Amber Archive Sep 2009: by subject

[AMBER] "nan" in gaussian input files generated by antechamber
- FyD (Sat Sep 12 2009 - 07:58:52 PDT)
- case (Sat Sep 12 2009 - 06:55:14 PDT)
- Yikan Chen (Fri Sep 11 2009 - 13:19:04 PDT)
[AMBER] (no subject)
- gunajyoti das (Mon Sep 07 2009 - 02:21:45 PDT)
[AMBER] about the number of residues after MD
- Qinghua Liao (Wed Sep 09 2009 - 00:23:03 PDT)
[AMBER] About the PMEMD compiling for CUDA
- Ross Walker (Tue Sep 15 2009 - 23:55:11 PDT)
- Ross Walker (Tue Sep 15 2009 - 22:26:19 PDT)
- wang (Tue Sep 15 2009 - 22:17:52 PDT)
[AMBER] ACE and NME patch: VMD ???
- Ross Walker (Tue Sep 01 2009 - 10:54:38 PDT)
- Siddharth Rastogi (Mon Aug 31 2009 - 17:25:47 PDT)
[AMBER] ACS COMP division awards- Oct 19th deadline
- Carlos Simmerling (Mon Sep 21 2009 - 10:49:28 PDT)
[AMBER] Active site - Ion - Search engine
- s. Bill (Wed Sep 02 2009 - 07:53:39 PDT)
[AMBER] AmberTools 1.3 / CHAMBER
- Mag. Thomas Taylor (Tue Sep 08 2009 - 07:29:23 PDT)
[AMBER] ambertools and Snow Leopard 64 bits kernel
- case (Wed Sep 23 2009 - 13:26:16 PDT)
- Alan (Wed Sep 23 2009 - 07:21:30 PDT)
- gilbert.bluemarble.net (Tue Sep 22 2009 - 19:18:12 PDT)
- Tom Joseph (Tue Sep 22 2009 - 17:18:17 PDT)
- Alan (Tue Sep 22 2009 - 14:41:18 PDT)
- Tom Joseph (Tue Sep 22 2009 - 11:12:55 PDT)
- Alan (Tue Sep 22 2009 - 06:55:25 PDT)
[AMBER] amoeba.prm problem?
- Ivan Gladich (Fri Sep 18 2009 - 12:57:39 PDT)
- case (Sat Sep 12 2009 - 06:46:52 PDT)
- Ivan Gladich (Fri Sep 11 2009 - 13:34:07 PDT)
- case (Wed Sep 09 2009 - 12:17:39 PDT)
- Ivan Gladich (Tue Sep 08 2009 - 07:31:43 PDT)
[AMBER] antechamber bug: output of incorrect bond character
- case (Thu Sep 03 2009 - 09:29:03 PDT)
- Matthew Walsh (Thu Sep 03 2009 - 08:15:00 PDT)
- case (Thu Sep 03 2009 - 04:26:19 PDT)
- Matthew Walsh (Wed Sep 02 2009 - 21:30:04 PDT)
- case (Wed Sep 02 2009 - 18:53:37 PDT)
- Matthew Walsh (Wed Sep 02 2009 - 11:37:44 PDT)
[AMBER] antechamber error
- Taufik Al-Sarraj (Wed Sep 16 2009 - 12:11:26 PDT)
- Taufik Al-Sarraj (Wed Sep 16 2009 - 11:52:26 PDT)
- case (Wed Sep 16 2009 - 11:43:56 PDT)
- Taufik Al-Sarraj (Wed Sep 16 2009 - 11:18:32 PDT)
[AMBER] Antechamber generate a prep file in a wrong order...
- case (Sun Sep 06 2009 - 05:26:02 PDT)
- Yikan Chen (Sat Sep 05 2009 - 12:37:53 PDT)
[AMBER] Any tutorial on the proper way to merge a ligand and protein?
- case (Fri Sep 11 2009 - 12:54:39 PDT)
- cc cc (Fri Sep 11 2009 - 11:16:55 PDT)
- Dean Cuebas (Wed Sep 09 2009 - 12:12:00 PDT)
- case (Wed Sep 09 2009 - 11:50:13 PDT)
- Dean Cuebas (Wed Sep 09 2009 - 11:26:02 PDT)
[AMBER] apbs-amber
- Rilei Yu (Tue Sep 22 2009 - 18:41:08 PDT)
- Robert Konecny (Tue Sep 22 2009 - 16:18:28 PDT)
- Rilei Yu (Tue Sep 22 2009 - 15:58:40 PDT)
[AMBER] ATP and GTP parameters
- E.M. (Thu Sep 03 2009 - 19:08:02 PDT)
- Carlos Simmerling (Thu Sep 03 2009 - 04:54:13 PDT)
- FyD (Thu Sep 03 2009 - 02:36:45 PDT)
- FyD (Thu Sep 03 2009 - 01:35:11 PDT)
- Sergey Samsonov (Wed Sep 02 2009 - 23:35:33 PDT)
- E.M. (Wed Sep 02 2009 - 23:30:31 PDT)
- FyD (Wed Sep 02 2009 - 23:15:54 PDT)
- E.M. (Wed Sep 02 2009 - 22:29:47 PDT)
[AMBER] ATP/GTP parameters
- Steve Seibold (Tue Sep 01 2009 - 09:29:59 PDT)
- FyD (Tue Sep 01 2009 - 09:25:45 PDT)
- Steve Seibold (Tue Sep 01 2009 - 04:42:09 PDT)
- FyD (Mon Aug 31 2009 - 23:10:41 PDT)
- wang (Mon Aug 31 2009 - 22:02:08 PDT)
- E.M. (Mon Aug 31 2009 - 21:48:39 PDT)
[AMBER] Attaching a ligand to a protein residue.
- Kipras Redeckas (Sun Sep 27 2009 - 03:23:42 PDT)
- case (Sat Sep 26 2009 - 07:23:18 PDT)
- Kipras Redeckas (Fri Sep 25 2009 - 14:33:58 PDT)
[AMBER] can antechamber convert a prep file from cartesian to internal coordinates?
- Paul Ledbetter (Tue Sep 15 2009 - 16:40:09 PDT)
- Paul Ledbetter (Tue Sep 15 2009 - 16:34:54 PDT)
- Bill Ross (Tue Sep 15 2009 - 15:15:38 PDT)
- case (Tue Sep 15 2009 - 15:12:25 PDT)
- Paul Ledbetter (Tue Sep 15 2009 - 13:25:56 PDT)
[AMBER] Carbon Nanotube Library file (CNT)
- Christopher Stiles (Mon Sep 14 2009 - 06:59:57 PDT)
[AMBER] CH3Hg+ parameters
- babak minoofar (Thu Sep 24 2009 - 05:08:12 PDT)
[AMBER] Changing pH of the system
- nicholus bhattacharjee (Tue Sep 01 2009 - 06:43:01 PDT)
[AMBER] charge consideration
- case (Sat Sep 12 2009 - 06:59:56 PDT)
- Jio M (Fri Sep 11 2009 - 13:17:34 PDT)
[AMBER] combining MD runs for post-MD analysis
- Bill Ross (Mon Sep 21 2009 - 10:32:53 PDT)
- case (Sun Sep 20 2009 - 18:35:08 PDT)
- Qinghua Liao (Sun Sep 20 2009 - 18:01:22 PDT)
- Jeff Yeo (Sun Sep 20 2009 - 17:02:12 PDT)
[AMBER] Compiling Amber with gfortran-4.5.0 on a mac
- Ben Roberts (Tue Sep 29 2009 - 14:37:31 PDT)
[AMBER] Compiling Amber10
- Williams, John (Tue Sep 22 2009 - 05:56:43 PDT)
[AMBER] cpin error
- case (Tue Sep 01 2009 - 05:23:04 PDT)
[AMBER] Creating new counterions
- case (Tue Sep 01 2009 - 13:03:48 PDT)
- Bill Ross (Tue Sep 01 2009 - 12:58:55 PDT)
[AMBER] Cygwin Home Directory
- Bill Ross (Mon Sep 21 2009 - 10:45:02 PDT)
- case (Mon Sep 21 2009 - 10:14:59 PDT)
- Wallace Kunin (Mon Sep 21 2009 - 09:29:11 PDT)
- Ashish Runthala (Sat Sep 19 2009 - 19:51:11 PDT)
- case (Sat Sep 19 2009 - 15:11:57 PDT)
- Bill Ross (Sat Sep 19 2009 - 10:29:59 PDT)
- Wallace Kunin (Sat Sep 19 2009 - 09:13:20 PDT)
- Bill Ross (Fri Sep 18 2009 - 13:56:17 PDT)
- manoj singh (Fri Sep 18 2009 - 12:30:28 PDT)
- Wallace Kunin (Fri Sep 18 2009 - 12:12:22 PDT)
- Bill Ross (Fri Sep 18 2009 - 11:19:44 PDT)
- Wallace Kunin (Fri Sep 18 2009 - 10:51:17 PDT)
[AMBER] database
- case (Fri Sep 18 2009 - 19:46:39 PDT)
- FyD (Fri Sep 18 2009 - 17:49:17 PDT)
- Steve Seibold (Fri Sep 18 2009 - 12:10:19 PDT)
- case (Fri Sep 18 2009 - 10:23:08 PDT)
- Steve Seibold (Fri Sep 18 2009 - 08:03:44 PDT)
- FyD (Fri Sep 18 2009 - 00:28:53 PDT)
- case (Thu Sep 17 2009 - 15:23:30 PDT)
- FyD (Thu Sep 17 2009 - 14:54:29 PDT)
- Jeff Yeo (Thu Sep 17 2009 - 14:01:48 PDT)
- Steve Seibold (Thu Sep 17 2009 - 12:46:20 PDT)
- FyD (Thu Sep 17 2009 - 09:00:22 PDT)
- Steve Seibold (Thu Sep 17 2009 - 06:43:25 PDT)
- FyD (Wed Sep 16 2009 - 11:58:38 PDT)
- FyD (Wed Sep 16 2009 - 11:56:16 PDT)
- Bill Ross (Wed Sep 16 2009 - 10:54:47 PDT)
- Steve Seibold (Wed Sep 16 2009 - 10:14:46 PDT)
- FyD (Wed Sep 16 2009 - 09:59:30 PDT)
- case (Wed Sep 16 2009 - 09:53:56 PDT)
- Steve Seibold (Wed Sep 16 2009 - 09:11:47 PDT)
- case (Wed Sep 16 2009 - 08:26:24 PDT)
- Steve Seibold (Wed Sep 16 2009 - 07:59:14 PDT)
[AMBER] dihedral force calculation
- case (Sat Sep 12 2009 - 07:04:34 PDT)
- Germain Vallverdu (Fri Sep 11 2009 - 07:35:08 PDT)
[AMBER] Discrepancy between AMBER and VMD calculation
- Sunita Patel (Thu Sep 17 2009 - 12:11:07 PDT)
[AMBER] DMF solvent box
- FyD (Fri Sep 18 2009 - 23:36:20 PDT)
- Abhishek Banerjee (Fri Sep 18 2009 - 22:24:08 PDT)
- FyD (Thu Sep 17 2009 - 00:00:06 PDT)
- Abhishek Banerjee (Wed Sep 16 2009 - 23:15:53 PDT)
- FyD (Tue Sep 15 2009 - 22:09:42 PDT)
- Abhishek Banerjee (Tue Sep 15 2009 - 21:33:23 PDT)
- FyD (Mon Sep 14 2009 - 08:04:58 PDT)
- Abhishek Banerjee (Mon Sep 14 2009 - 06:18:30 PDT)
- FyD (Sun Sep 13 2009 - 10:01:13 PDT)
- Abhishek Banerjee (Sun Sep 13 2009 - 07:24:04 PDT)
- FyD (Sun Sep 13 2009 - 02:25:33 PDT)
- Abhishek Banerjee (Sun Sep 13 2009 - 01:56:18 PDT)
- Abhishek Banerjee (Sat Sep 12 2009 - 22:33:39 PDT)
- FyD (Sat Sep 12 2009 - 07:07:30 PDT)
- Jio M (Fri Sep 11 2009 - 08:00:40 PDT)
- Abhishek Banerjee (Thu Sep 10 2009 - 19:40:21 PDT)
[AMBER] Docking with Amber
- case (Mon Aug 31 2009 - 17:58:49 PDT)
[AMBER] Dummy atoms and MM-PBSA
- Ray Luo (Fri Sep 04 2009 - 11:25:33 PDT)
- Alireza Shaneh (Fri Sep 04 2009 - 09:48:16 PDT)
[AMBER] Enquiry about MM/GBSA output file.
- Catein Catherine (Tue Sep 08 2009 - 00:14:19 PDT)
[AMBER] Error in minimal
- case (Tue Sep 15 2009 - 15:15:06 PDT)
- xuemeiwang1103 (Tue Sep 15 2009 - 06:54:58 PDT)
- case (Tue Sep 15 2009 - 04:56:02 PDT)
- xuemeiwang1103 (Tue Sep 15 2009 - 00:27:18 PDT)
[AMBER] error xleap: XaLeap_wcl is empty
- case (Mon Sep 14 2009 - 05:02:12 PDT)
- Mari Carmen Pérez (Mon Sep 14 2009 - 02:59:09 PDT)
[AMBER] Ewald error estimated
- Robert Duke (Fri Sep 25 2009 - 08:50:18 PDT)
- case (Fri Sep 25 2009 - 08:15:31 PDT)
- Qinghua Liao (Fri Sep 25 2009 - 00:48:14 PDT)
- xuemeiwang1103 (Thu Sep 24 2009 - 20:01:05 PDT)
- xuemeiwang1103 (Thu Sep 24 2009 - 20:01:02 PDT)
[AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex
- case (Thu Sep 24 2009 - 15:13:39 PDT)
- Jeff Yeo (Wed Sep 23 2009 - 16:24:51 PDT)
[AMBER] Force Field Fitting
- manoj singh (Thu Sep 17 2009 - 12:32:33 PDT)
- s. Bill (Thu Sep 17 2009 - 12:27:46 PDT)
- manoj singh (Thu Sep 17 2009 - 10:20:50 PDT)
- s. Bill (Thu Sep 17 2009 - 04:36:33 PDT)
[AMBER] gaff.dat questions
- case (Wed Sep 09 2009 - 07:16:23 PDT)
- gilbert.bluemarble.net (Wed Sep 09 2009 - 07:02:28 PDT)
[AMBER] Gap in rst file
- Katrina Lexa (Mon Sep 28 2009 - 07:47:43 PDT)
[AMBER] general query: implicit solvation
- Carlos Simmerling (Tue Sep 08 2009 - 03:11:24 PDT)
- Jio M (Tue Sep 08 2009 - 02:28:49 PDT)
[AMBER] generate prmtop file from CHARMM psf file
- Jeffrey (Mon Sep 21 2009 - 07:34:59 PDT)
[AMBER] group distance restraint
- XIAOHUICANG (Tue Sep 22 2009 - 12:36:03 PDT)
[AMBER] Hbond analysis: Direction of the hydrogen
- Age.Skjevik.biomed.uib.no (Tue Sep 08 2009 - 14:56:50 PDT)
- Shulin Zhuang (Tue Sep 08 2009 - 12:54:22 PDT)
- Age.Skjevik.biomed.uib.no (Tue Sep 08 2009 - 12:45:19 PDT)
[AMBER] Heme + Fe(II) + O2 + histidine parameter
- FyD (Fri Sep 04 2009 - 00:43:00 PDT)
- Haining Liu (Thu Sep 03 2009 - 14:13:09 PDT)
- FyD (Thu Sep 03 2009 - 00:03:45 PDT)
- Haining Liu (Wed Sep 02 2009 - 20:36:31 PDT)
[AMBER] how to calculate correct RMSF?
- Catein Catherine (Mon Sep 14 2009 - 17:57:20 PDT)
- case (Mon Sep 14 2009 - 05:33:29 PDT)
- Catein Catherine (Mon Sep 14 2009 - 04:21:52 PDT)
[AMBER] How to consider the off centre charges
- case (Wed Sep 02 2009 - 08:50:12 PDT)
- Ashish Runthala (Wed Sep 02 2009 - 08:28:40 PDT)
[AMBER] how to deal with aromatic nitro group with antechamber
- case (Wed Sep 02 2009 - 19:15:14 PDT)
- Lin Xu (Wed Sep 02 2009 - 15:04:13 PDT)
[AMBER] How to denature DNA
- balaji nagarajan (Wed Sep 09 2009 - 10:14:37 PDT)
- Bill Ross (Wed Sep 09 2009 - 09:38:04 PDT)
- balaji nagarajan (Tue Sep 08 2009 - 21:01:55 PDT)
- Bill Ross (Tue Sep 08 2009 - 10:33:09 PDT)
- Adrian Roitberg (Tue Sep 08 2009 - 10:12:00 PDT)
- balaji nagarajan (Tue Sep 08 2009 - 09:58:36 PDT)
- Adrian Roitberg (Tue Sep 08 2009 - 09:46:51 PDT)
- balaji nagarajan (Tue Sep 08 2009 - 09:29:57 PDT)
- Adrian Roitberg (Tue Sep 08 2009 - 07:04:30 PDT)
- balaji nagarajan (Tue Sep 08 2009 - 07:00:43 PDT)
[AMBER] How to derive charges from the output
- bharat lakhani (Tue Sep 01 2009 - 01:46:12 PDT)
[AMBER] How to find a protein's energy
- Ashish Runthala (Sun Sep 06 2009 - 05:30:26 PDT)
- Carlos Simmerling (Sun Sep 06 2009 - 04:49:53 PDT)
- Ashish Runthala (Sat Sep 05 2009 - 20:48:01 PDT)
[AMBER] How to find water-mediated hydrogen bond?
- Hannes Loeffler (Thu Sep 03 2009 - 00:53:51 PDT)
- Catein Catherine (Wed Sep 02 2009 - 07:10:37 PDT)
[AMBER] how to give force values in TMD
- balaji nagarajan (Wed Sep 02 2009 - 03:03:41 PDT)
[AMBER] how to make 50% aqueous TFE box?
- FyD (Fri Sep 18 2009 - 17:22:35 PDT)
- parul sharma (Fri Sep 18 2009 - 06:47:01 PDT)
[AMBER] How to obtain amber top and crd from pdb file with POPE lipids?
- Hannes Loeffler (Mon Sep 28 2009 - 00:34:12 PDT)
- decastro.physics.usyd.edu.au (Sun Sep 27 2009 - 21:52:20 PDT)
[AMBER] how to ouput the electrostatic potential at a single atomic position?
- Jose Borreguero (Thu Sep 17 2009 - 12:06:54 PDT)
[AMBER] How to prepare the coordinate and toplogy files in leap ?
- case (Mon Sep 14 2009 - 04:56:08 PDT)
- xuemeiwang1103 (Mon Sep 14 2009 - 02:03:59 PDT)
[AMBER] how to pull a dna
- balaji nagarajan (Tue Sep 01 2009 - 07:24:29 PDT)
- Sam Danziger (Tue Sep 01 2009 - 04:17:09 PDT)
- balaji nagarajan (Mon Aug 31 2009 - 19:39:10 PDT)
[AMBER] How to remove Hydrogen using ptraj
- Thomas Cheatham III (Tue Sep 01 2009 - 10:25:10 PDT)
- case (Tue Sep 01 2009 - 10:19:51 PDT)
- Thomas Cheatham III (Tue Sep 01 2009 - 08:55:43 PDT)
- Mannan (Tue Sep 01 2009 - 03:50:44 PDT)
[AMBER] How to use AMBER 10 for PCA analysis.
- Catein Catherine (Tue Sep 01 2009 - 08:30:56 PDT)
[AMBER] input file
- Bill Ross (Thu Sep 10 2009 - 09:51:10 PDT)
- Ashish Runthala (Thu Sep 10 2009 - 07:05:32 PDT)
- Jenny Iskrenova (Thu Sep 10 2009 - 06:05:03 PDT)
- Carlos Simmerling (Thu Sep 10 2009 - 04:03:17 PDT)
- Mag. Thomas Taylor (Thu Sep 10 2009 - 03:48:06 PDT)
[AMBER] input file / skinnb
- Mag. Thomas Taylor (Wed Sep 16 2009 - 22:50:16 PDT)
- Robert Duke (Wed Sep 16 2009 - 07:23:06 PDT)
- case (Wed Sep 16 2009 - 04:56:01 PDT)
- Mag. Thomas Taylor (Wed Sep 16 2009 - 00:49:32 PDT)
[AMBER] install ambertools
- case (Thu Sep 17 2009 - 06:40:28 PDT)
- Karl Kirschner (Thu Sep 17 2009 - 05:55:22 PDT)
[AMBER] Installation issue
- Bill Ross (Wed Sep 23 2009 - 09:36:59 PDT)
- Bill Ross (Wed Sep 23 2009 - 09:29:28 PDT)
- Tom Joseph (Wed Sep 23 2009 - 09:08:33 PDT)
- Ashveen Seenauth (Wed Sep 23 2009 - 08:54:27 PDT)
- Tom Joseph (Wed Sep 23 2009 - 08:43:42 PDT)
- Ashveen Seenauth (Wed Sep 23 2009 - 08:41:53 PDT)
- Tom Joseph (Wed Sep 23 2009 - 08:35:44 PDT)
- Ashveen Seenauth (Wed Sep 23 2009 - 08:28:55 PDT)
- Bill Ross (Tue Sep 22 2009 - 11:28:43 PDT)
- Tom Joseph (Tue Sep 22 2009 - 11:16:01 PDT)
- Ashveen Seenauth (Tue Sep 22 2009 - 10:59:46 PDT)
- Bill Ross (Tue Sep 22 2009 - 10:59:22 PDT)
- Bill Ross (Tue Sep 22 2009 - 10:55:34 PDT)
- Bill Ross (Tue Sep 22 2009 - 10:50:28 PDT)
- Tom Joseph (Tue Sep 22 2009 - 10:41:51 PDT)
- Ashveen Seenauth (Tue Sep 22 2009 - 10:25:12 PDT)
- Tom Joseph (Tue Sep 22 2009 - 09:55:20 PDT)
- Ashveen Seenauth (Tue Sep 22 2009 - 09:45:13 PDT)
- Bill Ross (Tue Sep 22 2009 - 09:31:47 PDT)
- Ashveen Seenauth (Tue Sep 22 2009 - 09:17:49 PDT)
[AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions.
- oguz gurbulak (Mon Sep 21 2009 - 23:46:27 PDT)
- David Dubins (Mon Sep 21 2009 - 16:02:47 PDT)
[AMBER] Ki and G
- Marek Maly (Tue Sep 15 2009 - 04:58:07 PDT)
- case (Mon Sep 14 2009 - 13:24:05 PDT)
- steinbrt.rci.rutgers.edu (Mon Sep 14 2009 - 13:09:55 PDT)
- Marek Maly (Mon Sep 14 2009 - 11:41:33 PDT)
- case (Mon Sep 14 2009 - 10:23:49 PDT)
- Marek Maly (Mon Sep 14 2009 - 10:02:36 PDT)
- Adrian Roitberg (Mon Sep 14 2009 - 07:28:57 PDT)
- steinbrt.rci.rutgers.edu (Mon Sep 14 2009 - 04:59:40 PDT)
- s. Bill (Mon Sep 14 2009 - 04:39:20 PDT)
[AMBER] Kinetics
- Soumya Lipsa Rath (Mon Sep 07 2009 - 23:36:18 PDT)
- case (Fri Sep 04 2009 - 12:29:24 PDT)
- Soumya Lipsa Rath (Thu Sep 03 2009 - 23:39:54 PDT)
[AMBER] Leap warning
- Bill Ross (Wed Sep 09 2009 - 09:49:05 PDT)
- case (Wed Sep 09 2009 - 04:31:36 PDT)
- Ashish Runthala (Wed Sep 09 2009 - 00:21:03 PDT)
- manoj singh (Tue Sep 08 2009 - 22:38:33 PDT)
[AMBER] LINMIN failure notice
- Ross Walker (Fri Sep 18 2009 - 16:41:33 PDT)
- Bill Ross (Fri Sep 18 2009 - 09:18:41 PDT)
- case (Fri Sep 18 2009 - 04:38:33 PDT)
- Ashish Runthala (Fri Sep 18 2009 - 03:46:09 PDT)
- Jio M (Fri Sep 18 2009 - 03:20:18 PDT)
[AMBER] LJ-partial charges and force field parameters for ethylene glycol and glycerol
- FyD (Mon Sep 28 2009 - 11:23:20 PDT)
- Ganesh Kamath (Mon Sep 28 2009 - 10:03:13 PDT)
[AMBER] load .crd & .top in xleap
- oguz gurbulak (Sun Sep 13 2009 - 12:20:26 PDT)
- vallespardojl.chem.leidenuniv.nl (Sun Sep 13 2009 - 07:21:15 PDT)
[AMBER] loading a following attached protein in amber 10
- albert albert (Tue Sep 08 2009 - 10:43:55 PDT)
- case (Tue Sep 08 2009 - 10:27:47 PDT)
- David Watson (Tue Sep 08 2009 - 10:26:19 PDT)
- albert albert (Tue Sep 08 2009 - 10:09:09 PDT)
[AMBER] loading PDB of a RNA sequence
- case (Tue Sep 08 2009 - 04:38:34 PDT)
- Carlos Simmerling (Tue Sep 08 2009 - 03:33:57 PDT)
- gunajyoti das (Tue Sep 08 2009 - 03:31:47 PDT)
[AMBER] loading RNA sequence in xleap
- case (Thu Sep 17 2009 - 05:13:38 PDT)
- FyD (Thu Sep 17 2009 - 02:39:09 PDT)
- gunajyoti das (Thu Sep 17 2009 - 01:27:49 PDT)
[AMBER] loadpdb
- Carlos Simmerling (Wed Sep 09 2009 - 04:35:04 PDT)
- Bill Ross (Tue Sep 08 2009 - 19:53:32 PDT)
- Jagdeesh C (Tue Sep 08 2009 - 18:55:36 PDT)
- Bill Ross (Tue Sep 08 2009 - 09:58:12 PDT)
- Bill Ross (Tue Sep 08 2009 - 09:53:03 PDT)
- Carlos Simmerling (Tue Sep 08 2009 - 06:39:12 PDT)
- Tom Joseph (Tue Sep 08 2009 - 05:31:56 PDT)
- Ashish Runthala (Mon Sep 07 2009 - 20:00:47 PDT)
- Jagdeesh C (Mon Sep 07 2009 - 11:31:42 PDT)
- Carlos Simmerling (Mon Sep 07 2009 - 11:01:10 PDT)
- Jagdeesh C (Mon Sep 07 2009 - 10:36:58 PDT)
[AMBER] logdvdl does not work
- steinbrt.rci.rutgers.edu (Tue Sep 08 2009 - 10:37:31 PDT)
- helde010.umn.edu (Tue Sep 08 2009 - 09:53:14 PDT)
[AMBER] makeDIST_RST: no map function
- Workalemahu Berhanu (Tue Sep 15 2009 - 08:24:56 PDT)
- Workalemahu Berhanu (Tue Sep 15 2009 - 08:11:27 PDT)
- case (Tue Sep 15 2009 - 07:38:23 PDT)
- Duggan, Brendan M. (Tue Sep 15 2009 - 06:40:00 PDT)
- Workalemahu Berhanu (Mon Sep 14 2009 - 12:30:15 PDT)
[AMBER] MM-GBAS decomp error
- Catein Catherine (Fri Sep 04 2009 - 03:29:35 PDT)
[AMBER] MM_PBSA
- Zhongjie Liang (Tue Sep 29 2009 - 18:30:40 PDT)
[AMBER] MM_PBSA decomp problem
- B. Nandy (Tue Sep 22 2009 - 05:29:23 PDT)
[AMBER] momentum in MD simulation
- case (Tue Sep 01 2009 - 04:48:52 PDT)
[AMBER] NAB syntax
- case (Thu Sep 17 2009 - 08:22:29 PDT)
- Andreas Svrcek-Seiler (Thu Sep 17 2009 - 08:21:51 PDT)
- Michael Durney (Thu Sep 17 2009 - 07:58:58 PDT)
[AMBER] nmropt option
- Carlos Simmerling (Sat Sep 05 2009 - 03:59:04 PDT)
- Jio M (Fri Sep 04 2009 - 22:23:09 PDT)
- Carlos Simmerling (Fri Sep 04 2009 - 11:15:13 PDT)
- Jio M (Fri Sep 04 2009 - 11:05:25 PDT)
[AMBER] No restrt file
- case (Wed Sep 30 2009 - 05:06:47 PDT)
- null (Wed Sep 30 2009 - 04:39:24 PDT)
- case (Wed Sep 30 2009 - 03:29:32 PDT)
- xuemeiwang1103 (Wed Sep 30 2009 - 02:32:38 PDT)
[AMBER] No sp2 improper torsion term for NB-CA-CB-CB
- case (Tue Sep 08 2009 - 05:58:33 PDT)
- qiaoyan (Tue Sep 08 2009 - 05:29:17 PDT)
[AMBER] parameter for manganese
- Mahmoud A. A. Ibrahim (Thu Sep 24 2009 - 05:17:29 PDT)
- Yuqin Cai (Tue Sep 22 2009 - 15:48:41 PDT)
[AMBER] Parameter Problem
- Manish Kumar (Wed Sep 23 2009 - 06:28:11 PDT)
- FyD (Wed Sep 23 2009 - 01:28:49 PDT)
- manoj singh (Tue Sep 22 2009 - 12:46:59 PDT)
- manoj singh (Tue Sep 22 2009 - 12:35:53 PDT)
[AMBER] parameterization of protein-ligand complex
- Jeff Yeo (Mon Sep 14 2009 - 08:03:25 PDT)
- cc cc (Wed Sep 09 2009 - 10:44:17 PDT)
- cc cc (Wed Sep 09 2009 - 10:41:52 PDT)
- Bill Ross (Wed Sep 09 2009 - 10:12:28 PDT)
- case (Wed Sep 09 2009 - 09:39:05 PDT)
- cc cc (Wed Sep 09 2009 - 09:29:07 PDT)
[AMBER] partial charges in Amber force field
- FyD (Mon Sep 28 2009 - 11:32:42 PDT)
- Jihang Wang (Mon Sep 28 2009 - 10:52:28 PDT)
[AMBER] PBSA for gp41 binding free energy
- Ray Luo (Fri Sep 11 2009 - 18:59:07 PDT)
- shuqing wang (Thu Sep 10 2009 - 23:42:59 PDT)
[AMBER] Pentane UA model
- FyD (Tue Sep 22 2009 - 00:02:50 PDT)
- aneesh cna (Mon Sep 21 2009 - 23:23:35 PDT)
[AMBER] periodic boundary condition for implicit solvent simulation and SHORT command
- case (Thu Sep 10 2009 - 19:04:53 PDT)
- Workalemahu Berhanu (Thu Sep 10 2009 - 15:37:32 PDT)
[AMBER] PES QM and MM
- Bill Ross (Thu Sep 17 2009 - 09:08:35 PDT)
- s. Bill (Thu Sep 17 2009 - 03:53:46 PDT)
[AMBER] pH calculations
- Michael Durney (Thu Sep 17 2009 - 08:01:08 PDT)
[AMBER] PK zero for specific dihedral and parmchk
- case (Wed Sep 09 2009 - 04:32:51 PDT)
- Carlos Simmerling (Wed Sep 09 2009 - 03:23:31 PDT)
[AMBER] pmemd and internal dielectric
- Robert Duke (Fri Sep 25 2009 - 15:19:10 PDT)
- case (Fri Sep 25 2009 - 14:59:56 PDT)
- Robert Duke (Fri Sep 25 2009 - 13:10:57 PDT)
- Serguei Vassiliev (Fri Sep 25 2009 - 12:47:46 PDT)
- Adrian Roitberg (Fri Sep 25 2009 - 09:44:56 PDT)
- Robert Duke (Fri Sep 25 2009 - 09:07:06 PDT)
- Serguei Vassiliev (Fri Sep 25 2009 - 08:47:50 PDT)
[AMBER] prep file
- case (Fri Sep 04 2009 - 07:09:06 PDT)
- Jio M (Fri Sep 04 2009 - 02:24:04 PDT)
[AMBER] Problem about adding a small residue to DNA
- FyD (Mon Sep 07 2009 - 02:53:14 PDT)
- case (Fri Sep 04 2009 - 12:32:53 PDT)
- Yikan Chen (Thu Sep 03 2009 - 21:33:52 PDT)
[AMBER] problem building sander.apbs
- Robert Konecny (Tue Sep 22 2009 - 12:55:40 PDT)
- case (Tue Sep 22 2009 - 12:12:50 PDT)
- Oliver Kuhn (Tue Sep 22 2009 - 01:10:10 PDT)
- case (Mon Sep 21 2009 - 07:38:20 PDT)
- Oliver Kuhn (Mon Sep 21 2009 - 07:03:34 PDT)
- case (Mon Sep 21 2009 - 04:39:41 PDT)
- Oliver Kuhn (Mon Sep 21 2009 - 03:49:48 PDT)
[AMBER] Problem in compiling AMBER9 in parallel !
- case (Tue Sep 29 2009 - 11:08:41 PDT)
- Abhishek Banerjee (Tue Sep 29 2009 - 10:25:36 PDT)
- Pradipta Bandyopadhyay (Tue Sep 29 2009 - 06:04:47 PDT)
[AMBER] problem in QM/MM input file
- Tom Joseph (Tue Sep 08 2009 - 05:37:56 PDT)
- gaurav panwar (Mon Sep 07 2009 - 10:33:20 PDT)
[AMBER] Problem in test run
- case (Tue Sep 29 2009 - 09:50:19 PDT)
- Kshatresh Dutta Dubey (Tue Sep 29 2009 - 08:23:29 PDT)
- Kshatresh Dutta Dubey (Tue Sep 29 2009 - 08:14:35 PDT)
- Carlos Simmerling (Tue Sep 29 2009 - 08:06:55 PDT)
- Kshatresh Dutta Dubey (Tue Sep 29 2009 - 08:05:13 PDT)
- Carlos Simmerling (Tue Sep 29 2009 - 07:26:38 PDT)
- Kshatresh Dutta Dubey (Tue Sep 29 2009 - 07:21:56 PDT)
[AMBER] problem of PBCAL/GB
- Qinghua Liao (Tue Sep 08 2009 - 02:40:42 PDT)
- Ray Luo (Mon Sep 07 2009 - 22:58:44 PDT)
- Qinghua Liao (Mon Sep 07 2009 - 22:05:37 PDT)
[AMBER] Problem on PMEMD
- Robert Duke (Mon Sep 14 2009 - 18:46:16 PDT)
- zyxism (Mon Sep 14 2009 - 18:41:50 PDT)
- Adrian Roitberg (Mon Sep 14 2009 - 18:40:35 PDT)
- Tom Joseph (Mon Sep 14 2009 - 18:34:11 PDT)
- zyxism (Mon Sep 14 2009 - 18:11:57 PDT)
[AMBER] Problem regarding Hbond analysis
- Bill Ross (Tue Sep 22 2009 - 13:00:55 PDT)
- Abhishek Singh (Tue Sep 22 2009 - 12:43:50 PDT)
[AMBER] problem running pmemd gbrna tests
- wong105.llnl.gov (Tue Sep 15 2009 - 11:07:14 PDT)
[AMBER] problem when doing mm/pbsa: bad atom type Br
- Baifan Wang (Mon Sep 28 2009 - 00:26:06 PDT)
- Ray Luo (Sun Sep 27 2009 - 20:10:25 PDT)
- Baifan Wang (Sun Sep 27 2009 - 19:50:46 PDT)
[AMBER] problem with 4-Hydroxyl-Proline tutorial
- Jia Xu (Mon Aug 31 2009 - 22:10:50 PDT)
[AMBER] PROBLEM WITH CHCL3BOX pdb
- case (Fri Sep 18 2009 - 15:01:23 PDT)
- Hannes Loeffler (Fri Sep 18 2009 - 08:16:06 PDT)
- case (Fri Sep 18 2009 - 06:26:40 PDT)
- Silvia Carlotto (Fri Sep 18 2009 - 05:49:12 PDT)
[AMBER] Problem with loading PDB into tleap
- Ashish Runthala (Tue Sep 08 2009 - 08:14:46 PDT)
- Kamali Sripathi (Tue Sep 08 2009 - 06:49:20 PDT)
[AMBER] Provisional Support for AMBER 10 PMEMD on NVIDIA GPUs
- Ross Walker (Fri Sep 04 2009 - 11:51:44 PDT)
[AMBER] QM/MM minimization
- Pansy Patel (Thu Sep 10 2009 - 07:09:48 PDT)
- gaurav panwar (Thu Sep 10 2009 - 07:05:37 PDT)
[AMBER] QM/MM simulation
- Ross Walker (Thu Sep 03 2009 - 13:43:45 PDT)
- gaurav panwar (Thu Sep 03 2009 - 13:11:42 PDT)
[AMBER] QMMM NEB with PM3-PDDG fails with ASSERTion 'ierr.eq.0' pimd_init.f line 320
- case (Sat Sep 12 2009 - 07:17:16 PDT)
- Keith Van Nostrand (Tue Sep 08 2009 - 12:26:14 PDT)
[AMBER] question about ptraj
- Niel Henriksen (Wed Sep 02 2009 - 07:37:39 PDT)
- Jeffrey (Wed Sep 02 2009 - 01:20:12 PDT)
[AMBER] Question about the debug forces
- Faezeh Salehi (Wed Sep 02 2009 - 14:30:47 PDT)
[AMBER] Question on ECAVITY term of MM_PBSA
- Ray Luo (Mon Sep 21 2009 - 18:28:32 PDT)
- Ray Luo (Mon Sep 21 2009 - 10:30:57 PDT)
- Gianluca Degliesposti (Mon Sep 21 2009 - 04:18:27 PDT)
- Gianluca Degliesposti (Mon Sep 14 2009 - 08:28:12 PDT)
[AMBER] Question regarding PCA analysis.
- Catein Catherine (Thu Sep 03 2009 - 19:55:42 PDT)
- Chris Moth (Thu Sep 03 2009 - 07:17:42 PDT)
- Catein Catherine (Tue Sep 01 2009 - 20:53:10 PDT)
[AMBER] question with hbond
- Ganesh Kamath (Wed Sep 16 2009 - 14:36:18 PDT)
[AMBER] question with radial distribution function
- Ganesh Kamath (Thu Sep 10 2009 - 15:08:34 PDT)
[AMBER] R.E.D. : Gaussian Error
- manoj singh (Sun Sep 06 2009 - 22:46:54 PDT)
- FyD (Sun Sep 06 2009 - 22:07:34 PDT)
- manoj singh (Sun Sep 06 2009 - 21:22:44 PDT)
- FyD (Sun Sep 06 2009 - 12:41:41 PDT)
- manoj singh (Sun Sep 06 2009 - 11:40:48 PDT)
[AMBER] radial distribution function in amber
- Ganesh Kamath (Mon Sep 14 2009 - 07:58:56 PDT)
[AMBER] RDC analysis: "No restraint defined"
- case (Wed Sep 16 2009 - 09:47:41 PDT)
- Michael Durney (Wed Sep 16 2009 - 09:10:34 PDT)
[AMBER] Reg. snapshot_statistics.out.snap
- Rose Tamil (Tue Sep 01 2009 - 10:04:08 PDT)
[AMBER] Regarding united atom force field
- FyD (Mon Sep 21 2009 - 23:13:03 PDT)
- Ray Luo (Mon Sep 21 2009 - 10:32:34 PDT)
- aneesh cna (Mon Sep 21 2009 - 03:17:20 PDT)
[AMBER] RESP RED
- FyD (Sat Sep 12 2009 - 07:35:16 PDT)
- s. Bill (Fri Sep 11 2009 - 11:40:24 PDT)
[AMBER] RMSDf of heavy atoms
- Syed Tarique Moin (Tue Sep 22 2009 - 04:45:26 PDT)
[AMBER] Simulation short peptide and protein interaction
- Carlos Simmerling (Thu Sep 03 2009 - 06:34:27 PDT)
- Rilei Yu (Thu Sep 03 2009 - 05:22:10 PDT)
- case (Wed Sep 02 2009 - 05:15:06 PDT)
- Rilei Yu (Tue Sep 01 2009 - 17:50:29 PDT)
[AMBER] Solvate in an alkaline solution
- case (Thu Sep 10 2009 - 05:05:44 PDT)
- vallespardojl.chem.leidenuniv.nl (Thu Sep 10 2009 - 01:07:07 PDT)
[AMBER] solvent accessible surface area
- Carlos Simmerling (Wed Sep 23 2009 - 12:29:57 PDT)
- Ganesh Kamath (Wed Sep 23 2009 - 12:26:33 PDT)
- Carlos Simmerling (Wed Sep 23 2009 - 12:20:24 PDT)
- Ganesh Kamath (Wed Sep 23 2009 - 12:07:23 PDT)
[AMBER] symbol lookup error
- Ross Walker (Tue Sep 01 2009 - 12:42:49 PDT)
- Bala subramanian (Tue Sep 01 2009 - 01:43:51 PDT)
[AMBER] Teragrid
- Carlos Simmerling (Thu Sep 24 2009 - 05:11:41 PDT)
- Beale, John (Thu Sep 24 2009 - 05:08:56 PDT)
[AMBER] TI in Amber9/10
- Ilyas Yildirim (Tue Sep 08 2009 - 11:07:40 PDT)
- steinbrt.rci.rutgers.edu (Tue Sep 08 2009 - 10:41:32 PDT)
- Alessandro S. Nascimento (Tue Sep 08 2009 - 08:47:26 PDT)
[AMBER] too many missing parameters in frcmod for the prep of my ligand
- FyD (Wed Sep 30 2009 - 03:30:32 PDT)
- xueqin pang (Wed Sep 30 2009 - 02:21:31 PDT)
[AMBER] trouble using iAPBS
- Robert Konecny (Mon Sep 28 2009 - 07:20:31 PDT)
- Oliver Kuhn (Mon Sep 28 2009 - 05:08:27 PDT)
[AMBER] unit of force constant
- balaji nagarajan (Tue Sep 08 2009 - 06:41:37 PDT)
- Carlos Simmerling (Tue Sep 08 2009 - 06:21:40 PDT)
- balaji nagarajan (Tue Sep 08 2009 - 06:16:08 PDT)
- balaji nagarajan (Wed Sep 02 2009 - 09:57:25 PDT)
[AMBER] variable header for ABMD
- stephane acoca (Sun Sep 13 2009 - 20:03:00 PDT)
[AMBER] warning in dispatchToken
- case (Sun Sep 20 2009 - 06:14:49 PDT)
- Jeff Yeo (Sun Sep 20 2009 - 03:30:57 PDT)
[AMBER] What is dual topology
- case (Wed Sep 02 2009 - 08:48:51 PDT)
- Ashish Runthala (Wed Sep 02 2009 - 08:25:19 PDT)
[AMBER] What is the Optimum Ph for solvating a protein
- case (Sun Sep 13 2009 - 14:19:24 PDT)
- Ashish Runthala (Sun Sep 13 2009 - 06:08:40 PDT)
[AMBER] What is the unit of RMSF?
- case (Sat Sep 12 2009 - 06:37:42 PDT)
- Catein Catherine (Sat Sep 12 2009 - 01:13:02 PDT)
[AMBER] What should be the standard input file when imin=5
- Carlos Simmerling (Thu Sep 03 2009 - 04:55:48 PDT)
- Ashish Runthala (Thu Sep 03 2009 - 00:25:49 PDT)
[AMBER] why should one restrain the position of the counterions?
- Jose Borreguero (Mon Sep 28 2009 - 11:28:20 PDT)
[AMBER] Your help about ptraj in AmberTools!]]
- Rosina Noto (Mon Sep 28 2009 - 02:59:09 PDT)
[AMBER] Zinc
- Roman Osman (Tue Sep 29 2009 - 17:08:28 PDT)
- Rubben Torella (Tue Sep 29 2009 - 14:31:31 PDT)
- Sel Ercan (Tue Sep 29 2009 - 14:26:53 PDT)
charge consideration
- Jio M (Mon Sep 14 2009 - 01:38:27 PDT)
charge interaction
- case (Sun Sep 13 2009 - 14:37:55 PDT)
- case (Sun Sep 13 2009 - 14:13:19 PDT)
- Jio M (Sun Sep 13 2009 - 07:38:43 PDT)
回复： [AMBER] Problem about adding a small residue to DNA
- Yikan Chen (Sun Sep 06 2009 - 08:47:04 PDT)
- case (Sun Sep 06 2009 - 05:30:23 PDT)
- Yikan Chen (Fri Sep 04 2009 - 14:38:27 PDT)
- case (Fri Sep 04 2009 - 13:37:23 PDT)
- Yikan Chen (Fri Sep 04 2009 - 13:03:54 PDT)
- Yikan Chen (Fri Sep 04 2009 - 12:51:38 PDT)
- Rilei Yu (Thu Sep 03 2009 - 23:33:50 PDT)

Amber Archive Sep 2009 by subject