AMBER Archive (2009) - Aug 2009 By Subject

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About this archive

Starting: Sat Aug 01 2009 - 00:33:58 CDT
Ending: Mon Aug 31 2009 - 23:48:39 CDT

[AMBER] (no subject)
- workalemahu berhanu (Mon Aug 31 2009 - 00:19:27 CDT)
- workalemahu berhanu (Sat Aug 29 2009 - 10:29:34 CDT)
- workalemahu berhanu (Fri Aug 28 2009 - 11:22:31 CDT)
- workalemahu berhanu (Fri Aug 28 2009 - 09:06:56 CDT)
- case (Fri Aug 07 2009 - 18:54:18 CDT)
- Ross Walker (Fri Aug 07 2009 - 10:35:32 CDT)
- Ashish Runthala (Fri Aug 07 2009 - 08:27:04 CDT)
- Beale, John (Fri Aug 07 2009 - 07:16:58 CDT)
[AMBER] ***PROBLEMS WITH GROUPLRES
- Maria Mirza (Tue Aug 18 2009 - 19:34:41 CDT)
[AMBER] [AmberTool] xleap problem
- ÁÖÅÂ¼º (Mon Aug 17 2009 - 03:57:37 CDT)
[AMBER] ABMD Reaction Coordinates
- stephane acoca (Mon Aug 24 2009 - 00:04:58 CDT)
- stephane acoca (Sun Aug 23 2009 - 22:25:43 CDT)
- stephane acoca (Sun Aug 23 2009 - 22:24:32 CDT)
- stephane acoca (Sun Aug 23 2009 - 22:11:09 CDT)
[AMBER] about file format
- Jia Xu (Sun Aug 30 2009 - 00:32:30 CDT)
- Tom Joseph (Sat Aug 29 2009 - 09:50:37 CDT)
- Jia Xu (Sat Aug 29 2009 - 02:55:49 CDT)
[AMBER] ACE and NME patch: VMD ???
- Siddharth Rastogi (Mon Aug 31 2009 - 19:25:47 CDT)
[AMBER] acetone lib and frcmod files?
- FyD (Tue Aug 25 2009 - 02:50:57 CDT)
- FyD (Tue Aug 25 2009 - 02:47:50 CDT)
- Jose Borreguero (Mon Aug 24 2009 - 16:34:07 CDT)
- FyD (Mon Aug 24 2009 - 15:13:33 CDT)
- Jose Borreguero (Mon Aug 24 2009 - 07:56:51 CDT)
- FyD (Mon Aug 24 2009 - 02:31:40 CDT)
- Ross Walker (Mon Aug 24 2009 - 00:08:16 CDT)
- Jose Borreguero (Sun Aug 23 2009 - 16:36:43 CDT)
[AMBER] amber 10 test fails with pathscale 3.2
- Ross Walker (Mon Aug 17 2009 - 11:34:28 CDT)
- Raj (Mon Aug 17 2009 - 07:54:45 CDT)
[AMBER] AMBER is running silently
- Kefa Lu (Mon Aug 17 2009 - 20:25:14 CDT)
- Ross Walker (Mon Aug 17 2009 - 18:33:09 CDT)
- Kefa Lu (Mon Aug 17 2009 - 18:10:17 CDT)
- Bill Ross (Mon Aug 17 2009 - 18:04:02 CDT)
- Kefa Lu (Mon Aug 17 2009 - 17:47:34 CDT)
[AMBER] AMBER job restart problem
- Kefa Lu (Sun Aug 16 2009 - 00:09:22 CDT)
- Thomas Cheatham (Sat Aug 15 2009 - 23:44:27 CDT)
- Kefa Lu (Sat Aug 15 2009 - 23:36:59 CDT)
- Thomas Cheatham (Sat Aug 15 2009 - 10:49:10 CDT)
- case (Sat Aug 15 2009 - 10:40:51 CDT)
- Ashish Runthala (Sat Aug 15 2009 - 09:39:56 CDT)
- case (Sat Aug 15 2009 - 08:49:44 CDT)
- Kefa Lu (Sat Aug 15 2009 - 05:12:21 CDT)
- Ashish Runthala (Sat Aug 15 2009 - 04:57:48 CDT)
- Kefa Lu (Sat Aug 15 2009 - 03:22:08 CDT)
[AMBER] AMBER on a Mac Mini cluster PoC
- Abdul Rehman Gani (Mon Aug 17 2009 - 07:31:37 CDT)
- Alan (Mon Aug 17 2009 - 05:50:30 CDT)
- Abdul Rehman Gani (Mon Aug 17 2009 - 03:13:38 CDT)
- Ross Walker (Sun Aug 16 2009 - 12:08:47 CDT)
- Abdul Rehman Gani (Sun Aug 16 2009 - 10:51:44 CDT)
[AMBER] AMBER on a Mac Mini cluster PoC - solved
- Abdul Rehman Gani (Mon Aug 17 2009 - 09:44:07 CDT)
[AMBER] amber test fails with ICC 11.0.081
- Carlos Simmerling (Mon Aug 17 2009 - 10:16:26 CDT)
- Raj (Mon Aug 17 2009 - 09:57:57 CDT)
[AMBER] Amber99SB
- Carlos Simmerling (Tue Aug 11 2009 - 09:42:44 CDT)
- eric johnson (Tue Aug 11 2009 - 09:33:34 CDT)
[AMBER] ambertools test faied
- case (Tue Aug 25 2009 - 06:39:16 CDT)
- subarna thakur (Tue Aug 25 2009 - 06:01:12 CDT)
[AMBER] ambpdb water removal for rst files
- Bill Ross (Sat Aug 22 2009 - 09:45:30 CDT)
- Andrew Voronkov (Sat Aug 22 2009 - 01:53:14 CDT)
[AMBER] angle with ptraj
- Seetin, Matthew (Wed Aug 19 2009 - 14:42:07 CDT)
- E.M. (Wed Aug 19 2009 - 14:27:29 CDT)
[AMBER] antechamber am1-bcc issues
- Ross Walker (Thu Aug 20 2009 - 09:29:14 CDT)
- Khavrutskii, Ilja (Thu Aug 20 2009 - 08:04:44 CDT)
- gilbert_at_bluemarble.net (Thu Aug 20 2009 - 07:37:53 CDT)
- Khavrutskii, Ilja (Thu Aug 20 2009 - 07:03:43 CDT)
- Khavrutskii, Ilja (Thu Aug 20 2009 - 06:37:47 CDT)
- case (Thu Aug 20 2009 - 06:18:52 CDT)
- Alan (Thu Aug 20 2009 - 03:28:09 CDT)
- Khavrutskii, Ilja (Tue Aug 18 2009 - 16:00:03 CDT)
- David Mobley (Fri Aug 07 2009 - 13:19:53 CDT)
[AMBER] antechamber bug report
- case (Mon Aug 31 2009 - 12:36:33 CDT)
- Matthew Walsh (Mon Aug 31 2009 - 11:43:08 CDT)
[AMBER] antechamber execution
- FyD (Tue Aug 18 2009 - 18:59:40 CDT)
- subarna thakur (Tue Aug 18 2009 - 01:06:52 CDT)
[AMBER] Any Comment, please
- s. Bill (Tue Aug 11 2009 - 02:56:20 CDT)
[AMBER] Appropriate nmode input file for gas and vacuum phase simulation
- Scott Pendley (Fri Aug 07 2009 - 12:48:52 CDT)
[AMBER] ATP/GTP parameters
- E.M. (Mon Aug 31 2009 - 23:48:39 CDT)
- E.M. (Mon Aug 31 2009 - 15:50:09 CDT)
- FyD (Mon Aug 31 2009 - 15:20:50 CDT)
- case (Mon Aug 31 2009 - 07:41:22 CDT)
- Steve Seibold (Mon Aug 31 2009 - 07:33:04 CDT)
[AMBER] box problem
- Nancy (Mon Aug 17 2009 - 22:27:59 CDT)
- Nancy (Mon Aug 17 2009 - 22:18:02 CDT)
- Ashish Runthala (Mon Aug 17 2009 - 22:08:28 CDT)
- Nancy (Mon Aug 17 2009 - 22:02:21 CDT)
- Nancy (Mon Aug 17 2009 - 21:49:20 CDT)
- Ross Walker (Sun Aug 16 2009 - 11:59:59 CDT)
- Ashish Runthala (Sun Aug 16 2009 - 09:00:50 CDT)
- Nancy (Sun Aug 16 2009 - 02:31:02 CDT)
- Ashish Runthala (Sat Aug 15 2009 - 01:12:10 CDT)
- Nancy (Thu Aug 13 2009 - 21:43:02 CDT)
- case (Thu Aug 13 2009 - 06:50:54 CDT)
- Nancy (Thu Aug 13 2009 - 06:20:20 CDT)
[AMBER] box volume not understood?
- Bill Ross (Fri Aug 21 2009 - 11:15:51 CDT)
- Jio M (Thu Aug 20 2009 - 23:43:31 CDT)
- Bill Ross (Thu Aug 20 2009 - 21:53:52 CDT)
- Ross Walker (Thu Aug 20 2009 - 18:21:00 CDT)
- Jio M (Thu Aug 20 2009 - 13:26:41 CDT)
- Ross Walker (Thu Aug 20 2009 - 10:43:42 CDT)
- Jio M (Thu Aug 20 2009 - 08:54:52 CDT)
[AMBER] Can I do DNA bending with AMBER?
- Catein Catherine (Mon Aug 17 2009 - 01:00:08 CDT)
- case (Sun Aug 16 2009 - 08:13:05 CDT)
- Catein Catherine (Sat Aug 15 2009 - 23:15:26 CDT)
[AMBER] Can i link and refine the modeled domains with different proteins bound on it
- Ashish Runthala (Tue Aug 18 2009 - 06:13:23 CDT)
[AMBER] Can i link and refine two domains of a single protein
- Ashish Runthala (Mon Aug 17 2009 - 10:32:33 CDT)
[AMBER] center of mass
- dhacademic (Thu Aug 20 2009 - 15:50:47 CDT)
[AMBER] Changing pH of the system
- Adrian Roitberg (Sun Aug 30 2009 - 11:18:32 CDT)
- nicholus bhattacharjee (Sun Aug 30 2009 - 10:40:42 CDT)
- Adrian Roitberg (Sun Aug 30 2009 - 10:26:01 CDT)
- nicholus bhattacharjee (Sun Aug 30 2009 - 06:13:17 CDT)
[AMBER] Charge Problem
- FyD (Sat Aug 15 2009 - 07:06:45 CDT)
- Karl Kirschner (Fri Aug 14 2009 - 03:55:07 CDT)
- s. Bill (Fri Aug 14 2009 - 03:25:05 CDT)
[AMBER] Chirality error in pdb
- case (Fri Aug 28 2009 - 06:33:41 CDT)
- xiawei (Fri Aug 28 2009 - 01:41:45 CDT)
- case (Wed Aug 26 2009 - 06:52:18 CDT)
- xiawei (Wed Aug 26 2009 - 02:02:43 CDT)
[AMBER] Computational Resources
- Ross Walker (Wed Aug 05 2009 - 11:08:21 CDT)
- s. Bill (Wed Aug 05 2009 - 10:17:34 CDT)
[AMBER] Conference or workshop on AMBER?
- Dharmik Meghana shankar (Tue Aug 18 2009 - 00:25:25 CDT)
- Ross Walker (Mon Aug 17 2009 - 23:15:52 CDT)
- Ashish Runthala (Mon Aug 17 2009 - 22:04:12 CDT)
- Ross Walker (Mon Aug 17 2009 - 22:00:14 CDT)
- Catein Catherine (Mon Aug 17 2009 - 21:30:04 CDT)
- Ross Walker (Mon Aug 17 2009 - 09:22:14 CDT)
- Catein Catherine (Mon Aug 17 2009 - 00:56:41 CDT)
[AMBER] Conference or workshop on AMBER? Thank you.
- Catein Catherine (Tue Aug 18 2009 - 01:44:45 CDT)
[AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB
- Hector A. Baldoni (Wed Aug 12 2009 - 15:43:28 CDT)
- case (Wed Aug 12 2009 - 14:57:33 CDT)
- Manish Kumar (Wed Aug 12 2009 - 14:44:37 CDT)
[AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates?
- Bill Ross (Tue Aug 18 2009 - 17:59:12 CDT)
- Jose Borreguero (Tue Aug 18 2009 - 17:33:32 CDT)
- FyD (Tue Aug 18 2009 - 19:05:19 CDT)
- Jose Borreguero (Tue Aug 18 2009 - 09:37:39 CDT)
[AMBER] Distance restraint and periodic boundary conditions
- Robert Duke (Sun Aug 23 2009 - 09:50:56 CDT)
- Peter Varnai (Thu Aug 20 2009 - 10:23:48 CDT)
- case (Wed Aug 19 2009 - 19:53:15 CDT)
- Keith Van Nostrand (Wed Aug 19 2009 - 11:44:49 CDT)
- Peter Varnai (Wed Aug 19 2009 - 11:16:01 CDT)
- Peter Varnai (Wed Aug 19 2009 - 10:13:04 CDT)
- case (Tue Aug 18 2009 - 21:02:45 CDT)
- Thomas Cheatham (Tue Aug 18 2009 - 20:23:56 CDT)
- Cyril Falvo (Tue Aug 18 2009 - 19:58:29 CDT)
[AMBER] DivCon - QM/MM
- s. Bill (Tue Aug 11 2009 - 02:54:38 CDT)
- s. Bill (Mon Aug 10 2009 - 09:11:39 CDT)
[AMBER] divcon question
- case (Mon Aug 31 2009 - 07:34:14 CDT)
- Andrei Neamtu (Mon Aug 31 2009 - 06:31:35 CDT)
[AMBER] Do we need to need to rms fit all atoms before calculating correlation motion between residues?
- Catein Catherine (Sun Aug 02 2009 - 22:45:19 CDT)
[AMBER] Docking with Amber
- case (Mon Aug 31 2009 - 19:58:49 CDT)
- Jordan, Brad (Mon Aug 31 2009 - 15:01:15 CDT)
[AMBER] drying of solvent possible ?
- Jio M (Sat Aug 15 2009 - 00:59:08 CDT)
- Bill Ross (Thu Aug 13 2009 - 11:21:35 CDT)
- Jio M (Thu Aug 13 2009 - 08:49:00 CDT)
[AMBER] Dyndom
- Loeffler, Hannes (STFC,DL,CSE) (Sat Aug 29 2009 - 10:18:18 CDT)
- Carlos Simmerling (Sat Aug 29 2009 - 09:59:23 CDT)
- Chunliyan (Sat Aug 29 2009 - 09:43:00 CDT)
[AMBER] Epsilon value for Iron
- bharat lakhani (Tue Aug 25 2009 - 07:24:10 CDT)
[AMBER] Error in equilibration: file _ew_box.f
- case (Fri Aug 07 2009 - 17:34:29 CDT)
- Biswaranjan Meher (Fri Aug 07 2009 - 15:39:00 CDT)
[AMBER] Extreme optimization problems
- case (Thu Aug 06 2009 - 10:51:23 CDT)
- ondrej.prenosil_at_marge.uochb.cas.cz (Thu Aug 06 2009 - 07:04:09 CDT)
[AMBER] gaussain output
- FyD (Mon Aug 17 2009 - 17:59:39 CDT)
- FyD (Mon Aug 17 2009 - 04:50:53 CDT)
- subarna thakur (Mon Aug 17 2009 - 02:11:00 CDT)
[AMBER] gaussian 98 input/output for antechamber/resp
- Karl Kirschner (Thu Aug 13 2009 - 02:26:12 CDT)
- Karl Kirschner (Thu Aug 13 2009 - 01:57:41 CDT)
- wong105_at_llnl.gov (Wed Aug 12 2009 - 13:41:45 CDT)
[AMBER] Gaussian network model (GNM)
- Adrian Roitberg (Fri Aug 21 2009 - 19:49:04 CDT)
- Chih-Ying Lin (Fri Aug 21 2009 - 19:39:07 CDT)
[AMBER] GTP/ATP parameters
- Steve Seibold (Mon Aug 31 2009 - 07:44:56 CDT)
[AMBER] how much % of the total protein motion are described by the first eigenvector?
- jackie (Thu Aug 27 2009 - 10:52:19 CDT)
- Catein Catherine (Thu Aug 27 2009 - 05:02:37 CDT)
- Hannes Loeffler (Thu Aug 27 2009 - 02:21:28 CDT)
- Catein Catherine (Thu Aug 27 2009 - 00:58:27 CDT)
- Hannes Loeffler (Wed Aug 26 2009 - 04:41:31 CDT)
- Catein Catherine (Wed Aug 26 2009 - 04:05:17 CDT)
[AMBER] how to add a new atomtype for MM/GB/SA decomposition analysis
- TaoPaul (Mon Aug 24 2009 - 09:03:51 CDT)
[AMBER] How to derive charges from the output
- FyD (Mon Aug 31 2009 - 15:35:46 CDT)
- bharat lakhani (Mon Aug 31 2009 - 08:43:15 CDT)
- Barbault Florent (Mon Aug 31 2009 - 02:38:09 CDT)
- bharat lakhani (Mon Aug 31 2009 - 00:33:21 CDT)
[AMBER] How to keep the closest solvent mols to each atoms by PTRAJ?
- u8613020_at_msg.ndhu.edu.tw (Thu Aug 06 2009 - 20:40:17 CDT)
[AMBER] how to pull a dna
- balaji nagarajan (Mon Aug 31 2009 - 21:39:10 CDT)
[AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE"
- Jianping Lin (Fri Aug 07 2009 - 15:32:47 CDT)
- Ross Walker (Mon Aug 03 2009 - 14:38:23 CDT)
- Jianping Lin (Mon Aug 03 2009 - 09:57:28 CDT)
[AMBER] How to strip water for MM/GBSA calculations?
- Carlos Simmerling (Fri Aug 21 2009 - 05:53:59 CDT)
- Catein Catherine (Fri Aug 21 2009 - 05:38:27 CDT)
[AMBER] hydrogen bond?
- Jio M (Sun Aug 09 2009 - 06:29:23 CDT)
[AMBER] implicit solvent simulation
- Manish Kumar (Thu Aug 06 2009 - 01:53:54 CDT)
- Ross Walker (Thu Aug 06 2009 - 01:32:24 CDT)
- Manish Kumar (Thu Aug 06 2009 - 00:19:11 CDT)
- Ashish Runthala (Thu Aug 06 2009 - 00:00:50 CDT)
- Manish Kumar (Wed Aug 05 2009 - 23:49:30 CDT)
[AMBER] implicit solvent simulation with new ligand
- Manish Kumar (Thu Aug 06 2009 - 22:29:37 CDT)
[AMBER] Inquiries about antechamber
- jackie (Thu Aug 27 2009 - 10:48:24 CDT)
- FyD (Thu Aug 27 2009 - 01:15:55 CDT)
- Yikan Chen (Wed Aug 26 2009 - 21:05:40 CDT)
- Nicholas Musolino (Wed Aug 26 2009 - 16:02:21 CDT)
- Yikan Chen (Wed Aug 26 2009 - 12:07:20 CDT)
[AMBER] Is it the correct procedures to strip water for MM/GBSA calculations?
- Catein Catherine (Tue Aug 18 2009 - 00:06:18 CDT)
[AMBER] Lennard Jones potential
- Ross Walker (Mon Aug 03 2009 - 14:28:06 CDT)
- Rizwan Tai (Mon Aug 03 2009 - 12:13:16 CDT)
[AMBER] Meaning of GMAX
- Ashish Runthala (Mon Aug 24 2009 - 10:38:46 CDT)
- Adrian Roitberg (Mon Aug 24 2009 - 10:05:36 CDT)
- Ashish Runthala (Mon Aug 24 2009 - 09:59:53 CDT)
- case (Mon Aug 24 2009 - 06:44:34 CDT)
- E.M. (Mon Aug 24 2009 - 04:05:10 CDT)
[AMBER] Measuring volume of the binding pocket
- Mannan (Tue Aug 11 2009 - 21:31:18 CDT)
- Mannan (Tue Aug 11 2009 - 21:03:49 CDT)
[AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?
- Ashish Runthala (Mon Aug 17 2009 - 22:02:43 CDT)
- case (Mon Aug 17 2009 - 21:56:17 CDT)
- Ashish Runthala (Mon Aug 17 2009 - 01:21:45 CDT)
- Catein Catherine (Mon Aug 17 2009 - 00:58:49 CDT)
- Ross Walker (Sat Aug 15 2009 - 23:40:26 CDT)
- Catein Catherine (Sat Aug 15 2009 - 23:12:42 CDT)
- Ashish Runthala (Sat Aug 15 2009 - 22:59:11 CDT)
- Catein Catherine (Sat Aug 15 2009 - 21:45:34 CDT)
- Ashish Runthala (Sat Aug 15 2009 - 01:05:53 CDT)
- Catein Catherine (Thu Aug 13 2009 - 22:38:02 CDT)
- case (Thu Aug 13 2009 - 06:46:02 CDT)
- Catein Catherine (Wed Aug 12 2009 - 21:23:40 CDT)
- case (Tue Aug 11 2009 - 06:54:43 CDT)
- Catein Catherine (Tue Aug 11 2009 - 06:10:09 CDT)
[AMBER] MM-PBSA results
- Dmitry Osolodkin (Fri Aug 07 2009 - 09:31:48 CDT)
[AMBER] MM-PBSA: decompose energy error
- Maria Mirza (Sun Aug 16 2009 - 14:49:06 CDT)
[AMBER] MM_PBSA not successful
- Ross Walker (Sun Aug 16 2009 - 13:15:42 CDT)
- workalemahu berhanu (Sun Aug 16 2009 - 12:22:01 CDT)
- monnet.jordan_at_free.fr (Sat Aug 15 2009 - 17:10:08 CDT)
- Qinghua Liao (Sat Aug 15 2009 - 01:55:40 CDT)
- workalemahu berhanu (Fri Aug 14 2009 - 23:22:57 CDT)
- Qinghua Liao (Fri Aug 14 2009 - 21:43:23 CDT)
- workalemahu berhanu (Fri Aug 14 2009 - 21:36:39 CDT)
- workalemahu berhanu (Fri Aug 14 2009 - 21:21:32 CDT)
- Qinghua Liao (Fri Aug 14 2009 - 20:20:55 CDT)
- Jordan Monnet (Fri Aug 14 2009 - 19:05:00 CDT)
- workalemahu berhanu (Fri Aug 14 2009 - 16:45:41 CDT)
[AMBER] mm_pbsa-Binding and Stability tests?
- Antonija TomiÄ‡ (Wed Aug 26 2009 - 04:15:54 CDT)
- Niel Henriksen (Mon Aug 24 2009 - 12:24:09 CDT)
- Antonija TomiÄ‡ (Mon Aug 24 2009 - 04:51:28 CDT)
- Ray Luo (Fri Aug 21 2009 - 16:29:58 CDT)
- Niel Henriksen (Fri Aug 21 2009 - 09:52:49 CDT)
- Antonija TomiÄ‡ (Fri Aug 21 2009 - 05:04:35 CDT)
[AMBER] Model(l)ing'09 in Erlangen, Germany: Registration Open Until August 31st
- Harald Lanig (Thu Aug 06 2009 - 03:39:07 CDT)
[AMBER] momentum in MD simulation
- dhacademic (Mon Aug 31 2009 - 09:37:42 CDT)
[AMBER] NAB optimization
- case (Thu Aug 13 2009 - 08:56:28 CDT)
- ondrej.prenosil_at_marge.uochb.cas.cz (Thu Aug 13 2009 - 08:45:26 CDT)
[AMBER] NATOM in prmtop and inpcrd files does not agree with the input
- Ross Walker (Tue Aug 25 2009 - 12:55:39 CDT)
- Ashish Runthala (Tue Aug 25 2009 - 00:45:33 CDT)
- Ross Walker (Mon Aug 24 2009 - 23:55:52 CDT)
- Maria Mirza (Mon Aug 24 2009 - 23:41:39 CDT)
[AMBER] Need you help
- Carlos Simmerling (Wed Aug 26 2009 - 08:48:20 CDT)
- bharat lakhani (Wed Aug 26 2009 - 08:41:17 CDT)
[AMBER] nmode output
- Vahdati N. (Wed Aug 05 2009 - 17:26:11 CDT)
[AMBER] nmr restraint for angle between vectors
- Peter Varnai (Fri Aug 28 2009 - 20:10:20 CDT)
[AMBER] nonbon.f question
- Ross Walker (Mon Aug 03 2009 - 13:32:18 CDT)
- Rizwan Tai (Mon Aug 03 2009 - 11:13:21 CDT)
[AMBER] Note regarding posting of the same message multiple times
- Ross Walker (Mon Aug 24 2009 - 00:19:36 CDT)
[AMBER] optimization step length
- Ashish Runthala (Mon Aug 03 2009 - 09:26:28 CDT)
- ondrej.prenosil_at_marge.uochb.cas.cz (Mon Aug 03 2009 - 05:40:15 CDT)
[AMBER] Parameters for haloacetates
- Joseph Nachman (Mon Aug 10 2009 - 09:54:13 CDT)
- Lili Peng (Fri Aug 07 2009 - 23:43:50 CDT)
- Joseph Nachman (Fri Aug 07 2009 - 13:22:34 CDT)
[AMBER] parameters for HIV protease inhibitors
- FyD (Wed Aug 12 2009 - 07:56:18 CDT)
- Oliver Kuhn (Tue Aug 11 2009 - 09:57:24 CDT)
- Carlos Simmerling (Thu Aug 06 2009 - 10:29:39 CDT)
- Oliver Kuhn (Thu Aug 06 2009 - 09:51:03 CDT)
[AMBER] parmchk problem
- case (Tue Aug 11 2009 - 08:51:57 CDT)
- isaac sugden (Wed Aug 05 2009 - 12:21:53 CDT)
- case (Wed Aug 05 2009 - 11:36:27 CDT)
- isaac sugden (Tue Aug 04 2009 - 09:12:29 CDT)
[AMBER] PCA analysis: the first vector is the movement of whole molecule.
- Catein Catherine (Sun Aug 02 2009 - 22:47:07 CDT)
[AMBER] pmemd
- Robert Duke (Mon Aug 24 2009 - 08:42:05 CDT)
- michael (Sat Aug 15 2009 - 06:30:28 CDT)
- Ross Walker (Mon Aug 10 2009 - 19:00:12 CDT)
- michael (Mon Aug 10 2009 - 14:51:59 CDT)
- case (Fri Aug 07 2009 - 10:18:52 CDT)
- michael (Fri Aug 07 2009 - 04:50:29 CDT)
[AMBER] PMEMD 10 overflow issues
- Ross Walker (Sat Aug 22 2009 - 12:25:31 CDT)
- Ross Walker (Sat Aug 22 2009 - 12:21:30 CDT)
- Ashish Runthala (Fri Aug 21 2009 - 21:52:55 CDT)
- ben rodriguez (Fri Aug 21 2009 - 16:17:36 CDT)
- Ross Walker (Fri Aug 21 2009 - 15:57:12 CDT)
- ben rodriguez (Fri Aug 21 2009 - 15:38:05 CDT)
[AMBER] problem compiling amber tools with gcc-4.4.1
- case (Tue Aug 25 2009 - 07:52:35 CDT)
- gilbert_at_bluemarble.net (Mon Aug 24 2009 - 22:07:44 CDT)
[AMBER] problem from xleap
- Tom Joseph (Sat Aug 01 2009 - 06:19:22 CDT)
[AMBER] problem of mm_pbsa
- Jordan Monnet (Thu Aug 13 2009 - 15:04:37 CDT)
- Qinghua Liao (Thu Aug 13 2009 - 08:58:24 CDT)
- Jordan Monnet (Mon Aug 10 2009 - 14:37:55 CDT)
- Qinghua Liao (Fri Aug 07 2009 - 20:11:43 CDT)
- Jordan Monnet (Fri Aug 07 2009 - 18:13:57 CDT)
- Qinghua Liao (Thu Aug 06 2009 - 18:58:55 CDT)
- Rubben Torella (Thu Aug 06 2009 - 10:53:47 CDT)
- Qinghua Liao (Wed Aug 05 2009 - 19:22:13 CDT)
- case (Wed Aug 05 2009 - 10:42:56 CDT)
- Qinghua Liao (Wed Aug 05 2009 - 00:46:51 CDT)
[AMBER] problem with 4-Hydroxyl-Proline tutorial
- FyD (Mon Aug 31 2009 - 15:10:52 CDT)
- Jia Xu (Sun Aug 30 2009 - 02:46:18 CDT)
[AMBER] Problem with Amber8
- Sebastian Petruczynik (Wed Aug 05 2009 - 06:33:05 CDT)
- Ross Walker (Mon Aug 03 2009 - 14:41:28 CDT)
- ondrej.prenosil_at_marge.uochb.cas.cz (Mon Aug 03 2009 - 08:37:01 CDT)
- Sebastian Petruczynik (Mon Aug 03 2009 - 08:28:56 CDT)
[AMBER] Problem with loading PDB into tleap
- Ashish Runthala (Wed Aug 19 2009 - 21:53:04 CDT)
- case (Wed Aug 19 2009 - 18:55:52 CDT)
- ksripath_at_umich.edu (Wed Aug 19 2009 - 14:00:22 CDT)
- Ashish Runthala (Wed Aug 19 2009 - 10:03:19 CDT)
- Kamali Sripathi (Wed Aug 19 2009 - 09:06:15 CDT)
- Ashish Runthala (Wed Aug 19 2009 - 08:56:59 CDT)
- Kamali Sripathi (Wed Aug 19 2009 - 08:21:30 CDT)
[AMBER] Protein Activity
- Ashish Runthala (Tue Aug 04 2009 - 22:42:11 CDT)
- Bill Ross (Tue Aug 04 2009 - 14:59:40 CDT)
- Chih-Ying Lin (Tue Aug 04 2009 - 14:42:42 CDT)
- Bill Ross (Tue Aug 04 2009 - 14:19:32 CDT)
- Chih-Ying Lin (Tue Aug 04 2009 - 12:57:54 CDT)
[AMBER] Protein Domain Motion
- Carlos Simmerling (Fri Aug 14 2009 - 07:17:28 CDT)
- Chih-Ying Lin (Thu Aug 13 2009 - 20:51:14 CDT)
- Carlos Simmerling (Thu Aug 13 2009 - 14:39:39 CDT)
- Chih-Ying Lin (Thu Aug 13 2009 - 14:20:09 CDT)
[AMBER] protein-ligand binding simulation times
- Andrew Voronkov (Sat Aug 22 2009 - 05:32:42 CDT)
- steinbrt_at_rci.rutgers.edu (Sat Aug 22 2009 - 04:50:35 CDT)
- Andrew Voronkov (Sat Aug 22 2009 - 00:09:54 CDT)
[AMBER] ptraj cluster - snapshot number of a representative structure
- Jianyin Shao (Thu Aug 20 2009 - 10:50:22 CDT)
- Marcin Krol (Thu Aug 20 2009 - 03:26:09 CDT)
[AMBER] ptraj failure to parse psf input
- Sasha Buzko (Thu Aug 13 2009 - 18:34:07 CDT)
- Sasha Buzko (Thu Aug 13 2009 - 11:25:32 CDT)
- Thomas Cheatham (Wed Aug 12 2009 - 23:27:34 CDT)
- Sasha Buzko (Wed Aug 12 2009 - 16:16:07 CDT)
- Sasha Buzko (Wed Aug 05 2009 - 14:33:54 CDT)
- case (Wed Aug 05 2009 - 12:32:00 CDT)
- Sasha Buzko (Wed Aug 05 2009 - 11:39:57 CDT)
[AMBER] ptraj imaging of namd generated trajectories
- Vlad Cojocaru (Thu Aug 13 2009 - 04:35:49 CDT)
[AMBER] ptraj limit on trajectory size
- Sasha Buzko (Mon Aug 24 2009 - 17:31:14 CDT)
- Ross Walker (Mon Aug 24 2009 - 17:07:00 CDT)
- Sasha Buzko (Mon Aug 24 2009 - 11:59:30 CDT)
[AMBER] ptraj-image
- Nancy (Thu Aug 13 2009 - 05:35:01 CDT)
[AMBER] ptraj-rms vs carnal; questions on RMSD of ligand drift
- Andrew Voronkov (Sun Aug 23 2009 - 06:55:01 CDT)
[AMBER] QM/MM types.
- Ross Walker (Thu Aug 13 2009 - 11:11:57 CDT)
- ros_at_servidor.unam.mx (Thu Aug 13 2009 - 10:49:02 CDT)
[AMBER] query
- bharat lakhani (Fri Aug 07 2009 - 04:11:42 CDT)
[AMBER] query regarding fes cluster
- FyD (Wed Aug 12 2009 - 08:00:37 CDT)
- subarna thakur (Wed Aug 12 2009 - 00:39:55 CDT)
[AMBER] query regarding resp
- Oliver Kuhn (Tue Aug 11 2009 - 09:24:19 CDT)
- subarna thakur (Fri Aug 07 2009 - 07:14:35 CDT)
[AMBER] Query regarding watershell command
- Mannan (Mon Aug 31 2009 - 05:38:08 CDT)
[AMBER] radial distribution function
- Dharmik Meghana shankar (Sat Aug 01 2009 - 00:33:58 CDT)
[AMBER] radius for Manganese ion
- E.M. (Sun Aug 30 2009 - 18:38:38 CDT)
- Chunliyan (Sat Aug 29 2009 - 09:43:00 CDT)
[AMBER] RDC import from PALES
- case (Fri Aug 28 2009 - 07:01:30 CDT)
- Thomas Pochapsky (Tue Aug 18 2009 - 09:33:42 CDT)
[AMBER] Regarding Minimization maxcyc
- case (Mon Aug 10 2009 - 09:43:00 CDT)
- Ashish Runthala (Sun Aug 09 2009 - 09:09:58 CDT)
[AMBER] Regarding principal component analysis using ptraj
- Arvind Marathe (Fri Aug 28 2009 - 06:56:53 CDT)
- Hannes Loeffler (Fri Aug 28 2009 - 06:45:05 CDT)
- Arvind Marathe (Fri Aug 28 2009 - 06:04:22 CDT)
- Hannes Loeffler (Fri Aug 28 2009 - 02:28:29 CDT)
- Arvind Marathe (Fri Aug 28 2009 - 01:54:40 CDT)
[AMBER] Regd : gaff force field
- Ashish Runthala (Sat Aug 08 2009 - 07:17:37 CDT)
- Ross Walker (Fri Aug 07 2009 - 10:52:07 CDT)
- Ashish Runthala (Fri Aug 07 2009 - 04:08:43 CDT)
- KIRTANA S (Thu Aug 06 2009 - 17:12:15 CDT)
- Ross Walker (Thu Aug 06 2009 - 15:42:14 CDT)
- Nicholas Musolino (Thu Aug 06 2009 - 15:22:37 CDT)
- KIRTANA S (Thu Aug 06 2009 - 15:09:14 CDT)
[AMBER] REMD using hybrid solvent model
- Morad Mustafa (Wed Aug 12 2009 - 14:05:40 CDT)
[AMBER] reset velocity
- Tom Joseph (Thu Aug 13 2009 - 01:26:48 CDT)
- Parimal Kar (Wed Aug 12 2009 - 20:01:33 CDT)
[AMBER] resp calculation for rubredoxin
- vhakkim boy (Wed Aug 19 2009 - 05:11:22 CDT)
[AMBER] RESP charges of Fe4S4 cluster
- case (Fri Aug 21 2009 - 09:13:23 CDT)
- vhakkim boy (Wed Aug 19 2009 - 03:40:59 CDT)
- subarna thakur (Wed Aug 19 2009 - 02:53:20 CDT)
[AMBER] sander does not print out all residues in range.
- Maria Mirza (Tue Aug 25 2009 - 00:17:59 CDT)
- Ross Walker (Tue Aug 25 2009 - 00:00:03 CDT)
- Maria Mirza (Mon Aug 24 2009 - 23:32:31 CDT)
[AMBER] SCC-DFTB MD for mercury ions in proteins
- Adrian Roitberg (Thu Aug 27 2009 - 11:51:21 CDT)
- Vaida Arciðauskaitë (Thu Aug 27 2009 - 11:41:17 CDT)
[AMBER] Setting a constrain in one direction
- matthew_seetin_at_urmc.rochester.edu (Fri Aug 28 2009 - 09:35:57 CDT)
- Nicholas Musolino (Thu Aug 27 2009 - 22:40:54 CDT)
- Darren Yang (Thu Aug 27 2009 - 22:15:30 CDT)
[AMBER] Should I neutralize the models with Na+ or Mg2+ containing DNA and protein residues
- case (Sun Aug 16 2009 - 08:14:14 CDT)
- Catein Catherine (Sat Aug 15 2009 - 23:18:28 CDT)
[AMBER] Showing error
- bharat lakhani (Sat Aug 01 2009 - 08:12:00 CDT)
[AMBER] Showing error in energy minimization
- Ashish Runthala (Sun Aug 02 2009 - 22:05:06 CDT)
- case (Sun Aug 02 2009 - 09:25:04 CDT)
- bharat lakhani (Sun Aug 02 2009 - 01:22:30 CDT)
[AMBER] showing error when creating topology and coordinate file
- bharat lakhani (Mon Aug 03 2009 - 02:19:59 CDT)
[AMBER] Single Adenine
- FyD (Thu Aug 27 2009 - 16:20:48 CDT)
- ros (Thu Aug 27 2009 - 11:27:06 CDT)
- FyD (Thu Aug 27 2009 - 02:05:54 CDT)
- Bill Ross (Wed Aug 26 2009 - 14:28:31 CDT)
- ros (Wed Aug 26 2009 - 12:50:54 CDT)
- case (Wed Aug 26 2009 - 06:48:36 CDT)
- case (Wed Aug 26 2009 - 06:36:09 CDT)
- ros (Wed Aug 26 2009 - 01:09:23 CDT)
[AMBER] sourcing leap commands in log file
- Ashish Runthala (Sat Aug 15 2009 - 01:50:31 CDT)
- Bill Ross (Wed Aug 12 2009 - 19:47:57 CDT)
- Donald Keidel (Wed Aug 12 2009 - 19:32:31 CDT)
[AMBER] Strange QM/MM Divcon - help me out
- Ross Walker (Sun Aug 16 2009 - 11:55:01 CDT)
- Ashish Runthala (Sat Aug 15 2009 - 01:42:38 CDT)
- case (Thu Aug 13 2009 - 10:52:34 CDT)
- s. Bill (Thu Aug 13 2009 - 10:37:54 CDT)
[AMBER] suggestions pls
- Jio M (Wed Aug 12 2009 - 08:04:16 CDT)
- Ashish Runthala (Tue Aug 11 2009 - 21:40:40 CDT)
- Jio M (Tue Aug 11 2009 - 12:44:19 CDT)
[AMBER] Timescales and restraints for protein-small ligands movement simulations
- Vivek Sharma (Sun Aug 02 2009 - 01:29:13 CDT)
- Andrew Voronkov (Sat Aug 01 2009 - 09:14:49 CDT)
- Andrew Voronkov (Sat Aug 01 2009 - 01:23:19 CDT)
[AMBER] TWO restraints with different force constants
- A. Gomez-Sicilia (Wed Aug 05 2009 - 07:20:54 CDT)
- s. Bill (Wed Aug 05 2009 - 06:54:18 CDT)
[AMBER] update on am1-bcc charge problem in antechamber
- case (Fri Aug 21 2009 - 11:32:30 CDT)
[AMBER] USE A VERSION COMPILED WITHOUT -DLES
- s. Bill (Wed Aug 05 2009 - 06:55:55 CDT)
- s. Bill (Wed Aug 05 2009 - 05:50:01 CDT)
[AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj
- Paul Frybarger (Mon Aug 17 2009 - 12:57:28 CDT)
- workalemahu berhanu (Mon Aug 17 2009 - 08:26:35 CDT)
- workalemahu berhanu (Sun Aug 16 2009 - 15:13:21 CDT)
[AMBER] WATERSHELL
- Mannan (Mon Aug 31 2009 - 00:02:51 CDT)
[AMBER] What is the meaning of IED values for PCA analysis?
- case (Wed Aug 05 2009 - 11:39:30 CDT)
- Catein Catherine (Mon Aug 03 2009 - 09:30:15 CDT)
[AMBER] What is the parameters for Mg2+?
- Catein Catherine (Mon Aug 17 2009 - 00:59:23 CDT)
- Tom Joseph (Sun Aug 16 2009 - 11:00:35 CDT)
- Catein Catherine (Sat Aug 15 2009 - 23:21:46 CDT)
[AMBER] why is nonpolar solvation energy not implemented for dynamic in amber
- TaoPaul (Wed Aug 19 2009 - 10:29:38 CDT)
[AMBER] Why..QM/MM
- Ross Walker (Sat Aug 08 2009 - 12:00:27 CDT)
- s. Bill (Sat Aug 08 2009 - 06:26:46 CDT)
[AMBER] xleap installation error
- Scott Brozell (Mon Aug 03 2009 - 11:57:18 CDT)
- Bokun Cho (Mon Aug 03 2009 - 00:18:00 CDT)
[AMBER] ZPVE simple question
- case (Wed Aug 26 2009 - 06:41:27 CDT)
- Jerome.GOLEBIOWSKI_at_unice.fr (Wed Aug 26 2009 - 06:15:00 CDT)
- ondrej.prenosil_at_marge.uochb.cas.cz (Wed Aug 26 2009 - 04:42:04 CDT)
[Amber]: REMD using hybrid solvent model
- Morad Mustafa (Fri Aug 14 2009 - 07:44:44 CDT)
- Carlos Simmerling (Wed Aug 12 2009 - 18:54:20 CDT)
- Carlos Simmerling (Wed Aug 12 2009 - 18:52:56 CDT)
- Morad Mustafa (Wed Aug 12 2009 - 16:30:01 CDT)
[q4md-fft] charge calculation
- FyD (Mon Aug 17 2009 - 18:40:49 CDT)
AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
- Andrew Voronkov (Sun Aug 23 2009 - 08:48:07 CDT)
angle with ptraj
- E.M. (Wed Aug 19 2009 - 14:44:56 CDT)
antechamber am1-bcc issues
- Khavrutskii, Ilja (Fri Aug 21 2009 - 14:32:34 CDT)
- Khavrutskii, Ilja (Fri Aug 21 2009 - 11:27:28 CDT)
- David Mobley (Thu Aug 13 2009 - 08:25:52 CDT)
- case (Sat Aug 08 2009 - 14:20:44 CDT)
- gilbert_at_bluemarble.net (Sat Aug 08 2009 - 08:55:40 CDT)
- case (Fri Aug 07 2009 - 18:54:38 CDT)
AW: [AMBER] Any Comment, please
- s. Bill (Tue Aug 11 2009 - 03:22:16 CDT)
- Aust, Susanne (Tue Aug 11 2009 - 03:17:18 CDT)
AW: [AMBER] Conference or workshop on AMBER?
- Aust, Susanne (Wed Aug 19 2009 - 03:16:21 CDT)
AW: [AMBER] TWO restraints with different force constants
- Aust, Susanne (Wed Aug 05 2009 - 07:31:38 CDT)
AW: AW: [AMBER] Any Comment, please
- Aust, Susanne (Tue Aug 11 2009 - 03:36:34 CDT)
How to solve the problem "RESTARTED DUE to LINMIN FAILURE"
- Bill Ross (Mon Aug 10 2009 - 20:30:07 CDT)
- Jianping Lin (Mon Aug 10 2009 - 20:23:44 CDT)
- Bill Ross (Mon Aug 10 2009 - 20:17:05 CDT)
- Jianping Lin (Mon Aug 10 2009 - 18:18:44 CDT)
implicit solvent simulation with new ligand
- Carlos Simmerling (Mon Aug 10 2009 - 09:42:33 CDT)
- Manish Kumar (Fri Aug 07 2009 - 14:08:59 CDT)
- Carlos Simmerling (Fri Aug 07 2009 - 13:29:46 CDT)
- Manish Kumar (Fri Aug 07 2009 - 13:22:57 CDT)
ptraj imaging of namd generated trajectories
- Vlad Cojocaru (Thu Aug 13 2009 - 05:10:54 CDT)
query
- Ashish Runthala (Sat Aug 01 2009 - 07:21:47 CDT)
- bharat lakhani (Sat Aug 01 2009 - 07:07:24 CDT)
question_on_MMPBSA
- jackie (Thu Aug 27 2009 - 10:41:28 CDT)
- Catein Catherine (Thu Aug 27 2009 - 00:55:59 CDT)
- jackie (Wed Aug 26 2009 - 10:08:01 CDT)
showing error when creating topology and coordinate file
- Olotu Odunayo (Tue Aug 04 2009 - 08:08:32 CDT)
- bharat lakhani (Mon Aug 03 2009 - 23:54:36 CDT)

Last message date: Mon Nov 23 2009 - 13:51:08 CST
Archived on: Mon Nov 23 2009 - 13:51:12 CST

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