Amber Archive May 2009: by subject

Marek Malý (Fri May 08 2009 - 12:12:39 PDT)
[AMBER] "Parameter file not generated"
- Remya S R (Sun May 03 2009 - 23:17:23 PDT)
[AMBER] 2 atoms not in residue template
- Workalemhu Berhanu (Sat May 23 2009 - 17:11:12 PDT)
[AMBER] A confusion about tutorial B1
- Houyang Chen (Tue May 05 2009 - 10:39:18 PDT)
- David A. Case (Tue May 05 2009 - 08:41:54 PDT)
- Ross Walker (Tue May 05 2009 - 08:29:23 PDT)
- Carlos Simmerling (Tue May 05 2009 - 03:11:43 PDT)
- Houyang Chen (Mon May 04 2009 - 22:24:39 PDT)
- Ross Walker (Mon May 04 2009 - 22:18:43 PDT)
- Houyang Chen (Mon May 04 2009 - 22:01:31 PDT)
[AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels
- David A. Case (Wed May 27 2009 - 04:57:07 PDT)
- Tomasio, Susana (Wed May 27 2009 - 04:25:35 PDT)
[AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off- different labels
- Tomasio, Susana (Wed May 27 2009 - 05:13:58 PDT)
[AMBER] adding a standard amino acid as ligand
- FyD (Fri May 15 2009 - 06:39:18 PDT)
- sheerychen (Fri May 15 2009 - 02:37:51 PDT)
[AMBER] Adding non standard residues
- Jorgen Simonsen (Mon May 11 2009 - 14:11:49 PDT)
- David A. Case (Mon May 11 2009 - 10:30:56 PDT)
- Jorgen Simonsen (Mon May 11 2009 - 01:54:25 PDT)
[AMBER] Alignment of small molecule on peptide fragment
- Workalemhu Berhanu (Sat May 16 2009 - 02:32:38 PDT)
- Workalemhu Berhanu (Sat May 16 2009 - 02:31:08 PDT)
[AMBER] Amber - Leap- SolvateBox help
- Ross Walker (Tue May 19 2009 - 22:20:50 PDT)
- David A. Case (Tue May 19 2009 - 04:48:39 PDT)
- Remya S R (Mon May 18 2009 - 23:22:12 PDT)
- Shubhra Gupta (Mon May 18 2009 - 20:54:23 PDT)
- David A. Case (Fri May 15 2009 - 16:57:00 PDT)
- Ross Walker (Thu May 14 2009 - 05:28:36 PDT)
- Shubhra Gupta (Wed May 13 2009 - 22:04:16 PDT)
[AMBER] Amber 10 install parallel problem
- Hopkins, Robert (Sat May 16 2009 - 17:38:16 PDT)
[AMBER] AMBER 10 output
- Sergey Samsonov (Tue May 19 2009 - 07:53:41 PDT)
- steinbrt.rci.rutgers.edu (Tue May 19 2009 - 06:53:03 PDT)
- Sergey Samsonov (Tue May 19 2009 - 00:33:21 PDT)
[AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases.
- todd.semichem.com (Sun May 10 2009 - 14:56:24 PDT)
- FyD (Sat May 09 2009 - 22:49:55 PDT)
- todd.semichem.com (Sat May 09 2009 - 11:36:17 PDT)
- Adrian Roitberg (Sat May 09 2009 - 11:07:08 PDT)
- todd.semichem.com (Sat May 09 2009 - 09:27:52 PDT)
[AMBER] Amber FF and Glycam
- Carlos Simmerling (Fri May 01 2009 - 05:41:35 PDT)
- Hannes Loeffler (Fri May 01 2009 - 01:33:34 PDT)
[AMBER] AMBER for dual core processor?
- Ross Walker (Thu May 07 2009 - 08:26:09 PDT)
- Catein Catherine (Thu May 07 2009 - 01:05:17 PDT)
[AMBER] Amber/CHARMM summer school
- CHAMI F. (Thu May 21 2009 - 04:56:23 PDT)
- David A. Case (Wed May 20 2009 - 05:40:39 PDT)
[AMBER] amber9 in fedora10
- Bala subramanian (Thu May 14 2009 - 01:18:07 PDT)
- Ross Walker (Wed May 13 2009 - 16:22:20 PDT)
- Bala subramanian (Wed May 13 2009 - 02:50:25 PDT)
[AMBER] ambertools for NAMD
- Jorgen Simonsen (Thu May 07 2009 - 11:29:41 PDT)
- Andrew Purkiss-Trew (Thu May 07 2009 - 08:16:40 PDT)
- Wei Huang (Thu May 07 2009 - 07:51:06 PDT)
- Andrew Purkiss-Trew (Thu May 07 2009 - 07:30:14 PDT)
- Carlos Simmerling (Thu May 07 2009 - 07:23:25 PDT)
- David A. Case (Thu May 07 2009 - 07:09:55 PDT)
- Carlos Simmerling (Thu May 07 2009 - 06:36:27 PDT)
- Jorgen Simonsen (Thu May 07 2009 - 05:35:24 PDT)
[AMBER] AMOEBA and carbon nanotubes + include parameters
- Tomasio, Susana (Thu May 28 2009 - 03:23:00 PDT)
[AMBER] anal output: Entalphy or Free Energy?
- Edward M (Tue May 12 2009 - 17:14:37 PDT)
- E.M. (Tue May 12 2009 - 15:25:41 PDT)
[AMBER] ask for parm99MOD
- David A. Case (Thu May 28 2009 - 14:52:29 PDT)
- xiaoqin huang (Thu May 28 2009 - 14:43:15 PDT)
- Carlos Simmerling (Thu May 28 2009 - 14:17:05 PDT)
- xiaoqin huang (Thu May 28 2009 - 14:09:26 PDT)
- Adrian Roitberg (Thu May 28 2009 - 13:56:14 PDT)
- Carlos Simmerling (Thu May 28 2009 - 13:52:56 PDT)
- xiaoqin huang (Thu May 28 2009 - 13:32:02 PDT)
- Carlos Simmerling (Thu May 28 2009 - 13:22:31 PDT)
- xiaoqin huang (Thu May 28 2009 - 13:09:28 PDT)
- Carlos Simmerling (Thu May 28 2009 - 12:57:24 PDT)
- Carlos Simmerling (Thu May 28 2009 - 12:56:26 PDT)
- xiaoqin huang (Thu May 28 2009 - 12:51:59 PDT)
- xiaoqin huang (Thu May 28 2009 - 12:46:23 PDT)
- Carlos Simmerling (Thu May 28 2009 - 12:44:41 PDT)
- Adrian Roitberg (Thu May 28 2009 - 12:44:08 PDT)
- xiaoqin huang (Thu May 28 2009 - 12:41:54 PDT)
- Carlos Simmerling (Thu May 28 2009 - 12:41:20 PDT)
- Adrian Roitberg (Thu May 28 2009 - 12:38:23 PDT)
- xiaoqin huang (Thu May 28 2009 - 12:31:14 PDT)
- xiaoqin huang (Thu May 28 2009 - 11:16:35 PDT)
[AMBER] broken Ligand
- David A. Case (Sun May 31 2009 - 05:50:57 PDT)
- Shubhra Gupta (Fri May 29 2009 - 23:35:46 PDT)
- David A. Case (Fri May 29 2009 - 07:45:20 PDT)
- Shubhra Gupta (Fri May 29 2009 - 06:28:22 PDT)
[AMBER] building quadruplex with NAB
- David A. Case (Wed May 13 2009 - 04:48:38 PDT)
- Peter Varnai (Sun May 10 2009 - 16:27:38 PDT)
[AMBER] Can bond clevage & formation conducted by qm/mm via sander?
- Gustavo Seabra (Tue May 05 2009 - 10:28:10 PDT)
- Mahmoud A. A. Ibrahim (Tue May 05 2009 - 10:15:18 PDT)
- Gustavo Seabra (Tue May 05 2009 - 10:04:37 PDT)
- sychen (Tue May 05 2009 - 06:12:32 PDT)
[AMBER] can I get partial charge for lipid membrane with Antechamber and RESP
- FyD (Sun May 31 2009 - 05:51:50 PDT)
- xueqin pang (Sun May 31 2009 - 05:43:09 PDT)
[AMBER] Can I use only a single point calculation to derive RESP charges?
- FyD (Sat May 09 2009 - 23:52:12 PDT)
- Josmar R. da Rocha (Sat May 09 2009 - 08:19:07 PDT)
- FyD (Fri May 08 2009 - 23:00:36 PDT)
- Josmar R. da Rocha (Fri May 08 2009 - 17:08:54 PDT)
[AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy
- xueqin pang (Sun May 31 2009 - 05:47:57 PDT)
[AMBER] chain restrain x TI
- Josmar R. da Rocha (Sat May 02 2009 - 10:09:53 PDT)
[AMBER] Changing bond length
- manoj singh (Thu May 28 2009 - 10:00:14 PDT)
- Ross Walker (Wed May 27 2009 - 21:38:59 PDT)
- manoj singh (Wed May 27 2009 - 20:47:52 PDT)
[AMBER] charge of Fe-heme
- FyD (Sat May 02 2009 - 09:02:48 PDT)
- David A. Case (Fri May 01 2009 - 15:52:45 PDT)
- 董昊 (Fri May 01 2009 - 12:08:12 PDT)
[AMBER] Charge problem
- Carlos Simmerling (Tue May 05 2009 - 05:58:31 PDT)
- Remya S R (Tue May 05 2009 - 05:19:51 PDT)
- Carlos Simmerling (Tue May 05 2009 - 05:16:32 PDT)
- Remya S R (Tue May 05 2009 - 04:43:47 PDT)
[AMBER] Choice of force feild
- manoj singh (Sun May 31 2009 - 10:12:23 PDT)
[AMBER] Choice of force field
- manoj singh (Sun May 31 2009 - 13:39:13 PDT)
[AMBER] Conformation of sulfated Glucosamine
- Matthew Tessier (Wed May 06 2009 - 08:19:22 PDT)
- Neha Gandhi (Wed May 06 2009 - 02:54:31 PDT)
[AMBER] contacts in ptraj
- 欧阳德方 (Thu May 28 2009 - 04:55:28 PDT)
[AMBER] create a simulation box
- Workalemhu Berhanu (Sat May 30 2009 - 20:06:24 PDT)
[AMBER] creating new residue adds none wanted ter
- David A. Case (Tue May 05 2009 - 05:07:53 PDT)
- Jorgen Simonsen (Tue May 05 2009 - 02:57:29 PDT)
- David A. Case (Mon May 04 2009 - 11:27:58 PDT)
- Jorgen Simonsen (Mon May 04 2009 - 07:09:08 PDT)
- David A. Case (Mon May 04 2009 - 06:35:41 PDT)
- Jorgen Simonsen (Mon May 04 2009 - 00:49:47 PDT)
[AMBER] Cyclodextrin forcefield
- Rajesh Raju (Fri May 01 2009 - 10:21:21 PDT)
- Lachele Foley (Lists) (Fri May 01 2009 - 08:23:37 PDT)
- Rajesh Raju (Fri May 01 2009 - 07:51:17 PDT)
[AMBER] decomposition and alanine scanning
- 廖青华 (Fri May 22 2009 - 07:13:49 PDT)
[AMBER] dftb_disper problem
- Fernando Martín García (Mon May 11 2009 - 05:34:01 PDT)
- Gustavo Seabra (Fri May 08 2009 - 09:34:39 PDT)
- fmgarcia.cbm.uam.es (Fri May 08 2009 - 09:27:30 PDT)
- Ross Walker (Fri May 08 2009 - 08:47:39 PDT)
- Fernando Martín García (Fri May 08 2009 - 05:43:19 PDT)
- Fernando Martín García (Thu May 07 2009 - 06:32:06 PDT)
- Gustavo Seabra (Thu May 07 2009 - 06:01:42 PDT)
- Fernando Martín García (Thu May 07 2009 - 05:30:25 PDT)
[AMBER] difference in temperature
- Naser Alijabbari (Wed May 06 2009 - 05:29:48 PDT)
- David A. Case (Wed May 06 2009 - 05:08:01 PDT)
- Naser Alijabbari (Tue May 05 2009 - 17:02:28 PDT)
[AMBER] equilibration stops for dimer simulation with REMD
- Sunita Patel (Thu May 07 2009 - 11:35:59 PDT)
- Carlos Simmerling (Tue May 05 2009 - 10:32:42 PDT)
- Sunita Patel (Tue May 05 2009 - 10:26:09 PDT)
- Carlos Simmerling (Tue May 05 2009 - 09:39:52 PDT)
- Sunita Patel (Tue May 05 2009 - 09:33:40 PDT)
- Sunita Patel (Sun May 03 2009 - 18:30:05 PDT)
- Carlos Simmerling (Sun May 03 2009 - 04:11:07 PDT)
- Sunita Patel (Sat May 02 2009 - 13:11:48 PDT)
[AMBER] Error in binding energy (MM PBSA)
- Vikas Sharma (Mon May 11 2009 - 22:05:08 PDT)
- Ray Luo (Mon May 11 2009 - 11:14:20 PDT)
- Vikas Sharma (Mon May 11 2009 - 01:08:28 PDT)
- Vikas Sharma (Sun May 10 2009 - 02:03:07 PDT)
- Ray Luo (Sat May 09 2009 - 18:39:05 PDT)
- Vikas Sharma (Sat May 09 2009 - 00:20:09 PDT)
- Vikas Sharma (Sat May 09 2009 - 00:19:20 PDT)
- Ray Luo (Fri May 08 2009 - 09:42:58 PDT)
- Vikas Sharma (Thu May 07 2009 - 23:50:40 PDT)
- Vikas Sharma (Thu May 07 2009 - 23:44:33 PDT)
- Vikas Sharma (Thu May 07 2009 - 23:42:32 PDT)
- Ray Luo (Thu May 07 2009 - 11:12:18 PDT)
- Vikas Sharma (Thu May 07 2009 - 06:29:22 PDT)
- David A. Case (Thu May 07 2009 - 04:33:20 PDT)
- Vikas Sharma (Wed May 06 2009 - 22:47:33 PDT)
[AMBER] Error in MM PBSA
- Vikas Sharma (Wed May 06 2009 - 01:35:57 PDT)
[AMBER] Error in parallel run
- Catein Catherine (Wed May 06 2009 - 19:46:02 PDT)
[AMBER] Error in PMEMD run
- Marek Malý (Fri May 08 2009 - 18:36:49 PDT)
- Robert Duke (Fri May 08 2009 - 18:26:37 PDT)
- Marek Malý (Fri May 08 2009 - 18:05:40 PDT)
- Robert Duke (Fri May 08 2009 - 17:01:23 PDT)
- Marek Malý (Fri May 08 2009 - 16:37:28 PDT)
- Robert Duke (Fri May 08 2009 - 12:44:08 PDT)
- Marek Malý (Fri May 08 2009 - 12:10:41 PDT)
- Marek Malý (Fri May 08 2009 - 11:27:20 PDT)
- Robert Duke (Fri May 08 2009 - 11:24:35 PDT)
- Robert Duke (Fri May 08 2009 - 11:14:12 PDT)
- Ross Walker (Fri May 08 2009 - 11:11:19 PDT)
- Robert Duke (Fri May 08 2009 - 11:06:17 PDT)
- Marek Malý (Fri May 08 2009 - 11:02:53 PDT)
- Marek Malý (Fri May 08 2009 - 10:57:36 PDT)
- Gustavo Seabra (Fri May 08 2009 - 10:28:35 PDT)
- Marek Malý (Fri May 08 2009 - 09:38:27 PDT)
- Robert Duke (Fri May 08 2009 - 06:29:48 PDT)
- Marek Malý (Fri May 08 2009 - 05:54:57 PDT)
- Robert Duke (Thu May 07 2009 - 17:11:25 PDT)
- Marek Malý (Thu May 07 2009 - 16:59:23 PDT)
- Robert Duke (Wed May 06 2009 - 16:04:10 PDT)
- Ross Walker (Wed May 06 2009 - 14:53:07 PDT)
- Marek Malý (Wed May 06 2009 - 14:27:17 PDT)
- Marek Malý (Wed May 06 2009 - 14:25:02 PDT)
- Robert Duke (Wed May 06 2009 - 13:40:29 PDT)
- Ross Walker (Wed May 06 2009 - 13:36:36 PDT)
- Marek Malý (Wed May 06 2009 - 13:26:58 PDT)
- Robert Duke (Wed May 06 2009 - 13:08:56 PDT)
- Marek Malý (Wed May 06 2009 - 13:02:11 PDT)
- Robert Duke (Wed May 06 2009 - 12:58:29 PDT)
- Robert Duke (Wed May 06 2009 - 12:55:49 PDT)
- Marek Malý (Wed May 06 2009 - 12:48:26 PDT)
- Ross Walker (Wed May 06 2009 - 12:41:10 PDT)
- Robert Duke (Wed May 06 2009 - 12:29:41 PDT)
- Robert Duke (Wed May 06 2009 - 12:20:37 PDT)
- Marek Malý (Wed May 06 2009 - 11:51:03 PDT)
- Marek Malý (Wed May 06 2009 - 11:42:36 PDT)
- Marek Malý (Wed May 06 2009 - 11:30:43 PDT)
- Robert Duke (Wed May 06 2009 - 10:30:43 PDT)
- Ross Walker (Wed May 06 2009 - 10:07:01 PDT)
- Marek Malý (Wed May 06 2009 - 08:58:33 PDT)
- Robert Duke (Mon May 04 2009 - 21:08:37 PDT)
- Marek Malý (Mon May 04 2009 - 19:19:20 PDT)
- Robert Duke (Mon May 04 2009 - 18:35:54 PDT)
- Marek Malý (Mon May 04 2009 - 18:23:33 PDT)
[AMBER] ERROR in ptrajInitializeState(): Attempting ....
- Siavoush Dastmalchi (Sat May 30 2009 - 09:06:51 PDT)
[AMBER] Error message for tutorial 1 (run in parallel)
- Catein Catherine (Mon May 04 2009 - 06:31:05 PDT)
- David A. Case (Mon May 04 2009 - 05:40:36 PDT)
- Catein Catherine (Mon May 04 2009 - 02:05:17 PDT)
[AMBER] Error message in "make test.sander"
- Catein Catherine (Tue May 05 2009 - 23:58:04 PDT)
- Ross Walker (Tue May 05 2009 - 23:28:01 PDT)
- Catein Catherine (Tue May 05 2009 - 22:40:54 PDT)
- Ross Walker (Tue May 05 2009 - 20:37:28 PDT)
- Catein Catherine (Tue May 05 2009 - 19:52:26 PDT)
[AMBER] Error message in "make test.sander" Is amber compatible with dual processors?
- Catein Catherine (Wed May 06 2009 - 06:08:49 PDT)
[AMBER] Error running MM _PBSA.pl script
- Vikas Sharma (Wed May 20 2009 - 01:29:42 PDT)
- liuhui (Tue May 19 2009 - 19:20:26 PDT)
- Vikas Sharma (Tue May 19 2009 - 11:21:47 PDT)
- liuhui (Tue May 19 2009 - 09:15:24 PDT)
- Vikas Sharma (Tue May 19 2009 - 08:02:21 PDT)
- liuhui (Tue May 19 2009 - 07:29:23 PDT)
- Vikas Sharma (Mon May 18 2009 - 21:34:18 PDT)
- Ray Luo (Mon May 18 2009 - 10:43:30 PDT)
- Vikas Sharma (Mon May 18 2009 - 05:00:13 PDT)
[AMBER] Error: cannot run prepgen
- Rose Tamil (Tue May 05 2009 - 08:20:52 PDT)
[AMBER] errors when add ions
- David A. Case (Thu May 21 2009 - 05:23:08 PDT)
- zgong.hust (Wed May 20 2009 - 19:51:48 PDT)
[AMBER] essential dynamics
- David A. Case (Wed May 13 2009 - 10:15:50 PDT)
- Chunliyan (Wed May 13 2009 - 09:23:23 PDT)
[AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber
- Rubben Torella (Tue May 26 2009 - 15:33:18 PDT)
- Workalemhu Berhanu (Tue May 26 2009 - 14:45:55 PDT)
[AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4'
- David A. Case (Fri May 15 2009 - 16:56:34 PDT)
- ben rodriguez (Fri May 15 2009 - 15:09:44 PDT)
[AMBER] file contains 2 atoms not in residue templates
- David A. Case (Sun May 24 2009 - 06:12:14 PDT)
- Workalemhu Berhanu (Sat May 23 2009 - 17:17:09 PDT)
[AMBER] free enrgy error in MM PBSA
- Vikas Sharma (Thu May 07 2009 - 03:11:44 PDT)
[AMBER] gaff and aromatic compounds
- Junmei Wang (Tue May 26 2009 - 09:03:53 PDT)
- rebeca (Fri May 22 2009 - 02:04:45 PDT)
- Junmei Wang (Thu May 21 2009 - 18:24:52 PDT)
- David A. Case (Wed May 20 2009 - 05:04:05 PDT)
- rebeca (Wed May 20 2009 - 01:54:43 PDT)
- David A. Case (Tue May 19 2009 - 09:07:29 PDT)
- rebeca (Tue May 19 2009 - 08:50:02 PDT)
[AMBER] get typeid of -1, sleap - AMBER with amoeba ff
- Tomasio, Susana (Tue May 26 2009 - 08:51:18 PDT)
[AMBER] hbond_ptraj
- Thomas Cheatham (Wed May 27 2009 - 17:39:15 PDT)
[AMBER] heating advice
- Mark M Huntress (Wed May 27 2009 - 13:44:26 PDT)
[AMBER] help with RESP tutorial using antechamber and gaussian
- Josmar R. da Rocha (Sun May 03 2009 - 10:59:23 PDT)
[AMBER] High energy during minimization
- Ross Walker (Tue May 05 2009 - 23:24:30 PDT)
- aneesh cna (Tue May 05 2009 - 22:58:00 PDT)
- Bill Ross (Sun May 03 2009 - 11:00:32 PDT)
- David A. Case (Sun May 03 2009 - 06:40:22 PDT)
- aneesh cna (Sat May 02 2009 - 21:26:16 PDT)
[AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber
- FyD (Sat May 02 2009 - 09:06:28 PDT)
- Ye MEI (Sat May 02 2009 - 05:01:20 PDT)
- Ye MEI (Sat May 02 2009 - 05:00:06 PDT)
[AMBER] How to choose the counter ions for proteins?
- Chih-Ying Lin (Sat May 23 2009 - 11:16:49 PDT)
- Ross Walker (Sat May 23 2009 - 11:09:27 PDT)
- Chih-Ying Lin (Fri May 22 2009 - 22:42:40 PDT)
[AMBER] how to know that adequate equilibration from rmsd curve of equilibration
- Carlos Simmerling (Thu May 28 2009 - 11:15:09 PDT)
- nicholus bhattacharjee (Thu May 28 2009 - 11:08:52 PDT)
- Bill Ross (Thu May 28 2009 - 08:42:13 PDT)
- nicholus bhattacharjee (Thu May 28 2009 - 06:37:29 PDT)
[AMBER] How to know that the md is stable in equilibration run
- nicholus bhattacharjee (Mon May 25 2009 - 04:54:25 PDT)
[AMBER] how to make the different/specific displacement of ligand around protein?
- Chih-Ying Lin (Fri May 15 2009 - 16:55:49 PDT)
[AMBER] How to setup the pH value?
- David A. Case (Tue May 19 2009 - 12:08:53 PDT)
- Chih-Ying Lin (Sat May 16 2009 - 10:29:21 PDT)
[AMBER] How to take into account the charge in GAFF parameterization
- cgji (Thu May 28 2009 - 23:49:44 PDT)
- Workalemhu Berhanu (Thu May 28 2009 - 16:22:07 PDT)
[AMBER] how to use two dimensions periodic boundary ?
- Nancy (Wed May 20 2009 - 18:32:50 PDT)
[AMBER] Influence about HIS-HIE-HIS-HIP
- Rilei Yu (Thu Apr 30 2009 - 17:37:17 PDT)
[AMBER] Installation directory
- Atro Tossavainen (Mon May 25 2009 - 01:10:34 PDT)
- Thomas Spraggins (Thu May 21 2009 - 12:18:13 PDT)
- David A. Case (Thu May 21 2009 - 11:19:28 PDT)
- Thomas Spraggins (Thu May 21 2009 - 11:02:59 PDT)
[AMBER] Issue related to saving the vector in ptraj
- S.Sundar Raman (Sat May 16 2009 - 05:41:10 PDT)
[AMBER] Issue related to vector saving
- S.Sundar Raman (Fri May 15 2009 - 06:35:01 PDT)
[AMBER] J coupling constant calculation
- Dechang Li (Thu May 28 2009 - 22:31:06 PDT)
- Neha Gandhi (Thu May 28 2009 - 22:24:37 PDT)
[AMBER] LCPO or Molsurf?
- Dong Xu (Sat May 02 2009 - 20:14:55 PDT)
[AMBER] ligand QM/semi-empirical coords optmisation
- David A. Case (Tue May 26 2009 - 04:41:25 PDT)
- Alan (Tue May 26 2009 - 03:55:09 PDT)
[AMBER] lipid membrane(dppc) in amber
- Myunggi Yi (Fri May 22 2009 - 06:45:20 PDT)
- xueqin pang (Fri May 22 2009 - 02:01:26 PDT)
- xueqin pang (Fri May 22 2009 - 01:42:54 PDT)
[AMBER] Loading PDB of complex
- Vikas Sharma (Thu May 21 2009 - 22:56:36 PDT)
- Carlos Simmerling (Thu May 21 2009 - 06:48:06 PDT)
- Vikas Sharma (Thu May 21 2009 - 06:13:36 PDT)
[AMBER] loadpdb atom type
- David A. Case (Tue May 19 2009 - 11:19:44 PDT)
- Mark M Huntress (Tue May 19 2009 - 11:15:02 PDT)
- Carlos Simmerling (Tue May 19 2009 - 10:09:29 PDT)
- Mark M Huntress (Tue May 19 2009 - 09:20:20 PDT)
[AMBER] make test.parallel.MM error
- Collins Nganou (Sun May 03 2009 - 14:20:51 PDT)
[AMBER] makeDIST_RST: no map function for ambiguous restraint
- David A. Case (Tue May 19 2009 - 05:35:31 PDT)
- Peter Varnai (Sun May 17 2009 - 11:41:24 PDT)
[AMBER] mdfil: Error unknown flag during sander minimization
- Shubhra Gupta (Tue May 26 2009 - 21:07:25 PDT)
- David A. Case (Tue May 26 2009 - 07:05:37 PDT)
- Workalemhu Berhanu (Tue May 26 2009 - 06:57:29 PDT)
[AMBER] Minimization error on protonated system? Please help. Thanks!
- David A. Case (Thu May 28 2009 - 08:17:59 PDT)
[AMBER] Minimization on MM-PBSA
- Rubben Torella (Thu May 28 2009 - 08:23:07 PDT)
[AMBER] MM PBSA output
- Vikas Sharma (Wed May 20 2009 - 04:53:57 PDT)
[AMBER] MM-GBSA energy decomposition and pairwise decomposition question
- Dong Xu (Fri May 15 2009 - 15:05:52 PDT)
[AMBER] MM-PBSA and NetCDF
- Bradshaw, Richard (Wed May 27 2009 - 08:38:13 PDT)
[AMBER] MM-PBSA nmode statistics
- Ray Luo (Sun May 31 2009 - 10:32:49 PDT)
- Dmitry Osolodkin (Sat May 30 2009 - 10:25:46 PDT)
- Ray Luo (Fri May 29 2009 - 11:01:36 PDT)
- Dmitry Osolodkin (Fri May 29 2009 - 03:53:27 PDT)
- Kshatresh Dutta Dubey (Thu May 28 2009 - 22:13:34 PDT)
- Dmitry Osolodkin (Thu May 28 2009 - 04:54:18 PDT)
[AMBER] MM-PBSA statistics
- Musa Ozboyaci (Sun May 10 2009 - 03:00:19 PDT)
[AMBER] MM-PBSA tutorial
- Cihan Aydin (Thu May 14 2009 - 18:19:04 PDT)
- Workalemhu Berhanu (Thu May 14 2009 - 11:53:25 PDT)
- steinbrt.rci.rutgers.edu (Thu May 14 2009 - 10:26:50 PDT)
- Workalemhu Berhanu (Thu May 14 2009 - 10:16:55 PDT)
[AMBER] MM-PBSA with explicit water
- mathew k varghese (Thu May 14 2009 - 23:45:23 PDT)
[AMBER] MM_PBSA problem in Amber 9
- Sean Zhao (Mon May 04 2009 - 02:09:14 PDT)
[AMBER] MMPBSA extract coordinate
- vijayaraj.clri.res.in (Fri May 22 2009 - 11:00:57 PDT)
[AMBER] MMPBSA- interaction energy for every frame
- Jack Colis (Tue May 05 2009 - 01:22:35 PDT)
- Wei Huang (Mon May 04 2009 - 07:58:26 PDT)
- Jack Colis (Mon May 04 2009 - 07:38:38 PDT)
[AMBER] Modification of His
- Bill Ross (Mon May 18 2009 - 13:06:16 PDT)
- David A. Case (Mon May 18 2009 - 05:31:33 PDT)
- Jorgen Simonsen (Mon May 18 2009 - 05:16:10 PDT)
- David A. Case (Mon May 18 2009 - 04:58:34 PDT)
- Jorgen Simonsen (Mon May 18 2009 - 03:51:50 PDT)
[AMBER] Modifying a water molecule
- Jorgen Simonsen (Sat May 09 2009 - 06:16:54 PDT)
[AMBER] molecular crystal simulation
- David A. Case (Wed May 13 2009 - 15:28:37 PDT)
- Simona Irrera (Tue May 12 2009 - 04:04:26 PDT)
[AMBER] Molecular simulation of a protein using special H2O cluster
- Carlos Simmerling (Tue May 26 2009 - 17:25:03 PDT)
- Rilei Yu (Tue May 26 2009 - 17:21:15 PDT)
- Carlos Simmerling (Tue May 26 2009 - 04:45:50 PDT)
- Rilei Yu (Tue May 26 2009 - 01:20:56 PDT)
[AMBER] molsurf and probe radius
- David A. Case (Mon May 11 2009 - 08:03:10 PDT)
- David Watson (Sat May 09 2009 - 10:32:43 PDT)
[AMBER] multiple chain specification in Sander
- Siddharth Rastogi (Thu May 07 2009 - 13:29:28 PDT)
- Carlos Simmerling (Thu May 07 2009 - 03:19:09 PDT)
- Siddharth Rastogi (Wed May 06 2009 - 20:17:57 PDT)
[AMBER] Nab units ?
- Marek Maly (Fri May 22 2009 - 18:43:41 PDT)
- David A. Case (Fri May 22 2009 - 18:33:34 PDT)
- Marek Maly (Fri May 22 2009 - 17:20:14 PDT)
[AMBER] nanoseconds of simulation with nscm=0
- Thomas Cheatham (Sun May 24 2009 - 13:37:23 PDT)
- Naser Alijabbari (Sun May 24 2009 - 12:56:28 PDT)
- Thomas Cheatham (Sun May 24 2009 - 11:27:33 PDT)
- Naser Alijabbari (Sun May 24 2009 - 10:20:18 PDT)
[AMBER] no equilibrium
- steinbrt.rci.rutgers.edu (Mon May 18 2009 - 20:00:40 PDT)
- Nancy (Mon May 18 2009 - 19:44:03 PDT)
- Nancy (Mon May 18 2009 - 19:32:01 PDT)
[AMBER] Non-zero internal energy in single trajectory MM-PBSA calculations
- Dmitry Osolodkin (Mon May 04 2009 - 02:24:59 PDT)
[AMBER] normal mode analysis
- David A. Case (Mon May 04 2009 - 11:06:32 PDT)
- Hannes Wallnoefer (Mon May 04 2009 - 08:56:11 PDT)
- David A. Case (Mon May 04 2009 - 06:37:02 PDT)
- Hannes Wallnoefer (Mon May 04 2009 - 02:39:16 PDT)
[AMBER] normal modes calculation
- chaitanya koppisetty (Thu May 14 2009 - 01:51:28 PDT)
- Neha Gandhi (Wed May 13 2009 - 20:12:13 PDT)
[AMBER] ntf, ntc with softcore potentials and TI in amber10
- steinbrt.rci.rutgers.edu (Tue May 05 2009 - 20:39:02 PDT)
- Matthew Wilce (Tue May 05 2009 - 18:33:28 PDT)
[AMBER] Number of processor in pmemd
- Robert Duke (Mon May 04 2009 - 10:28:11 PDT)
- Carlos Simmerling (Mon May 04 2009 - 10:27:06 PDT)
- Hemant Kumar (Mon May 04 2009 - 10:17:13 PDT)
[AMBER] ongoing issues using sander with AMOEBA
- Tomasio, Susana (Wed May 13 2009 - 03:00:00 PDT)
[AMBER] parallel amber on cluster
- David A. Case (Mon May 18 2009 - 04:54:18 PDT)
- Siavoush Dastmalchi (Sun May 17 2009 - 23:04:58 PDT)
[AMBER] Parameter file content
- Tom Joseph (Sat May 30 2009 - 19:23:48 PDT)
- manoj singh (Sat May 30 2009 - 18:53:37 PDT)
[AMBER] Parameter file not saved
- Carlos Simmerling (Mon May 04 2009 - 05:19:14 PDT)
- Remya S R (Mon May 04 2009 - 05:03:08 PDT)
- Remya S R (Sun May 03 2009 - 23:30:19 PDT)
[AMBER] PARMCAL calculation ?
- Marek Maly (Wed May 27 2009 - 07:19:48 PDT)
[AMBER] partial charge and topology of intrastrand cross-link DNA
- FyD (Tue May 26 2009 - 22:27:40 PDT)
- Shuang Ding (Mon May 25 2009 - 19:27:43 PDT)
[AMBER] partial charges of lipid membrane for GPCR system
- xueqin pang (Tue May 26 2009 - 06:34:34 PDT)
[AMBER] please help me out
- Wei Zhang (Sun May 10 2009 - 06:21:06 PDT)
- Nancy (Sun May 10 2009 - 00:56:33 PDT)
[AMBER] pmemd compilation error
- john smith (Tue May 05 2009 - 04:20:08 PDT)
[AMBER] pmemd running very slow in amber10
- Robert Duke (Thu May 14 2009 - 06:38:29 PDT)
- Ross Walker (Thu May 14 2009 - 05:57:43 PDT)
- Carlos Simmerling (Thu May 14 2009 - 03:09:11 PDT)
- Vijay Manickam Achari (Wed May 13 2009 - 22:41:40 PDT)
[AMBER] positive value of binding enrgy after MM PBSA
- Vikas Sharma (Wed May 06 2009 - 08:07:03 PDT)
[AMBER] prmtop
- Ross Walker (Sun May 03 2009 - 19:18:04 PDT)
- Mark M Huntress (Sun May 03 2009 - 16:20:39 PDT)
[AMBER] Problem in Nmode
- Kshatresh Dutta Dubey (Sun May 17 2009 - 23:07:52 PDT)
[AMBER] Problem in production run
- Carlos Simmerling (Tue May 05 2009 - 03:07:11 PDT)
- nicholus bhattacharjee (Mon May 04 2009 - 22:50:07 PDT)
[AMBER] problem with cutoff
- Ross Walker (Mon May 04 2009 - 08:35:40 PDT)
- Yunjie Zhao (Mon May 04 2009 - 05:58:00 PDT)
- Ross Walker (Sun May 03 2009 - 22:02:04 PDT)
- Yunjie Zhao (Sun May 03 2009 - 20:53:00 PDT)
[AMBER] problem with MM-PBSA
- Bill Ross (Wed May 27 2009 - 17:52:19 PDT)
- Thomas Cheatham (Wed May 27 2009 - 17:35:30 PDT)
- Ray Luo (Tue May 26 2009 - 09:44:14 PDT)
- David A. Case (Tue May 26 2009 - 04:37:31 PDT)
- Maryam Hamzehee (Mon May 25 2009 - 21:52:29 PDT)
- Maryam Hamzehee (Sat May 23 2009 - 21:48:05 PDT)
[AMBER] Problem with MM-PBSA energy calculation
- Rubben Torella (Tue May 26 2009 - 04:24:56 PDT)
- Barbault Florent (Mon May 25 2009 - 11:57:19 PDT)
- Rubben Torella (Mon May 25 2009 - 08:58:41 PDT)
[AMBER] Problem with Nmode
- David A. Case (Thu May 21 2009 - 05:29:06 PDT)
- Kshatresh Dutta Dubey (Wed May 20 2009 - 22:14:50 PDT)
- David A. Case (Wed May 20 2009 - 11:02:44 PDT)
- Kshatresh Dutta Dubey (Mon May 18 2009 - 21:25:05 PDT)
[AMBER] Problem with nonstandard residues
- moitrayee.mbu.iisc.ernet.in (Tue May 19 2009 - 09:47:38 PDT)
- David A. Case (Tue May 19 2009 - 08:22:15 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue May 19 2009 - 06:10:00 PDT)
- David A. Case (Tue May 19 2009 - 05:54:14 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue May 19 2009 - 04:48:33 PDT)
[AMBER] problem with parmchk
- David A. Case (Mon May 18 2009 - 13:00:07 PDT)
- rebeca (Mon May 18 2009 - 07:34:31 PDT)
- David A. Case (Mon May 18 2009 - 07:19:54 PDT)
- rebeca (Mon May 18 2009 - 06:59:51 PDT)
[AMBER] problem with program anal within Amber10
- David A. Case (Tue May 26 2009 - 05:03:01 PDT)
- Marina Grabar (Tue May 26 2009 - 04:48:38 PDT)
[AMBER] Problems in the result of MM_PBSA
- Ray Luo (Mon May 11 2009 - 10:55:12 PDT)
- Sean Zhao (Sun May 10 2009 - 01:23:19 PDT)
- Ray Luo (Sat May 09 2009 - 18:36:04 PDT)
- Sean Zhao (Fri May 08 2009 - 20:44:29 PDT)
- David A. Case (Fri May 08 2009 - 05:45:19 PDT)
- Ray Luo (Thu May 07 2009 - 19:02:58 PDT)
- Sean Zhao (Thu May 07 2009 - 18:30:24 PDT)
[AMBER] Problems with PMEMD installation for AMBER10
- German Erlenkamp (Thu May 07 2009 - 00:18:36 PDT)
- Robert Duke (Tue May 05 2009 - 06:48:06 PDT)
- German Erlenkamp (Tue May 05 2009 - 06:07:13 PDT)
- Robert Duke (Tue May 05 2009 - 06:00:54 PDT)
- German Erlenkamp (Tue May 05 2009 - 05:40:56 PDT)
[AMBER] Protein Docking
- Chih-Ying Lin (Thu May 14 2009 - 21:28:43 PDT)
- Simon Becker (Tue May 12 2009 - 08:23:02 PDT)
- steinbrt.rci.rutgers.edu (Mon May 11 2009 - 13:33:15 PDT)
- Chih-Ying Lin (Mon May 11 2009 - 13:21:45 PDT)
[AMBER] protein molecular weight?
- Tom Joseph (Fri May 29 2009 - 16:40:58 PDT)
- Chih-Ying Lin (Fri May 29 2009 - 15:44:24 PDT)
[AMBER] Protein with HETATM, am I doing the
- amit (Mon May 25 2009 - 08:26:15 PDT)
- nicholus bhattacharjee (Wed May 20 2009 - 23:43:37 PDT)
- Amit Bajaj (Wed May 20 2009 - 22:26:49 PDT)
- nicholus bhattacharjee (Wed May 20 2009 - 21:48:42 PDT)
[AMBER] Protein with HETATM, am I doing the right thing
- David A. Case (Sat May 23 2009 - 05:13:01 PDT)
- nicholus bhattacharjee (Thu May 21 2009 - 09:28:52 PDT)
- David A. Case (Thu May 21 2009 - 05:39:14 PDT)
- nicholus bhattacharjee (Thu May 21 2009 - 04:21:15 PDT)
[AMBER] ptraj netcdf
- Chris Moth (Tue May 12 2009 - 08:46:31 PDT)
- Bala subramanian (Tue May 12 2009 - 05:04:00 PDT)
[AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated?
- Hannes Loeffler (Thu May 07 2009 - 00:47:23 PDT)
- Patrick Gedeon (Wed May 06 2009 - 21:12:39 PDT)
[AMBER] ptraj questions
- Jia Xu (Sat May 23 2009 - 22:06:10 PDT)
- Myunggi Yi (Fri May 22 2009 - 06:57:08 PDT)
- Jia Xu (Wed May 20 2009 - 07:39:13 PDT)
[AMBER] QM/MM
- Syed Tarique Moin (Wed May 06 2009 - 00:12:17 PDT)
- Syed Tarique Moin (Wed May 06 2009 - 00:11:54 PDT)
- Catein Catherine (Tue May 05 2009 - 19:48:44 PDT)
- Ross Walker (Tue May 05 2009 - 15:16:26 PDT)
- Syed Tarique Moin (Mon May 04 2009 - 15:13:22 PDT)
- Ross Walker (Mon May 04 2009 - 10:47:21 PDT)
- Syed Tarique Moin (Mon May 04 2009 - 08:32:29 PDT)
[AMBER] QM/MM assigns Cd to C, Se to S
- Ross Walker (Fri May 08 2009 - 00:16:09 PDT)
- Ross Walker (Sat May 02 2009 - 21:45:41 PDT)
- C Liu (Sat May 02 2009 - 19:09:27 PDT)
[AMBER] QQD psuedoatom restraints
- David A. Case (Fri May 29 2009 - 12:26:27 PDT)
- Titus, Jamie (bairdje) (Fri May 29 2009 - 12:01:34 PDT)
- David A. Case (Fri May 29 2009 - 08:18:29 PDT)
- Titus, Jamie (bairdje) (Fri May 29 2009 - 07:02:31 PDT)
[AMBER] Question about &dipoles printing in AMBER 8
- Karen Callahan (Mon May 25 2009 - 16:46:00 PDT)
[AMBER] Question about Thermal Integration with Softcore
- steinbrt.rci.rutgers.edu (Wed May 13 2009 - 08:11:16 PDT)
- Elodie Laine (Wed May 13 2009 - 02:13:22 PDT)
[AMBER] Radius for Bromine in MMPBSA calculation
- Ray Luo (Tue May 26 2009 - 12:02:27 PDT)
- john smith (Mon May 25 2009 - 22:00:52 PDT)
- Ray Luo (Mon May 25 2009 - 14:10:41 PDT)
- john smith (Sun May 24 2009 - 21:52:48 PDT)
- Ray Luo (Thu May 21 2009 - 09:32:41 PDT)
- john smith (Wed May 20 2009 - 22:24:05 PDT)
[AMBER] resp charge
- Ross Walker (Wed May 20 2009 - 08:05:20 PDT)
- FyD (Wed May 20 2009 - 00:42:07 PDT)
- R. A. (Tue May 19 2009 - 19:35:25 PDT)
[AMBER] Running PTRAJ command line scripts in background
- Hopkins, Robert (Mon May 18 2009 - 15:50:06 PDT)
- Ross Walker (Sun May 17 2009 - 20:35:09 PDT)
- Hopkins, Robert (Sun May 17 2009 - 09:55:48 PDT)
- Jia Xu (Sun May 17 2009 - 00:16:49 PDT)
- Hopkins, Robert (Sat May 16 2009 - 17:47:38 PDT)
[AMBER] SANDER BOMB
- David A. Case (Thu May 28 2009 - 07:29:50 PDT)
- PRADEEP VENKATARAMAN (Wed May 27 2009 - 19:39:56 PDT)
[AMBER] scee term
- Ross Walker (Fri May 15 2009 - 08:02:09 PDT)
- Neha Gandhi (Fri May 15 2009 - 02:03:48 PDT)
[AMBER] Script for parallel runs
- Gustavo Seabra (Tue May 05 2009 - 09:31:38 PDT)
- Catein Catherine (Mon May 04 2009 - 02:17:42 PDT)
[AMBER] Script for parallel runs 2
- Ross Walker (Mon May 04 2009 - 08:39:27 PDT)
- Catein Catherine (Mon May 04 2009 - 02:41:58 PDT)
[AMBER] secstruct with ptraj
- Bala subramanian (Fri May 15 2009 - 03:19:54 PDT)
[AMBER] Segmentation error in Ptraj
- Kshatresh Dutta Dubey (Fri May 22 2009 - 00:17:27 PDT)
[AMBER] skip parallel test
- Ross Walker (Tue May 05 2009 - 08:43:34 PDT)
- David A. Case (Tue May 05 2009 - 08:34:14 PDT)
- Collins Nganou (Tue May 05 2009 - 06:09:00 PDT)
[AMBER] solutes in a simulation box
- Workalemhu Berhanu (Sun May 31 2009 - 09:59:39 PDT)
[AMBER] Strange high temperature in softcore TI
- steinbrt.rci.rutgers.edu (Sun May 24 2009 - 21:13:38 PDT)
- Tom Joseph (Sun May 24 2009 - 20:20:20 PDT)
- steinbrt.rci.rutgers.edu (Sun May 24 2009 - 19:26:28 PDT)
- Tom Joseph (Sun May 24 2009 - 18:54:43 PDT)
[AMBER] Suggestion for restraining chain of a protein
- Carlos Simmerling (Tue May 05 2009 - 05:27:05 PDT)
- nicholus bhattacharjee (Tue May 05 2009 - 05:20:44 PDT)
- Carlos Simmerling (Tue May 05 2009 - 03:05:16 PDT)
- nicholus bhattacharjee (Mon May 04 2009 - 23:29:54 PDT)
[AMBER] Targeted MD and QM/MM
- Gabriel Urquiza (Fri May 29 2009 - 13:09:31 PDT)
[AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically
- David A. Case (Sat May 30 2009 - 06:11:59 PDT)
- Workalemhu Berhanu (Sat May 30 2009 - 04:20:03 PDT)
[AMBER] The largest AMBER calculation(s)?
- Vlad (Mon May 18 2009 - 19:58:27 PDT)
[AMBER] The protein swell?
- Chih-Ying Lin (Sun May 17 2009 - 15:17:51 PDT)
[AMBER] The resonable way to create single strand DNA with NAB ?
- Marek Malý (Mon May 11 2009 - 05:18:06 PDT)
- David A. Case (Mon May 11 2009 - 04:34:16 PDT)
- Marek Malý (Sun May 10 2009 - 10:12:09 PDT)
[AMBER] Tutorial 4 Parameter file was not saved
- Ross Walker (Wed May 27 2009 - 10:31:30 PDT)
- Workalemhu Berhanu (Wed May 27 2009 - 09:00:30 PDT)
[AMBER] Tutorial 4 Please check the total charge and your -nc flag
- David A. Case (Wed May 27 2009 - 04:42:29 PDT)
- Workalemhu Berhanu (Tue May 26 2009 - 12:47:07 PDT)
[AMBER] Tutorial A1
- Workalemhu Berhanu (Tue May 19 2009 - 16:05:15 PDT)
[AMBER] unable to start xleap
- Wei Zhang (Fri May 01 2009 - 11:39:03 PDT)
- Jayalakshmi Sridhar (Fri May 01 2009 - 11:32:27 PDT)
[AMBER] Unit 8 Error on OPEN: prmtop
- Workalemhu Berhanu (Sun May 24 2009 - 15:12:00 PDT)
- Peter Gannett (Sun May 24 2009 - 12:29:58 PDT)
- Alessandro Nascimento (Sun May 24 2009 - 11:28:26 PDT)
- Peter Gannett (Sun May 24 2009 - 10:46:47 PDT)
- Workalemhu Berhanu (Sun May 24 2009 - 10:27:38 PDT)
[AMBER] unnatural amino acid
- FyD (Thu May 28 2009 - 11:46:27 PDT)
[AMBER] What are the elements to speed up the simulation?
- Chih-Ying Lin (Tue May 19 2009 - 15:17:07 PDT)
[AMBER] What is the purpose to do the bond constraints?
- Bill Ross (Mon May 18 2009 - 12:39:42 PDT)
- Ross Walker (Sun May 17 2009 - 20:38:52 PDT)
- Chih-Ying Lin (Sun May 17 2009 - 15:09:04 PDT)
[AMBER] Why does protein carry charges?
- Ross Walker (Sat May 23 2009 - 11:06:57 PDT)
- Chih-Ying Lin (Fri May 22 2009 - 21:09:21 PDT)
[AMBER] Why NaCl or KCl solution?
- Chih-Ying Lin (Wed May 27 2009 - 19:11:21 PDT)
- Thomas Cheatham (Wed May 27 2009 - 17:50:56 PDT)
- Chih-Ying Lin (Sat May 23 2009 - 09:41:33 PDT)
[AMBER] Why the job idle before the sentence "| Running AMBER/MPI version on 2 nodes"?
- Catein Catherine (Mon May 04 2009 - 08:16:08 PDT)
[AMBER] xleap input pdb problem
- David A. Case (Wed May 06 2009 - 19:16:10 PDT)
- Majeed Shaik (Wed May 06 2009 - 11:47:45 PDT)
[AMBER] xleap reading hydrogens giving error
- David A. Case (Fri May 15 2009 - 09:25:11 PDT)
- Jorgen Simonsen (Fri May 15 2009 - 08:54:17 PDT)
- David A. Case (Fri May 15 2009 - 07:17:04 PDT)
- Jorgen Simonsen (Fri May 15 2009 - 00:47:10 PDT)
[AMBER] xleap segmentation fault
- Jayalakshmi Sridhar (Fri May 29 2009 - 08:45:25 PDT)
- David A. Case (Thu May 28 2009 - 13:05:12 PDT)
- Jayalakshmi Sridhar (Thu May 28 2009 - 09:29:47 PDT)
- Jayalakshmi Sridhar (Mon May 04 2009 - 08:50:06 PDT)
[AMBER] xleap, mac number problem
- Mark M Huntress (Sat May 09 2009 - 12:46:46 PDT)
[AMBER] xmin
- Scott Brozell (Mon May 18 2009 - 13:30:17 PDT)
- Peter Varnai (Sun May 17 2009 - 17:58:00 PDT)
- Scott Brozell (Sun May 17 2009 - 13:45:27 PDT)
- Peter Varnai (Thu May 14 2009 - 14:29:09 PDT)
[Subject Filtered] [AMBER] hbond-error in amber9 8%
- Thomas Cheatham III (Fri May 01 2009 - 11:07:40 PDT)
- Hopkins, Robert (Thu Apr 30 2009 - 17:02:34 PDT)
About Amber installations
- jacky zhao (Tue May 26 2009 - 04:18:25 PDT)
- Alan (Tue May 26 2009 - 02:53:37 PDT)
About Amber10 installation "Possible Failure"
- Ross Walker (Thu May 28 2009 - 07:06:31 PDT)
- Ross Walker (Tue May 26 2009 - 08:38:19 PDT)
add magnesium
- Ross Walker (Wed May 20 2009 - 14:30:09 PDT)
ERROR in ptrajInitializeState(): Attempting ....
- Siavoush Dastmalchi (Sat May 30 2009 - 10:11:55 PDT)
essential dynamics
- Niel Henriksen (Wed May 13 2009 - 11:28:22 PDT)
- David A. Case (Wed May 13 2009 - 10:48:42 PDT)
- Chunliyan (Wed May 13 2009 - 10:25:57 PDT)
Help with xleap
- Taufik Al-Sarraj (Tue May 26 2009 - 16:58:00 PDT)
How to know that the md is stable in equilibration run
- nicholus bhattacharjee (Mon May 25 2009 - 09:11:39 PDT)
Listing gaff parameters in frcmod
- steinbrt.rci.rutgers.edu (Fri May 08 2009 - 07:23:45 PDT)
- Bokun Cho (Thu May 07 2009 - 22:00:47 PDT)
- Ross Walker (Thu May 07 2009 - 21:34:08 PDT)
- Bokun Cho (Thu May 07 2009 - 21:20:46 PDT)
MM-PBSA with explicit water
- mathew k varghese (Thu May 14 2009 - 23:43:46 PDT)
xleap, mac number problem
- Mark M Huntress (Sat May 09 2009 - 15:29:50 PDT)
回复： [AMBER] Error running MM _PBSA.pl script
- Vikas Sharma (Mon May 18 2009 - 07:06:49 PDT)
- 廖青华 (Mon May 18 2009 - 05:08:47 PDT)
回复： [AMBER] MM PBSA output
- Vikas Sharma (Wed May 20 2009 - 10:54:32 PDT)
- 廖青华 (Wed May 20 2009 - 05:15:04 PDT)
回复：回复： [AMBER] Error running MM _PBSA.pl script
- 廖青华 (Mon May 18 2009 - 07:41:14 PDT)

Amber Archive May 2009 by subject