)
- AMBER: changing pdb structure taufik.alsarraj_at_utoronto.ca (Thu Oct 09 2008 - 21:35:07 CDT)
Re: [Jmol-users] AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files Robert Hanson (Thu Oct 09 2008 - 18:12:52 CDT)
AMBER: nscm code Naser Alijabbari (Fri Oct 10 2008 - 00:05:59 CDT)
- Re: AMBER: nscm code Carlos Simmerling (Fri Oct 10 2008 - 05:32:25 CDT)
  - Re: AMBER: nscm code Andreas Svrcek-Seiler (Fri Oct 10 2008 - 06:37:09 CDT)
AMBER: Question about resp charges for a charged molecule... Alberto Sergio Garay (Fri Oct 10 2008 - 05:54:22 CDT)
- Re: AMBER: Question about resp charges for a charged molecule... Germain Vallverdu (Fri Oct 10 2008 - 06:20:45 CDT)
- Re: AMBER: Question about resp charges for a charged molecule... FyD (Fri Oct 10 2008 - 08:37:48 CDT)
AMBER: AddIons approach parul sharma (Fri Oct 10 2008 - 06:13:51 CDT)
- Re: AMBER: AddIons approach Carlos Simmerling (Fri Oct 10 2008 - 06:17:08 CDT)
  - Re: AMBER: AddIons approach Germain Vallverdu (Fri Oct 10 2008 - 06:23:00 CDT)
  - Re: AMBER: AddIons approach parul sharma (Fri Oct 10 2008 - 06:44:41 CDT)
    - Re: AMBER: AddIons approach David A. Case (Fri Oct 10 2008 - 06:52:52 CDT)
AMBER: Radius of Gyration Beale, John (Fri Oct 10 2008 - 06:27:22 CDT)
- Re: AMBER: Radius of Gyration Carlos Simmerling (Fri Oct 10 2008 - 06:48:21 CDT)
AMBER: Ring flips Beale, John (Fri Oct 10 2008 - 12:09:52 CDT)
- Re: AMBER: Ring flips David Watson (Fri Oct 10 2008 - 12:30:37 CDT)
- Re: AMBER: Ring flips David Watson (Fri Oct 10 2008 - 12:36:36 CDT)
AMBER: antechamber dipti lele (Sat Oct 11 2008 - 23:43:33 CDT)
- Re: AMBER: antechamber David A. Case (Mon Oct 13 2008 - 17:43:00 CDT)
AMBER: removing COM and rotation in explicit solvation Naser Alijabbari (Sun Oct 12 2008 - 15:02:22 CDT)
- Re: AMBER: removing COM and rotation in explicit solvation David A. Case (Sun Oct 12 2008 - 16:32:54 CDT)
AMBER: pairwise interaction energies Thomas Leonard (Mon Oct 13 2008 - 01:12:11 CDT)
- Re: AMBER: pairwise interaction energies Alessandro Nascimento (Mon Oct 13 2008 - 05:35:39 CDT)
AMBER: PDB standards Francesco Pietra (Mon Oct 13 2008 - 03:18:23 CDT)
AMBER: Ptraj pucker for pyranose Neha Gandhi (Mon Oct 13 2008 - 04:43:33 CDT)
AMBER: question about pression Yunierkis Perez Castillo (Mon Oct 13 2008 - 09:45:38 CDT)
- Re: AMBER: question about pression David A. Case (Mon Oct 13 2008 - 09:55:57 CDT)
  - RE: AMBER: question about pression Yunierkis Perez Castillo (Mon Oct 13 2008 - 10:33:45 CDT)
AMBER: LEU as first residue Francesco Pietra (Mon Oct 13 2008 - 11:20:00 CDT)
AMBER: amber: parameters for 5' nucleotide monophosphates Jeff Schwinefus (Mon Oct 13 2008 - 12:52:55 CDT)
- Re: AMBER: amber: parameters for 5' nucleotide monophosphates FyD (Mon Oct 13 2008 - 14:44:47 CDT)
AMBER: High Bfactor values for the terminal residues/atoms Siddharth Rastogi (Mon Oct 13 2008 - 23:19:52 CDT)
- AMBER: Segmentation fault hklwatergod (Tue Oct 14 2008 - 01:52:36 CDT)
  - RE: AMBER: Segmentation fault Ross Walker (Tue Oct 14 2008 - 09:53:08 CDT)
- Re: AMBER: High Bfactor values for the terminal residues/atoms Carlos Simmerling (Tue Oct 14 2008 - 05:25:25 CDT)
AMBER: large number of solvent molecules were added for protein with 221 AA residues Siddharth Rastogi (Mon Oct 13 2008 - 23:34:58 CDT)
- Re: AMBER: large number of solvent molecules were added for protein with 221 AA residues Carlos Simmerling (Tue Oct 14 2008 - 05:21:46 CDT)
AMBER: antechamber test failure john smith (Tue Oct 14 2008 - 00:47:28 CDT)
- Re: AMBER: antechamber test failure David A. Case (Wed Oct 15 2008 - 08:16:06 CDT)
  - Re: AMBER: antechamber test failure john smith (Thu Oct 16 2008 - 00:53:50 CDT)
    - Re: AMBER: antechamber test failure David A. Case (Thu Oct 16 2008 - 06:04:13 CDT)
AMBER: LEaP problem with LEU first residue? Francesco Pietra (Tue Oct 14 2008 - 05:26:25 CDT)
- Re: AMBER: LEaP problem with LEU first residue? Carlos Simmerling (Tue Oct 14 2008 - 05:41:01 CDT)
  - Re: AMBER: LEaP problem with LEU first residue? Francesco Pietra (Tue Oct 14 2008 - 08:42:55 CDT)
- Re: AMBER: LEaP problem with LEU first residue? David A. Case (Wed Oct 15 2008 - 08:18:58 CDT)
- Re: AMBER: LEaP problem with LEU first residue? KazuoOhta (Sun Oct 19 2008 - 22:04:38 CDT)
  - Re: AMBER: LEaP problem with LEU first residue? David A. Case (Mon Oct 20 2008 - 06:00:09 CDT)
AMBER: amber10 installation problem in cygwin vijayaraj_at_clri.res.in (Tue Oct 14 2008 - 10:21:19 CDT)
- Re: AMBER: amber10 installation problem in cygwin Gustavo Seabra (Tue Oct 14 2008 - 10:56:20 CDT)
- RE: AMBER: amber10 installation problem in cygwin Ross Walker (Tue Oct 14 2008 - 11:32:06 CDT)
AMBER: Amber dipole printout. Zhao, Zhen (zhaozh) (Tue Oct 14 2008 - 12:25:40 CDT)
- Re: AMBER: Amber dipole printout. Dave Rogers (Tue Oct 14 2008 - 13:14:21 CDT)
- RE: AMBER: Amber dipole printout. Ross Walker (Tue Oct 14 2008 - 15:05:38 CDT)
AMBER: Installation Error Jagan Mohan (Wed Oct 15 2008 - 02:50:18 CDT)
- Re: AMBER: Installation Error Scott Brozell (Wed Oct 15 2008 - 03:05:48 CDT)
  - Re: AMBER: Installation Error Jagan Mohan (Wed Oct 15 2008 - 03:51:03 CDT)
AMBER: Amber10: Problem with tgtmd and ncsu testing Dmitri Nilov (Wed Oct 15 2008 - 08:00:11 CDT)
AMBER: Origin of periodic box Naser Alijabbari (Wed Oct 15 2008 - 20:34:00 CDT)
- RE: AMBER: Origin of periodic box Ross Walker (Wed Oct 15 2008 - 20:57:47 CDT)
- Re: AMBER: Origin of periodic box Gustavo Seabra (Thu Oct 16 2008 - 08:24:50 CDT)
AMBER: Differentiating the force constant of distance restraints Francesca Poletti (Thu Oct 16 2008 - 03:40:16 CDT)
- Re: AMBER: Differentiating the force constant of distance restraints Germain Vallverdu (Thu Oct 16 2008 - 04:07:07 CDT)
AMBER: regarding rigid molecules aneesh cna (Thu Oct 16 2008 - 04:34:36 CDT)
- Re: AMBER: regarding rigid molecules Germain Vallverdu (Thu Oct 16 2008 - 06:02:49 CDT)
- Re: AMBER: regarding rigid molecules David A. Case (Thu Oct 16 2008 - 06:06:42 CDT)
  - Re: AMBER: regarding rigid molecules Steven Winfield (Thu Oct 16 2008 - 06:30:31 CDT)
- Re: AMBER: regarding rigid molecules Gustavo Seabra (Thu Oct 16 2008 - 08:34:56 CDT)
  - RE: AMBER: regarding rigid molecules Ross Walker (Thu Oct 16 2008 - 09:53:29 CDT)
    - Re: AMBER: regarding rigid molecules Gustavo Seabra (Thu Oct 16 2008 - 10:16:39 CDT)
AMBER: Clarification re qmmask Benjamin Roberts (Thu Oct 16 2008 - 12:24:45 CDT)
- RE: AMBER: Clarification re qmmask Ross Walker (Thu Oct 16 2008 - 13:14:04 CDT)
- Re: AMBER: Clarification re qmmask Gustavo Seabra (Thu Oct 16 2008 - 13:22:41 CDT)
AMBER: antechamber Marcela Madrid (Thu Oct 16 2008 - 15:37:07 CDT)
- Re: AMBER: antechamber David A. Case (Thu Oct 16 2008 - 16:25:17 CDT)
  - Re: AMBER: antechamber Marcela Madrid (Tue Oct 21 2008 - 12:02:54 CDT)
    - AMBER: HOLD fixed vs restraint mask Taufik Al-Sarraj (Tue Oct 21 2008 - 13:02:34 CDT)
    - RE: AMBER: HOLD fixed vs restraint mask Ross Walker (Tue Oct 21 2008 - 13:33:32 CDT)
AMBER: Using charmm force field in amber Harry (Yicun) Ni (Thu Oct 16 2008 - 16:20:45 CDT)
- RE: AMBER: Using charmm force field in amber Ross Walker (Thu Oct 16 2008 - 16:44:30 CDT)
- Re: AMBER: Using charmm force field in amber David A. Case (Thu Oct 16 2008 - 16:51:45 CDT)
AMBER: capping with non charged residues Francesco Pietra (Thu Oct 16 2008 - 17:24:44 CDT)
AMBER: antechamber errors oguz gurbulak (Fri Oct 17 2008 - 08:07:37 CDT)
- Re: AMBER: antechamber errors David A. Case (Fri Oct 17 2008 - 09:20:51 CDT)
AMBER: Restricting the system to simulate Francesco Pietra (Fri Oct 17 2008 - 11:00:50 CDT)
- Fwd: AMBER: Restricting the system to simulate Francesco Pietra (Sat Oct 18 2008 - 02:44:19 CDT)
AMBER: NAD+ parameters problem using tleap Dmitri Nilov (Fri Oct 17 2008 - 11:24:50 CDT)
- RE: AMBER: NAD+ parameters problem using tleap Ross Walker (Fri Oct 17 2008 - 13:16:41 CDT)
AMBER: using ptraj Adrien Delmont (Fri Oct 17 2008 - 16:44:16 CDT)
- AMBER: How to assign /make the ionion bond? Chih-Ying Lin (Fri Oct 17 2008 - 17:30:07 CDT)
  - Re: AMBER: How to assign /make the ionion bond? steinbrt_at_rci.rutgers.edu (Fri Oct 17 2008 - 18:06:26 CDT)
- Re: AMBER: using ptraj Gustavo Seabra (Fri Oct 17 2008 - 20:35:23 CDT)
AMBER: REDvIII_I_lack_of_charges_in_mol2 Karol Kaszuba (Sat Oct 18 2008 - 06:08:53 CDT)
- Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 FyD (Sat Oct 18 2008 - 06:54:56 CDT)
  - Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 Karol Kaszuba (Sat Oct 18 2008 - 11:32:58 CDT)
- Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 FyD (Wed Oct 22 2008 - 10:15:15 CDT)
AMBER: Addions in GB Mode? Rogelio Hernández (Sun Oct 19 2008 - 12:04:32 CDT)
- Re: AMBER: Addions in GB Mode? parul sharma (Mon Oct 20 2008 - 04:25:22 CDT)
  - Re: AMBER: Addions in GB Mode? Carlos Simmerling (Mon Oct 20 2008 - 05:12:52 CDT)
AMBER: question about simulation box Adrien Delmont (Sun Oct 19 2008 - 16:04:24 CDT)
- Re: AMBER: question about simulation box Gustavo Seabra (Mon Oct 20 2008 - 08:09:03 CDT)
- Re: AMBER: question about simulation box Adrien Delmont (Tue Oct 21 2008 - 08:43:24 CDT)
AMBER: Error in creating topology file musa özboyacý (Mon Oct 20 2008 - 06:00:48 CDT)
- Re: AMBER: Error in creating topology file Wei Zhang (Mon Oct 20 2008 - 07:34:40 CDT)
AMBER: Contacts Beale, John (Mon Oct 20 2008 - 09:29:06 CDT)
AMBER: about SASA and AMBER Yunierkis Perez Castillo (Mon Oct 20 2008 - 10:58:06 CDT)
- Re: AMBER: about SASA and AMBER Lachele Foley (Lists) (Mon Oct 20 2008 - 12:07:06 CDT)
  - Re: AMBER: about SASA and AMBER Carlos Simmerling (Mon Oct 20 2008 - 12:17:42 CDT)
AMBER: mm_pbsa_statistics / 3 traj Arturas Ziemys (Mon Oct 20 2008 - 11:18:26 CDT)
AMBER: drug/protein interaction modeling setup Sean Johnston (Mon Oct 20 2008 - 15:10:52 CDT)
- Re: AMBER: drug/protein interaction modeling setup Alessandro Nascimento (Mon Oct 20 2008 - 15:21:05 CDT)
- Re: AMBER: drug/protein interaction modeling setup Barbault Florent (Mon Oct 20 2008 - 15:37:24 CDT)
- Re: AMBER: drug/protein interaction modeling setup Bill Ross (Mon Oct 20 2008 - 17:39:04 CDT)
  - Re: AMBER: drug/protein interaction modeling setup Sean Johnston (Fri Oct 31 2008 - 14:31:56 CDT)
AMBER: cnstph test case failure or expected divergence? Melinda Layten (Mon Oct 20 2008 - 15:23:08 CDT)
- RE: AMBER: cnstph test case failure or expected divergence? Ross Walker (Mon Oct 20 2008 - 15:41:27 CDT)
  - Re: AMBER: cnstph test case failure or expected divergence? Melinda Layten (Tue Oct 21 2008 - 10:38:31 CDT)
AMBER: scyld beowulf --amber10--openmpi Rima Chaudhuri (Mon Oct 20 2008 - 19:00:27 CDT)
- RE: AMBER: scyld beowulf --amber10--openmpi Ross Walker (Mon Oct 20 2008 - 20:38:04 CDT)
  - Re: AMBER: scyld beowulf --amber10--openmpi Rima Chaudhuri (Mon Oct 20 2008 - 20:46:13 CDT)
    - Re: AMBER: scyld beowulf --amber10--openmpi Gustavo Seabra (Mon Oct 20 2008 - 21:56:35 CDT)
AMBER: Heme cysteine Shaikh Abdul R S Ramaju (Tue Oct 21 2008 - 02:16:50 CDT)
- RE: AMBER: Heme cysteine Ross Walker (Tue Oct 21 2008 - 10:17:08 CDT)
  - RE: AMBER: Heme cysteine Shaikh Abdul R S Ramaju (Tue Oct 21 2008 - 21:46:09 CDT)
AMBER: ptraj John Bennett (Tue Oct 21 2008 - 09:32:07 CDT)
AMBER: Does LEaP understant capping with ACE/NME? Francesco Pietra (Tue Oct 21 2008 - 10:57:12 CDT)
- Re: AMBER: Does LEaP understant capping with ACE/NME? Carlos Simmerling (Tue Oct 21 2008 - 11:02:41 CDT)
  - Re: AMBER: Does LEaP understant capping with ACE/NME? Francesco Pietra (Tue Oct 21 2008 - 12:31:36 CDT)
Re: AMBER: Heme cysteine Bill Ross (Tue Oct 21 2008 - 11:20:38 CDT)
AMBER: Again: Installation problem of AMBER on cluster Dmitri Nilov (Tue Oct 21 2008 - 11:31:52 CDT)
- RE: AMBER: Again: Installation problem of AMBER on cluster Ross Walker (Tue Oct 21 2008 - 11:49:50 CDT)
  - Re: AMBER: Again: Installation problem of AMBER on cluster Dmitri Nilov (Sat Oct 25 2008 - 07:30:43 CDT)
AMBER: MM_PBSA doesn't terminate Khaled Barakat (Tue Oct 21 2008 - 11:58:12 CDT)
AMBER: DNA structure analysis Bert (Wed Oct 22 2008 - 06:27:38 CDT)
AMBER: MM_PBSA doesn't terminate Khaled Barakat (Wed Oct 22 2008 - 10:27:55 CDT)
AMBER: stripping water from a restart file CHAMI F. (Wed Oct 22 2008 - 11:11:46 CDT)
- Re: AMBER: stripping water from a restart file Carlos Simmerling (Wed Oct 22 2008 - 11:29:32 CDT)
AMBER: stripping water from a restart file CHAMI F. (Wed Oct 22 2008 - 11:11:46 CDT)
- RE: AMBER: stripping water from a restart file Bill Ross (Wed Oct 22 2008 - 15:38:11 CDT)
  - RE: AMBER: stripping water from a restart file CHAMI F. (Thu Oct 23 2008 - 06:33:29 CDT)
    - Re: AMBER: stripping water from a restart file Carlos Simmerling (Thu Oct 23 2008 - 07:22:00 CDT)
    - RE: AMBER: stripping water from a restart file CHAMI F. (Thu Oct 23 2008 - 07:45:19 CDT)
- RE: AMBER: stripping water from a restart file Bill Ross (Thu Oct 23 2008 - 13:13:43 CDT)
  - RE: AMBER: stripping water from a restart file CHAMI F. (Thu Oct 23 2008 - 16:59:03 CDT)
    - Re: AMBER: stripping water from a restart file Carlos Simmerling (Thu Oct 23 2008 - 17:05:07 CDT)
- RE: AMBER: stripping water from a restart file Bill Ross (Thu Oct 23 2008 - 18:48:59 CDT)
  - RE: AMBER: stripping water from a restart file CHAMI F. (Fri Oct 24 2008 - 04:58:58 CDT)
    - Re: AMBER: stripping water from a restart file Gustavo Seabra (Mon Oct 27 2008 - 12:12:04 CDT)
- RE: AMBER: stripping water from a restart file Bill Ross (Fri Oct 24 2008 - 10:21:59 CDT)
Re: AMBER: stripping water from a restart file Bill Ross (Wed Oct 22 2008 - 12:12:29 CDT)
- RE: AMBER: stripping water from a restart file CHAMI F. (Wed Oct 22 2008 - 15:29:45 CDT)
AMBER: installing amber on new linux Jan Goeman (Wed Oct 22 2008 - 16:06:48 CDT)
- Re: AMBER: installing amber on new linux Scott Brozell (Wed Oct 22 2008 - 18:53:50 CDT)
  - Re: AMBER: installing amber on new linux Jan Goeman (Sun Oct 26 2008 - 19:25:49 CDT)
AMBER: MM-PBSA -energy decomposition error Cristina Sisu (Wed Oct 22 2008 - 17:07:43 CDT)
AMBER: energy leakage? Sally Pias (Thu Oct 23 2008 - 02:25:59 CDT)
- Re: AMBER: energy leakage? David A. Case (Thu Oct 23 2008 - 06:00:29 CDT)
  - Re: AMBER: energy leakage? Sally Pias (Thu Oct 23 2008 - 09:47:28 CDT)
AMBER: Metal parameter values musa özboyacý (Thu Oct 23 2008 - 06:59:13 CDT)
AMBER: Non bond list error Wang,Ying (Thu Oct 23 2008 - 12:19:49 CDT)
- RE: AMBER: Non bond list error Ross Walker (Thu Oct 23 2008 - 13:38:09 CDT)
- RE: AMBER: Non bond list error Wang,Ying (Thu Oct 23 2008 - 14:26:26 CDT)
  - AMBER: pdb structure is only half the molecule. Taufik Al-Sarraj (Thu Oct 23 2008 - 14:42:24 CDT)
  - Re: AMBER: Non bond list error Robert Duke (Thu Oct 23 2008 - 15:14:13 CDT)
- Re: AMBER: Non bond list error Wang,Ying (Thu Oct 23 2008 - 16:58:06 CDT)
- Fw: AMBER: Non bond list error Robert Duke (Fri Oct 24 2008 - 08:20:29 CDT)
Re: AMBER: Metal parameter values Bill Ross (Thu Oct 23 2008 - 13:23:08 CDT)
- Re: AMBER: Metal parameter values musa özboyacý (Thu Oct 23 2008 - 14:09:35 CDT)
AMBER: problem with running mm-pbsa moitrayee_at_mbu.iisc.ernet.in (Fri Oct 24 2008 - 02:14:49 CDT)
- Re: AMBER: problem with running mm-pbsa Ray Luo (Fri Oct 24 2008 - 11:24:59 CDT)
  - Re: AMBER: problem with running mm-pbsa moitrayee_at_mbu.iisc.ernet.in (Sat Oct 25 2008 - 01:30:11 CDT)
AMBER: something puzzled with mm_pbsa TaoPaul (Fri Oct 24 2008 - 05:50:04 CDT)
- Re: AMBER: something puzzled with mm_pbsa Ray Luo (Fri Oct 24 2008 - 11:21:59 CDT)
  - RE: AMBER: something puzzled with mm_pbsa TaoPaul (Fri Oct 24 2008 - 21:08:50 CDT)
    - RE: AMBER: something puzzled with mm_pbsa Ray Luo (Mon Oct 27 2008 - 11:56:54 CDT)
AMBER: problem with amber8 installation moitrayee_at_mbu.iisc.ernet.in (Fri Oct 24 2008 - 07:22:40 CDT)
- RE: AMBER: problem with amber8 installation Ross Walker (Fri Oct 24 2008 - 09:57:52 CDT)
  - RE: AMBER: problem with amber8 installation moitrayee_at_mbu.iisc.ernet.in (Sat Oct 25 2008 - 01:36:27 CDT)
    - Re: AMBER: problem with amber8 installation David A. Case (Sat Oct 25 2008 - 08:30:30 CDT)
AMBER: problem with amber8 installation moitrayee_at_mbu.iisc.ernet.in (Fri Oct 24 2008 - 07:20:17 CDT)
AMBER: Regarding sleap - documentation and output behavior Keith Van Nostrand (Fri Oct 24 2008 - 10:26:58 CDT)
AMBER: Atom names CL and four characters Francesco Pietra (Fri Oct 24 2008 - 13:55:05 CDT)
- Re: AMBER: Atom names CL and four characters David A. Case (Fri Oct 24 2008 - 14:21:51 CDT)
  - Re: AMBER: Atom names CL and four characters Francesco Pietra (Fri Oct 24 2008 - 17:44:31 CDT)
AMBER: Restraining with PMEMD 10 Francesco Pietra (Sat Oct 25 2008 - 04:32:39 CDT)
- Re: AMBER: Restraining with PMEMD 10 Robert Duke (Sat Oct 25 2008 - 07:57:03 CDT)
  - Re: AMBER: Restraining with PMEMD 10 Francesco Pietra (Sat Oct 25 2008 - 11:33:57 CDT)
AMBER: the question about "RADIOPT" option in mm_pbsa TaoPaul (Sat Oct 25 2008 - 06:11:04 CDT)
AMBER: Is it possible to recover the umbrella file in ABMD simulation after hard disk failure? Ye Mei (Sat Oct 25 2008 - 07:32:25 CDT)
AMBER: Conversion between truncated octahedron and orthorohombic box #NGUYEN CONG TRI# (Sat Oct 25 2008 - 21:36:30 CDT)
- RE: AMBER: Conversion between truncated octahedron and orthorohombic box Ross Walker (Sun Oct 26 2008 - 11:56:50 CDT)
- Re: AMBER: Conversion between truncated octahedron and orthorohombic box Gustavo Seabra (Mon Oct 27 2008 - 12:19:59 CDT)
AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 John Chodera (Sun Oct 26 2008 - 20:16:48 CDT)
AMBER: atom type for carbon and nitrogen atoms Catein Catherine (Mon Oct 27 2008 - 03:56:06 CDT)
- Re: AMBER: atom type for carbon and nitrogen atoms Gustavo Seabra (Mon Oct 27 2008 - 12:28:31 CDT)
AMBER: atom type for carbon and nitrogen atoms Catein Catherine (Mon Oct 27 2008 - 03:58:51 CDT)
AMBER: peptide MD Beale, John (Mon Oct 27 2008 - 10:38:48 CDT)
- Re: AMBER: peptide MD Carlos Simmerling (Mon Oct 27 2008 - 12:05:00 CDT)
  - RE: AMBER: peptide MD Beale, John (Mon Oct 27 2008 - 12:13:47 CDT)
AMBER: 2'-5'-branched RNA Volodymyr Zloy (Mon Oct 27 2008 - 11:10:00 CDT)
AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber John Chodera (Mon Oct 27 2008 - 17:12:31 CDT)
- Re: AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber David A. Case (Tue Oct 28 2008 - 07:57:22 CDT)
  - Re: AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber John Chodera (Tue Oct 28 2008 - 10:57:42 CDT)
    - Re: AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber David A. Case (Tue Oct 28 2008 - 17:15:11 CDT)
AMBER: aromatic bent ligand Arturas Ziemys (Mon Oct 27 2008 - 21:34:49 CDT)
AMBER: SPCFW problems Naser Alijabbari (Mon Oct 27 2008 - 21:37:12 CDT)
- Re: AMBER: SPCFW problems David A. Case (Tue Oct 28 2008 - 05:49:37 CDT)
  - Re: AMBER: SPCFW problems Naser Alijabbari (Tue Oct 28 2008 - 10:50:49 CDT)
AMBER: antechamber bug? produces incorrect NEWPDB.PDB file Robert Hanson (Tue Oct 28 2008 - 11:46:08 CDT)
- Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file David A. Case (Tue Oct 28 2008 - 12:41:45 CDT)
  - Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file David A. Case (Tue Oct 28 2008 - 12:57:49 CDT)
AMBER: Problem installing PMEMD with intel mpi, ifort Rupesh Nanjunda (Tue Oct 28 2008 - 16:07:01 CDT)
- RE: AMBER: Problem installing PMEMD with intel mpi, ifort Ross Walker (Tue Oct 28 2008 - 19:41:39 CDT)
- Re: AMBER: Problem installing PMEMD with intel mpi, ifort Robert Duke (Tue Oct 28 2008 - 20:12:17 CDT)
  - Re: AMBER: Problem installing PMEMD with intel mpi, ifort Rupesh Nanjunda (Wed Oct 29 2008 - 12:57:06 CDT)
  - Re: AMBER: Problem installing PMEMD with intel mpi, ifort Rupesh Nanjunda (Thu Oct 30 2008 - 10:07:56 CDT)
AMBER: ANAL Madhumalar Arumugam (Wed Oct 29 2008 - 03:44:57 CDT)
AMBER: problem with Dihedral angle potentials aneesh cna (Wed Oct 29 2008 - 04:23:57 CDT)
- Re: AMBER: problem with Dihedral angle potentials Carlos Simmerling (Wed Oct 29 2008 - 05:09:15 CDT)
  - Re: AMBER: problem with Dihedral angle potentials aneesh cna (Thu Oct 30 2008 - 04:11:48 CDT)
AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations moitrayee_at_mbu.iisc.ernet.in (Wed Oct 29 2008 - 08:07:23 CDT)
- RE: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations Ray Luo (Wed Oct 29 2008 - 11:41:38 CDT)
  - RE: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations moitrayee_at_mbu.iisc.ernet.in (Thu Oct 30 2008 - 00:56:51 CDT)
AMBER: Folate parameters Michael Lerner (Wed Oct 29 2008 - 12:03:06 CDT)
- Re: AMBER: Folate parameters Barbault Florent (Thu Oct 30 2008 - 09:03:09 CDT)
AMBER: Optimal compiling of amber on XT3 Patrick McCarren (Wed Oct 29 2008 - 23:30:56 CDT)
- Re: AMBER: Optimal compiling of amber on XT3 Robert Duke (Thu Oct 30 2008 - 00:31:49 CDT)
  - Re: AMBER: Optimal compiling of amber on XT3 Patrick McCarren (Sat Nov 01 2008 - 02:13:08 CDT)
- RE: AMBER: Optimal compiling of amber on XT3 Ross Walker (Thu Oct 30 2008 - 00:33:35 CDT)
  - Re: AMBER: Optimal compiling of amber on XT3 Robert Duke (Thu Oct 30 2008 - 00:59:21 CDT)
    - Re: AMBER: Optimal compiling of amber on XT3 Carlos Simmerling (Thu Oct 30 2008 - 05:22:35 CDT)
AMBER: Packing density calculation Siddharth Rastogi (Thu Oct 30 2008 - 05:41:58 CDT)
AMBER: Lone pairs in antechamber Diddo Diddens (Thu Oct 30 2008 - 08:25:35 CDT)
- Re: AMBER: Lone pairs in antechamber David A. Case (Thu Oct 30 2008 - 09:27:31 CDT)
AMBER: minimization Jacopo Sgrignani (Thu Oct 30 2008 - 13:03:29 CDT)
- RE: AMBER: minimization Ross Walker (Thu Oct 30 2008 - 13:48:11 CDT)
AMBER: MM_PBSA binding error Larry Layne (Thu Oct 30 2008 - 13:54:24 CDT)
- RE: AMBER: MM_PBSA binding error Ray Luo (Thu Oct 30 2008 - 14:35:36 CDT)
  - RE: AMBER: MM_PBSA binding error Larry Layne (Fri Oct 31 2008 - 07:56:42 CDT)
AMBER: Setting GROUP for pmemd Francesco Pietra (Thu Oct 30 2008 - 14:10:39 CDT)
- Re: AMBER: Setting GROUP for pmemd Robert Duke (Thu Oct 30 2008 - 14:29:27 CDT)
AMBER: Query on restart file Neha Gandhi (Thu Oct 30 2008 - 20:49:30 CDT)
- Re: AMBER: Query on restart file Carlos Simmerling (Thu Oct 30 2008 - 21:03:53 CDT)
- Re: AMBER: Query on restart file Robert Duke (Thu Oct 30 2008 - 21:14:40 CDT)
  - Re: AMBER: Query on restart file Neha Gandhi (Thu Oct 30 2008 - 21:22:49 CDT)
AMBER: error message of xleap Catein Catherine (Thu Oct 30 2008 - 22:40:49 CDT)
- RE: AMBER: error message of xleap Ross Walker (Thu Oct 30 2008 - 23:09:47 CDT)
  - RE: AMBER: error message of xleap Catein Catherine (Mon Nov 03 2008 - 03:52:24 CST)
AMBER: how to ger resp charge for a residue? WJ Ding (Thu Oct 30 2008 - 23:20:05 CDT)
- RE: AMBER: how to ger resp charge for a residue? Ross Walker (Thu Oct 30 2008 - 23:46:43 CDT)
- Re: AMBER: how to ger resp charge for a residue? FyD (Fri Oct 31 2008 - 01:33:42 CDT)
  - Re: AMBER: how to ger resp charge for a residue? Francesco Pietra (Fri Oct 31 2008 - 02:59:31 CDT)
    - Re: AMBER: how to ger resp charge for a residue? FyD (Fri Oct 31 2008 - 08:21:13 CDT)
    - Re: AMBER: how to ger resp charge for a residue? WJ Ding (Fri Oct 31 2008 - 09:26:48 CDT)
AMBER: problem with zMatrix in tleap WJ Ding (Thu Oct 30 2008 - 23:40:59 CDT)
- Re: AMBER: problem with zMatrix in tleap David A. Case (Fri Oct 31 2008 - 07:33:44 CDT)
  - Re: AMBER: problem with zMatrix in tleap WJ Ding (Fri Oct 31 2008 - 09:23:45 CDT)
AMBER: minimization Jacopo Sgrignani (Fri Oct 31 2008 - 03:52:12 CDT)
- RE: AMBER: minimization Ross Walker (Fri Oct 31 2008 - 10:44:49 CDT)
AMBER: Question on AMBER MD Implications Campbell, Patrick (Fri Oct 31 2008 - 11:27:41 CDT)
- Re: AMBER: Question on AMBER MD Implications Carlos Simmerling (Fri Oct 31 2008 - 11:51:21 CDT)
AMBER: Trouble compiling Amber 9 leap programs on SGI Altix system John Finke (Fri Oct 31 2008 - 13:05:57 CDT)
- RE: AMBER: Trouble compiling Amber 9 leap programs on SGI Altix system Ross Walker (Fri Oct 31 2008 - 13:22:13 CDT)
AMBER: MM-PBSA error in Amber10: possible bug? Pablo Englebienne (Fri Oct 31 2008 - 22:38:15 CDT)
AMBER: Question on AMBER MD Implications Campbell, Patrick (Sat Nov 01 2008 - 05:01:17 CDT)
AMBER: Minimisation and heating under GB conditions Francesco Pietra (Mon Nov 03 2008 - 02:58:58 CST)
- Re: AMBER: Minimisation and heating under GB conditions Carlos Simmerling (Mon Nov 03 2008 - 05:29:25 CST)
  - Re: AMBER: Minimisation and heating under GB conditions David A. Case (Mon Nov 03 2008 - 08:01:59 CST)
  - Re: AMBER: Minimisation and heating under GB conditions Francesco Pietra (Mon Nov 03 2008 - 08:08:42 CST)
    - Re: AMBER: Minimisation and heating under GB conditions Carlos Simmerling (Mon Nov 03 2008 - 08:45:22 CST)
AMBER: Problems compiling leap on Altix Cluster John Finke (Mon Nov 03 2008 - 14:51:54 CST)
- RE: AMBER: Problems compiling leap on Altix Cluster Ross Walker (Mon Nov 03 2008 - 15:47:06 CST)
  - Re: AMBER: Problems compiling leap on Altix Cluster John Finke (Mon Nov 03 2008 - 17:43:09 CST)
    - RE: AMBER: Problems compiling leap on Altix Cluster Ross Walker (Mon Nov 03 2008 - 18:06:07 CST)
AMBER: Prem Prakash Pathak (Mon Nov 03 2008 - 21:20:09 CST)
AMBER: process_mdout modify Naser Alijabbari (Tue Nov 04 2008 - 00:20:07 CST)
- RE: AMBER: process_mdout modify Ross Walker (Tue Nov 04 2008 - 09:41:33 CST)
AMBER: problem with group input and NMR restaints priya priya (Tue Nov 04 2008 - 09:20:09 CST)
- Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Tue Nov 04 2008 - 09:35:46 CST)
- RE: AMBER: problem with group input and NMR restaints Ross Walker (Tue Nov 04 2008 - 09:46:17 CST)
  - RE: AMBER: problem with group input and NMR restaints priya priya (Tue Nov 04 2008 - 10:16:34 CST)
AMBER: Steered MD and Jarzynski in pulling simulations Samuel Genheden (Wed Nov 05 2008 - 08:48:33 CST)
- Re: AMBER: Steered MD and Jarzynski in pulling simulations M. L. Dodson (Wed Nov 05 2008 - 09:04:23 CST)
- Re: AMBER: Steered MD and Jarzynski in pulling simulations Gustavo Seabra (Sun Nov 09 2008 - 20:36:38 CST)
AMBER: Glycam Neha Gandhi (Wed Nov 05 2008 - 22:02:01 CST)
- Re: AMBER: Glycam Lachele Foley (Lists) (Thu Nov 06 2008 - 09:01:48 CST)
AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query Ross Walker (Thu Nov 06 2008 - 02:18:22 CST)
AMBER: Force field for Gd (gadolinium)? Lili Peng (Thu Nov 06 2008 - 03:05:26 CST)
AMBER: gigabit ethernet cards and switches Alessandro Nascimento (Thu Nov 06 2008 - 10:51:43 CST)
- RE: AMBER: gigabit ethernet cards and switches Ross Walker (Thu Nov 06 2008 - 12:37:04 CST)
  - Re: AMBER: gigabit ethernet cards and switches Alessandro Nascimento (Thu Nov 06 2008 - 13:28:46 CST)
    - Re: AMBER: gigabit ethernet cards and switches Mengjuei Hsieh (Thu Nov 06 2008 - 20:39:23 CST)
AMBER: ptraj new mask parser: differences from ambmask and core dumps M. L. Dodson (Thu Nov 06 2008 - 12:31:07 CST)
- Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps Jianyin Shao (Thu Nov 06 2008 - 16:48:47 CST)
  - Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps M. L. Dodson (Thu Nov 06 2008 - 17:49:49 CST)
AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query Ross Walker (Thu Nov 06 2008 - 12:37:04 CST)
AMBER: RE: QUERRY? Ross Walker (Thu Nov 06 2008 - 12:37:04 CST)
AMBER: RE: Problem with the NEB tutorial Ross Walker (Thu Nov 06 2008 - 13:24:30 CST)
AMBER: RE: problems about TMD in your tutorial Ross Walker (Thu Nov 06 2008 - 13:32:58 CST)
- AMBER: coot mutation Taufik Al-Sarraj (Thu Nov 06 2008 - 14:19:00 CST)
AMBER: Extracting periodic box size deviation CJ Dickson (Thu Nov 06 2008 - 17:29:20 CST)
AMBER: using "EP" for dummy atom Ashish Sangwai (Thu Nov 06 2008 - 19:24:23 CST)
- RE: AMBER: using "EP" for dummy atom Ross Walker (Thu Nov 06 2008 - 20:05:22 CST)
Re: AMBER: Extracting periodic box size deviation Bill Ross (Thu Nov 06 2008 - 19:42:35 CST)
AMBER: AMBER : Inconsistent MD length and no of angles after ptraj parul sharma (Fri Nov 07 2008 - 03:52:07 CST)
- Re: AMBER: AMBER : Inconsistent MD length and no of angles after ptraj David A. Case (Fri Nov 07 2008 - 23:33:48 CST)
AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters Francois Theillet (Fri Nov 07 2008 - 09:24:36 CST)
- Re: AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters Lachele Foley (Lists) (Fri Nov 07 2008 - 15:25:18 CST)
AMBER: AMBER question: perturbed charge twice the unperturbed Edward M (Sat Nov 08 2008 - 23:36:54 CST)
- Re: AMBER: AMBER question: perturbed charge twice the unperturbed David A. Case (Sun Nov 09 2008 - 11:16:52 CST)
  - Re: AMBER: AMBER question: perturbed charge twice the unperturbed E.M. (Sun Nov 09 2008 - 17:08:05 CST)
    - Re: AMBER: AMBER question: perturbed charge twice the unperturbed David A. Case (Thu Nov 13 2008 - 14:39:41 CST)
AMBER: looks like I have problem with "make clean" command drugdesign (Mon Nov 10 2008 - 01:27:22 CST)
- Re: AMBER: looks like I have problem with "make clean" command David A. Case (Mon Nov 10 2008 - 06:39:26 CST)
AMBER: RE: problems about TMD in your tutorial Ross Walker (Mon Nov 10 2008 - 02:20:18 CST)
AMBER: ff02 in nmode gives error "too many dihedrals" ? Jacob Kongsted (Mon Nov 10 2008 - 03:16:36 CST)
- Re: AMBER: ff02 in nmode gives error "too many dihedrals" ? David A. Case (Wed Nov 12 2008 - 09:13:45 CST)
AMBER: test sander error in amber7 Saiful Islam (Mon Nov 10 2008 - 07:43:45 CST)
- Re: AMBER: test sander error in amber7 Saiful Islam (Tue Nov 11 2008 - 01:36:30 CST)
  - Re: AMBER: test sander error in amber7 David A. Case (Tue Nov 11 2008 - 06:15:51 CST)
AMBER: mm_pbsa.pl and Amber10 Stephan.Reiling_at_sanofi-aventis.com (Mon Nov 10 2008 - 10:05:27 CST)
- Re: AMBER: mm_pbsa.pl and Amber10 Holger Gohlke (Mon Nov 10 2008 - 11:12:16 CST)
AMBER: Amber 9 installation problems drugdesign (Mon Nov 10 2008 - 05:27:39 CST)
- Re: AMBER: Amber 9 installation problems Shozeb Haider (Mon Nov 10 2008 - 10:37:54 CST)
- Re: AMBER: Amber 9 installation problems David A. Case (Mon Nov 10 2008 - 11:32:39 CST)
- Re: AMBER: Amber 9 installation problems drugdesign (Tue Nov 11 2008 - 08:13:32 CST)
  - Re: AMBER: Amber 9 installation problems David A. Case (Tue Nov 11 2008 - 17:22:54 CST)
- Re: AMBER: Amber 9 installation problems drugdesign (Wed Nov 12 2008 - 01:36:51 CST)
  - RE: AMBER: Amber 9 installation problems Ross Walker (Wed Nov 12 2008 - 09:21:59 CST)
AMBER: xLeap error Lili Peng (Mon Nov 10 2008 - 14:45:58 CST)
- Re: AMBER: xLeap error Lili Peng (Mon Nov 10 2008 - 15:49:53 CST)
- Re: AMBER: xLeap error Mark Williamson (Mon Nov 10 2008 - 15:58:27 CST)
AMBER: resp charges in parameterization Mark M Huntress (Wed Nov 12 2008 - 10:24:55 CST)
- Re: AMBER: resp charges in parameterization steinbrt_at_rci.rutgers.edu (Wed Nov 12 2008 - 10:44:17 CST)
AMBER: Newbie question: partial minimization in implicit solvent Jochen Heil (Wed Nov 12 2008 - 11:48:38 CST)
- Re: AMBER: Newbie question: partial minimization in implicit solvent Carlos Simmerling (Wed Nov 12 2008 - 14:47:56 CST)
- RE: AMBER: Newbie question: partial minimization in implicit solvent Ross Walker (Wed Nov 12 2008 - 15:00:39 CST)
AMBER: Problem with evaporating water over longer simulation times Sasha Buzko (Wed Nov 12 2008 - 13:14:00 CST)
- Re: AMBER: Problem with evaporating water over longer simulation times Gustavo Seabra (Wed Nov 12 2008 - 13:48:01 CST)
  - Re: AMBER: Problem with evaporating water over longer simulation times steinbrt_at_rci.rutgers.edu (Wed Nov 12 2008 - 13:57:33 CST)
  - Re: AMBER: Problem with evaporating water over longer simulation times steinbrt_at_rci.rutgers.edu (Wed Nov 12 2008 - 13:57:33 CST)
AMBER: question about ptraj rai001_at_student.ucr.edu (Thu Nov 13 2008 - 00:30:48 CST)
- Re: AMBER: question about ptraj Jianyin Shao (Thu Nov 13 2008 - 17:38:44 CST)
- Re: AMBER: question about ptraj rai001_at_student.ucr.edu (Thu Nov 13 2008 - 17:56:49 CST)
AMBER: PB Radii Swarup Gupta (Thu Nov 13 2008 - 01:06:34 CST)
- Re: AMBER: PB Radii David A. Case (Thu Nov 13 2008 - 06:01:57 CST)
  - Re: AMBER: PB Radii Swarup Gupta (Sat Nov 15 2008 - 21:44:25 CST)
- Re: AMBER: PB Radii Swarup Gupta (Mon Nov 17 2008 - 05:24:42 CST)
  - Re: AMBER: PB Radii Carlos Simmerling (Mon Nov 17 2008 - 05:30:41 CST)
AMBER: load opls force field oguz gurbulak (Thu Nov 13 2008 - 04:38:11 CST)
- Re: AMBER: load opls force field David A. Case (Thu Nov 13 2008 - 06:06:40 CST)
- Re: AMBER: load opls force field Bill Ross (Thu Nov 13 2008 - 14:32:19 CST)
AMBER: Chloride anion ligands leave the protein during MD Francesco Pietra (Thu Nov 13 2008 - 09:06:06 CST)
- Re: AMBER: Chloride anion ligands leave the protein during MD Gustavo Seabra (Fri Nov 14 2008 - 07:40:45 CST)
  - Re: AMBER: Chloride anion ligands leave the protein during MD Adrian Roitberg (Fri Nov 14 2008 - 08:00:33 CST)
    - Re: AMBER: Chloride anion ligands leave the protein during MD Jiri Sponer (Fri Nov 14 2008 - 08:19:33 CST)
  - Re: AMBER: Chloride anion ligands leave the protein during MD Francesco Pietra (Sun Nov 16 2008 - 05:17:00 CST)
AMBER: MM-PBSA and trajectory input Arturas Ziemys (Thu Nov 13 2008 - 11:22:36 CST)
AMBER: segmentation fault when restarting periodic structure Diddo Diddens (Fri Nov 14 2008 - 06:47:23 CST)
- AMBER: subroutine for torsional potential CHAMI F. (Fri Nov 14 2008 - 08:16:37 CST)
  - Re: AMBER: subroutine for torsional potential steinbrt_at_rci.rutgers.edu (Fri Nov 14 2008 - 08:49:25 CST)
- Re: AMBER: segmentation fault when restarting periodic structure David A. Case (Tue Nov 18 2008 - 08:20:41 CST)
AMBER: how to remove counter ions ( K+ / Cl- ions) using rdparm? Siddharth Rastogi (Fri Nov 14 2008 - 08:02:34 CST)
AMBER: NMR optimization with group averages (IGR1 / IGR2) Ryan Pavlovicz (Fri Nov 14 2008 - 09:59:36 CST)
AMBER: Sander *.top and *.crd file from PDB file Chin, Keith B (Fri Nov 14 2008 - 13:43:41 CST)
- Re: AMBER: Sander *.top and *.crd file from PDB file Gustavo Seabra (Fri Nov 14 2008 - 14:30:21 CST)
  - RE: AMBER: Sander *.top and *.crd file from PDB file Chin, Keith B (Fri Nov 14 2008 - 14:55:57 CST)
    - Re: AMBER: Sander *.top and *.crd file from PDB file Carlos Simmerling (Fri Nov 14 2008 - 15:00:30 CST)
AMBER: Ptraj Normal Mode Analysis Jesse Jun (Fri Nov 14 2008 - 15:19:31 CST)
AMBER: organic solvents Marcelo Puiatti (Fri Nov 14 2008 - 17:20:30 CST)
- Re: AMBER: organic solvents Mark Williamson (Fri Nov 14 2008 - 17:28:10 CST)
- Re: AMBER: organic solvents FyD (Sat Nov 15 2008 - 01:56:30 CST)
AMBER: Trajectory file ended and unit 24 error on open inptraj Siddharth Rastogi (Sat Nov 15 2008 - 09:33:10 CST)
- Re: AMBER: Trajectory file ended and unit 24 error on open inptraj Carlos Simmerling (Sat Nov 15 2008 - 09:44:32 CST)
  - Re: AMBER: Trajectory file ended and unit 24 error on open inptraj Siddharth Rastogi (Sun Nov 16 2008 - 00:18:59 CST)
    - Re: AMBER: Trajectory file ended and unit 24 error on open inptraj Carlos Simmerling (Sun Nov 16 2008 - 06:42:22 CST)
- Re: AMBER: Trajectory file ended and unit 24 error on open inptraj Gustavo Seabra (Sun Nov 16 2008 - 10:05:42 CST)
AMBER: How to create *.top & *.crd file with hexagonal lattice Chin, Keith B (Sun Nov 16 2008 - 19:02:05 CST)
- Re: AMBER: How to create *.top & *.crd file with hexagonal lattice David A. Case (Tue Nov 18 2008 - 08:05:12 CST)
AMBER: problem Arturas Ziemys (Sun Nov 16 2008 - 23:07:38 CST)
- Re: AMBER: problem FyD (Mon Nov 17 2008 - 01:40:33 CST)
  - RE: AMBER: problem Arturas Ziemys (Mon Nov 17 2008 - 22:36:25 CST)
    - Re: AMBER: problem David A. Case (Tue Nov 18 2008 - 06:15:57 CST)
    - Re: AMBER: problem Arturas Ziemys (Tue Nov 18 2008 - 09:07:19 CST)
AMBER: High ESURF Siddharth Rastogi (Mon Nov 17 2008 - 02:07:57 CST)
- Re: AMBER: High ESURF Andreas Svrcek-Seiler (Mon Nov 17 2008 - 02:24:02 CST)
AMBER: velocity units? Jose Borreguero (Mon Nov 17 2008 - 10:14:35 CST)
- Re: AMBER: velocity units? David A. Case (Mon Nov 17 2008 - 10:53:19 CST)
AMBER: ptraj closest command steinbrt_at_rci.rutgers.edu (Mon Nov 17 2008 - 10:14:11 CST)
- Re: AMBER: ptraj closest command Gustavo Seabra (Mon Nov 17 2008 - 10:51:42 CST)
AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 11:15:17 CST)
- Re: AMBER: RESTRAINTS: no valid redirection found Robert Duke (Mon Nov 17 2008 - 11:34:50 CST)
  - Re: AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 12:00:25 CST)
  - Re: AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 13:21:01 CST)
    - Re: AMBER: RESTRAINTS: no valid redirection found Robert Duke (Mon Nov 17 2008 - 13:58:18 CST)
    - Re: AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 15:30:54 CST)
- Fwd: AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 11:35:04 CST)
AMBER: AMBER10 installation question Jeffrey (Mon Nov 17 2008 - 21:20:14 CST)
- Re: AMBER: AMBER10 installation question David A. Case (Tue Nov 18 2008 - 06:05:07 CST)
  - Re: Re: AMBER: AMBER10 installation question Jeffrey (Wed Nov 19 2008 - 07:27:13 CST)
AMBER: SPCFW temperature oscillations Naser Alijabbari (Mon Nov 17 2008 - 22:19:12 CST)
- Re: AMBER: SPCFW temperature oscillations David A. Case (Tue Nov 18 2008 - 06:13:16 CST)
  - Re: AMBER: SPCFW temperature oscillations Robert Duke (Tue Nov 18 2008 - 07:16:27 CST)
AMBER: Equilibration protocol for large protein Dmitri Nilov (Tue Nov 18 2008 - 10:33:26 CST)
AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) John Chodera (Tue Nov 18 2008 - 13:58:22 CST)
- Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) David A. Case (Wed Nov 19 2008 - 08:35:45 CST)
  - Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) Alan (Thu Nov 20 2008 - 05:48:56 CST)
AMBER: AMBER10 compiling SANDER parallel problem Hazard, E. Starr (Tue Nov 18 2008 - 14:48:31 CST)
- Re: AMBER: AMBER10 compiling SANDER parallel problem David A. Case (Tue Nov 18 2008 - 15:25:23 CST)
AMBER: Chin, Keith B (Tue Nov 18 2008 - 17:39:26 CST)
AMBER: PMEMD with AMOEBA parms including a lone pair site Margaret Johnson (Tue Nov 18 2008 - 20:29:04 CST)
- Re: AMBER: PMEMD with AMOEBA parms including a lone pair site Robert Duke (Tue Nov 18 2008 - 20:50:14 CST)
AMBER: question - gaff and leaprc.ff03ua oguz gurbulak (Wed Nov 19 2008 - 07:56:17 CST)
- Re: AMBER: question - gaff and leaprc.ff03ua David A. Case (Wed Nov 19 2008 - 09:08:02 CST)
  - Re: AMBER: question - gaff and leaprc.ff03ua oguz gurbulak (Sun Nov 23 2008 - 10:43:48 CST)
    - Re: AMBER: question - gaff and leaprc.ff03ua David A. Case (Sun Nov 23 2008 - 15:49:37 CST)
AMBER: MOLYBDENUM Joachim Reichelt (Wed Nov 19 2008 - 08:14:31 CST)
AMBER: problem with cartesian restraints with NTP simulations Barbault Florent (Wed Nov 19 2008 - 08:50:13 CST)
- Re: AMBER: problem with cartesian restraints with NTP simulations David A. Case (Wed Nov 19 2008 - 09:02:56 CST)
AMBER: Amber on linux Marudachalam S (Wed Nov 19 2008 - 11:58:10 CST)
- Re: AMBER: Amber on linux steinbrt_at_rci.rutgers.edu (Wed Nov 19 2008 - 13:47:45 CST)
AMBER: How to manually adjust periodic boundary conditions (PBC) Chin, Keith B (Wed Nov 19 2008 - 13:58:41 CST)
- Re: AMBER: How to manually adjust periodic boundary conditions (PBC) David A. Case (Wed Nov 19 2008 - 17:35:33 CST)
  - RE: AMBER: How to manually adjust periodic boundary conditions (PBC) Chin, Keith B (Wed Nov 19 2008 - 19:15:17 CST)
    - Re: AMBER: How to manually adjust periodic boundary conditions (PBC) David A. Case (Thu Nov 20 2008 - 14:52:57 CST)
AMBER: compiling ambertools with intel compilers Alan (Thu Nov 20 2008 - 04:27:26 CST)
- Re: AMBER: compiling ambertools with intel compilers David A. Case (Thu Nov 20 2008 - 06:04:22 CST)
AMBER: CG and HC atoms partial charges in AMBER Stephane Abel (Thu Nov 20 2008 - 09:40:17 CST)
- Re: AMBER: CG and HC atoms partial charges in AMBER David A. Case (Thu Nov 20 2008 - 09:56:15 CST)
  - Re: AMBER: CG and HC atoms partial charges in AMBER Stephane Abel (Thu Nov 20 2008 - 10:26:10 CST)
- RE: AMBER: CG and HC atoms partial charges in AMBER Matthew Tessier (Thu Nov 20 2008 - 10:15:56 CST)
AMBER: pmemd Jeremy Harris (Thu Nov 20 2008 - 10:27:14 CST)
- RE: AMBER: pmemd Ross Walker (Thu Nov 20 2008 - 10:36:51 CST)
- Re: AMBER: pmemd Robert Duke (Thu Nov 20 2008 - 10:40:36 CST)
AMBER: AMBER forfield choose Wang,Ying (Thu Nov 20 2008 - 08:32:24 CST)
- Re: AMBER: AMBER forfield choose Wang,Ying (Thu Nov 20 2008 - 09:05:28 CST)
  - Re: AMBER: AMBER forfield choose mori_at_cerm.unifi.it (Thu Nov 20 2008 - 09:09:28 CST)
- Re: AMBER: AMBER forfield choose Wang,Ying (Thu Nov 20 2008 - 09:17:45 CST)
- Re: AMBER: AMBER forfield choose Barbault Florent (Thu Nov 20 2008 - 08:45:20 CST)
  - Re: AMBER: AMBER forfield choose Carlos Simmerling (Thu Nov 20 2008 - 09:51:18 CST)
    - Re: AMBER: AMBER forfield choose Barbault Florent (Thu Nov 20 2008 - 10:21:17 CST)
    - Re: AMBER: AMBER forfield choose Carlos Simmerling (Thu Nov 20 2008 - 10:21:51 CST)
Re: AMBER: Force field for Gd3+ (metal ion)? Lili Peng (Thu Nov 20 2008 - 18:00:29 CST)
- AMBER: Problems for use manganese molecules vallespardojl_at_chem.leidenuniv.nl (Fri Nov 21 2008 - 03:06:37 CST)
  - Re: AMBER: Problems for use manganese molecules David A. Case (Fri Nov 21 2008 - 06:46:22 CST)
AMBER: ptraj center problem robaldo_at_dna.uba.ar (Fri Nov 21 2008 - 11:31:27 CST)
- Re: AMBER: ptraj center problem Carlos Simmerling (Fri Nov 21 2008 - 12:42:17 CST)
  - Re: AMBER: ptraj center problem robaldo_at_dna.uba.ar (Fri Nov 21 2008 - 14:04:56 CST)
AMBER: Electrostatic Energy Components guardiani_at_fi.infn.it (Fri Nov 21 2008 - 13:29:08 CST)
- RE: AMBER: Electrostatic Energy Components Ross Walker (Fri Nov 21 2008 - 15:36:20 CST)
  - RE: AMBER: Electrostatic Energy Components Ilyas Yildirim (Fri Nov 21 2008 - 16:11:14 CST)
- Re: AMBER: Electrostatic Energy Components Junmei Wang (Sun Nov 23 2008 - 21:36:38 CST)
AMBER: RE: About restart amber Ross Walker (Fri Nov 21 2008 - 15:45:16 CST)
- Re: AMBER: RE: About restart amber Francesco Pietra (Sat Nov 22 2008 - 10:03:02 CST)
  - RE: AMBER: RE: About restart amber Ross Walker (Sat Nov 22 2008 - 11:18:57 CST)
AMBER: compiling amber 10 Andrei Neamtu (Sat Nov 22 2008 - 01:26:58 CST)
- Re: AMBER: compiling amber 10 David A. Case (Sat Nov 22 2008 - 14:33:54 CST)
AMBER: QM/MM simulation Syed Tarique Moin (Sat Nov 22 2008 - 02:00:36 CST)
- Re: AMBER: QM/MM simulation David A. Case (Sat Nov 22 2008 - 08:53:50 CST)
  - Re: AMBER: QM/MM simulation Syed Tarique Moin (Sat Nov 22 2008 - 09:11:12 CST)
    - RE: AMBER: QM/MM simulation Ross Walker (Sat Nov 22 2008 - 10:59:49 CST)
    - Re: AMBER: QM/MM simulation Gustavo Seabra (Sat Nov 22 2008 - 13:19:22 CST)
AMBER: AMBER10 failing to compile PMEMD Hazard, E. Starr (Sat Nov 22 2008 - 16:06:03 CST)
- Re: AMBER: AMBER10 failing to compile PMEMD Robert Duke (Sat Nov 22 2008 - 16:42:50 CST)
AMBER: AdoMet parameterization with antechamber Jeffrey (Sun Nov 23 2008 - 09:55:30 CST)
- Re: AMBER: AdoMet parameterization with antechamber David A. Case (Sun Nov 23 2008 - 15:13:23 CST)
  - Re: AMBER: AdoMet parameterization with antechamber Alan (Mon Nov 24 2008 - 04:46:52 CST)
AMBER: Running Amber8 - Sander tri nam Vo (Mon Nov 24 2008 - 00:28:31 CST)
- Re: AMBER: Running Amber8 - Sander David A. Case (Mon Dec 01 2008 - 09:37:32 CST)
AMBER: GB versus explicit medium Francesco Pietra (Mon Nov 24 2008 - 03:39:58 CST)
- Re: AMBER: GB versus explicit medium Carlos Simmerling (Mon Nov 24 2008 - 05:08:40 CST)
  - Re: AMBER: GB versus explicit medium Francesco Pietra (Mon Nov 24 2008 - 09:33:43 CST)
    - Re: AMBER: GB versus explicit medium M. L. Dodson (Mon Nov 24 2008 - 09:43:52 CST)
AMBER: Ewald troubles when running very big boxes steinbrt_at_rci.rutgers.edu (Mon Nov 24 2008 - 14:50:50 CST)
- Re: AMBER: Ewald troubles when running very big boxes Robert Duke (Mon Nov 24 2008 - 20:09:23 CST)
RE: AMBER: Fully QM periodic runs hfox1_at_nd.edu (Mon Nov 24 2008 - 15:28:36 CST)
- Re: AMBER: Fully QM periodic runs David A. Case (Tue Nov 25 2008 - 05:56:51 CST)
- RE: AMBER: Fully QM periodic runs Ross Walker (Tue Nov 25 2008 - 10:54:24 CST)
AMBER: unsubscribe amber Su Nwe (Tue Nov 25 2008 - 01:12:02 CST)
AMBER: Gradual releasing of position restraints Dmitri Nilov (Tue Nov 25 2008 - 08:23:02 CST)
- RE: AMBER: Gradual releasing of position restraints Ross Walker (Tue Nov 25 2008 - 10:48:13 CST)
- Re: AMBER: Gradual releasing of position restraints David A. Case (Wed Nov 26 2008 - 11:00:41 CST)
AMBER: molsurf fails Arturas Ziemys (Tue Nov 25 2008 - 09:27:27 CST)
- Re: AMBER: molsurf fails David A. Case (Tue Nov 25 2008 - 13:26:14 CST)
AMBER: using packmol file in Amber oguz gurbulak (Tue Nov 25 2008 - 09:49:19 CST)
- Re: AMBER: using packmol file in Amber David A. Case (Tue Nov 25 2008 - 13:45:29 CST)
- Re: AMBER: using packmol file in Amber oguz gurbulak (Tue Dec 02 2008 - 05:06:10 CST)
  - Re: AMBER: using packmol file in Amber David A. Case (Tue Dec 02 2008 - 06:14:47 CST)
AMBER: Test failure with Amber 10 Kevin Parkes (Wed Nov 26 2008 - 04:33:35 CST)
- Re: AMBER: Test failure with Amber 10 David A. Case (Wed Nov 26 2008 - 06:46:41 CST)
  - RE: AMBER: Test failure with Amber 10 Kevin Parkes (Wed Nov 26 2008 - 08:36:36 CST)
AMBER: About antechamber and GAFF Stephane Abel (Wed Nov 26 2008 - 05:02:00 CST)
AMBER: About antechamber and GAFF [UPDATED] Stephane Abel (Wed Nov 26 2008 - 05:21:52 CST)
- AMBER: subroutine Work : Jarynski work theorem CHAMI F. (Wed Nov 26 2008 - 06:21:07 CST)
  - Re: AMBER: subroutine Work : Jarynski work theorem Gustavo Seabra (Wed Dec 03 2008 - 07:59:06 CST)
- Re: AMBER: About antechamber and GAFF [UPDATED] Navnit Kumar Mishra (Wed Nov 26 2008 - 07:04:20 CST)
- RE: AMBER: About antechamber and GAFF [UPDATED] Ross Walker (Wed Nov 26 2008 - 10:39:30 CST)
  - Re: AMBER: About antechamber and GAFF [UPDATED] Wenyong Tong (Wed Nov 26 2008 - 11:13:34 CST)
  - Re: AMBER: About antechamber and GAFF [UPDATED] Stephane Abel (Thu Nov 27 2008 - 05:33:56 CST)
AMBER: Problem running NEB in AMBER10 Chris C. (Wed Nov 26 2008 - 12:38:17 CST)
- RE: AMBER: Problem running NEB in AMBER10 Ross Walker (Wed Nov 26 2008 - 13:04:55 CST)
  - Re: AMBER: Problem running NEB in AMBER10 Chris C. (Wed Dec 03 2008 - 12:29:48 CST)
AMBER: problem with AMOEBA j00323240_at_students.jsums.edu (Wed Nov 26 2008 - 13:07:13 CST)
AMBER: Question fot Amber 10 Benchmarks sychen (Thu Nov 27 2008 - 01:50:11 CST)
- Re: AMBER: Question fot Amber 10 Benchmarks Robert Duke (Thu Nov 27 2008 - 08:37:20 CST)
- RE: AMBER: Question fot Amber 10 Benchmarks Ross Walker (Thu Nov 27 2008 - 10:57:06 CST)
  - Re[2]: AMBER: Question fot Amber 10 Benchmarks sychen (Thu Nov 27 2008 - 20:18:00 CST)
AMBER: Problems of MM/MM-GBSA calculations Sergey Samsonov (Thu Nov 27 2008 - 04:53:53 CST)
AMBER: antechamber and gaff for a homodimer rebeca (Thu Nov 27 2008 - 05:12:23 CST)
- Re: AMBER: antechamber and gaff for a homodimer Alan (Thu Nov 27 2008 - 06:27:31 CST)
  - Re: AMBER: antechamber and gaff for a homodimer rebeca (Thu Nov 27 2008 - 07:33:19 CST)
    - Re: AMBER: antechamber and gaff for a homodimer FyD (Thu Nov 27 2008 - 10:02:55 CST)
AMBER: seeking help regrading Zinc protein GBSA minimization S.Sundar Raman (Thu Nov 27 2008 - 06:32:08 CST)
- Re: AMBER: seeking help regrading Zinc protein GBSA minimization Carlos Simmerling (Fri Nov 28 2008 - 06:33:16 CST)
  - Re: AMBER: seeking help regrading Zinc protein GBSA minimization Sergey Samsonov (Mon Dec 01 2008 - 02:14:36 CST)
    - Re: AMBER: seeking help regrading Zinc protein GBSA minimization Carlos Simmerling (Mon Dec 01 2008 - 05:16:02 CST)
AMBER: cis - trans isomerization Nina Fischer (Thu Nov 27 2008 - 08:39:21 CST)
AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms Ye Mei (Thu Nov 27 2008 - 09:12:51 CST)
- Re: AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms David A. Case (Mon Dec 01 2008 - 09:34:47 CST)
AMBER: Heating up Francesco Pietra (Thu Nov 27 2008 - 12:29:30 CST)
- Re: AMBER: Heating up Carlos Simmerling (Fri Nov 28 2008 - 06:30:29 CST)
  - Re: AMBER: Heating up Francesco Pietra (Fri Nov 28 2008 - 09:57:49 CST)
AMBER: normal-vector of a plane with 'corrplane' Gert Kiss (Thu Nov 27 2008 - 14:28:46 CST)
AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? jitrayut jitonnom (Thu Nov 27 2008 - 19:26:54 CST)
- Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? Guillermo Mulliert Carlín (Fri Nov 28 2008 - 01:20:30 CST)
  - Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? jitrayut jitonnom (Fri Nov 28 2008 - 17:34:43 CST)
    - Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? FyD (Sat Nov 29 2008 - 01:30:19 CST)
- RE: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? Ross Walker (Fri Nov 28 2008 - 20:11:49 CST)
AMBER: N(CN2)- ion babak minoofar (Fri Nov 28 2008 - 07:12:26 CST)
- Re: AMBER: N(CN2)- ion David A. Case (Mon Dec 01 2008 - 08:47:14 CST)
  - Re: AMBER: N(CN2)- ion babak minoofar (Thu Dec 04 2008 - 10:00:58 CST)
    - Re: AMBER: N(CN2)- ion David A. Case (Fri Dec 05 2008 - 06:23:05 CST)
    - Re: AMBER: N(CN2)- ion babak minoofar (Fri Dec 12 2008 - 03:29:54 CST)
AMBER: Questions on TIP4P model? Chin, Keith B (Fri Nov 28 2008 - 13:20:38 CST)
- Re: AMBER: Questions on TIP4P model? Carlos Simmerling (Fri Nov 28 2008 - 14:03:14 CST)
- Re: AMBER: Questions on TIP4P model? David A. Case (Sat Nov 29 2008 - 13:21:01 CST)
  - RE: AMBER: Questions on TIP4P model? Chin, Keith B (Sat Nov 29 2008 - 17:43:21 CST)
AMBER: RED vIII-lack of charges in mol2 Neha Gandhi (Sat Nov 29 2008 - 08:24:30 CST)
- Re: AMBER: RED vIII-lack of charges in mol2 FyD (Sat Nov 29 2008 - 10:23:34 CST)
AMBER: QM/MM and unpaired spin Markus Kaukonen (Mon Dec 01 2008 - 01:30:02 CST)
- RE: AMBER: QM/MM and unpaired spin Ross Walker (Mon Dec 01 2008 - 10:40:20 CST)
- Re: AMBER: QM/MM and unpaired spin Gustavo Seabra (Tue Dec 02 2008 - 21:11:25 CST)
  - RE: AMBER: QM/MM and unpaired spin Ross Walker (Tue Dec 02 2008 - 21:42:37 CST)
    - AMBER: DNA-Gold parameters Xioling Chuang (Wed Dec 03 2008 - 05:37:55 CST)
    - Re: AMBER: QM/MM and unpaired spin Gustavo Seabra (Wed Dec 03 2008 - 07:53:00 CST)
AMBER: reg.dnasaveparm&tcrd balaji nagarajan (Mon Dec 01 2008 - 08:05:52 CST)
- Re: AMBER: reg.dnasaveparm&tcrd David A. Case (Mon Dec 01 2008 - 08:29:41 CST)
  - RE: AMBER: reg.dnasaveparm&tcrd balaji nagarajan (Mon Dec 01 2008 - 10:51:00 CST)
- RE: AMBER: reg.dnasaveparm&tcrd Ross Walker (Mon Dec 01 2008 - 10:44:57 CST)
  - RE: AMBER: reg.dnasaveparm&tcrd balaji nagarajan (Mon Dec 01 2008 - 10:56:44 CST)
AMBER: How do you evaluate forces on a fixed atom? Bill K (Mon Dec 01 2008 - 12:45:42 CST)
- Re: AMBER: How do you evaluate forces on a fixed atom? David A. Case (Tue Dec 02 2008 - 08:39:37 CST)
  - Re: AMBER: How do you evaluate forces on a fixed atom? Bill K (Tue Dec 02 2008 - 19:54:35 CST)
AMBER: makeDIST_RST error -- no map function for HH TYR Ryan Pavlovicz (Mon Dec 01 2008 - 13:30:01 CST)
- Re: AMBER: makeDIST_RST error -- no map function for HH TYR David A. Case (Mon Dec 01 2008 - 15:22:46 CST)
AMBER: Variable PBCAL values in MM-PBSA calculations Daniel Oehme (Mon Dec 01 2008 - 17:45:23 CST)
- RE: AMBER: Variable PBCAL values in MM-PBSA calculations Ray Luo (Mon Dec 01 2008 - 19:55:37 CST)
  - Re: AMBER: Variable PBCAL values in MM-PBSA calculations Daniel Oehme (Thu Dec 04 2008 - 00:34:42 CST)
    - RE: AMBER: Variable PBCAL values in MM-PBSA calculations Ray Luo (Thu Dec 04 2008 - 13:06:45 CST)
    - Re: AMBER: Variable PBCAL values in MM-PBSA calculations Daniel Oehme (Sun Dec 07 2008 - 23:56:58 CST)
AMBER: Simulating peptide linkers with AMBER Sasha Buzko (Tue Dec 02 2008 - 14:03:42 CST)
AMBER: MM/GBSA Error during deccomposition N.R. Jena (Wed Dec 03 2008 - 06:01:04 CST)
- Re: AMBER: MM/GBSA Error during deccomposition Barbault Florent (Wed Dec 03 2008 - 14:32:14 CST)
  - Re: AMBER: MM/GBSA Error during deccomposition N.R. Jena (Thu Dec 04 2008 - 05:01:36 CST)
AMBER: ptraj: how to select all non-hydrogen atoms Mingfeng Yang (Wed Dec 03 2008 - 13:37:00 CST)
- Re: AMBER: ptraj: how to select all non-hydrogen atoms Hannes Kopitz (Wed Dec 03 2008 - 14:27:33 CST)
  - AMBER: unable to open pdb file Taufik Al-Sarraj (Wed Dec 03 2008 - 20:44:09 CST)
    - Re: AMBER: unable to open pdb file David A. Case (Thu Dec 04 2008 - 05:41:32 CST)
AMBER: makeDIST_RST computation of r3 value with IAT < 0 Ryan Pavlovicz (Wed Dec 03 2008 - 17:13:32 CST)
- Re: AMBER: makeDIST_RST computation of r3 value with IAT < 0 David A. Case (Fri Dec 05 2008 - 10:45:20 CST)
AMBER: reg unstability of structure in md balaji nagarajan (Wed Dec 03 2008 - 22:17:51 CST)
- Re: AMBER: reg unstability of structure in md Carlos Simmerling (Thu Dec 04 2008 - 05:28:12 CST)
  - RE: AMBER: reg unstability of structure in md balaji nagarajan (Thu Dec 04 2008 - 22:32:21 CST)
    - Re: AMBER: reg unstability of structure in md N.R. Jena (Fri Dec 05 2008 - 00:48:50 CST)
    - Re: AMBER: reg unstability of structure in md Carlos Simmerling (Fri Dec 05 2008 - 05:41:40 CST)
AMBER: side chain expression Yunierkis Perez Castillo (Thu Dec 04 2008 - 10:43:14 CST)
AMBER: LINMIN error in geometrically constrained minimization @ MM-PB/SA conditions Alexander Metz (Thu Dec 04 2008 - 11:04:03 CST)
AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Hazard, E. Starr (Fri Dec 05 2008 - 14:12:54 CST)
- RE: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Ross Walker (Fri Dec 05 2008 - 14:26:30 CST)
  - Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Starr Hazard (Fri Dec 05 2008 - 14:53:14 CST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 David Watson (Fri Dec 05 2008 - 14:32:45 CST)
  - Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Starr Hazard (Fri Dec 05 2008 - 15:10:11 CST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Robert Duke (Fri Dec 05 2008 - 14:32:04 CST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 sychen (Fri Dec 05 2008 - 21:46:20 CST)
AMBER: regad-tutorial-dna-polyAT balaji nagarajan (Sun Dec 07 2008 - 22:45:10 CST)
- Re: AMBER: regad-tutorial-dna-polyAT jani sahil (Sun Dec 07 2008 - 23:13:30 CST)
  - RE: AMBER: regad-tutorial-dna-polyAT balaji nagarajan (Mon Dec 08 2008 - 00:40:39 CST)
AMBER: GB offset for proteins Sally Pias (Sun Dec 07 2008 - 23:14:58 CST)
- Re: AMBER: GB offset for proteins David A. Case (Wed Dec 24 2008 - 13:11:21 CST)
AMBER: reg-adding ions balaji nagarajan (Mon Dec 08 2008 - 02:20:05 CST)
- RE: AMBER: reg-adding ions Ross Walker (Mon Dec 08 2008 - 10:33:18 CST)
  - RE: AMBER: reg-adding ions balaji nagarajan (Mon Dec 08 2008 - 22:32:14 CST)
    - RE: AMBER: reg-adding ions Ross Walker (Tue Dec 09 2008 - 09:05:04 CST)
AMBER: interaction energies Marina Grabar (Mon Dec 08 2008 - 05:29:36 CST)
- Re: AMBER: interaction energies David A. Case (Mon Dec 08 2008 - 10:59:28 CST)
  - AMBER: prep files ATP-MG++ and for phosphorylated threonine mirzo_at_jinr.ru (Tue Dec 09 2008 - 02:01:42 CST)
    - Re: AMBER: prep files ATP-MG++ and for phosphorylated threonine Anselm Horn (Tue Dec 09 2008 - 04:06:17 CST)
    - Re: AMBER: prep files ATP-MG++ and for phosphorylated threonine mirzo_at_jinr.ru (Tue Dec 09 2008 - 04:23:08 CST)
AMBER: Problem with MMPBSA Daniel Emery (Mon Dec 08 2008 - 10:28:22 CST)
- RE: AMBER: Problem with MMPBSA Ray Luo (Mon Dec 08 2008 - 13:47:15 CST)
AMBER: MM-PBSA : bad atom type: ZN jitrayut jitonnom (Mon Dec 08 2008 - 10:51:12 CST)
AMBER: RESP GAUSSIAN AMBER SilasConnor_at_gmx.at (Mon Dec 08 2008 - 12:31:24 CST)
- Re: AMBER: RESP GAUSSIAN AMBER FyD (Thu Dec 11 2008 - 05:42:20 CST)
  - RE: AMBER: RESP GAUSSIAN AMBER Ross Walker (Thu Dec 11 2008 - 22:00:27 CST)
AMBER: RE: bugfix 11 & 12 Ross Walker (Mon Dec 08 2008 - 15:12:42 CST)
AMBER: how to add new solvent type in Amber iccy liu (Mon Dec 08 2008 - 18:23:11 CST)
- Re: AMBER: how to add new solvent type in Amber David A. Case (Wed Dec 10 2008 - 17:18:56 CST)
  - AMBER: solvent box again iccy liu (Tue Dec 16 2008 - 12:32:32 CST)
AMBER: Radial Distribution Function prabhakar g (Mon Dec 08 2008 - 20:37:52 CST)
- Re: AMBER: Radial Distribution Function Gustavo Seabra (Tue Dec 09 2008 - 09:38:54 CST)
  - Re: AMBER: Radial Distribution Function prabhakar g (Tue Dec 09 2008 - 21:33:27 CST)
AMBER: (no subject) waleed zalloum (Tue Dec 09 2008 - 06:22:39 CST)
- RE: AMBER: (no subject) Ross Walker (Tue Dec 09 2008 - 09:07:18 CST)
  - RE: AMBER: (no subject) Scott Brozell (Tue Dec 09 2008 - 09:17:06 CST)
AMBER: Constant pH dynamics Beale, John (Tue Dec 09 2008 - 06:51:39 CST)
- Re: AMBER: Constant pH dynamics Adrian Roitberg (Tue Dec 09 2008 - 10:24:17 CST)
- Re: AMBER: Constant pH dynamics David A. Case (Tue Dec 09 2008 - 09:27:51 CST)
AMBER: parallel installation balaji nagarajan (Tue Dec 09 2008 - 21:56:20 CST)
- Re: AMBER: parallel installation David A. Case (Wed Dec 10 2008 - 07:09:00 CST)
AMBER: forrtl severe(174) error with minimization and md john smith (Wed Dec 10 2008 - 00:20:57 CST)
- RE: AMBER: forrtl severe(174) error with minimization and md Ross Walker (Wed Dec 10 2008 - 09:57:42 CST)
  - Re: AMBER: forrtl severe(174) error with minimization and md john smith (Mon Dec 15 2008 - 02:46:56 CST)
AMBER: reg-antichamber run balaji nagarajan (Wed Dec 10 2008 - 11:08:17 CST)
- Re: AMBER: reg-antichamber run David A. Case (Wed Dec 10 2008 - 17:14:31 CST)
  - Re: AMBER: reg-antichamber run FyD (Thu Dec 11 2008 - 03:57:26 CST)
AMBER: Building Amber 10 with Intel MKL and compiler mini howto Ben Eisenbraun (Wed Dec 10 2008 - 11:45:04 CST)
AMBER: Running md using glycam in AMBER Neha Gandhi (Thu Dec 11 2008 - 01:15:54 CST)
- RE: AMBER: Running md using glycam in AMBER Matthew Tessier (Thu Dec 11 2008 - 14:52:28 CST)
AMBER: Distorted ring... Waqas Nasir (Thu Dec 11 2008 - 05:48:45 CST)
- Re: AMBER: Distorted ring... Carlos Simmerling (Thu Dec 11 2008 - 06:15:57 CST)
AMBER: tutorial A1, file missing readit.f ABEL Stephane 175950 (Thu Dec 11 2008 - 06:22:41 CST)
- Re: AMBER: tutorial A1, file missing readit.f David A. Case (Thu Dec 11 2008 - 07:19:38 CST)
AMBER: Pulling using restraintmask Dirar Homouz (Thu Dec 11 2008 - 14:30:00 CST)
- Re: AMBER: Pulling using restraintmask Alessandro Nascimento (Thu Dec 11 2008 - 14:58:51 CST)
AMBER: reg.building ions balaji nagarajan (Fri Dec 12 2008 - 04:40:07 CST)
- Re: AMBER: reg.building ions David A. Case (Fri Dec 12 2008 - 06:04:58 CST)
  - RE: AMBER: reg.building ions balaji nagarajan (Fri Dec 12 2008 - 06:14:57 CST)
    - Re: AMBER: reg.building ions David A. Case (Fri Dec 12 2008 - 06:42:28 CST)
  - AMBER: building new ions CHAMI F. (Fri Dec 12 2008 - 06:23:20 CST)
    - AMBER: building new ions CHAMI F. (Mon Dec 15 2008 - 07:50:50 CST)
    - Re: AMBER: building new ions FyD (Mon Dec 15 2008 - 08:09:04 CST)
AMBER: ff99 (PK/IDIVF) saurabh agrawal (Fri Dec 12 2008 - 07:26:58 CST)
- Re: AMBER: ff99 (PK/IDIVF) Carlos Simmerling (Fri Dec 12 2008 - 08:05:11 CST)
  - RE: AMBER: ff99 (PK/IDIVF) Ross Walker (Fri Dec 12 2008 - 11:06:22 CST)
AMBER: ld: cannot find -lgcc_s moitrayee_at_mbu.iisc.ernet.in (Fri Dec 12 2008 - 07:52:08 CST)
- Re: AMBER: ld: cannot find -lgcc_s David A. Case (Fri Dec 12 2008 - 08:26:00 CST)
AMBER: reg.concentration of ions balaji nagarajan (Fri Dec 12 2008 - 10:34:49 CST)
AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems ABEL Stephane 175950 (Fri Dec 12 2008 - 10:41:19 CST)
- Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems Jifeng Wang (Fri Dec 12 2008 - 10:50:56 CST)
  - Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems FyD (Fri Dec 12 2008 - 11:14:05 CST)
AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems ABEL Stephane 175950 (Fri Dec 12 2008 - 11:33:44 CST)
- Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems FyD (Fri Dec 12 2008 - 12:24:25 CST)
AMBER: sgi4700 the time of MD simulation is 30 minute for 1ps about 2500 atom using 1cpu llduan_at_itcc.nju.edu.cn (Sat Dec 13 2008 - 08:36:45 CST)
- Re: AMBER: sgi4700 the time of MD simulation is 30 minute for 1ps about 2500 atom using 1cpu steinbrt_at_rci.rutgers.edu (Sat Dec 13 2008 - 12:58:18 CST)
AMBER: problem with toturial A3 (MM-PBSA) Maryam Hamzehee (Sat Dec 13 2008 - 09:22:58 CST)
- Re: AMBER: problem with toturial A3 (MM-PBSA) Carlos Simmerling (Sat Dec 13 2008 - 09:35:13 CST)
  - Re: AMBER: problem with toturial A3 (MM-PBSA) Maryam Hamzehee (Sun Dec 14 2008 - 05:25:00 CST)
    - Re: AMBER: problem with toturial A3 (MM-PBSA) Carlos Simmerling (Tue Dec 16 2008 - 07:57:42 CST)
AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Sat Dec 13 2008 - 15:18:45 CST)
- Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Sat Dec 13 2008 - 16:12:30 CST)
- Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC David A. Case (Sun Dec 14 2008 - 08:20:36 CST)
  - Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Sun Dec 14 2008 - 14:11:53 CST)
AMBER: Calculating the dielectrostatic constant from simulation? Jeffrey (Mon Dec 15 2008 - 01:07:25 CST)
- Re: AMBER: Calculating the dielectrostatic constant from simulation? Adrian Roitberg (Mon Dec 15 2008 - 07:44:09 CST)
  - Re: Re: AMBER: Calculating the dielectrostatic constant from simulation? Jeffrey (Mon Dec 15 2008 - 19:34:54 CST)
AMBER: pressure component chengtao_at_sjtu.edu.cn (Mon Dec 15 2008 - 02:17:21 CST)
- Re: AMBER: pressure component David A. Case (Mon Dec 15 2008 - 06:43:44 CST)
  - Re: AMBER: pressure component chengtao_at_sjtu.edu.cn (Tue Dec 16 2008 - 02:42:00 CST)
AMBER: AMBER 10 PMEMD / SGI_MIPS Atro Tossavainen (Mon Dec 15 2008 - 06:51:16 CST)
- Re: AMBER: AMBER 10 PMEMD / SGI_MIPS Robert Duke (Mon Dec 15 2008 - 07:45:34 CST)
  - Re: AMBER: AMBER 10 PMEMD / SGI_MIPS Atro Tossavainen (Mon Dec 15 2008 - 08:40:41 CST)
AMBER: Initial velocities based on date and time are NOT changing ? Markus Kaukonen (Mon Dec 15 2008 - 07:14:38 CST)
- Re: AMBER: Initial velocities based on date and time are NOT changing ? David A. Case (Mon Dec 15 2008 - 07:38:03 CST)
  - Re: AMBER: Initial velocities based on date and time are NOT changing ? Markus Kaukonen (Tue Dec 16 2008 - 03:41:40 CST)
AMBER: launching a job works with sander.MPI and fail with pmemd.MPI Thérèse Malliavin (Mon Dec 15 2008 - 08:41:55 CST)
- RE: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI Ross Walker (Mon Dec 15 2008 - 09:18:04 CST)
  - RE: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI Thérèse Malliavin (Tue Dec 16 2008 - 06:57:05 CST)
- Fw: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI Robert Duke (Tue Dec 16 2008 - 08:56:13 CST)
  - AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) wl2290_at_columbia.edu (Fri Dec 19 2008 - 12:16:39 CST)
AMBER: relative weight of RDC constraints David Witte (Mon Dec 15 2008 - 10:21:34 CST)
- Re: AMBER: relative weight of RDC constraints David A. Case (Mon Dec 15 2008 - 10:44:19 CST)
  - AMBER: distance restraint in minimization Taufik Al-Sarraj (Tue Dec 16 2008 - 12:46:22 CST)
AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III ABEL Stephane 175950 (Tue Dec 16 2008 - 05:28:56 CST)
- Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III FyD (Tue Dec 16 2008 - 06:17:15 CST)
AMBER: alascan MUTANT_KEEP error Larry Layne (Tue Dec 16 2008 - 13:07:51 CST)
AMBER: restraintmask - reference file is not working Dirar Homouz (Tue Dec 16 2008 - 18:05:24 CST)
- Re: AMBER: restraintmask - reference file is not working Carlos Simmerling (Tue Dec 16 2008 - 18:38:14 CST)
  - RE: AMBER: restraintmask - reference file is not working Dirar Homouz (Tue Dec 16 2008 - 18:45:44 CST)
  - RE: AMBER: restraintmask - reference file is not working Dirar Homouz (Tue Dec 16 2008 - 18:51:08 CST)
AMBER: unsubscribe amber Prem Prakash Pathak (Tue Dec 16 2008 - 21:09:54 CST)
AMBER: AMBER minimization problems Lili Peng (Wed Dec 17 2008 - 01:14:00 CST)
- RE: AMBER: AMBER minimization problems Ross Walker (Wed Dec 17 2008 - 10:18:06 CST)
  - Re: AMBER: AMBER minimization problems Lili Peng (Wed Dec 17 2008 - 10:35:58 CST)
AMBER: from dihe parameters to torsional energy Jeffrey (Wed Dec 17 2008 - 03:15:17 CST)
- RE: AMBER: from dihe parameters to torsional energy Ross Walker (Wed Dec 17 2008 - 10:36:14 CST)
  - RE: AMBER: from dihe parameters to torsional energy Ilyas Yildirim (Wed Dec 17 2008 - 11:10:13 CST)
    - RE: AMBER: from dihe parameters to torsional energy Ross Walker (Wed Dec 17 2008 - 11:28:21 CST)
    - Re: RE: AMBER: from dihe parameters to torsional energy Jeffrey (Wed Dec 17 2008 - 20:18:29 CST)
AMBER: alascan error Larry Layne (Wed Dec 17 2008 - 14:19:22 CST)
AMBER: Hydroxide ion in POL3 water D.J. Cole (Thu Dec 18 2008 - 06:13:58 CST)
AMBER: Solvatebox problem musa özboyacý (Fri Dec 19 2008 - 04:24:56 CST)
- Re: AMBER: Solvatebox problem David A. Case (Fri Dec 19 2008 - 07:19:18 CST)
Re: AMBER: distance restraint between non-bonded molecules] Ilyas Yildirim (Fri Dec 19 2008 - 17:06:35 CST)
- Re: AMBER: distance restraint between non-bonded molecules] Taufik Al-Sarraj (Sat Dec 20 2008 - 12:44:43 CST)
  - AMBER: xleap (measureGeom) Taufik Al-Sarraj (Sat Dec 20 2008 - 15:02:56 CST)
    - Re: AMBER: xleap (measureGeom) Scott Brozell (Mon Dec 22 2008 - 16:10:46 CST)
  - Re: AMBER: distance restraint between non-bonded molecules] Ilyas Yildirim (Sun Dec 21 2008 - 21:08:38 CST)
    - AMBER: Re: Taufik Al-Sarraj (Mon Dec 22 2008 - 12:08:17 CST)
AMBER: idecomp=2 & RRES/LRES group specification In Hee Park (Fri Dec 19 2008 - 19:19:43 CST)
AMBER: amber 9 compilation error with mvapich and intel compilers Amit Bajaj (Sat Dec 20 2008 - 08:17:03 CST)
- Re: AMBER: amber 9 compilation error with mvapich and intel compilers David A. Case (Sat Dec 20 2008 - 16:42:28 CST)
  - Re: AMBER: amber 9 compilation error with mvapich and intel compilers Amit Bajaj (Sun Dec 21 2008 - 23:41:35 CST)
AMBER: Error: tutorial one for md simulation of DNA Catein Catherine (Sun Dec 21 2008 - 21:33:41 CST)
- RE: AMBER: Error: tutorial one for md simulation of DNA balaji nagarajan (Sun Dec 21 2008 - 22:06:55 CST)
  - RE: AMBER: Error: tutorial one for md simulation of DNA Catein Catherine (Sun Dec 21 2008 - 23:12:32 CST)
AMBER: balaji nagarajan (Mon Dec 22 2008 - 07:36:38 CST)
- RE: AMBER: Ross Walker (Mon Dec 22 2008 - 10:41:23 CST)
AMBER: Playstation 3 Benchmarks Andrew Ring (Mon Dec 22 2008 - 18:40:44 CST)
- Re: AMBER: Playstation 3 Benchmarks David Watson (Mon Dec 22 2008 - 19:17:57 CST)
- RE: AMBER: Playstation 3 Benchmarks Ross Walker (Mon Dec 22 2008 - 19:20:38 CST)
AMBER: installation amber9 in fedora9 Vijay Manickam Achari (Mon Dec 22 2008 - 22:44:12 CST)
- Re: AMBER: installation amber9 in fedora9 Scott Brozell (Mon Dec 22 2008 - 23:41:22 CST)
- Re: AMBER: installation amber9 in fedora9 sobereva (Tue Dec 23 2008 - 03:52:00 CST)
AMBER: AMBER10 AMBERTools antechamber Starr Hazard (Tue Dec 23 2008 - 10:36:05 CST)
- Re: AMBER: AMBER10 AMBERTools antechamber M. L. Dodson (Tue Dec 23 2008 - 10:45:46 CST)
- RE: AMBER: AMBER10 AMBERTools antechamber Ross Walker (Tue Dec 23 2008 - 11:09:54 CST)
  - Re: AMBER: AMBER10 AMBERTools antechamber David A. Case (Tue Dec 23 2008 - 13:45:06 CST)
    - Re: AMBER: AMBER10 AMBERTools antechamber M. L. Dodson (Tue Dec 23 2008 - 14:00:13 CST)
AMBER: Switching function in NAMD musa özboyacý (Tue Dec 23 2008 - 13:52:37 CST)
- Re: AMBER: Switching function in NAMD Adrian Roitberg (Tue Dec 23 2008 - 13:56:58 CST)
AMBER: about mmpbsa out data ecustipp (Tue Dec 23 2008 - 20:21:22 CST)
- Re: AMBER: about mmpbsa out data steinbrt_at_rci.rutgers.edu (Tue Dec 23 2008 - 22:53:02 CST)
  - Re:Re: AMBER: about mmpbsa out data ecustipp (Wed Dec 24 2008 - 03:11:50 CST)
AMBER: installation amber9 in fedora9 using bash shell Vijay Manickam Achari (Tue Dec 23 2008 - 22:05:28 CST)
- Re: AMBER: installation amber9 in fedora9 using bash shell David A. Case (Wed Dec 24 2008 - 13:07:35 CST)
AMBER: How to build a cubic box of a newly synthesized compound? Jeffrey (Wed Dec 24 2008 - 00:34:13 CST)
- Re: AMBER: How to build a cubic box of a newly synthesized compound? M. L. Dodson (Wed Dec 24 2008 - 11:45:23 CST)
AMBER: xleap error Vijay Manickam Achari (Wed Dec 24 2008 - 03:58:17 CST)
- Re: AMBER: xleap error David A. Case (Wed Dec 24 2008 - 13:02:11 CST)
AMBER: Beale, John (Wed Dec 24 2008 - 07:19:48 CST)
AMBER: mpirun Permission denied. drugdesign (Thu Dec 25 2008 - 00:49:31 CST)
- Re: AMBER: mpirun Permission denied. Jackie. J. Shen (Tue Dec 30 2008 - 20:32:17 CST)
  - Re: AMBER: mpirun Permission denied. David Watson (Tue Dec 30 2008 - 23:04:40 CST)
AMBER: a question about ff03ua oguz gurbulak (Thu Dec 25 2008 - 08:06:33 CST)
- Re: AMBER: a question about ff03ua David A. Case (Thu Dec 25 2008 - 15:01:56 CST)
AMBER: definition of dihedral in amber Jeffrey (Thu Dec 25 2008 - 09:38:38 CST)
AMBER: vertex atom mismatch ecustipp (Fri Dec 26 2008 - 04:09:45 CST)
AMBER: (no subject) Rajendra P. OJHA (Fri Dec 26 2008 - 06:35:12 CST)
- Re: AMBER: (no subject) ecustipp_at_163.com (Mon Dec 29 2008 - 01:58:20 CST)
AMBER: SMD-related questions Alessandro Nascimento (Mon Dec 29 2008 - 07:07:05 CST)
- Re: AMBER: SMD-related questions M. L. Dodson (Mon Dec 29 2008 - 12:25:19 CST)
- Re: AMBER: SMD-related questions Jackie. J. Shen (Tue Dec 30 2008 - 20:27:16 CST)
AMBER: mwcovar limit? Carra, Claudio (JSC-SK)[USRA] (Mon Dec 29 2008 - 16:31:27 CST)
- RE: AMBER: mwcovar limit? Ross Walker (Wed Dec 31 2008 - 22:44:33 CST)
AMBER: FAD RESP charges and parameters Cenk $Jenk$ Andac (Mon Dec 29 2008 - 16:51:49 CST)
- Re: AMBER: FAD RESP charges and parameters FyD (Tue Dec 30 2008 - 02:45:01 CST)
  - Re: AMBER: FAD RESP charges and parameters Cenk $Jenk$ Andac (Tue Dec 30 2008 - 06:28:41 CST)
    - Re: AMBER: FAD RESP charges and parameters FyD (Tue Dec 30 2008 - 08:19:15 CST)
    - Re: AMBER: FAD RESP charges and parameters Cenk $Jenk$ Andac (Tue Dec 30 2008 - 10:03:17 CST)
AMBER: mdout file details aneesh cna (Tue Dec 30 2008 - 00:20:40 CST)
- Re: AMBER: mdout file details David A. Case (Wed Dec 31 2008 - 10:50:05 CST)
AMBER: periodic boundary Sally Pias (Wed Dec 31 2008 - 02:37:25 CST)
AMBER: RMS plot Beale, John (Wed Dec 31 2008 - 13:11:39 CST)

Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:46 CST

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