Amber Archive Aug 2009: by subject

[AMBER] (no subject)
- workalemahu berhanu (Sun Aug 30 2009 - 22:19:27 PDT)
- workalemahu berhanu (Sat Aug 29 2009 - 08:29:34 PDT)
- workalemahu berhanu (Fri Aug 28 2009 - 09:22:31 PDT)
- workalemahu berhanu (Fri Aug 28 2009 - 07:06:56 PDT)
- case (Fri Aug 07 2009 - 16:54:18 PDT)
- Ross Walker (Fri Aug 07 2009 - 08:35:32 PDT)
- Ashish Runthala (Fri Aug 07 2009 - 06:27:04 PDT)
- Beale, John (Fri Aug 07 2009 - 05:16:58 PDT)
[AMBER] ***PROBLEMS WITH GROUPLRES
- Maria Mirza (Tue Aug 18 2009 - 17:34:41 PDT)
[AMBER] [AmberTool] xleap problem
- 주태성 (Mon Aug 17 2009 - 01:57:37 PDT)
[AMBER] ABMD Reaction Coordinates
- stephane acoca (Sun Aug 23 2009 - 22:04:58 PDT)
- stephane acoca (Sun Aug 23 2009 - 20:25:43 PDT)
- stephane acoca (Sun Aug 23 2009 - 20:24:32 PDT)
- stephane acoca (Sun Aug 23 2009 - 20:11:09 PDT)
[AMBER] about file format
- Jia Xu (Sat Aug 29 2009 - 22:32:30 PDT)
- Tom Joseph (Sat Aug 29 2009 - 07:50:37 PDT)
- Jia Xu (Sat Aug 29 2009 - 00:55:49 PDT)
[AMBER] acetone lib and frcmod files?
- FyD (Tue Aug 25 2009 - 00:50:57 PDT)
- FyD (Tue Aug 25 2009 - 00:47:50 PDT)
- Jose Borreguero (Mon Aug 24 2009 - 14:34:07 PDT)
- FyD (Mon Aug 24 2009 - 13:13:33 PDT)
- Jose Borreguero (Mon Aug 24 2009 - 05:56:51 PDT)
- FyD (Mon Aug 24 2009 - 00:31:40 PDT)
- Ross Walker (Sun Aug 23 2009 - 22:08:16 PDT)
- Jose Borreguero (Sun Aug 23 2009 - 14:36:43 PDT)
[AMBER] amber 10 test fails with pathscale 3.2
- Ross Walker (Mon Aug 17 2009 - 09:34:28 PDT)
- Raj (Mon Aug 17 2009 - 05:54:45 PDT)
[AMBER] AMBER is running silently
- Kefa Lu (Mon Aug 17 2009 - 18:25:14 PDT)
- Ross Walker (Mon Aug 17 2009 - 16:33:09 PDT)
- Kefa Lu (Mon Aug 17 2009 - 16:10:17 PDT)
- Bill Ross (Mon Aug 17 2009 - 16:04:02 PDT)
- Kefa Lu (Mon Aug 17 2009 - 15:47:34 PDT)
[AMBER] AMBER job restart problem
- Kefa Lu (Sat Aug 15 2009 - 22:09:22 PDT)
- Thomas Cheatham (Sat Aug 15 2009 - 21:44:27 PDT)
- Kefa Lu (Sat Aug 15 2009 - 21:36:59 PDT)
- Thomas Cheatham (Sat Aug 15 2009 - 08:49:10 PDT)
- case (Sat Aug 15 2009 - 08:40:51 PDT)
- Ashish Runthala (Sat Aug 15 2009 - 07:39:56 PDT)
- case (Sat Aug 15 2009 - 06:49:44 PDT)
- Kefa Lu (Sat Aug 15 2009 - 03:12:21 PDT)
- Ashish Runthala (Sat Aug 15 2009 - 02:57:48 PDT)
- Kefa Lu (Sat Aug 15 2009 - 01:22:08 PDT)
[AMBER] AMBER on a Mac Mini cluster PoC
- Abdul Rehman Gani (Mon Aug 17 2009 - 05:31:37 PDT)
- Alan (Mon Aug 17 2009 - 03:50:30 PDT)
- Abdul Rehman Gani (Mon Aug 17 2009 - 01:13:38 PDT)
- Alan (Sun Aug 16 2009 - 15:30:19 PDT)
- Ross Walker (Sun Aug 16 2009 - 10:08:47 PDT)
- Abdul Rehman Gani (Sun Aug 16 2009 - 08:51:44 PDT)
[AMBER] AMBER on a Mac Mini cluster PoC - solved
- Abdul Rehman Gani (Mon Aug 17 2009 - 07:44:07 PDT)
[AMBER] amber test fails with ICC 11.0.081
- Carlos Simmerling (Mon Aug 17 2009 - 08:16:26 PDT)
- Raj (Mon Aug 17 2009 - 07:57:57 PDT)
[AMBER] Amber99SB
- Carlos Simmerling (Tue Aug 11 2009 - 07:42:44 PDT)
- eric johnson (Tue Aug 11 2009 - 07:33:34 PDT)
[AMBER] ambertools test faied
- case (Tue Aug 25 2009 - 04:39:16 PDT)
- subarna thakur (Tue Aug 25 2009 - 04:01:12 PDT)
[AMBER] ambpdb problem
- Ashish Runthala (Fri Jul 31 2009 - 18:28:42 PDT)
[AMBER] ambpdb water removal for rst files
- Bill Ross (Sat Aug 22 2009 - 07:45:30 PDT)
- Andrew Voronkov (Fri Aug 21 2009 - 23:53:14 PDT)
[AMBER] angle with ptraj
- Seetin, Matthew (Wed Aug 19 2009 - 12:42:07 PDT)
- E.M. (Wed Aug 19 2009 - 12:27:29 PDT)
[AMBER] antechamber am1-bcc issues
- Ross Walker (Thu Aug 20 2009 - 07:29:14 PDT)
- Khavrutskii, Ilja (Thu Aug 20 2009 - 06:04:44 PDT)
- gilbert.bluemarble.net (Thu Aug 20 2009 - 05:37:53 PDT)
- Khavrutskii, Ilja (Thu Aug 20 2009 - 05:03:43 PDT)
- Khavrutskii, Ilja (Thu Aug 20 2009 - 04:37:47 PDT)
- case (Thu Aug 20 2009 - 04:18:52 PDT)
- Alan (Thu Aug 20 2009 - 01:28:09 PDT)
- Khavrutskii, Ilja (Tue Aug 18 2009 - 14:00:03 PDT)
- David Mobley (Fri Aug 07 2009 - 11:19:53 PDT)
[AMBER] antechamber bug report
- case (Mon Aug 31 2009 - 10:36:33 PDT)
- Matthew Walsh (Mon Aug 31 2009 - 09:43:08 PDT)
[AMBER] antechamber execution
- FyD (Tue Aug 18 2009 - 16:59:40 PDT)
- subarna thakur (Mon Aug 17 2009 - 23:06:52 PDT)
[AMBER] Any Comment, please
- s. Bill (Tue Aug 11 2009 - 00:56:20 PDT)
[AMBER] Appropriate nmode input file for gas and vacuum phase simulation
- case (Sat Aug 08 2009 - 12:20:37 PDT)
- Scott Pendley (Fri Aug 07 2009 - 10:48:52 PDT)
[AMBER] ATP/GTP parameters
- E.M. (Mon Aug 31 2009 - 13:50:09 PDT)
- FyD (Mon Aug 31 2009 - 13:20:50 PDT)
- case (Mon Aug 31 2009 - 05:41:22 PDT)
[AMBER] box problem
- Nancy (Mon Aug 17 2009 - 20:27:59 PDT)
- Nancy (Mon Aug 17 2009 - 20:18:02 PDT)
- Ashish Runthala (Mon Aug 17 2009 - 20:08:28 PDT)
- Nancy (Mon Aug 17 2009 - 20:02:21 PDT)
- Nancy (Mon Aug 17 2009 - 19:49:20 PDT)
- Ross Walker (Sun Aug 16 2009 - 09:59:59 PDT)
- Ashish Runthala (Sun Aug 16 2009 - 07:00:50 PDT)
- Nancy (Sun Aug 16 2009 - 00:31:02 PDT)
- Ashish Runthala (Fri Aug 14 2009 - 23:12:10 PDT)
- Nancy (Thu Aug 13 2009 - 19:43:02 PDT)
- case (Thu Aug 13 2009 - 04:50:54 PDT)
- Nancy (Thu Aug 13 2009 - 04:20:20 PDT)
[AMBER] box volume not understood?
- Bill Ross (Fri Aug 21 2009 - 09:15:51 PDT)
- Jio M (Thu Aug 20 2009 - 21:43:31 PDT)
- Bill Ross (Thu Aug 20 2009 - 19:53:52 PDT)
- Ross Walker (Thu Aug 20 2009 - 16:21:00 PDT)
- Jio M (Thu Aug 20 2009 - 11:26:41 PDT)
- Ross Walker (Thu Aug 20 2009 - 08:43:42 PDT)
- Jio M (Thu Aug 20 2009 - 06:54:52 PDT)
[AMBER] Can I do DNA bending with AMBER?
- Catein Catherine (Sun Aug 16 2009 - 23:00:08 PDT)
- case (Sun Aug 16 2009 - 06:13:05 PDT)
- Catein Catherine (Sat Aug 15 2009 - 21:15:26 PDT)
[AMBER] Can i link and refine the modeled domains with different proteins bound on it
- Ashish Runthala (Tue Aug 18 2009 - 04:13:23 PDT)
[AMBER] Can i link and refine two domains of a single protein
- Ashish Runthala (Mon Aug 17 2009 - 08:32:33 PDT)
[AMBER] center of mass
- dhacademic (Thu Aug 20 2009 - 13:50:47 PDT)
[AMBER] Changing pH of the system
- Adrian Roitberg (Sun Aug 30 2009 - 09:18:32 PDT)
- nicholus bhattacharjee (Sun Aug 30 2009 - 08:40:42 PDT)
- Adrian Roitberg (Sun Aug 30 2009 - 08:26:01 PDT)
- nicholus bhattacharjee (Sun Aug 30 2009 - 04:13:17 PDT)
[AMBER] Charge Problem
- FyD (Sat Aug 15 2009 - 05:06:45 PDT)
- Karl Kirschner (Fri Aug 14 2009 - 01:55:07 PDT)
- s. Bill (Fri Aug 14 2009 - 01:25:05 PDT)
[AMBER] Chirality error in pdb
- case (Fri Aug 28 2009 - 04:33:41 PDT)
- xiawei (Thu Aug 27 2009 - 23:41:45 PDT)
- case (Wed Aug 26 2009 - 04:52:18 PDT)
- xiawei (Wed Aug 26 2009 - 00:02:43 PDT)
[AMBER] Computational Resources
- Ross Walker (Wed Aug 05 2009 - 09:08:21 PDT)
- s. Bill (Wed Aug 05 2009 - 08:17:34 PDT)
[AMBER] Conference or workshop on AMBER?
- Dharmik Meghana shankar (Mon Aug 17 2009 - 22:25:25 PDT)
- Ross Walker (Mon Aug 17 2009 - 21:15:52 PDT)
- Ashish Runthala (Mon Aug 17 2009 - 20:04:12 PDT)
- Ross Walker (Mon Aug 17 2009 - 20:00:14 PDT)
- Catein Catherine (Mon Aug 17 2009 - 19:30:04 PDT)
- Ross Walker (Mon Aug 17 2009 - 07:22:14 PDT)
- Catein Catherine (Sun Aug 16 2009 - 22:56:41 PDT)
[AMBER] Conference or workshop on AMBER? Thank you.
- Catein Catherine (Mon Aug 17 2009 - 23:44:45 PDT)
[AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB
- Hector A. Baldoni (Wed Aug 12 2009 - 13:43:28 PDT)
- case (Wed Aug 12 2009 - 12:57:33 PDT)
- Manish Kumar (Wed Aug 12 2009 - 12:44:37 PDT)
[AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates?
- Bill Ross (Tue Aug 18 2009 - 15:59:12 PDT)
- Jose Borreguero (Tue Aug 18 2009 - 15:33:32 PDT)
- FyD (Tue Aug 18 2009 - 17:05:19 PDT)
- Jose Borreguero (Tue Aug 18 2009 - 07:37:39 PDT)
[AMBER] Distance restraint and periodic boundary conditions
- Robert Duke (Sun Aug 23 2009 - 07:50:56 PDT)
- Peter Varnai (Thu Aug 20 2009 - 08:23:48 PDT)
- case (Wed Aug 19 2009 - 17:53:15 PDT)
- Keith Van Nostrand (Wed Aug 19 2009 - 09:44:49 PDT)
- Peter Varnai (Wed Aug 19 2009 - 09:16:01 PDT)
- Peter Varnai (Wed Aug 19 2009 - 08:13:04 PDT)
- case (Tue Aug 18 2009 - 19:02:45 PDT)
- Thomas Cheatham (Tue Aug 18 2009 - 18:23:56 PDT)
- Cyril Falvo (Tue Aug 18 2009 - 17:58:29 PDT)
[AMBER] DivCon - QM/MM
- s. Bill (Tue Aug 11 2009 - 00:54:38 PDT)
- s. Bill (Mon Aug 10 2009 - 07:11:39 PDT)
[AMBER] divcon question
- case (Mon Aug 31 2009 - 05:34:14 PDT)
- Andrei Neamtu (Mon Aug 31 2009 - 04:31:35 PDT)
[AMBER] Do we need to need to rms fit all atoms before calculating correlation motion between residues?
- Catein Catherine (Sun Aug 02 2009 - 20:45:19 PDT)
[AMBER] drying of solvent possible ?
- Jio M (Fri Aug 14 2009 - 22:59:08 PDT)
- Bill Ross (Thu Aug 13 2009 - 09:21:35 PDT)
- Jio M (Thu Aug 13 2009 - 06:49:00 PDT)
[AMBER] Dyndom
- Loeffler, Hannes (STFC,DL,CSE) (Sat Aug 29 2009 - 08:18:18 PDT)
- Carlos Simmerling (Sat Aug 29 2009 - 07:59:23 PDT)
- Chunliyan (Sat Aug 29 2009 - 07:43:00 PDT)
[AMBER] Epsilon value for Iron
- bharat lakhani (Tue Aug 25 2009 - 05:24:10 PDT)
[AMBER] Error in equilibration: file _ew_box.f
- case (Fri Aug 07 2009 - 15:34:29 PDT)
- Biswaranjan Meher (Fri Aug 07 2009 - 13:39:00 PDT)
[AMBER] Extreme optimization problems
- case (Thu Aug 06 2009 - 08:51:23 PDT)
- ondrej.prenosil.marge.uochb.cas.cz (Thu Aug 06 2009 - 05:04:09 PDT)
[AMBER] gaussain output
- FyD (Mon Aug 17 2009 - 15:59:39 PDT)
- FyD (Mon Aug 17 2009 - 02:50:53 PDT)
- subarna thakur (Mon Aug 17 2009 - 00:11:00 PDT)
[AMBER] gaussian 98 input/output for antechamber/resp
- Karl Kirschner (Thu Aug 13 2009 - 00:26:12 PDT)
- Karl Kirschner (Wed Aug 12 2009 - 23:57:41 PDT)
- wong105.llnl.gov (Wed Aug 12 2009 - 11:41:45 PDT)
[AMBER] Gaussian network model (GNM)
- Adrian Roitberg (Fri Aug 21 2009 - 17:49:04 PDT)
- Chih-Ying Lin (Fri Aug 21 2009 - 17:39:07 PDT)
[AMBER] how much % of the total protein motion are described by the first eigenvector?
- jackie (Thu Aug 27 2009 - 08:52:19 PDT)
- Catein Catherine (Thu Aug 27 2009 - 03:02:37 PDT)
- Hannes Loeffler (Thu Aug 27 2009 - 00:21:28 PDT)
- Catein Catherine (Wed Aug 26 2009 - 22:58:27 PDT)
- Hannes Loeffler (Wed Aug 26 2009 - 02:41:31 PDT)
- Catein Catherine (Wed Aug 26 2009 - 02:05:17 PDT)
[AMBER] how to add a new atomtype for MM/GB/SA decomposition analysis
- TaoPaul (Mon Aug 24 2009 - 07:03:51 PDT)
[AMBER] How to derive charges from the output
- FyD (Mon Aug 31 2009 - 13:35:46 PDT)
- bharat lakhani (Mon Aug 31 2009 - 06:43:15 PDT)
- Barbault Florent (Mon Aug 31 2009 - 00:38:09 PDT)
- bharat lakhani (Sun Aug 30 2009 - 22:33:21 PDT)
[AMBER] How to keep the closest solvent mols to each atoms by PTRAJ?
- u8613020.msg.ndhu.edu.tw (Thu Aug 06 2009 - 18:40:17 PDT)
[AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE"
- Jianping Lin (Fri Aug 07 2009 - 13:32:47 PDT)
- Ross Walker (Mon Aug 03 2009 - 12:38:23 PDT)
- Jianping Lin (Mon Aug 03 2009 - 07:57:28 PDT)
[AMBER] How to strip water for MM/GBSA calculations?
- Carlos Simmerling (Fri Aug 21 2009 - 03:53:59 PDT)
- Catein Catherine (Fri Aug 21 2009 - 03:38:27 PDT)
[AMBER] hydrogen bond?
- Jio M (Sun Aug 09 2009 - 04:29:23 PDT)
[AMBER] implicit solvent simulation
- Manish Kumar (Wed Aug 05 2009 - 23:53:54 PDT)
- Ross Walker (Wed Aug 05 2009 - 23:32:24 PDT)
- Manish Kumar (Wed Aug 05 2009 - 22:19:11 PDT)
- Ashish Runthala (Wed Aug 05 2009 - 22:00:50 PDT)
- Manish Kumar (Wed Aug 05 2009 - 21:49:30 PDT)
[AMBER] implicit solvent simulation with new ligand
- Manish Kumar (Thu Aug 06 2009 - 20:29:37 PDT)
[AMBER] Inquiries about antechamber
- jackie (Thu Aug 27 2009 - 08:48:24 PDT)
- FyD (Wed Aug 26 2009 - 23:15:55 PDT)
- Yikan Chen (Wed Aug 26 2009 - 19:05:40 PDT)
- Nicholas Musolino (Wed Aug 26 2009 - 14:02:21 PDT)
- Yikan Chen (Wed Aug 26 2009 - 10:07:20 PDT)
[AMBER] Is it the correct procedures to strip water for MM/GBSA calculations?
- Catein Catherine (Mon Aug 17 2009 - 22:06:18 PDT)
[AMBER] Lennard Jones potential
- Ross Walker (Mon Aug 03 2009 - 12:28:06 PDT)
- Rizwan Tai (Mon Aug 03 2009 - 10:13:16 PDT)
[AMBER] Meaning of GMAX
- Ashish Runthala (Mon Aug 24 2009 - 08:38:46 PDT)
- Adrian Roitberg (Mon Aug 24 2009 - 08:05:36 PDT)
- Ashish Runthala (Mon Aug 24 2009 - 07:59:53 PDT)
- case (Mon Aug 24 2009 - 04:44:34 PDT)
- E.M. (Mon Aug 24 2009 - 02:05:10 PDT)
[AMBER] Measuring volume of the binding pocket
- Mannan (Tue Aug 11 2009 - 19:31:18 PDT)
- Mannan (Tue Aug 11 2009 - 19:03:49 PDT)
[AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?
- Ashish Runthala (Mon Aug 17 2009 - 20:02:43 PDT)
- case (Mon Aug 17 2009 - 19:56:17 PDT)
- Ashish Runthala (Sun Aug 16 2009 - 23:21:45 PDT)
- Catein Catherine (Sun Aug 16 2009 - 22:58:49 PDT)
- Ross Walker (Sat Aug 15 2009 - 21:40:26 PDT)
- Catein Catherine (Sat Aug 15 2009 - 21:12:42 PDT)
- Ashish Runthala (Sat Aug 15 2009 - 20:59:11 PDT)
- Catein Catherine (Sat Aug 15 2009 - 19:45:34 PDT)
- Ashish Runthala (Fri Aug 14 2009 - 23:05:53 PDT)
- Catein Catherine (Thu Aug 13 2009 - 20:38:02 PDT)
- case (Thu Aug 13 2009 - 04:46:02 PDT)
- Catein Catherine (Wed Aug 12 2009 - 19:23:40 PDT)
- case (Tue Aug 11 2009 - 04:54:43 PDT)
- Catein Catherine (Tue Aug 11 2009 - 04:10:09 PDT)
[AMBER] MM-PBSA results
- Dmitry Osolodkin (Fri Aug 07 2009 - 07:31:48 PDT)
[AMBER] MM-PBSA: decompose energy error
- Maria Mirza (Sun Aug 16 2009 - 12:49:06 PDT)
[AMBER] MM_PBSA not successful
- Ross Walker (Sun Aug 16 2009 - 11:15:42 PDT)
- workalemahu berhanu (Sun Aug 16 2009 - 10:22:01 PDT)
- monnet.jordan.free.fr (Sat Aug 15 2009 - 15:10:08 PDT)
- Qinghua Liao (Fri Aug 14 2009 - 23:55:40 PDT)
- workalemahu berhanu (Fri Aug 14 2009 - 21:22:57 PDT)
- Qinghua Liao (Fri Aug 14 2009 - 19:43:23 PDT)
- workalemahu berhanu (Fri Aug 14 2009 - 19:36:39 PDT)
- workalemahu berhanu (Fri Aug 14 2009 - 19:21:32 PDT)
- Qinghua Liao (Fri Aug 14 2009 - 18:20:55 PDT)
- Jordan Monnet (Fri Aug 14 2009 - 17:05:00 PDT)
- workalemahu berhanu (Fri Aug 14 2009 - 14:45:41 PDT)
[AMBER] mm_pbsa-Binding and Stability tests?
- Antonija Tomić (Wed Aug 26 2009 - 02:15:54 PDT)
- Niel Henriksen (Mon Aug 24 2009 - 10:24:09 PDT)
- Antonija Tomić (Mon Aug 24 2009 - 02:51:28 PDT)
- Ray Luo (Fri Aug 21 2009 - 14:29:58 PDT)
- Niel Henriksen (Fri Aug 21 2009 - 07:52:49 PDT)
- Antonija Tomić (Fri Aug 21 2009 - 03:04:35 PDT)
[AMBER] Model(l)ing'09 in Erlangen, Germany: Registration Open Until August 31st
- Harald Lanig (Thu Aug 06 2009 - 01:39:07 PDT)
[AMBER] momentum in MD simulation
- dhacademic (Mon Aug 31 2009 - 07:37:42 PDT)
[AMBER] NAB optimization
- case (Thu Aug 13 2009 - 06:56:28 PDT)
- ondrej.prenosil.marge.uochb.cas.cz (Thu Aug 13 2009 - 06:45:26 PDT)
[AMBER] NATOM in prmtop and inpcrd files does not agree with the input
- Ross Walker (Tue Aug 25 2009 - 10:55:39 PDT)
- Ashish Runthala (Mon Aug 24 2009 - 22:45:33 PDT)
- Ross Walker (Mon Aug 24 2009 - 21:55:52 PDT)
- Maria Mirza (Mon Aug 24 2009 - 21:41:39 PDT)
[AMBER] Need you help
- Carlos Simmerling (Wed Aug 26 2009 - 06:48:20 PDT)
- bharat lakhani (Wed Aug 26 2009 - 06:41:17 PDT)
[AMBER] nmode output
- Vahdati N. (Wed Aug 05 2009 - 15:26:11 PDT)
[AMBER] nmr restraint for angle between vectors
- Peter Varnai (Fri Aug 28 2009 - 18:10:20 PDT)
[AMBER] Non-Standard Amino Acid Residue LEAP ERROR
- Ashish Runthala (Fri Jul 31 2009 - 18:39:54 PDT)
[AMBER] nonbon.f question
- Ross Walker (Mon Aug 03 2009 - 11:32:18 PDT)
- Rizwan Tai (Mon Aug 03 2009 - 09:13:21 PDT)
[AMBER] Note regarding posting of the same message multiple times
- Ross Walker (Sun Aug 23 2009 - 22:19:36 PDT)
[AMBER] optimization step length
- Ashish Runthala (Mon Aug 03 2009 - 07:26:28 PDT)
- ondrej.prenosil.marge.uochb.cas.cz (Mon Aug 03 2009 - 03:40:15 PDT)
[AMBER] Parameters for haloacetates
- Joseph Nachman (Mon Aug 10 2009 - 07:54:13 PDT)
- Lili Peng (Fri Aug 07 2009 - 21:43:50 PDT)
- Joseph Nachman (Fri Aug 07 2009 - 11:22:34 PDT)
[AMBER] parameters for HIV protease inhibitors
- FyD (Wed Aug 12 2009 - 05:56:18 PDT)
- Oliver Kuhn (Tue Aug 11 2009 - 07:57:24 PDT)
- Carlos Simmerling (Thu Aug 06 2009 - 08:29:39 PDT)
[AMBER] parmchk problem
- case (Tue Aug 11 2009 - 06:51:57 PDT)
- isaac sugden (Wed Aug 05 2009 - 10:21:53 PDT)
- case (Wed Aug 05 2009 - 09:36:27 PDT)
- isaac sugden (Tue Aug 04 2009 - 07:12:29 PDT)
[AMBER] PCA analysis: the first vector is the movement of whole molecule.
- Catein Catherine (Sun Aug 02 2009 - 20:47:07 PDT)
[AMBER] pmemd
- Robert Duke (Mon Aug 24 2009 - 06:42:05 PDT)
- michael (Sat Aug 15 2009 - 04:30:28 PDT)
- Ross Walker (Mon Aug 10 2009 - 17:00:12 PDT)
- michael (Mon Aug 10 2009 - 12:51:59 PDT)
- case (Fri Aug 07 2009 - 08:18:52 PDT)
- michael (Fri Aug 07 2009 - 02:50:29 PDT)
[AMBER] PMEMD 10 overflow issues
- Ross Walker (Sat Aug 22 2009 - 10:25:31 PDT)
- Ross Walker (Sat Aug 22 2009 - 10:21:30 PDT)
- Ashish Runthala (Fri Aug 21 2009 - 19:52:55 PDT)
- ben rodriguez (Fri Aug 21 2009 - 14:17:36 PDT)
- Ross Walker (Fri Aug 21 2009 - 13:57:12 PDT)
[AMBER] problem compiling amber tools with gcc-4.4.1
- case (Tue Aug 25 2009 - 05:52:35 PDT)
- gilbert.bluemarble.net (Mon Aug 24 2009 - 20:07:44 PDT)
[AMBER] problem from xleap
- Tom Joseph (Sat Aug 01 2009 - 04:19:22 PDT)
- Ashish Runthala (Fri Jul 31 2009 - 20:33:10 PDT)
- Qinghua Liao (Fri Jul 31 2009 - 18:38:19 PDT)
[AMBER] problem of mm_pbsa
- Jordan Monnet (Thu Aug 13 2009 - 13:04:37 PDT)
- Qinghua Liao (Thu Aug 13 2009 - 06:58:24 PDT)
- Jordan Monnet (Mon Aug 10 2009 - 12:37:55 PDT)
- Qinghua Liao (Fri Aug 07 2009 - 18:11:43 PDT)
- Jordan Monnet (Fri Aug 07 2009 - 16:13:57 PDT)
- Qinghua Liao (Thu Aug 06 2009 - 16:58:55 PDT)
- Rubben Torella (Thu Aug 06 2009 - 08:53:47 PDT)
- Qinghua Liao (Wed Aug 05 2009 - 17:22:13 PDT)
- case (Wed Aug 05 2009 - 08:42:56 PDT)
- Qinghua Liao (Tue Aug 04 2009 - 22:46:51 PDT)
[AMBER] problem with 4-Hydroxyl-Proline tutorial
- FyD (Mon Aug 31 2009 - 13:10:52 PDT)
- Jia Xu (Sun Aug 30 2009 - 00:46:18 PDT)
[AMBER] Problem with Amber8
- Sebastian Petruczynik (Wed Aug 05 2009 - 04:33:05 PDT)
- Ross Walker (Mon Aug 03 2009 - 12:41:28 PDT)
- ondrej.prenosil.marge.uochb.cas.cz (Mon Aug 03 2009 - 06:37:01 PDT)
- Sebastian Petruczynik (Mon Aug 03 2009 - 06:28:56 PDT)
[AMBER] Problem with loading PDB into tleap
- Ashish Runthala (Wed Aug 19 2009 - 19:53:04 PDT)
- case (Wed Aug 19 2009 - 16:55:52 PDT)
- ksripath.umich.edu (Wed Aug 19 2009 - 12:00:22 PDT)
- Ashish Runthala (Wed Aug 19 2009 - 08:03:19 PDT)
- Kamali Sripathi (Wed Aug 19 2009 - 07:06:15 PDT)
- Ashish Runthala (Wed Aug 19 2009 - 06:56:59 PDT)
- Kamali Sripathi (Wed Aug 19 2009 - 06:21:30 PDT)
[AMBER] Protein Activity
- Ashish Runthala (Tue Aug 04 2009 - 20:42:11 PDT)
- Bill Ross (Tue Aug 04 2009 - 12:59:40 PDT)
- Chih-Ying Lin (Tue Aug 04 2009 - 12:42:42 PDT)
- Bill Ross (Tue Aug 04 2009 - 12:19:32 PDT)
- Chih-Ying Lin (Tue Aug 04 2009 - 10:57:54 PDT)
[AMBER] Protein Domain Motion
- Carlos Simmerling (Fri Aug 14 2009 - 05:17:28 PDT)
- Chih-Ying Lin (Thu Aug 13 2009 - 18:51:14 PDT)
- Carlos Simmerling (Thu Aug 13 2009 - 12:39:39 PDT)
- Chih-Ying Lin (Thu Aug 13 2009 - 12:20:09 PDT)
[AMBER] protein-ligand binding simulation times
- Andrew Voronkov (Sat Aug 22 2009 - 03:32:42 PDT)
- steinbrt.rci.rutgers.edu (Sat Aug 22 2009 - 02:50:35 PDT)
- Andrew Voronkov (Fri Aug 21 2009 - 22:09:54 PDT)
[AMBER] ptraj cluster - snapshot number of a representative structure
- Jianyin Shao (Thu Aug 20 2009 - 08:50:22 PDT)
- Marcin Krol (Thu Aug 20 2009 - 01:26:09 PDT)
[AMBER] ptraj failure to parse psf input
- Sasha Buzko (Thu Aug 13 2009 - 16:34:07 PDT)
- Sasha Buzko (Thu Aug 13 2009 - 09:25:32 PDT)
- Thomas Cheatham (Wed Aug 12 2009 - 21:27:34 PDT)
- Sasha Buzko (Wed Aug 12 2009 - 14:16:07 PDT)
- Sasha Buzko (Wed Aug 05 2009 - 12:33:54 PDT)
- case (Wed Aug 05 2009 - 10:32:00 PDT)
- Sasha Buzko (Wed Aug 05 2009 - 09:39:57 PDT)
[AMBER] ptraj imaging of namd generated trajectories
- Vlad Cojocaru (Thu Aug 13 2009 - 02:35:49 PDT)
[AMBER] ptraj limit on trajectory size
- Sasha Buzko (Mon Aug 24 2009 - 15:31:14 PDT)
- Ross Walker (Mon Aug 24 2009 - 15:07:00 PDT)
- Sasha Buzko (Mon Aug 24 2009 - 09:59:30 PDT)
[AMBER] ptraj-image
- Nancy (Thu Aug 13 2009 - 03:35:01 PDT)
[AMBER] ptraj-rms vs carnal; questions on RMSD of ligand drift
- Andrew Voronkov (Sun Aug 23 2009 - 04:55:01 PDT)
[AMBER] QM/MM types.
- Ross Walker (Thu Aug 13 2009 - 09:11:57 PDT)
- ros.servidor.unam.mx (Thu Aug 13 2009 - 08:49:02 PDT)
[AMBER] query
- bharat lakhani (Fri Aug 07 2009 - 02:11:42 PDT)
- Ashish Runthala (Fri Jul 31 2009 - 18:23:07 PDT)
[AMBER] query regarding fes cluster
- FyD (Wed Aug 12 2009 - 06:00:37 PDT)
- subarna thakur (Tue Aug 11 2009 - 22:39:55 PDT)
[AMBER] query regarding resp
- Oliver Kuhn (Tue Aug 11 2009 - 07:24:19 PDT)
- subarna thakur (Fri Aug 07 2009 - 05:14:35 PDT)
[AMBER] Query regarding watershell command
- Mannan (Mon Aug 31 2009 - 03:38:08 PDT)
[AMBER] radial distribution function
- Dharmik Meghana shankar (Fri Jul 31 2009 - 22:33:58 PDT)
[AMBER] radius for Manganese ion
- E.M. (Sun Aug 30 2009 - 16:38:38 PDT)
- Chunliyan (Sat Aug 29 2009 - 07:43:00 PDT)
[AMBER] RDC import from PALES
- case (Fri Aug 28 2009 - 05:01:30 PDT)
- Thomas Pochapsky (Tue Aug 18 2009 - 07:33:42 PDT)
[AMBER] Regarding Minimization maxcyc
- case (Mon Aug 10 2009 - 07:43:00 PDT)
- Ashish Runthala (Sun Aug 09 2009 - 07:09:58 PDT)
[AMBER] Regarding principal component analysis using ptraj
- Arvind Marathe (Fri Aug 28 2009 - 04:56:53 PDT)
- Hannes Loeffler (Fri Aug 28 2009 - 04:45:05 PDT)
- Arvind Marathe (Fri Aug 28 2009 - 04:04:22 PDT)
- Hannes Loeffler (Fri Aug 28 2009 - 00:28:29 PDT)
- Arvind Marathe (Thu Aug 27 2009 - 23:54:40 PDT)
[AMBER] Regd : gaff force field
- Ashish Runthala (Sat Aug 08 2009 - 05:17:37 PDT)
- Ross Walker (Fri Aug 07 2009 - 08:52:07 PDT)
- Ashish Runthala (Fri Aug 07 2009 - 02:08:43 PDT)
- KIRTANA S (Thu Aug 06 2009 - 15:12:15 PDT)
- Ross Walker (Thu Aug 06 2009 - 13:42:14 PDT)
- Nicholas Musolino (Thu Aug 06 2009 - 13:22:37 PDT)
- KIRTANA S (Thu Aug 06 2009 - 13:09:14 PDT)
[AMBER] REMD using hybrid solvent model
- Morad Mustafa (Wed Aug 12 2009 - 12:05:40 PDT)
[AMBER] reset velocity
- Tom Joseph (Wed Aug 12 2009 - 23:26:48 PDT)
- Parimal Kar (Wed Aug 12 2009 - 18:01:33 PDT)
[AMBER] resp calculation for rubredoxin
- vhakkim boy (Wed Aug 19 2009 - 03:11:22 PDT)
[AMBER] RESP charges of Fe4S4 cluster
- case (Fri Aug 21 2009 - 07:13:23 PDT)
- vhakkim boy (Wed Aug 19 2009 - 01:40:59 PDT)
- subarna thakur (Wed Aug 19 2009 - 00:53:20 PDT)
[AMBER] sander does not print out all residues in range.
- Maria Mirza (Mon Aug 24 2009 - 22:17:59 PDT)
- Ross Walker (Mon Aug 24 2009 - 22:00:03 PDT)
- Maria Mirza (Mon Aug 24 2009 - 21:32:31 PDT)
[AMBER] SCC-DFTB MD for mercury ions in proteins
- Adrian Roitberg (Thu Aug 27 2009 - 09:51:21 PDT)
- Vaida Arcišauskaitė (Thu Aug 27 2009 - 09:41:17 PDT)
[AMBER] Setting a constrain in one direction
- matthew_seetin.urmc.rochester.edu (Fri Aug 28 2009 - 07:35:57 PDT)
- Nicholas Musolino (Thu Aug 27 2009 - 20:40:54 PDT)
- Darren Yang (Thu Aug 27 2009 - 20:15:30 PDT)
[AMBER] Should I neutralize the models with Na+ or Mg2+ containing DNA and protein residues
- case (Sun Aug 16 2009 - 06:14:14 PDT)
- Catein Catherine (Sat Aug 15 2009 - 21:18:28 PDT)
[AMBER] Showing error
- bharat lakhani (Sat Aug 01 2009 - 06:12:00 PDT)
[AMBER] Showing error in energy minimization
- Ashish Runthala (Sun Aug 02 2009 - 20:05:06 PDT)
- case (Sun Aug 02 2009 - 07:25:04 PDT)
- bharat lakhani (Sat Aug 01 2009 - 23:22:30 PDT)
[AMBER] showing error when creating topology and coordinate file
- bharat lakhani (Mon Aug 03 2009 - 00:19:59 PDT)
[AMBER] Single Adenine
- FyD (Thu Aug 27 2009 - 14:20:48 PDT)
- ros (Thu Aug 27 2009 - 09:27:06 PDT)
- FyD (Thu Aug 27 2009 - 00:05:54 PDT)
- Bill Ross (Wed Aug 26 2009 - 12:28:31 PDT)
- ros (Wed Aug 26 2009 - 10:50:54 PDT)
- case (Wed Aug 26 2009 - 04:48:36 PDT)
- case (Wed Aug 26 2009 - 04:36:09 PDT)
- ros (Tue Aug 25 2009 - 23:09:23 PDT)
[AMBER] sourcing leap commands in log file
- Ashish Runthala (Fri Aug 14 2009 - 23:50:31 PDT)
- Bill Ross (Wed Aug 12 2009 - 17:47:57 PDT)
- Donald Keidel (Wed Aug 12 2009 - 17:32:31 PDT)
[AMBER] Strange QM/MM Divcon - help me out
- Ross Walker (Sun Aug 16 2009 - 09:55:01 PDT)
- Ashish Runthala (Fri Aug 14 2009 - 23:42:38 PDT)
- case (Thu Aug 13 2009 - 08:52:34 PDT)
- s. Bill (Thu Aug 13 2009 - 08:37:54 PDT)
[AMBER] suggestions pls
- Jio M (Wed Aug 12 2009 - 06:04:16 PDT)
- Ashish Runthala (Tue Aug 11 2009 - 19:40:40 PDT)
- Jio M (Tue Aug 11 2009 - 10:44:19 PDT)
[AMBER] Timescales and restraints for protein-small ligands movement simulations
- Vivek Sharma (Sat Aug 01 2009 - 23:29:13 PDT)
- Andrew Voronkov (Sat Aug 01 2009 - 07:14:49 PDT)
- Andrew Voronkov (Fri Jul 31 2009 - 23:23:19 PDT)
[AMBER] TWO restraints with different force constants
- A. Gomez-Sicilia (Wed Aug 05 2009 - 05:20:54 PDT)
- s. Bill (Wed Aug 05 2009 - 04:54:18 PDT)
[AMBER] update on am1-bcc charge problem in antechamber
- case (Fri Aug 21 2009 - 09:32:30 PDT)
[AMBER] USE A VERSION COMPILED WITHOUT -DLES
- s. Bill (Wed Aug 05 2009 - 04:55:55 PDT)
- s. Bill (Wed Aug 05 2009 - 03:50:01 PDT)
[AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj
- Paul Frybarger (Mon Aug 17 2009 - 10:57:28 PDT)
- workalemahu berhanu (Mon Aug 17 2009 - 06:26:35 PDT)
- Ross Walker (Sun Aug 16 2009 - 17:30:47 PDT)
- workalemahu berhanu (Sun Aug 16 2009 - 13:13:21 PDT)
[AMBER] WATERSHELL
- Mannan (Sun Aug 30 2009 - 22:02:51 PDT)
[AMBER] What is the meaning of IED values for PCA analysis?
- case (Wed Aug 05 2009 - 09:39:30 PDT)
- Catein Catherine (Mon Aug 03 2009 - 07:30:15 PDT)
[AMBER] What is the parameters for Mg2+?
- Catein Catherine (Sun Aug 16 2009 - 22:59:23 PDT)
- Tom Joseph (Sun Aug 16 2009 - 09:00:35 PDT)
- Catein Catherine (Sat Aug 15 2009 - 21:21:46 PDT)
[AMBER] why is nonpolar solvation energy not implemented for dynamic in amber
- TaoPaul (Wed Aug 19 2009 - 08:29:38 PDT)
[AMBER] Why..QM/MM
- Ross Walker (Sat Aug 08 2009 - 10:00:27 PDT)
- s. Bill (Sat Aug 08 2009 - 04:26:46 PDT)
[AMBER] xleap installation error
- Scott Brozell (Mon Aug 03 2009 - 09:57:18 PDT)
- Bokun Cho (Sun Aug 02 2009 - 22:18:00 PDT)
[AMBER] ZPVE simple question
- case (Wed Aug 26 2009 - 04:41:27 PDT)
- Jerome.GOLEBIOWSKI.unice.fr (Wed Aug 26 2009 - 04:15:00 PDT)
- ondrej.prenosil.marge.uochb.cas.cz (Wed Aug 26 2009 - 02:42:04 PDT)
[Amber]: REMD using hybrid solvent model
- Morad Mustafa (Fri Aug 14 2009 - 05:44:44 PDT)
- Carlos Simmerling (Wed Aug 12 2009 - 16:54:20 PDT)
- Carlos Simmerling (Wed Aug 12 2009 - 16:52:56 PDT)
- Morad Mustafa (Wed Aug 12 2009 - 14:30:01 PDT)
[q4md-fft] charge calculation
- FyD (Mon Aug 17 2009 - 16:40:49 PDT)
AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
- Andrew Voronkov (Sun Aug 23 2009 - 06:48:07 PDT)
angle with ptraj
- E.M. (Wed Aug 19 2009 - 12:44:56 PDT)
antechamber am1-bcc issues
- Khavrutskii, Ilja (Fri Aug 21 2009 - 12:32:34 PDT)
- Khavrutskii, Ilja (Fri Aug 21 2009 - 09:27:28 PDT)
- David Mobley (Thu Aug 13 2009 - 06:25:52 PDT)
- case (Sat Aug 08 2009 - 12:20:44 PDT)
- gilbert.bluemarble.net (Sat Aug 08 2009 - 06:55:40 PDT)
- case (Fri Aug 07 2009 - 16:54:38 PDT)
AW: [AMBER] Any Comment, please
- s. Bill (Tue Aug 11 2009 - 01:22:16 PDT)
- Aust, Susanne (Tue Aug 11 2009 - 01:17:18 PDT)
AW: [AMBER] Conference or workshop on AMBER?
- Aust, Susanne (Wed Aug 19 2009 - 01:16:21 PDT)
AW: [AMBER] TWO restraints with different force constants
- Aust, Susanne (Wed Aug 05 2009 - 05:31:38 PDT)
AW: AW: [AMBER] Any Comment, please
- Aust, Susanne (Tue Aug 11 2009 - 01:36:34 PDT)
How to solve the problem "RESTARTED DUE to LINMIN FAILURE"
- Bill Ross (Mon Aug 10 2009 - 18:30:07 PDT)
- Jianping Lin (Mon Aug 10 2009 - 18:23:44 PDT)
- Bill Ross (Mon Aug 10 2009 - 18:17:05 PDT)
- Jianping Lin (Mon Aug 10 2009 - 16:18:44 PDT)
implicit solvent simulation with new ligand
- Carlos Simmerling (Mon Aug 10 2009 - 07:42:33 PDT)
- Manish Kumar (Fri Aug 07 2009 - 12:08:59 PDT)
- Carlos Simmerling (Fri Aug 07 2009 - 11:29:46 PDT)
- Manish Kumar (Fri Aug 07 2009 - 11:22:57 PDT)
ptraj imaging of namd generated trajectories
- Vlad Cojocaru (Thu Aug 13 2009 - 03:10:54 PDT)
query
- Ashish Runthala (Sat Aug 01 2009 - 05:21:47 PDT)
- bharat lakhani (Sat Aug 01 2009 - 05:07:24 PDT)
question_on_MMPBSA
- jackie (Thu Aug 27 2009 - 08:41:28 PDT)
- Catein Catherine (Wed Aug 26 2009 - 22:55:59 PDT)
- jackie (Wed Aug 26 2009 - 08:08:01 PDT)
showing error when creating topology and coordinate file
- Olotu Odunayo (Tue Aug 04 2009 - 06:08:32 PDT)
- bharat lakhani (Mon Aug 03 2009 - 21:54:36 PDT)

Amber Archive Aug 2009 by subject