AMBER Archive (2009) - Sep 2009 By Subject

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About this archive

Starting: Tue Sep 01 2009 - 00:02:08 CDT
Ending: Wed Sep 30 2009 - 13:40:58 CDT

[AMBER] "nan" in gaussian input files generated by antechamber
- FyD (Sat Sep 12 2009 - 09:58:52 CDT)
- case (Sat Sep 12 2009 - 08:55:14 CDT)
- Yikan Chen (Fri Sep 11 2009 - 15:19:04 CDT)
[AMBER] (no subject)
- gunajyoti das (Mon Sep 07 2009 - 04:21:45 CDT)
[AMBER] about the number of residues after MD
- Qinghua Liao (Wed Sep 09 2009 - 02:23:03 CDT)
[AMBER] About the PMEMD compiling for CUDA
- Ross Walker (Wed Sep 16 2009 - 01:55:11 CDT)
- Ross Walker (Wed Sep 16 2009 - 00:26:19 CDT)
- wang (Wed Sep 16 2009 - 00:17:52 CDT)
[AMBER] ACE and NME patch: VMD ???
- Ross Walker (Tue Sep 01 2009 - 12:54:38 CDT)
[AMBER] ACS COMP division awards- Oct 19th deadline
- Carlos Simmerling (Mon Sep 21 2009 - 12:49:28 CDT)
[AMBER] Active site - Ion - Search engine
- s. Bill (Wed Sep 02 2009 - 09:53:39 CDT)
[AMBER] AmberTools 1.3 / CHAMBER
- Mag. Thomas Taylor (Tue Sep 08 2009 - 09:29:23 CDT)
[AMBER] ambertools and Snow Leopard 64 bits kernel
- case (Wed Sep 23 2009 - 15:26:16 CDT)
- Alan (Wed Sep 23 2009 - 09:21:30 CDT)
- gilbert_at_bluemarble.net (Tue Sep 22 2009 - 21:18:12 CDT)
- Tom Joseph (Tue Sep 22 2009 - 19:18:17 CDT)
- Alan (Tue Sep 22 2009 - 16:41:18 CDT)
- Tom Joseph (Tue Sep 22 2009 - 13:12:55 CDT)
- Alan (Tue Sep 22 2009 - 08:55:25 CDT)
[AMBER] amoeba.prm problem?
- Ivan Gladich (Fri Sep 18 2009 - 14:57:39 CDT)
- case (Sat Sep 12 2009 - 08:46:52 CDT)
- Ivan Gladich (Fri Sep 11 2009 - 15:34:07 CDT)
- case (Wed Sep 09 2009 - 14:17:39 CDT)
- Ivan Gladich (Tue Sep 08 2009 - 09:31:43 CDT)
[AMBER] antechamber bug: output of incorrect bond character
- case (Thu Sep 03 2009 - 11:29:03 CDT)
- Matthew Walsh (Thu Sep 03 2009 - 10:15:00 CDT)
- case (Thu Sep 03 2009 - 06:26:19 CDT)
- Matthew Walsh (Wed Sep 02 2009 - 23:30:04 CDT)
- case (Wed Sep 02 2009 - 20:53:37 CDT)
- Matthew Walsh (Wed Sep 02 2009 - 13:37:44 CDT)
[AMBER] antechamber error
- Taufik Al-Sarraj (Wed Sep 16 2009 - 14:11:26 CDT)
- Taufik Al-Sarraj (Wed Sep 16 2009 - 13:52:26 CDT)
- case (Wed Sep 16 2009 - 13:43:56 CDT)
- Taufik Al-Sarraj (Wed Sep 16 2009 - 13:18:32 CDT)
[AMBER] Antechamber generate a prep file in a wrong order...
- case (Sun Sep 06 2009 - 07:26:02 CDT)
- Yikan Chen (Sat Sep 05 2009 - 14:37:53 CDT)
[AMBER] Any tutorial on the proper way to merge a ligand and protein?
- case (Fri Sep 11 2009 - 14:54:39 CDT)
- cc cc (Fri Sep 11 2009 - 13:16:55 CDT)
- Dean Cuebas (Wed Sep 09 2009 - 14:12:00 CDT)
- case (Wed Sep 09 2009 - 13:50:13 CDT)
- Dean Cuebas (Wed Sep 09 2009 - 13:26:02 CDT)
[AMBER] apbs-amber
- Rilei Yu (Tue Sep 22 2009 - 20:41:08 CDT)
- Robert Konecny (Tue Sep 22 2009 - 18:18:28 CDT)
- Rilei Yu (Tue Sep 22 2009 - 17:58:40 CDT)
[AMBER] ATP and GTP parameters
- E.M. (Thu Sep 03 2009 - 21:08:02 CDT)
- Carlos Simmerling (Thu Sep 03 2009 - 06:54:13 CDT)
- FyD (Thu Sep 03 2009 - 04:36:45 CDT)
- FyD (Thu Sep 03 2009 - 03:35:11 CDT)
- Sergey Samsonov (Thu Sep 03 2009 - 01:35:33 CDT)
- E.M. (Thu Sep 03 2009 - 01:30:31 CDT)
- FyD (Thu Sep 03 2009 - 01:15:54 CDT)
- E.M. (Thu Sep 03 2009 - 00:29:47 CDT)
[AMBER] ATP/GTP parameters
- Steve Seibold (Tue Sep 01 2009 - 11:29:59 CDT)
- FyD (Tue Sep 01 2009 - 11:25:45 CDT)
- Steve Seibold (Tue Sep 01 2009 - 06:42:09 CDT)
- FyD (Tue Sep 01 2009 - 01:10:41 CDT)
- wang (Tue Sep 01 2009 - 00:02:08 CDT)
[AMBER] Attaching a ligand to a protein residue.
- Kipras Redeckas (Sun Sep 27 2009 - 05:23:42 CDT)
- case (Sat Sep 26 2009 - 09:23:18 CDT)
- Kipras Redeckas (Fri Sep 25 2009 - 16:33:58 CDT)
[AMBER] can antechamber convert a prep file from cartesian to internal coordinates?
- Paul Ledbetter (Tue Sep 15 2009 - 18:40:09 CDT)
- Paul Ledbetter (Tue Sep 15 2009 - 18:34:54 CDT)
- Bill Ross (Tue Sep 15 2009 - 17:15:38 CDT)
- case (Tue Sep 15 2009 - 17:12:25 CDT)
- Paul Ledbetter (Tue Sep 15 2009 - 15:25:56 CDT)
[AMBER] Carbon Nanotube Library file (CNT)
- Christopher Stiles (Mon Sep 14 2009 - 08:59:57 CDT)
[AMBER] CH3Hg+ parameters
- babak minoofar (Thu Sep 24 2009 - 07:08:12 CDT)
[AMBER] Changing pH of the system
- nicholus bhattacharjee (Tue Sep 01 2009 - 08:43:01 CDT)
[AMBER] charge consideration
- case (Sat Sep 12 2009 - 08:59:56 CDT)
- Jio M (Fri Sep 11 2009 - 15:17:34 CDT)
[AMBER] combining MD runs for post-MD analysis
- Bill Ross (Mon Sep 21 2009 - 12:32:53 CDT)
- case (Sun Sep 20 2009 - 20:35:08 CDT)
- Qinghua Liao (Sun Sep 20 2009 - 20:01:22 CDT)
- Jeff Yeo (Sun Sep 20 2009 - 19:02:12 CDT)
[AMBER] Compiling Amber with gfortran-4.5.0 on a mac
- Ben Roberts (Tue Sep 29 2009 - 16:37:31 CDT)
[AMBER] Compiling Amber10
- Williams, John (Tue Sep 22 2009 - 07:56:43 CDT)
[AMBER] cpin error
- case (Tue Sep 01 2009 - 07:23:04 CDT)
[AMBER] Creating new counterions
- case (Tue Sep 01 2009 - 15:03:48 CDT)
- Bill Ross (Tue Sep 01 2009 - 14:58:55 CDT)
- Timothy Robbins (trobbins) (Tue Sep 01 2009 - 14:00:37 CDT)
[AMBER] Cygwin Home Directory
- Bill Ross (Mon Sep 21 2009 - 12:45:02 CDT)
- case (Mon Sep 21 2009 - 12:14:59 CDT)
- Wallace Kunin (Mon Sep 21 2009 - 11:29:11 CDT)
- Ashish Runthala (Sat Sep 19 2009 - 21:51:11 CDT)
- case (Sat Sep 19 2009 - 17:11:57 CDT)
- Bill Ross (Sat Sep 19 2009 - 12:29:59 CDT)
- Wallace Kunin (Sat Sep 19 2009 - 11:13:20 CDT)
- Bill Ross (Fri Sep 18 2009 - 15:56:17 CDT)
- manoj singh (Fri Sep 18 2009 - 14:30:28 CDT)
- Wallace Kunin (Fri Sep 18 2009 - 14:12:22 CDT)
- Bill Ross (Fri Sep 18 2009 - 13:19:44 CDT)
- Wallace Kunin (Fri Sep 18 2009 - 12:51:17 CDT)
[AMBER] database
- case (Fri Sep 18 2009 - 21:46:39 CDT)
- FyD (Fri Sep 18 2009 - 19:49:17 CDT)
- Steve Seibold (Fri Sep 18 2009 - 14:10:19 CDT)
- case (Fri Sep 18 2009 - 12:23:08 CDT)
- Steve Seibold (Fri Sep 18 2009 - 10:03:44 CDT)
- FyD (Fri Sep 18 2009 - 02:28:53 CDT)
- case (Thu Sep 17 2009 - 17:23:30 CDT)
- FyD (Thu Sep 17 2009 - 16:54:29 CDT)
- Jeff Yeo (Thu Sep 17 2009 - 16:01:48 CDT)
- Steve Seibold (Thu Sep 17 2009 - 14:46:20 CDT)
- FyD (Thu Sep 17 2009 - 11:00:22 CDT)
- Steve Seibold (Thu Sep 17 2009 - 08:43:25 CDT)
- FyD (Wed Sep 16 2009 - 13:58:38 CDT)
- FyD (Wed Sep 16 2009 - 13:56:16 CDT)
- Bill Ross (Wed Sep 16 2009 - 12:54:47 CDT)
- Steve Seibold (Wed Sep 16 2009 - 12:14:46 CDT)
- FyD (Wed Sep 16 2009 - 11:59:30 CDT)
- case (Wed Sep 16 2009 - 11:53:56 CDT)
- Steve Seibold (Wed Sep 16 2009 - 11:11:47 CDT)
- case (Wed Sep 16 2009 - 10:26:24 CDT)
- Steve Seibold (Wed Sep 16 2009 - 09:59:14 CDT)
[AMBER] dihedral force calculation
- case (Sat Sep 12 2009 - 09:04:34 CDT)
- Germain Vallverdu (Fri Sep 11 2009 - 09:35:08 CDT)
[AMBER] Discrepancy between AMBER and VMD calculation
- Sunita Patel (Thu Sep 17 2009 - 14:11:07 CDT)
[AMBER] DMF solvent box
- FyD (Sat Sep 19 2009 - 01:36:20 CDT)
- Abhishek Banerjee (Sat Sep 19 2009 - 00:24:08 CDT)
- FyD (Thu Sep 17 2009 - 02:00:06 CDT)
- Abhishek Banerjee (Thu Sep 17 2009 - 01:15:53 CDT)
- FyD (Wed Sep 16 2009 - 00:09:42 CDT)
- Abhishek Banerjee (Tue Sep 15 2009 - 23:33:23 CDT)
- FyD (Mon Sep 14 2009 - 10:04:58 CDT)
- Abhishek Banerjee (Mon Sep 14 2009 - 08:18:30 CDT)
- FyD (Sun Sep 13 2009 - 12:01:13 CDT)
- Abhishek Banerjee (Sun Sep 13 2009 - 09:24:04 CDT)
- FyD (Sun Sep 13 2009 - 04:25:33 CDT)
- Abhishek Banerjee (Sun Sep 13 2009 - 03:56:18 CDT)
- Abhishek Banerjee (Sun Sep 13 2009 - 00:33:39 CDT)
- FyD (Sat Sep 12 2009 - 09:07:30 CDT)
- Jio M (Fri Sep 11 2009 - 10:00:40 CDT)
- Abhishek Banerjee (Thu Sep 10 2009 - 21:40:21 CDT)
[AMBER] Dummy atoms and MM-PBSA
- Ray Luo (Fri Sep 04 2009 - 13:25:33 CDT)
- Alireza Shaneh (Fri Sep 04 2009 - 11:48:16 CDT)
[AMBER] Enquiry about MM/GBSA output file.
- Catein Catherine (Tue Sep 08 2009 - 02:14:19 CDT)
[AMBER] Error in minimal
- case (Tue Sep 15 2009 - 17:15:06 CDT)
- xuemeiwang1103 (Tue Sep 15 2009 - 08:54:58 CDT)
- case (Tue Sep 15 2009 - 06:56:02 CDT)
- xuemeiwang1103 (Tue Sep 15 2009 - 02:27:18 CDT)
[AMBER] error xleap: XaLeap_wcl is empty
- case (Mon Sep 14 2009 - 07:02:12 CDT)
- Mari Carmen Pérez (Mon Sep 14 2009 - 04:59:09 CDT)
[AMBER] Ewald error estimated
- Robert Duke (Fri Sep 25 2009 - 10:50:18 CDT)
- case (Fri Sep 25 2009 - 10:15:31 CDT)
- Qinghua Liao (Fri Sep 25 2009 - 02:48:14 CDT)
- xuemeiwang1103 (Thu Sep 24 2009 - 22:01:05 CDT)
- xuemeiwang1103 (Thu Sep 24 2009 - 22:01:02 CDT)
[AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex
- case (Thu Sep 24 2009 - 17:13:39 CDT)
- Jeff Yeo (Wed Sep 23 2009 - 18:24:51 CDT)
[AMBER] Force Field Fitting
- manoj singh (Thu Sep 17 2009 - 14:32:33 CDT)
- s. Bill (Thu Sep 17 2009 - 14:27:46 CDT)
- manoj singh (Thu Sep 17 2009 - 12:20:50 CDT)
- s. Bill (Thu Sep 17 2009 - 06:36:33 CDT)
[AMBER] gaff.dat questions
- case (Wed Sep 09 2009 - 09:16:23 CDT)
- gilbert_at_bluemarble.net (Wed Sep 09 2009 - 09:02:28 CDT)
[AMBER] Gap in rst file
- Katrina Lexa (Mon Sep 28 2009 - 09:47:43 CDT)
[AMBER] general query: implicit solvation
- Carlos Simmerling (Tue Sep 08 2009 - 05:11:24 CDT)
- Jio M (Tue Sep 08 2009 - 04:28:49 CDT)
[AMBER] generate prmtop file from CHARMM psf file
- Jeffrey (Mon Sep 21 2009 - 09:34:59 CDT)
[AMBER] group distance restraint
- XIAOHUICANG (Tue Sep 22 2009 - 14:36:03 CDT)
[AMBER] Hbond analysis: Direction of the hydrogen
- Age.Skjevik_at_biomed.uib.no (Tue Sep 08 2009 - 16:56:50 CDT)
- Shulin Zhuang (Tue Sep 08 2009 - 14:54:22 CDT)
- Age.Skjevik_at_biomed.uib.no (Tue Sep 08 2009 - 14:45:19 CDT)
[AMBER] Heme + Fe(II) + O2 + histidine parameter
- FyD (Fri Sep 04 2009 - 02:43:00 CDT)
- Haining Liu (Thu Sep 03 2009 - 16:13:09 CDT)
- FyD (Thu Sep 03 2009 - 02:03:45 CDT)
- Haining Liu (Wed Sep 02 2009 - 22:36:31 CDT)
[AMBER] how to calculate correct RMSF?
- Catein Catherine (Mon Sep 14 2009 - 19:57:20 CDT)
- case (Mon Sep 14 2009 - 07:33:29 CDT)
- Catein Catherine (Mon Sep 14 2009 - 06:21:52 CDT)
[AMBER] How to consider the off centre charges
- case (Wed Sep 02 2009 - 10:50:12 CDT)
- Ashish Runthala (Wed Sep 02 2009 - 10:28:40 CDT)
[AMBER] how to deal with aromatic nitro group with antechamber
- case (Wed Sep 02 2009 - 21:15:14 CDT)
- Lin Xu (Wed Sep 02 2009 - 17:04:13 CDT)
[AMBER] How to denature DNA
- balaji nagarajan (Wed Sep 09 2009 - 12:14:37 CDT)
- Bill Ross (Wed Sep 09 2009 - 11:38:04 CDT)
- balaji nagarajan (Tue Sep 08 2009 - 23:01:55 CDT)
- Bill Ross (Tue Sep 08 2009 - 12:33:09 CDT)
- Adrian Roitberg (Tue Sep 08 2009 - 12:12:00 CDT)
- balaji nagarajan (Tue Sep 08 2009 - 11:58:36 CDT)
- Adrian Roitberg (Tue Sep 08 2009 - 11:46:51 CDT)
- balaji nagarajan (Tue Sep 08 2009 - 11:29:57 CDT)
- Adrian Roitberg (Tue Sep 08 2009 - 09:04:30 CDT)
- balaji nagarajan (Tue Sep 08 2009 - 09:00:43 CDT)
[AMBER] How to derive charges from the output
- bharat lakhani (Tue Sep 01 2009 - 03:46:12 CDT)
[AMBER] How to find a protein's energy
- Ashish Runthala (Sun Sep 06 2009 - 07:30:26 CDT)
- Carlos Simmerling (Sun Sep 06 2009 - 06:49:53 CDT)
- Ashish Runthala (Sat Sep 05 2009 - 22:48:01 CDT)
[AMBER] How to find water-mediated hydrogen bond?
- Hannes Loeffler (Thu Sep 03 2009 - 02:53:51 CDT)
- Catein Catherine (Wed Sep 02 2009 - 09:10:37 CDT)
[AMBER] how to give force values in TMD
- balaji nagarajan (Wed Sep 02 2009 - 05:03:41 CDT)
[AMBER] how to make 50% aqueous TFE box?
- FyD (Fri Sep 18 2009 - 19:22:35 CDT)
- parul sharma (Fri Sep 18 2009 - 08:47:01 CDT)
[AMBER] How to obtain amber top and crd from pdb file with POPE lipids?
- Hannes Loeffler (Mon Sep 28 2009 - 02:34:12 CDT)
- decastro_at_physics.usyd.edu.au (Sun Sep 27 2009 - 23:52:20 CDT)
[AMBER] how to ouput the electrostatic potential at a single atomic position?
- Jose Borreguero (Thu Sep 17 2009 - 14:06:54 CDT)
[AMBER] How to prepare the coordinate and toplogy files in leap ?
- case (Mon Sep 14 2009 - 06:56:08 CDT)
- xuemeiwang1103 (Mon Sep 14 2009 - 04:03:59 CDT)
[AMBER] how to pull a dna
- balaji nagarajan (Tue Sep 01 2009 - 09:24:29 CDT)
- Sam Danziger (Tue Sep 01 2009 - 06:17:09 CDT)
[AMBER] How to remove Hydrogen using ptraj
- Thomas Cheatham III (Tue Sep 01 2009 - 12:25:10 CDT)
- case (Tue Sep 01 2009 - 12:19:51 CDT)
- Thomas Cheatham III (Tue Sep 01 2009 - 10:55:43 CDT)
- Mannan (Tue Sep 01 2009 - 05:50:44 CDT)
[AMBER] How to use AMBER 10 for PCA analysis.
- Catein Catherine (Tue Sep 01 2009 - 10:30:56 CDT)
[AMBER] input file
- Bill Ross (Thu Sep 10 2009 - 11:51:10 CDT)
- Ashish Runthala (Thu Sep 10 2009 - 09:05:32 CDT)
- Jenny Iskrenova (Thu Sep 10 2009 - 08:05:03 CDT)
- Carlos Simmerling (Thu Sep 10 2009 - 06:03:17 CDT)
- Mag. Thomas Taylor (Thu Sep 10 2009 - 05:48:06 CDT)
[AMBER] input file / skinnb
- Mag. Thomas Taylor (Thu Sep 17 2009 - 00:50:16 CDT)
- Robert Duke (Wed Sep 16 2009 - 09:23:06 CDT)
- case (Wed Sep 16 2009 - 06:56:01 CDT)
- Mag. Thomas Taylor (Wed Sep 16 2009 - 02:49:32 CDT)
[AMBER] install ambertools
- case (Thu Sep 17 2009 - 08:40:28 CDT)
- Karl Kirschner (Thu Sep 17 2009 - 07:55:22 CDT)
[AMBER] Installation issue
- Bill Ross (Wed Sep 23 2009 - 11:36:59 CDT)
- Bill Ross (Wed Sep 23 2009 - 11:29:28 CDT)
- Tom Joseph (Wed Sep 23 2009 - 11:08:33 CDT)
- Ashveen Seenauth (Wed Sep 23 2009 - 10:54:27 CDT)
- Tom Joseph (Wed Sep 23 2009 - 10:43:42 CDT)
- Ashveen Seenauth (Wed Sep 23 2009 - 10:41:53 CDT)
- Tom Joseph (Wed Sep 23 2009 - 10:35:44 CDT)
- Ashveen Seenauth (Wed Sep 23 2009 - 10:28:55 CDT)
- Bill Ross (Tue Sep 22 2009 - 13:28:43 CDT)
- Tom Joseph (Tue Sep 22 2009 - 13:16:01 CDT)
- Ashveen Seenauth (Tue Sep 22 2009 - 12:59:46 CDT)
- Bill Ross (Tue Sep 22 2009 - 12:59:22 CDT)
- Bill Ross (Tue Sep 22 2009 - 12:55:34 CDT)
- Bill Ross (Tue Sep 22 2009 - 12:50:28 CDT)
- Tom Joseph (Tue Sep 22 2009 - 12:41:51 CDT)
- Ashveen Seenauth (Tue Sep 22 2009 - 12:25:12 CDT)
- Tom Joseph (Tue Sep 22 2009 - 11:55:20 CDT)
- Ashveen Seenauth (Tue Sep 22 2009 - 11:45:13 CDT)
- Bill Ross (Tue Sep 22 2009 - 11:31:47 CDT)
- Ashveen Seenauth (Tue Sep 22 2009 - 11:17:49 CDT)
[AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions.
- oguz gurbulak (Tue Sep 22 2009 - 01:46:27 CDT)
- David Dubins (Mon Sep 21 2009 - 18:02:47 CDT)
[AMBER] Ki and G
- Marek Maly (Tue Sep 15 2009 - 06:58:07 CDT)
- case (Mon Sep 14 2009 - 15:24:05 CDT)
- steinbrt_at_rci.rutgers.edu (Mon Sep 14 2009 - 15:09:55 CDT)
- Marek Maly (Mon Sep 14 2009 - 13:41:33 CDT)
- case (Mon Sep 14 2009 - 12:23:49 CDT)
- Marek Maly (Mon Sep 14 2009 - 12:02:36 CDT)
- Adrian Roitberg (Mon Sep 14 2009 - 09:28:57 CDT)
- steinbrt_at_rci.rutgers.edu (Mon Sep 14 2009 - 06:59:40 CDT)
- s. Bill (Mon Sep 14 2009 - 06:39:20 CDT)
[AMBER] Kinetics
- Soumya Lipsa Rath (Tue Sep 08 2009 - 01:36:18 CDT)
- case (Fri Sep 04 2009 - 14:29:24 CDT)
- Soumya Lipsa Rath (Fri Sep 04 2009 - 01:39:54 CDT)
[AMBER] Leap warning
- Bill Ross (Wed Sep 09 2009 - 11:49:05 CDT)
- case (Wed Sep 09 2009 - 06:31:36 CDT)
- Ashish Runthala (Wed Sep 09 2009 - 02:21:03 CDT)
- manoj singh (Wed Sep 09 2009 - 00:38:33 CDT)
[AMBER] LINMIN failure notice
- Ross Walker (Fri Sep 18 2009 - 18:41:33 CDT)
- Bill Ross (Fri Sep 18 2009 - 11:18:41 CDT)
- case (Fri Sep 18 2009 - 06:38:33 CDT)
- Ashish Runthala (Fri Sep 18 2009 - 05:46:09 CDT)
- Jio M (Fri Sep 18 2009 - 05:20:18 CDT)
[AMBER] LJ-partial charges and force field parameters for ethylene glycol and glycerol
- FyD (Mon Sep 28 2009 - 13:23:20 CDT)
- Ganesh Kamath (Mon Sep 28 2009 - 12:03:13 CDT)
[AMBER] load .crd & .top in xleap
- oguz gurbulak (Sun Sep 13 2009 - 14:20:26 CDT)
- vallespardojl_at_chem.leidenuniv.nl (Sun Sep 13 2009 - 09:21:15 CDT)
[AMBER] loading a following attached protein in amber 10
- albert albert (Tue Sep 08 2009 - 12:43:55 CDT)
- case (Tue Sep 08 2009 - 12:27:47 CDT)
- David Watson (Tue Sep 08 2009 - 12:26:19 CDT)
- albert albert (Tue Sep 08 2009 - 12:09:09 CDT)
[AMBER] loading PDB of a RNA sequence
- case (Tue Sep 08 2009 - 06:38:34 CDT)
- Carlos Simmerling (Tue Sep 08 2009 - 05:33:57 CDT)
- gunajyoti das (Tue Sep 08 2009 - 05:31:47 CDT)
[AMBER] loading RNA sequence in xleap
- case (Thu Sep 17 2009 - 07:13:38 CDT)
- FyD (Thu Sep 17 2009 - 04:39:09 CDT)
- gunajyoti das (Thu Sep 17 2009 - 03:27:49 CDT)
[AMBER] loadpdb
- Carlos Simmerling (Wed Sep 09 2009 - 06:35:04 CDT)
- Bill Ross (Tue Sep 08 2009 - 21:53:32 CDT)
- Jagdeesh C (Tue Sep 08 2009 - 20:55:36 CDT)
- Bill Ross (Tue Sep 08 2009 - 11:58:12 CDT)
- Bill Ross (Tue Sep 08 2009 - 11:53:03 CDT)
- Carlos Simmerling (Tue Sep 08 2009 - 08:39:12 CDT)
- Tom Joseph (Tue Sep 08 2009 - 07:31:56 CDT)
- Ashish Runthala (Mon Sep 07 2009 - 22:00:47 CDT)
- Jagdeesh C (Mon Sep 07 2009 - 13:31:42 CDT)
- Carlos Simmerling (Mon Sep 07 2009 - 13:01:10 CDT)
- Jagdeesh C (Mon Sep 07 2009 - 12:36:58 CDT)
[AMBER] logdvdl does not work
- steinbrt_at_rci.rutgers.edu (Tue Sep 08 2009 - 12:37:31 CDT)
- helde010_at_umn.edu (Tue Sep 08 2009 - 11:53:14 CDT)
[AMBER] makeDIST_RST: no map function
- Workalemahu Berhanu (Tue Sep 15 2009 - 10:24:56 CDT)
- Workalemahu Berhanu (Tue Sep 15 2009 - 10:11:27 CDT)
- case (Tue Sep 15 2009 - 09:38:23 CDT)
- Duggan, Brendan M. (Tue Sep 15 2009 - 08:40:00 CDT)
- Workalemahu Berhanu (Mon Sep 14 2009 - 14:30:15 CDT)
[AMBER] MM-GBAS decomp error
- Catein Catherine (Fri Sep 04 2009 - 05:29:35 CDT)
[AMBER] MM_PBSA
- Zhongjie Liang (Tue Sep 29 2009 - 20:30:40 CDT)
[AMBER] MM_PBSA decomp problem
- B. Nandy (Tue Sep 22 2009 - 07:29:23 CDT)
[AMBER] momentum in MD simulation
- dhacademic (Wed Sep 02 2009 - 12:37:50 CDT)
- case (Tue Sep 01 2009 - 06:48:52 CDT)
[AMBER] NAB syntax
- case (Thu Sep 17 2009 - 10:22:29 CDT)
- Andreas Svrcek-Seiler (Thu Sep 17 2009 - 10:21:51 CDT)
- Michael Durney (Thu Sep 17 2009 - 09:58:58 CDT)
[AMBER] nmropt option
- Carlos Simmerling (Sat Sep 05 2009 - 05:59:04 CDT)
- Jio M (Sat Sep 05 2009 - 00:23:09 CDT)
- Carlos Simmerling (Fri Sep 04 2009 - 13:15:13 CDT)
- Jio M (Fri Sep 04 2009 - 13:05:25 CDT)
[AMBER] No restrt file
- case (Wed Sep 30 2009 - 07:06:47 CDT)
- null (Wed Sep 30 2009 - 06:39:24 CDT)
- case (Wed Sep 30 2009 - 05:29:32 CDT)
- xuemeiwang1103 (Wed Sep 30 2009 - 04:32:38 CDT)
[AMBER] No sp2 improper torsion term for NB-CA-CB-CB
- case (Tue Sep 08 2009 - 07:58:33 CDT)
- qiaoyan (Tue Sep 08 2009 - 07:29:17 CDT)
[AMBER] parameter for manganese
- Mahmoud A. A. Ibrahim (Thu Sep 24 2009 - 07:17:29 CDT)
- Yuqin Cai (Tue Sep 22 2009 - 17:48:41 CDT)
[AMBER] Parameter Problem
- Manish Kumar (Wed Sep 23 2009 - 08:28:11 CDT)
- FyD (Wed Sep 23 2009 - 03:28:49 CDT)
- manoj singh (Tue Sep 22 2009 - 14:46:59 CDT)
- manoj singh (Tue Sep 22 2009 - 14:35:53 CDT)
[AMBER] parameterization of protein-ligand complex
- Jeff Yeo (Mon Sep 14 2009 - 10:03:25 CDT)
- cc cc (Wed Sep 09 2009 - 12:44:17 CDT)
- cc cc (Wed Sep 09 2009 - 12:41:52 CDT)
- Bill Ross (Wed Sep 09 2009 - 12:12:28 CDT)
- case (Wed Sep 09 2009 - 11:39:05 CDT)
- cc cc (Wed Sep 09 2009 - 11:29:07 CDT)
[AMBER] partial charges in Amber force field
- FyD (Mon Sep 28 2009 - 13:32:42 CDT)
- Jihang Wang (Mon Sep 28 2009 - 12:52:28 CDT)
[AMBER] PBSA for gp41 binding free energy
- Ray Luo (Fri Sep 11 2009 - 20:59:07 CDT)
- shuqing wang (Fri Sep 11 2009 - 01:42:59 CDT)
[AMBER] Pentane UA model
- FyD (Tue Sep 22 2009 - 02:02:50 CDT)
- aneesh cna (Tue Sep 22 2009 - 01:23:35 CDT)
[AMBER] periodic boundary condition for implicit solvent simulation and SHORT command
- case (Thu Sep 10 2009 - 21:04:53 CDT)
- Workalemahu Berhanu (Thu Sep 10 2009 - 17:37:32 CDT)
[AMBER] PES QM and MM
- Bill Ross (Thu Sep 17 2009 - 11:08:35 CDT)
- s. Bill (Thu Sep 17 2009 - 05:53:46 CDT)
[AMBER] pH calculations
- Michael Durney (Thu Sep 17 2009 - 10:01:08 CDT)
[AMBER] PK zero for specific dihedral and parmchk
- case (Wed Sep 09 2009 - 06:32:51 CDT)
- Carlos Simmerling (Wed Sep 09 2009 - 05:23:31 CDT)
- Loeffler, Hannes (STFC,DL,CSE) (Wed Sep 09 2009 - 03:00:20 CDT)
[AMBER] pmemd and internal dielectric
- Robert Duke (Fri Sep 25 2009 - 17:19:10 CDT)
- case (Fri Sep 25 2009 - 16:59:56 CDT)
- Robert Duke (Fri Sep 25 2009 - 15:10:57 CDT)
- Serguei Vassiliev (Fri Sep 25 2009 - 14:47:46 CDT)
- Adrian Roitberg (Fri Sep 25 2009 - 11:44:56 CDT)
- Robert Duke (Fri Sep 25 2009 - 11:07:06 CDT)
- Serguei Vassiliev (Fri Sep 25 2009 - 10:47:50 CDT)
[AMBER] prep file
- case (Fri Sep 04 2009 - 09:09:06 CDT)
- Jio M (Fri Sep 04 2009 - 04:24:04 CDT)
[AMBER] Problem about adding a small residue to DNA
- FyD (Mon Sep 07 2009 - 04:53:14 CDT)
- case (Fri Sep 04 2009 - 14:32:53 CDT)
- Yikan Chen (Thu Sep 03 2009 - 23:33:52 CDT)
[AMBER] problem building sander.apbs
- Robert Konecny (Tue Sep 22 2009 - 14:55:40 CDT)
- case (Tue Sep 22 2009 - 14:12:50 CDT)
- Oliver Kuhn (Tue Sep 22 2009 - 03:10:10 CDT)
- case (Mon Sep 21 2009 - 09:38:20 CDT)
- Oliver Kuhn (Mon Sep 21 2009 - 09:03:34 CDT)
- case (Mon Sep 21 2009 - 06:39:41 CDT)
- Oliver Kuhn (Mon Sep 21 2009 - 05:49:48 CDT)
[AMBER] Problem in compiling AMBER9 in parallel !
- case (Tue Sep 29 2009 - 13:08:41 CDT)
- Abhishek Banerjee (Tue Sep 29 2009 - 12:25:36 CDT)
- Pradipta Bandyopadhyay (Tue Sep 29 2009 - 08:04:47 CDT)
[AMBER] problem in QM/MM input file
- Tom Joseph (Tue Sep 08 2009 - 07:37:56 CDT)
- gaurav panwar (Mon Sep 07 2009 - 12:33:20 CDT)
[AMBER] Problem in test run
- case (Tue Sep 29 2009 - 11:50:19 CDT)
- Kshatresh Dutta Dubey (Tue Sep 29 2009 - 10:23:29 CDT)
- Kshatresh Dutta Dubey (Tue Sep 29 2009 - 10:14:35 CDT)
- Carlos Simmerling (Tue Sep 29 2009 - 10:06:55 CDT)
- Kshatresh Dutta Dubey (Tue Sep 29 2009 - 10:05:13 CDT)
- Carlos Simmerling (Tue Sep 29 2009 - 09:26:38 CDT)
- Kshatresh Dutta Dubey (Tue Sep 29 2009 - 09:21:56 CDT)
[AMBER] problem of PBCAL/GB
- Qinghua Liao (Tue Sep 08 2009 - 04:40:42 CDT)
- Ray Luo (Tue Sep 08 2009 - 00:58:44 CDT)
- Qinghua Liao (Tue Sep 08 2009 - 00:05:37 CDT)
[AMBER] Problem on PMEMD
- Robert Duke (Mon Sep 14 2009 - 20:46:16 CDT)
- zyxism (Mon Sep 14 2009 - 20:41:50 CDT)
- Adrian Roitberg (Mon Sep 14 2009 - 20:40:35 CDT)
- Tom Joseph (Mon Sep 14 2009 - 20:34:11 CDT)
- zyxism (Mon Sep 14 2009 - 20:11:57 CDT)
[AMBER] Problem regarding Hbond analysis
- Bill Ross (Tue Sep 22 2009 - 15:00:55 CDT)
- Abhishek Singh (Tue Sep 22 2009 - 14:43:50 CDT)
[AMBER] problem running pmemd gbrna tests
- wong105_at_llnl.gov (Tue Sep 15 2009 - 13:07:14 CDT)
[AMBER] problem when doing mm/pbsa: bad atom type Br
- Baifan Wang (Mon Sep 28 2009 - 02:26:06 CDT)
- Ray Luo (Sun Sep 27 2009 - 22:10:25 CDT)
- Baifan Wang (Sun Sep 27 2009 - 21:50:46 CDT)
[AMBER] problem with 4-Hydroxyl-Proline tutorial
- Jia Xu (Tue Sep 01 2009 - 00:10:50 CDT)
[AMBER] PROBLEM WITH CHCL3BOX pdb
- case (Fri Sep 18 2009 - 17:01:23 CDT)
- Hannes Loeffler (Fri Sep 18 2009 - 10:16:06 CDT)
- case (Fri Sep 18 2009 - 08:26:40 CDT)
- Silvia Carlotto (Fri Sep 18 2009 - 07:49:12 CDT)
[AMBER] Problem with GROUP input
- Jordan, Brad (Wed Sep 09 2009 - 18:58:36 CDT)
[AMBER] Problem with loading PDB into tleap
- Ashish Runthala (Tue Sep 08 2009 - 10:14:46 CDT)
- Kamali Sripathi (Tue Sep 08 2009 - 08:49:20 CDT)
[AMBER] Provisional Support for AMBER 10 PMEMD on NVIDIA GPUs
- Ross Walker (Fri Sep 04 2009 - 13:51:44 CDT)
[AMBER] QM/MM minimization
- Pansy Patel (Thu Sep 10 2009 - 09:09:48 CDT)
- gaurav panwar (Thu Sep 10 2009 - 09:05:37 CDT)
[AMBER] QM/MM simulation
- Ross Walker (Thu Sep 03 2009 - 15:43:45 CDT)
- gaurav panwar (Thu Sep 03 2009 - 15:11:42 CDT)
[AMBER] QMMM NEB with PM3-PDDG fails with ASSERTion 'ierr.eq.0' pimd_init.f line 320
- case (Sat Sep 12 2009 - 09:17:16 CDT)
- Keith Van Nostrand (Tue Sep 08 2009 - 14:26:14 CDT)
[AMBER] question about ptraj
- Niel Henriksen (Wed Sep 02 2009 - 09:37:39 CDT)
- Jeffrey (Wed Sep 02 2009 - 03:20:12 CDT)
[AMBER] Question about the debug forces
- Faezeh Salehi (Wed Sep 02 2009 - 16:30:47 CDT)
[AMBER] Question on ECAVITY term of MM_PBSA
- Ray Luo (Mon Sep 21 2009 - 20:28:32 CDT)
- Ray Luo (Mon Sep 21 2009 - 12:30:57 CDT)
- Gianluca Degliesposti (Mon Sep 21 2009 - 06:18:27 CDT)
- Gianluca Degliesposti (Mon Sep 14 2009 - 10:28:12 CDT)
[AMBER] Question regarding PCA analysis.
- Catein Catherine (Thu Sep 03 2009 - 21:55:42 CDT)
- Chris Moth (Thu Sep 03 2009 - 09:17:42 CDT)
- Catein Catherine (Tue Sep 01 2009 - 22:53:10 CDT)
[AMBER] question with hbond
- Ganesh Kamath (Wed Sep 16 2009 - 16:36:18 CDT)
[AMBER] question with radial distribution function
- Ganesh Kamath (Thu Sep 10 2009 - 17:08:34 CDT)
[AMBER] R.E.D. : Gaussian Error
- manoj singh (Mon Sep 07 2009 - 00:46:54 CDT)
- FyD (Mon Sep 07 2009 - 00:07:34 CDT)
- manoj singh (Sun Sep 06 2009 - 23:22:44 CDT)
- FyD (Sun Sep 06 2009 - 14:41:41 CDT)
- manoj singh (Sun Sep 06 2009 - 13:40:48 CDT)
[AMBER] radial distribution function in amber
- Ganesh Kamath (Mon Sep 14 2009 - 09:58:56 CDT)
[AMBER] RDC analysis: "No restraint defined"
- case (Wed Sep 16 2009 - 11:47:41 CDT)
- Michael Durney (Wed Sep 16 2009 - 11:10:34 CDT)
[AMBER] Reg. snapshot_statistics.out.snap
- Rose Tamil (Tue Sep 01 2009 - 12:04:08 CDT)
[AMBER] Regarding united atom force field
- FyD (Tue Sep 22 2009 - 01:13:03 CDT)
- Ray Luo (Mon Sep 21 2009 - 12:32:34 CDT)
- aneesh cna (Mon Sep 21 2009 - 05:17:20 CDT)
[AMBER] RESP RED
- FyD (Sat Sep 12 2009 - 09:35:16 CDT)
- s. Bill (Fri Sep 11 2009 - 13:40:24 CDT)
[AMBER] RMSDf of heavy atoms
- Syed Tarique Moin (Tue Sep 22 2009 - 06:45:26 CDT)
[AMBER] Simulation short peptide and protein interaction
- Carlos Simmerling (Thu Sep 03 2009 - 08:34:27 CDT)
- Rilei Yu (Thu Sep 03 2009 - 07:22:10 CDT)
- case (Wed Sep 02 2009 - 07:15:06 CDT)
- Rilei Yu (Tue Sep 01 2009 - 19:50:29 CDT)
[AMBER] Solvate in an alkaline solution
- case (Thu Sep 10 2009 - 07:05:44 CDT)
- vallespardojl_at_chem.leidenuniv.nl (Thu Sep 10 2009 - 03:07:07 CDT)
[AMBER] solvent accessible surface area
- Carlos Simmerling (Wed Sep 23 2009 - 14:29:57 CDT)
- Ganesh Kamath (Wed Sep 23 2009 - 14:26:33 CDT)
- Carlos Simmerling (Wed Sep 23 2009 - 14:20:24 CDT)
- Ganesh Kamath (Wed Sep 23 2009 - 14:07:23 CDT)
[AMBER] symbol lookup error
- Ross Walker (Tue Sep 01 2009 - 14:42:49 CDT)
- Bala subramanian (Tue Sep 01 2009 - 03:43:51 CDT)
[AMBER] Teragrid
- Carlos Simmerling (Thu Sep 24 2009 - 07:11:41 CDT)
- Beale, John (Thu Sep 24 2009 - 07:08:56 CDT)
[AMBER] TI in Amber9/10
- Ilyas Yildirim (Tue Sep 08 2009 - 13:07:40 CDT)
- steinbrt_at_rci.rutgers.edu (Tue Sep 08 2009 - 12:41:32 CDT)
- Alessandro S. Nascimento (Tue Sep 08 2009 - 10:47:26 CDT)
[AMBER] too many missing parameters in frcmod for the prep of my ligand
- FyD (Wed Sep 30 2009 - 05:30:32 CDT)
- xueqin pang (Wed Sep 30 2009 - 04:21:31 CDT)
[AMBER] trouble using iAPBS
- Robert Konecny (Mon Sep 28 2009 - 09:20:31 CDT)
- Oliver Kuhn (Mon Sep 28 2009 - 07:08:27 CDT)
[AMBER] unit of force constant
- balaji nagarajan (Tue Sep 08 2009 - 08:41:37 CDT)
- Carlos Simmerling (Tue Sep 08 2009 - 08:21:40 CDT)
- balaji nagarajan (Tue Sep 08 2009 - 08:16:08 CDT)
- balaji nagarajan (Wed Sep 02 2009 - 11:57:25 CDT)
[AMBER] variable header for ABMD
- stephane acoca (Sun Sep 13 2009 - 22:03:00 CDT)
[AMBER] warning in dispatchToken
- case (Sun Sep 20 2009 - 08:14:49 CDT)
- Jeff Yeo (Sun Sep 20 2009 - 05:30:57 CDT)
[AMBER] What is dual topology
- case (Wed Sep 02 2009 - 10:48:51 CDT)
- Ashish Runthala (Wed Sep 02 2009 - 10:25:19 CDT)
[AMBER] What is the Optimum Ph for solvating a protein
- case (Sun Sep 13 2009 - 16:19:24 CDT)
- Ashish Runthala (Sun Sep 13 2009 - 08:08:40 CDT)
[AMBER] What is the unit of RMSF?
- case (Sat Sep 12 2009 - 08:37:42 CDT)
- Catein Catherine (Sat Sep 12 2009 - 03:13:02 CDT)
[AMBER] What should be the standard input file when imin=5
- Carlos Simmerling (Thu Sep 03 2009 - 06:55:48 CDT)
- Ashish Runthala (Thu Sep 03 2009 - 02:25:49 CDT)
[AMBER] why should one restrain the position of the counterions?
- Jose Borreguero (Mon Sep 28 2009 - 13:28:20 CDT)
[AMBER] xleap problem !
- balaji nagarajan (Wed Sep 30 2009 - 13:40:58 CDT)
[AMBER] Your help about ptraj in AmberTools!]]
- Rosina Noto (Mon Sep 28 2009 - 04:59:09 CDT)
[AMBER] Zinc
- Roman Osman (Tue Sep 29 2009 - 19:08:28 CDT)
- Rubben Torella (Tue Sep 29 2009 - 16:31:31 CDT)
- Sel Ercan (Tue Sep 29 2009 - 16:26:53 CDT)
charge consideration
- Jio M (Mon Sep 14 2009 - 03:38:27 CDT)
charge interaction
- case (Sun Sep 13 2009 - 16:37:55 CDT)
- case (Sun Sep 13 2009 - 16:13:19 CDT)
- Jio M (Sun Sep 13 2009 - 09:38:43 CDT)
Problem with GROUP input
- Jordan, Brad (Wed Sep 09 2009 - 19:11:51 CDT)
»Ø¸´£º [AMBER] Problem about adding a small residue to DNA
- Yikan Chen (Fri Sep 04 2009 - 15:03:54 CDT)
- Yikan Chen (Fri Sep 04 2009 - 14:51:38 CDT)
å›žå¤ï¼š [AMBER] Problem about adding a small residue to DNA
- Yikan Chen (Sun Sep 06 2009 - 10:47:04 CDT)
- case (Sun Sep 06 2009 - 07:30:23 CDT)
- Yikan Chen (Fri Sep 04 2009 - 16:38:27 CDT)
- case (Fri Sep 04 2009 - 15:37:23 CDT)
- Rilei Yu (Fri Sep 04 2009 - 01:33:50 CDT)

Last message date: Mon Nov 23 2009 - 13:25:08 CST
Archived on: Mon Nov 23 2009 - 13:25:11 CST

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