Amber Archive Mar 2011: by subject

[AMBER] a question about using oplsaa ff in amber
- Junjian Miao (Tue Mar 08 2011 - 17:13:58 PST)
- Ben Roberts (Tue Mar 08 2011 - 08:44:05 PST)
- Junjian Miao (Mon Mar 07 2011 - 20:12:35 PST)
[AMBER] about Nmod in amber11
- juan zeng (Tue Mar 08 2011 - 23:25:11 PST)
[AMBER] acceptance probabilities remd
- Carlos Simmerling (Tue Mar 08 2011 - 04:00:14 PST)
- Jorgen Simonsen (Tue Mar 08 2011 - 03:58:18 PST)
- Carlos Simmerling (Tue Mar 08 2011 - 03:49:14 PST)
- Adrian Roitberg (Tue Mar 08 2011 - 03:17:58 PST)
- Jorgen Simonsen (Tue Mar 08 2011 - 02:02:59 PST)
[AMBER] ACS COMP division awards for Fall 2011 meeting
- Carlos Simmerling (Sat Mar 05 2011 - 07:44:30 PST)
[AMBER] Add Residue at N-terminal
- setyanto md (Thu Mar 31 2011 - 07:17:59 PDT)
- Dmitry Nilov (Thu Mar 31 2011 - 07:09:54 PDT)
- setyanto md (Thu Mar 31 2011 - 06:57:17 PDT)
[AMBER] Add residue copied from other unit
- Vlastimil Zíma (Tue Mar 15 2011 - 08:24:14 PDT)
[AMBER] Amber
- David A Case (Thu Mar 24 2011 - 08:34:47 PDT)
- Jason Swails (Thu Mar 24 2011 - 08:21:56 PDT)
- 姜笑楠 (Wed Mar 23 2011 - 23:50:08 PDT)
[AMBER] AMBER 10 serial compile problem
- Dmitry Osolodkin (Tue Mar 15 2011 - 13:22:01 PDT)
- Jason Swails (Tue Mar 15 2011 - 11:09:46 PDT)
- Dmitry Osolodkin (Tue Mar 15 2011 - 10:45:07 PDT)
- Jason Swails (Tue Mar 15 2011 - 10:41:28 PDT)
- Dmitry Osolodkin (Tue Mar 15 2011 - 10:29:59 PDT)
- David A Case (Tue Mar 15 2011 - 10:24:19 PDT)
- Jason Swails (Tue Mar 15 2011 - 10:06:17 PDT)
- Dmitry Osolodkin (Tue Mar 15 2011 - 09:52:50 PDT)
- Jason Swails (Tue Mar 15 2011 - 09:57:54 PDT)
- David Watson (Tue Mar 15 2011 - 09:53:41 PDT)
- Dmitry Osolodkin (Tue Mar 15 2011 - 09:35:37 PDT)
[AMBER] Amber archive mailing list is not working
- David Watson (Mon Mar 14 2011 - 10:37:50 PDT)
- Ross Walker (Mon Mar 14 2011 - 09:57:23 PDT)
- Hirdesh Kumar (Sun Mar 13 2011 - 22:04:51 PDT)
- Bill Ross (Sat Mar 12 2011 - 23:50:21 PST)
- Ross Walker (Sat Mar 12 2011 - 10:50:07 PST)
- Gustavo Seabra (Sat Mar 12 2011 - 03:56:02 PST)
- Gustavo Seabra (Sat Mar 12 2011 - 03:53:53 PST)
- Ilyas Yildirim (Fri Mar 11 2011 - 23:29:31 PST)
- Jason Swails (Fri Mar 11 2011 - 23:18:58 PST)
- Hirdesh Kumar (Fri Mar 11 2011 - 23:07:13 PST)
- Jason Swails (Fri Mar 11 2011 - 22:55:01 PST)
- Hirdesh Kumar (Fri Mar 11 2011 - 22:50:55 PST)
[AMBER] Amber CUDA calcualtion on GeForce GTX 590 ?
- Scott Le Grand (Thu Mar 31 2011 - 12:33:49 PDT)
- Ross Walker (Thu Mar 31 2011 - 11:23:31 PDT)
- Marek Maly (Thu Mar 31 2011 - 02:34:38 PDT)
- filip fratev (Wed Mar 30 2011 - 16:17:34 PDT)
- Ross Walker (Wed Mar 30 2011 - 15:48:37 PDT)
- filip fratev (Wed Mar 30 2011 - 15:16:54 PDT)
- Marek Maly (Wed Mar 30 2011 - 12:26:50 PDT)
- Dmitry Mukha (Wed Mar 30 2011 - 12:24:15 PDT)
- Ross Walker (Wed Mar 30 2011 - 12:21:54 PDT)
- Marek Maly (Wed Mar 30 2011 - 11:59:20 PDT)
- Scott Le Grand (Wed Mar 30 2011 - 11:37:21 PDT)
- Ross Walker (Wed Mar 30 2011 - 11:29:58 PDT)
- Marek Maly (Wed Mar 30 2011 - 08:24:07 PDT)
- filip fratev (Wed Mar 30 2011 - 08:29:13 PDT)
- filip fratev (Wed Mar 30 2011 - 08:26:29 PDT)
- Marek Maly (Wed Mar 30 2011 - 06:48:35 PDT)
- Gould, Ian R (Wed Mar 30 2011 - 06:09:19 PDT)
- Marek Maly (Wed Mar 30 2011 - 05:34:30 PDT)
- filip fratev (Wed Mar 30 2011 - 05:08:35 PDT)
- Marek Maly (Wed Mar 30 2011 - 02:39:41 PDT)
[AMBER] Amber Installation error
- Jason Swails (Fri Mar 25 2011 - 08:12:38 PDT)
- Hirdesh Kumar (Fri Mar 25 2011 - 05:22:25 PDT)
[AMBER] AMBER parameters for lead
- Ganesh Kamath (Fri Mar 04 2011 - 12:24:48 PST)
[AMBER] Amber Training Workshop Announcement - Barcelona, Spain. 3-6 May 2011
- Ross Walker (Fri Mar 11 2011 - 10:24:53 PST)
[AMBER] AMBER Workshop in Shanghai, China, August 22-26 2011
- Andreas Goetz (Tue Mar 15 2011 - 13:29:25 PDT)
[AMBER] amber11 Installation Test Failures
- Jason Swails (Sun Mar 20 2011 - 07:36:09 PDT)
- David Cantu (Sun Mar 20 2011 - 01:34:55 PDT)
- David Cantu (Sat Mar 19 2011 - 23:39:08 PDT)
- David Cantu (Sat Mar 19 2011 - 23:16:27 PDT)
- Tru Huynh (Sat Mar 19 2011 - 17:30:40 PDT)
- case (Tue Mar 15 2011 - 18:58:06 PDT)
- David Cantu (Tue Mar 15 2011 - 19:08:04 PDT)
- David Cantu (Tue Mar 15 2011 - 18:40:15 PDT)
- Jason Swails (Tue Mar 15 2011 - 17:14:05 PDT)
- David Cantu (Tue Mar 15 2011 - 16:58:06 PDT)
- Daniel Roe (Tue Mar 15 2011 - 16:55:28 PDT)
- David Cantu (Tue Mar 15 2011 - 16:16:02 PDT)
- David Cantu (Tue Mar 15 2011 - 14:31:24 PDT)
- Jason Swails (Mon Mar 14 2011 - 07:08:52 PDT)
- David Cantu (Mon Mar 14 2011 - 00:16:41 PDT)
- Daniel Roe (Sun Mar 13 2011 - 19:21:21 PDT)
- David Cantu (Sun Mar 13 2011 - 18:11:59 PDT)
[AMBER] amber11 intel mpi compile on altix 450 problem
- Lisa Perez (Wed Mar 16 2011 - 09:45:03 PDT)
- Jason Swails (Tue Mar 15 2011 - 07:38:03 PDT)
- Lisa Perez (Mon Mar 14 2011 - 22:09:01 PDT)
[AMBER] Amber11 make test FAILURE and ERROR
- David Cantu (Mon Mar 21 2011 - 18:57:02 PDT)
- Jason Swails (Sun Mar 20 2011 - 07:33:14 PDT)
- David Cantu (Sun Mar 20 2011 - 01:45:34 PDT)
[AMBER] Amber11 on osx using port and gcc4.5
- case (Fri Mar 18 2011 - 14:31:17 PDT)
- Joachim Reichelt (Fri Mar 18 2011 - 05:42:58 PDT)
[AMBER] AmberTools 1.4 make test Error
- David Cantu (Sun Mar 20 2011 - 01:39:50 PDT)
[AMBER] AmberTools 1.4 possible bug for secstruct (test case attached)
- Tru Huynh (Mon Mar 14 2011 - 10:46:34 PDT)
- Crowley, Michael (Sun Mar 13 2011 - 12:55:31 PDT)
- case (Sat Mar 12 2011 - 05:54:02 PST)
- Tru Huynh (Fri Mar 11 2011 - 16:30:57 PST)
[AMBER] AmberTools and GROMACS
- Francesco Oteri (Sat Mar 19 2011 - 11:31:04 PDT)
[AMBER] AmberTools1.4 question
- Carlos Simmerling (Sat Mar 26 2011 - 10:46:24 PDT)
- markus metz (Sat Mar 26 2011 - 10:40:56 PDT)
[AMBER] AMD Opteron system - compiling pmemd with intel or gfortran?
- Jason Swails (Fri Mar 25 2011 - 22:44:48 PDT)
- Sergio R Aragon (Fri Mar 25 2011 - 22:21:39 PDT)
- Jason Swails (Fri Mar 25 2011 - 19:21:07 PDT)
- Sergio R Aragon (Fri Mar 25 2011 - 16:42:19 PDT)
- Ilyas Yildirim (Fri Mar 25 2011 - 13:54:22 PDT)
[AMBER] angle in h-bond analysis
- Daniel Roe (Mon Mar 14 2011 - 05:58:22 PDT)
- mirage . (Mon Mar 14 2011 - 00:40:47 PDT)
- mirage . (Fri Mar 11 2011 - 06:10:20 PST)
[AMBER] Any manual for python or perl to transform a matrix for data analysis?
- M. Shahid (Fri Mar 25 2011 - 13:57:33 PDT)
- Jason Swails (Fri Mar 25 2011 - 08:23:50 PDT)
- steinbrt.rci.rutgers.edu (Fri Mar 25 2011 - 01:31:02 PDT)
- Catein Catherine (Fri Mar 25 2011 - 01:06:14 PDT)
- Per Jr. Greisen (Fri Mar 25 2011 - 00:55:13 PDT)
- Catein Catherine (Fri Mar 25 2011 - 00:46:53 PDT)
[AMBER] Assertion failed: nat < 5000, file makeDIST_RST
- case (Thu Mar 17 2011 - 05:34:51 PDT)
- Andre Serobian (Wed Mar 16 2011 - 17:51:37 PDT)
- case (Wed Mar 16 2011 - 04:47:37 PDT)
- Andre Serobian (Tue Mar 15 2011 - 18:44:02 PDT)
- case (Tue Mar 15 2011 - 17:51:21 PDT)
- Andre Serobian (Tue Mar 15 2011 - 13:20:47 PDT)
[AMBER] Atom distribution in PMEMD.cuda
- Francesco Oteri (Wed Mar 30 2011 - 07:02:31 PDT)
[AMBER] Atom name convention/conversion in antechamber
- Jason Swails (Tue Mar 29 2011 - 08:46:23 PDT)
- David A Case (Tue Mar 29 2011 - 04:54:04 PDT)
- thomas.fox.boehringer-ingelheim.com (Mon Mar 28 2011 - 23:45:09 PDT)
- Francesco Pietra (Sun Mar 27 2011 - 02:11:56 PDT)
- case (Sat Mar 26 2011 - 17:32:53 PDT)
- Mahmoud Soliman (Thu Mar 24 2011 - 09:12:47 PDT)
- thomas.fox.boehringer-ingelheim.com (Thu Mar 24 2011 - 08:42:50 PDT)
- David A Case (Thu Mar 24 2011 - 06:24:11 PDT)
- thomas.fox.boehringer-ingelheim.com (Wed Mar 23 2011 - 03:47:26 PDT)
[AMBER] Atom Types involved in Carbon monoxide and Cyanide bonds
- Naveen Samala (Wed Mar 09 2011 - 12:45:39 PST)
[AMBER] average structure pdb file looks wrong
- Thomas Cheatham III (Tue Mar 22 2011 - 16:19:03 PDT)
- Bingwu Yu (Tue Mar 22 2011 - 13:39:03 PDT)
[AMBER] Bad magic number ?
- Jason Swails (Sat Mar 12 2011 - 08:20:59 PST)
- Bill Miller III (Sat Mar 12 2011 - 07:02:56 PST)
- Hector A. Baldoni (Sat Mar 12 2011 - 06:41:19 PST)
[AMBER] Blowing array; too many frames!!
- Bill Ross (Fri Mar 04 2011 - 15:30:14 PST)
- Sangita Kachhap (Fri Mar 04 2011 - 11:24:04 PST)
- Sangita Kachhap (Thu Mar 03 2011 - 20:37:48 PST)
- Sangita Kachhap (Thu Mar 03 2011 - 19:56:52 PST)
- Daniel Roe (Thu Mar 03 2011 - 10:48:15 PST)
- Sangita Kachhap (Thu Mar 03 2011 - 09:00:18 PST)
- Daniel Roe (Thu Mar 03 2011 - 08:31:29 PST)
- Sangita Kachhap (Thu Mar 03 2011 - 08:25:01 PST)
- Daniel Roe (Thu Mar 03 2011 - 08:06:05 PST)
- Sangita Kachhap (Thu Mar 03 2011 - 07:59:50 PST)
- Daniel Roe (Thu Mar 03 2011 - 06:38:50 PST)
- Sangita Kachhap (Thu Mar 03 2011 - 04:33:30 PST)
[AMBER] building HA8 (hyaluronic acid 8-mer) using amber leap
- Madhurima Jana (Fri Mar 04 2011 - 21:36:04 PST)
[AMBER] calculation of population of each conformers
- Bingwu Yu (Mon Mar 21 2011 - 14:45:22 PDT)
[AMBER] Calculation with CUTCAP
- Roman Osman (Tue Mar 15 2011 - 07:51:16 PDT)
- Jason Swails (Tue Mar 15 2011 - 07:43:50 PDT)
- Osman, Roman (Tue Mar 15 2011 - 06:34:22 PDT)
- Dwight McGee (Mon Mar 14 2011 - 20:28:35 PDT)
- Roman Osman (Mon Mar 14 2011 - 20:20:43 PDT)
[AMBER] can I calculate binding energy with some restraints
- Mahmoud Soliman (Mon Mar 21 2011 - 10:40:24 PDT)
- case (Mon Mar 21 2011 - 10:23:35 PDT)
- Mahmoud Soliman (Mon Mar 21 2011 - 08:06:17 PDT)
[AMBER] Can we relax protein and ligand separately?
- kurisaki.ncube.human.nagoya-u.ac.jp (Wed Mar 09 2011 - 17:34:38 PST)
[AMBER] chamber
- Mark Williamson (Thu Mar 03 2011 - 01:53:24 PST)
- colvin (Thu Mar 03 2011 - 01:24:53 PST)
- Mark Williamson (Wed Mar 02 2011 - 08:18:27 PST)
[AMBER] CHAMBER prmtop
- colvin (Thu Mar 03 2011 - 01:22:39 PST)
- Mark Williamson (Wed Mar 02 2011 - 09:48:02 PST)
- colvin (Tue Mar 01 2011 - 22:36:36 PST)
- Ross Walker (Tue Mar 01 2011 - 20:30:08 PST)
- Bill Ross (Tue Mar 01 2011 - 20:05:29 PST)
- colvin (Tue Mar 01 2011 - 19:58:06 PST)
- Bill Ross (Tue Mar 01 2011 - 19:51:11 PST)
- colvin (Tue Mar 01 2011 - 19:46:50 PST)
[AMBER] changing maximum number of frames for mmpbsa.py
- Bill Miller III (Sat Mar 19 2011 - 09:40:39 PDT)
- Chris Chris (Sat Mar 19 2011 - 09:27:03 PDT)
[AMBER] changing X Y Z orientation
- Vijay Manickam Achari (Fri Mar 18 2011 - 03:47:21 PDT)
[AMBER] charmmgen issues
- Francesco Pietra (Mon Mar 21 2011 - 04:04:03 PDT)
[AMBER] checking interaction between periodic images
- Hannes Loeffler (Tue Mar 01 2011 - 08:29:18 PST)
- Daniel Roe (Tue Mar 01 2011 - 06:54:42 PST)
- Jason Swails (Tue Mar 01 2011 - 05:29:33 PST)
- Bala subramanian (Tue Mar 01 2011 - 02:37:04 PST)
[AMBER] clustering MD results
- Thomas Cheatham III (Wed Mar 30 2011 - 14:28:39 PDT)
- Jack Lee (Wed Mar 30 2011 - 01:34:06 PDT)
[AMBER] Compatibility Question
- Ross Walker (Mon Mar 14 2011 - 18:44:29 PDT)
- Azat Mukhametov (Mon Mar 14 2011 - 17:57:09 PDT)
[AMBER] compiling AmberTools1.4 with -cuda flag
- Ross Walker (Tue Mar 22 2011 - 16:09:24 PDT)
- Jason Swails (Tue Mar 22 2011 - 16:06:36 PDT)
- Robert Wohlhueter (Tue Mar 22 2011 - 15:46:56 PDT)
[AMBER] compiling with cuda
- Scott Le Grand (Fri Mar 25 2011 - 08:53:55 PDT)
- Jacopo Sgrignani (Fri Mar 25 2011 - 08:21:44 PDT)
- Jason Swails (Fri Mar 25 2011 - 08:16:04 PDT)
- Jacopo Sgrignani (Fri Mar 25 2011 - 01:47:49 PDT)
[AMBER] continuum solvation with low viscosity
- Mahmoud Soliman (Wed Mar 09 2011 - 06:17:36 PST)
- Carlos Simmerling (Wed Mar 09 2011 - 04:19:58 PST)
- Mahmoud Soliman (Tue Mar 08 2011 - 12:28:05 PST)
[AMBER] convert the atomic b factor to residual b factor
- zhihong ke (Fri Mar 18 2011 - 14:27:45 PDT)
[AMBER] Creating distaint restaint in Amber
- David A Case (Thu Mar 24 2011 - 06:18:14 PDT)
- Vivien Landre (Wed Mar 23 2011 - 00:26:30 PDT)
- David A Case (Thu Mar 10 2011 - 05:56:18 PST)
- Vivien Landre (Wed Mar 09 2011 - 19:40:37 PST)
[AMBER] CUDA 4.0 RC
- Scott Le Grand (Tue Mar 08 2011 - 20:04:31 PST)
- Ross Walker (Mon Mar 07 2011 - 20:53:14 PST)
- filip fratev (Mon Mar 07 2011 - 18:35:28 PST)
[AMBER] CUDA Installation URL
- ros (Fri Mar 25 2011 - 09:40:22 PDT)
[AMBER] deleting protein atoms from prmtop topology files using rdparm
- g t (Wed Mar 30 2011 - 08:14:59 PDT)
- Bill Ross (Fri Mar 25 2011 - 10:38:19 PDT)
- g t (Fri Mar 25 2011 - 03:41:55 PDT)
- Chris Chris (Thu Mar 24 2011 - 14:29:25 PDT)
- Jason Swails (Thu Mar 24 2011 - 13:05:58 PDT)
- g t (Thu Mar 24 2011 - 12:01:36 PDT)
[AMBER] Differences in the periodic box dimensions
- Bill Ross (Tue Mar 22 2011 - 10:07:37 PDT)
- Jason Swails (Sat Mar 19 2011 - 16:39:15 PDT)
- Vijay Manickam Achari (Sat Mar 19 2011 - 14:38:25 PDT)
[AMBER] Diffusion coefficient
- setyanto md (Tue Mar 08 2011 - 20:33:40 PST)
- case (Mon Mar 07 2011 - 04:58:38 PST)
- Chih-Ying Lin (Fri Mar 04 2011 - 09:41:42 PST)
[AMBER] Dihedral angles does not match VMD vs ptraj
- Bingwu Yu (Fri Mar 18 2011 - 21:08:04 PDT)
- Lachele Foley (Lists) (Fri Mar 18 2011 - 14:42:04 PDT)
- Lachele Foley (Lists) (Fri Mar 18 2011 - 14:40:48 PDT)
- Bingwu Yu (Fri Mar 18 2011 - 14:24:12 PDT)
- Lachele Foley (Lists) (Fri Mar 18 2011 - 14:08:33 PDT)
- Bingwu Yu (Fri Mar 18 2011 - 13:30:42 PDT)
[AMBER] discrepancy after sieve in ptraj
- Jojart_Balazs (Thu Mar 17 2011 - 05:24:46 PDT)
[AMBER] distance cutoff of closest command
- Sangita Kachhap (Wed Mar 16 2011 - 11:05:50 PDT)
- Sangita Kachhap (Wed Mar 16 2011 - 10:24:38 PDT)
- Daniel Roe (Wed Mar 16 2011 - 06:02:12 PDT)
- Daniel Roe (Wed Mar 16 2011 - 05:59:43 PDT)
- Sangita Kachhap (Wed Mar 16 2011 - 03:07:36 PDT)
[AMBER] docking evaluation using amber
- George Tzotzos (Mon Mar 14 2011 - 11:57:20 PDT)
- Dmitry Nilov (Mon Mar 14 2011 - 06:32:02 PDT)
- erik zuiderweg (Sat Mar 12 2011 - 08:17:07 PST)
- filip fratev (Fri Mar 11 2011 - 21:15:23 PST)
- David Case (Fri Mar 11 2011 - 18:18:26 PST)
- erik zuiderweg (Fri Mar 11 2011 - 17:33:00 PST)
[AMBER] Doubts in MM-PBSA
- Bill Miller III (Wed Mar 23 2011 - 06:57:05 PDT)
- vani panguluri (Tue Mar 22 2011 - 21:44:52 PDT)
- Jason Swails (Tue Mar 22 2011 - 18:23:29 PDT)
- vani panguluri (Tue Mar 22 2011 - 18:01:30 PDT)
- Jason Swails (Tue Mar 22 2011 - 16:05:02 PDT)
- vani panguluri (Tue Mar 22 2011 - 14:52:00 PDT)
[AMBER] Energy Decomposition using mmpbsa script
- Eliac Brown (Sat Mar 12 2011 - 10:05:47 PST)
- Bill Miller III (Sat Mar 12 2011 - 07:47:56 PST)
- Eliac Brown (Sat Mar 12 2011 - 07:32:36 PST)
- Bill Miller III (Sat Mar 12 2011 - 05:31:16 PST)
- Eliac Brown (Sat Mar 12 2011 - 05:05:20 PST)
[AMBER] enzyme MD trajectory looks funny
- Jason Swails (Mon Mar 28 2011 - 08:34:23 PDT)
- Mahmoud Soliman (Mon Mar 28 2011 - 06:37:21 PDT)
- Mahmoud Soliman (Mon Mar 28 2011 - 06:34:35 PDT)
- Dmitry Nilov (Mon Mar 28 2011 - 06:20:53 PDT)
- Rajeswari A. (Mon Mar 28 2011 - 06:19:02 PDT)
- Per Jr. Greisen (Mon Mar 28 2011 - 06:07:55 PDT)
- Mahmoud Soliman (Mon Mar 28 2011 - 06:10:38 PDT)
[AMBER] error in creating prmtop and inpcrd files
- Chris Bryant (Sun Mar 13 2011 - 15:47:45 PDT)
- Jason Swails (Sun Mar 13 2011 - 14:55:13 PDT)
- Ben Roberts (Sun Mar 13 2011 - 14:34:48 PDT)
- Chris Bryant (Sun Mar 13 2011 - 13:55:51 PDT)
- Ben Roberts (Sun Mar 13 2011 - 11:42:29 PDT)
- Chris Bryant (Sun Mar 13 2011 - 10:48:56 PDT)
[AMBER] error installing AmberTools-1.2 in ubuntu 10.10
- juzer stationwala (Fri Mar 18 2011 - 02:02:50 PDT)
- Jason Swails (Fri Mar 18 2011 - 01:58:34 PDT)
- Vijay Manickam Achari (Thu Mar 17 2011 - 19:57:11 PDT)
- Jason Swails (Thu Mar 17 2011 - 14:21:25 PDT)
- Ben Roberts (Thu Mar 17 2011 - 12:52:26 PDT)
- Vijay Manickam Achari (Thu Mar 17 2011 - 12:24:46 PDT)
[AMBER] error on atom parameters
- Jason Swails (Wed Mar 23 2011 - 12:03:56 PDT)
- John S (Wed Mar 23 2011 - 11:07:47 PDT)
[AMBER] error reading NMR restraints
- Jason Swails (Wed Mar 02 2011 - 16:25:59 PST)
- Wong, Sergio E. (Wed Mar 02 2011 - 15:59:56 PST)
[AMBER] Error with MM-PBSA perl file for pairwise residue decomposition
- Bill Miller III (Fri Mar 25 2011 - 04:07:45 PDT)
- Monika Sharma (Fri Mar 25 2011 - 03:18:59 PDT)
- Jason Swails (Thu Mar 24 2011 - 20:31:44 PDT)
- Monika Sharma (Thu Mar 24 2011 - 20:09:16 PDT)
[AMBER] Error: vlimit exceeded for step
- Jason Swails (Fri Mar 25 2011 - 08:09:43 PDT)
- pankhuri arora (Fri Mar 25 2011 - 04:38:11 PDT)
[AMBER] Exchange Acceptance Ratio
- Daniel Sindhikara (Wed Mar 30 2011 - 05:00:02 PDT)
- Alessio Atzori (Wed Mar 30 2011 - 03:57:36 PDT)
[AMBER] Explicit and implicit n-octanol solvent
- Eliac Brown (Tue Mar 15 2011 - 07:03:47 PDT)
[AMBER] Extract binding free energy for each snapshot
- Wei Huang (Fri Mar 25 2011 - 08:17:07 PDT)
- Jason Swails (Fri Mar 25 2011 - 07:56:36 PDT)
- Jason Swails (Fri Mar 25 2011 - 07:54:57 PDT)
- Dwight McGee (Fri Mar 25 2011 - 07:39:05 PDT)
- Wei Huang (Fri Mar 25 2011 - 07:18:07 PDT)
[AMBER] extract vdw energy
- Yuan Ding (Wed Mar 23 2011 - 18:41:07 PDT)
- Jason Swails (Wed Mar 23 2011 - 18:35:31 PDT)
- Yuan Ding (Wed Mar 23 2011 - 17:41:33 PDT)
[AMBER] ff10
- Jorgen Simonsen (Sun Mar 27 2011 - 01:47:53 PDT)
- Jason Swails (Sun Mar 27 2011 - 01:45:06 PDT)
- Jorgen Simonsen (Sun Mar 27 2011 - 01:40:55 PDT)
- Jason Swails (Sun Mar 27 2011 - 01:32:19 PDT)
- Jorgen Simonsen (Sun Mar 27 2011 - 00:30:28 PDT)
- case (Sat Mar 26 2011 - 14:26:17 PDT)
- Jorgen Simonsen (Sat Mar 26 2011 - 11:39:44 PDT)
[AMBER] Flags of secstruct
- Daniel Roe (Tue Mar 22 2011 - 10:46:46 PDT)
- Alessio Atzori (Tue Mar 22 2011 - 08:14:11 PDT)
[AMBER] Force Field question - DLPOLY to AMBER
- Lorenzo Gontrani (Tue Mar 22 2011 - 10:09:51 PDT)
[AMBER] forefile of acetyl coenzyme A
- asakiayumikio.gmail.com (Mon Mar 07 2011 - 06:30:06 PST)
- Ganesh Kamath (Mon Mar 07 2011 - 06:19:03 PST)
- asakiayumikio.gmail.com (Mon Mar 07 2011 - 06:16:54 PST)
- Ganesh Kamath (Mon Mar 07 2011 - 06:11:37 PST)
- asakiayumikio.gmail.com (Mon Mar 07 2011 - 06:07:27 PST)
[AMBER] free energy calculation with TI
- steinbrt.rci.rutgers.edu (Wed Mar 16 2011 - 02:25:15 PDT)
- steinbrt.rci.rutgers.edu (Wed Mar 16 2011 - 02:21:52 PDT)
- Dian Jiao (Tue Mar 15 2011 - 20:17:44 PDT)
- Dian Jiao (Tue Mar 15 2011 - 15:12:19 PDT)
- steinbrt.rci.rutgers.edu (Tue Mar 15 2011 - 14:31:38 PDT)
- Dian Jiao (Tue Mar 15 2011 - 13:55:04 PDT)
[AMBER] free energy profile for water slab
- Martina Roeselova (Fri Mar 11 2011 - 10:24:04 PST)
[AMBER] Fwd: Implicit solvent GB calculation
- Rubben Torella (Mon Mar 07 2011 - 08:03:16 PST)
- Daniel Roe (Mon Mar 07 2011 - 07:42:19 PST)
- Daniel Roe (Mon Mar 07 2011 - 07:40:34 PST)
- Rubben Torella (Mon Mar 07 2011 - 07:17:59 PST)
- Carlos Simmerling (Mon Mar 07 2011 - 07:10:41 PST)
- Rubben Torella (Mon Mar 07 2011 - 07:04:35 PST)
[AMBER] GB parameters for Octane
- Eliac Brown (Sat Mar 12 2011 - 10:10:49 PST)
[AMBER] GBSA calculations using mm_pbsa.pl
- manikanthan bhavaraju (Sat Mar 26 2011 - 17:59:38 PDT)
[AMBER] generalized Born question
- Francesco Oteri (Tue Mar 01 2011 - 10:21:00 PST)
[AMBER] Generating an average structure from a rst/pdb list?
- Baptiste Legrand (Fri Mar 04 2011 - 02:06:25 PST)
- Baptiste Legrand (Thu Mar 03 2011 - 13:02:04 PST)
- Daniel Roe (Thu Mar 03 2011 - 10:54:31 PST)
- Baptiste Legrand (Thu Mar 03 2011 - 09:21:14 PST)
[AMBER] grid action command in ptraj
- mish (Wed Mar 09 2011 - 04:41:06 PST)
[AMBER] h-bond donor acceptor definition confusion
- case (Mon Mar 07 2011 - 06:13:48 PST)
- Jio M (Mon Mar 07 2011 - 06:06:51 PST)
[AMBER] Help: Clustering trajectories based on dihedral angle?
- Rajeswari A. (Mon Mar 28 2011 - 05:40:37 PDT)
- Daniel Roe (Fri Mar 25 2011 - 18:43:59 PDT)
- Thomas Cheatham III (Fri Mar 25 2011 - 15:35:25 PDT)
- Rajeswari A. (Fri Mar 25 2011 - 01:38:00 PDT)
[AMBER] HEME parameters
- Scott Brozell (Thu Mar 03 2011 - 19:10:11 PST)
- CHAMI F. (Wed Mar 02 2011 - 03:53:54 PST)
[AMBER] how critical charge neutralization of a system
- Jason Swails (Fri Mar 25 2011 - 15:39:52 PDT)
- Mahmoud Soliman (Fri Mar 25 2011 - 14:02:35 PDT)
[AMBER] How do I plot the angle population distribution
- Jason Swails (Thu Mar 24 2011 - 08:31:21 PDT)
- Bingwu Yu (Thu Mar 24 2011 - 06:42:36 PDT)
[AMBER] How to analysis radius of gyration?
- Carlos Simmerling (Thu Mar 24 2011 - 07:56:14 PDT)
- Catein Catherine (Thu Mar 24 2011 - 07:50:34 PDT)
[AMBER] how to calculate scattering trajectory
- Adrian Roitberg (Mon Mar 21 2011 - 08:16:50 PDT)
- Wen Xu (Mon Mar 21 2011 - 08:11:41 PDT)
- Adrian Roitberg (Sun Mar 20 2011 - 14:09:47 PDT)
- Bill Ross (Sun Mar 20 2011 - 14:06:52 PDT)
- Wen Xu (Sun Mar 20 2011 - 12:51:01 PDT)
[AMBER] how to calculate the B-factor of crystal pdb
- asakiayumikio.gmail.com (Mon Mar 14 2011 - 07:59:10 PDT)
- Carlos Simmerling (Mon Mar 14 2011 - 04:23:49 PDT)
- asakiayumikio.gmail.com (Sun Mar 13 2011 - 23:58:43 PDT)
[AMBER] How to calculate water density around the certain residue or ligand
- mish (Tue Mar 15 2011 - 07:47:54 PDT)
[AMBER] how to choose the biasing potential based on the coarse free energy curve
- Daniel Sindhikara (Mon Mar 14 2011 - 23:03:15 PDT)
- Ye MEI (Mon Mar 14 2011 - 21:21:12 PDT)
[AMBER] how to choose the biasing potential based on the coarsefree energy curve
- Daniel Sindhikara (Tue Mar 15 2011 - 07:48:55 PDT)
- Carlos Simmerling (Tue Mar 15 2011 - 07:24:17 PDT)
- Ye MEI (Tue Mar 15 2011 - 06:41:53 PDT)
[AMBER] how to choose the biasing potential based on thecoarsefree energy curve
- Ye MEI (Tue Mar 15 2011 - 20:28:05 PDT)
[AMBER] how to create periodic box similar to TIP3PBOX?
- Junjian Miao (Thu Mar 03 2011 - 17:32:35 PST)
[AMBER] how to deal with flexibility of peptide during prod. process
- asakiayumikio.gmail.com (Mon Mar 07 2011 - 06:28:24 PST)
- Carlos Simmerling (Mon Mar 07 2011 - 06:18:39 PST)
- asakiayumikio.gmail.com (Mon Mar 07 2011 - 05:57:37 PST)
[AMBER] How to defining a bond between the Cβ of the substrate and the Cα of the catalytic serine
- py (Tue Mar 01 2011 - 06:28:17 PST)
- Jason Swails (Tue Mar 01 2011 - 05:41:15 PST)
[AMBER] How to get the free energy landscape from a MD simulation?
- Mahmoud Soliman (Thu Mar 24 2011 - 12:08:30 PDT)
- Ilyas Yildirim (Thu Mar 24 2011 - 11:33:28 PDT)
- Mahmoud Soliman (Thu Mar 24 2011 - 10:50:19 PDT)
- Ilyas Yildirim (Thu Mar 24 2011 - 09:25:00 PDT)
- Mahmoud Soliman (Thu Mar 24 2011 - 09:06:25 PDT)
- David A Case (Thu Mar 24 2011 - 08:44:16 PDT)
- steinbrt.rci.rutgers.edu (Thu Mar 24 2011 - 08:27:48 PDT)
- Adrian Roitberg (Thu Mar 24 2011 - 08:23:24 PDT)
- Mahmoud Soliman (Thu Mar 24 2011 - 08:23:10 PDT)
- steinbrt.rci.rutgers.edu (Thu Mar 24 2011 - 08:04:03 PDT)
- Catein Catherine (Thu Mar 24 2011 - 07:55:19 PDT)
[AMBER] how to minimize a protein-ligand system with the protein constrained
- Jason Swails (Wed Mar 23 2011 - 17:40:46 PDT)
- Haldoupis I. (Wed Mar 23 2011 - 14:28:41 PDT)
- Per Jr. Greisen (Wed Mar 23 2011 - 13:14:44 PDT)
- I.Haldoupis (Wed Mar 23 2011 - 13:09:13 PDT)
[AMBER] how to obtain 4x4x1.1nm water; how to add polarizable models
- David A Case (Mon Mar 14 2011 - 08:16:30 PDT)
- gromacs (Mon Mar 14 2011 - 05:44:42 PDT)
[AMBER] how to print out frames from conflib and lmod_traj arrays in NAB
- Sidney Elmer (Tue Mar 22 2011 - 18:10:43 PDT)
[AMBER] how to run amber on mutli-gpu/muti-nodes
- Jason Swails (Tue Mar 15 2011 - 17:23:29 PDT)
- Haipeng Wei (Tue Mar 15 2011 - 17:04:52 PDT)
- Ross Walker (Tue Mar 15 2011 - 15:13:44 PDT)
- Haipeng Wei (Tue Mar 15 2011 - 15:08:40 PDT)
[AMBER] how to run PIMD
- Sangita Kachhap (Fri Mar 11 2011 - 11:15:35 PST)
- David A Case (Fri Mar 11 2011 - 10:31:03 PST)
- Sangita Kachhap (Fri Mar 11 2011 - 09:29:20 PST)
[AMBER] How to save a restart file
- Jason Swails (Fri Mar 11 2011 - 12:13:04 PST)
- Bill Ross (Fri Mar 11 2011 - 10:52:24 PST)
- Jason Swails (Fri Mar 11 2011 - 09:52:29 PST)
- david condon (Fri Mar 11 2011 - 09:14:43 PST)
- Rahul Banerjee (Fri Mar 11 2011 - 09:04:58 PST)
- david condon (Fri Mar 11 2011 - 08:56:14 PST)
- Rahul Banerjee (Fri Mar 11 2011 - 08:51:50 PST)
[AMBER] How to use perl to replace number to txt?
- M. L. Dodson (Thu Mar 31 2011 - 07:31:36 PDT)
- Chris Chris (Thu Mar 31 2011 - 05:17:14 PDT)
- Hannes Loeffler (Thu Mar 31 2011 - 03:19:11 PDT)
- Catein Catherine (Thu Mar 31 2011 - 02:48:48 PDT)
[AMBER] hydrogen bonding facility in ptraj
- Beale, John (Fri Mar 04 2011 - 05:38:11 PST)
[AMBER] igb=1 and gbsa=0
- David A Case (Tue Mar 08 2011 - 05:00:11 PST)
- Francesco Oteri (Mon Mar 07 2011 - 15:38:43 PST)
[AMBER] Implicit simulation
- Elisa Frezza (Wed Mar 30 2011 - 10:17:12 PDT)
- Jason Swails (Wed Mar 30 2011 - 10:13:40 PDT)
- Elisa Frezza (Wed Mar 30 2011 - 10:03:30 PDT)
[AMBER] implicit solvent with cuda
- Ross Walker (Thu Mar 03 2011 - 06:21:56 PST)
- Francesco Oteri (Thu Mar 03 2011 - 04:44:07 PST)
[AMBER] Important Notice Re Sleap (especially with Glycam)
- Lachele Foley (Lists) (Mon Mar 14 2011 - 07:27:12 PDT)
[AMBER] Inconsistencies between reported lines and executed lines in source code
- Albert Lee (Thu Mar 31 2011 - 12:39:13 PDT)
- Jason Swails (Thu Mar 31 2011 - 12:22:01 PDT)
- Albert Lee (Thu Mar 31 2011 - 11:56:06 PDT)
- Adrian Roitberg (Thu Mar 31 2011 - 11:33:19 PDT)
- Albert Lee (Thu Mar 31 2011 - 11:12:23 PDT)
[AMBER] interaction energy
- Aust, Susanne (Mon Mar 14 2011 - 06:32:01 PDT)
- Jason Swails (Thu Mar 10 2011 - 07:24:40 PST)
- steinbrt.rci.rutgers.edu (Thu Mar 10 2011 - 03:42:48 PST)
- Bill Miller III (Thu Mar 10 2011 - 03:38:51 PST)
- Aust, Susanne (Thu Mar 10 2011 - 03:24:16 PST)
- steinbrt.rci.rutgers.edu (Thu Mar 10 2011 - 01:39:43 PST)
- Aust, Susanne (Thu Mar 10 2011 - 00:34:28 PST)
[AMBER] irest
- Cenk \(Jenk\) Andac (Wed Mar 09 2011 - 07:07:05 PST)
- Burcu Aykac Fas (Wed Mar 09 2011 - 06:38:38 PST)
[AMBER] is it possible to identify each mode in Nmode calculation?
- Bill Miller III (Mon Mar 07 2011 - 04:54:57 PST)
- zhihong ke (Fri Mar 04 2011 - 12:44:28 PST)
[AMBER] Is rst file the last frame of output crd file?
- Bingwu Yu (Fri Mar 18 2011 - 11:24:40 PDT)
- Gustavo Seabra (Fri Mar 18 2011 - 11:20:01 PDT)
- Bingwu Yu (Fri Mar 18 2011 - 11:10:14 PDT)
- Jason Swails (Fri Mar 18 2011 - 10:36:07 PDT)
- Mark Williamson (Fri Mar 18 2011 - 10:21:15 PDT)
- Bingwu Yu (Fri Mar 18 2011 - 10:07:04 PDT)
[AMBER] Is the neutralization necessary for the GB model?
- zhihong ke (Mon Mar 07 2011 - 13:51:00 PST)
- Jason Swails (Mon Mar 07 2011 - 13:42:07 PST)
- zhihong ke (Mon Mar 07 2011 - 13:24:19 PST)
[AMBER] Keep getting LINMIN error. Not sure how to progress.
- I.Haldoupis (Tue Mar 29 2011 - 03:15:15 PDT)
- Bill Ross (Mon Mar 28 2011 - 11:39:39 PDT)
- Jason Swails (Mon Mar 28 2011 - 08:32:14 PDT)
- Hugh Heldenbrand (Mon Mar 28 2011 - 05:40:50 PDT)
- Carlos Simmerling (Mon Mar 28 2011 - 05:39:07 PDT)
- I.Haldoupis (Mon Mar 28 2011 - 05:27:00 PDT)
[AMBER] Loading .mol2 file in sleap
- Ben Roberts (Wed Mar 30 2011 - 20:16:59 PDT)
- case (Wed Mar 30 2011 - 18:52:36 PDT)
- Ben Roberts (Wed Mar 30 2011 - 13:19:21 PDT)
- r smith (Wed Mar 30 2011 - 12:30:46 PDT)
- Ben Roberts (Wed Mar 30 2011 - 12:16:20 PDT)
- r smith (Wed Mar 30 2011 - 09:19:21 PDT)
- r smith (Wed Mar 30 2011 - 09:08:07 PDT)
- Ben Roberts (Wed Mar 30 2011 - 07:43:00 PDT)
- r smith (Wed Mar 30 2011 - 06:12:15 PDT)
[AMBER] MD simulation of protein with Calcium ion
- Dmitry Nilov (Wed Mar 02 2011 - 03:02:46 PST)
[AMBER] MD- the enzyme bouncing
- Gustavo Seabra (Mon Mar 14 2011 - 17:19:47 PDT)
- Jason Swails (Mon Mar 14 2011 - 15:07:40 PDT)
- Mahmoud Soliman (Mon Mar 14 2011 - 13:44:41 PDT)
- Mahmoud Soliman (Mon Mar 14 2011 - 13:44:11 PDT)
[AMBER] missing AMBER features for simulating surfaces and linear assemblies
- Andrew Jewett (Wed Mar 09 2011 - 13:08:31 PST)
- Andrew Jewett (Wed Mar 09 2011 - 13:00:22 PST)
- David A Case (Wed Mar 09 2011 - 08:54:27 PST)
- Andrew Jewett (Mon Mar 07 2011 - 02:18:31 PST)
[AMBER] Missing Parameters
- case (Sat Mar 19 2011 - 07:14:43 PDT)
- Ilyas Yildirim (Fri Mar 18 2011 - 22:39:11 PDT)
- Ilyas Yildirim (Fri Mar 18 2011 - 21:31:00 PDT)
- Melanie (Fri Mar 18 2011 - 21:05:47 PDT)
- Marek Maly (Thu Mar 17 2011 - 13:05:02 PDT)
- Ilyas Yildirim (Thu Mar 17 2011 - 12:59:00 PDT)
- Melanie (Thu Mar 17 2011 - 12:27:35 PDT)
- Ilyas Yildirim (Tue Mar 15 2011 - 11:18:49 PDT)
- Melanie (Tue Mar 15 2011 - 10:29:32 PDT)
[AMBER] MM-PBSA Error
- N.R. Jena (Mon Mar 21 2011 - 04:38:59 PDT)
- Bill Miller III (Mon Mar 21 2011 - 04:30:33 PDT)
- N.R. Jena (Mon Mar 21 2011 - 04:25:31 PDT)
[AMBER] MM/PBSA (Problem in snapshot generation)
- Dwight McGee (Mon Mar 21 2011 - 12:14:00 PDT)
- mish (Mon Mar 21 2011 - 11:06:34 PDT)
- Dwight McGee (Mon Mar 21 2011 - 10:43:56 PDT)
- mish (Mon Mar 21 2011 - 10:00:37 PDT)
[AMBER] mm_pbsa input for energy decomposition
- Lihua Wang (Mon Mar 14 2011 - 16:23:06 PDT)
[AMBER] MMPBSA energy contribution
- Jason Swails (Thu Mar 17 2011 - 08:40:34 PDT)
- John S (Thu Mar 17 2011 - 08:05:12 PDT)
[AMBER] MMPBSA question
- Jason Swails (Sat Mar 19 2011 - 19:11:16 PDT)
- Eliac Brown (Sat Mar 19 2011 - 17:57:52 PDT)
- Jason Swails (Sat Mar 19 2011 - 17:31:02 PDT)
- Eliac Brown (Sat Mar 19 2011 - 16:35:42 PDT)
[AMBER] mmpbsa.pl energy decompistion stopped
- Eliac Brown (Mon Mar 21 2011 - 19:37:26 PDT)
- Jason Swails (Mon Mar 21 2011 - 18:24:01 PDT)
- Eliac Brown (Mon Mar 21 2011 - 16:41:36 PDT)
[AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1.
- hari krishna (Mon Mar 07 2011 - 20:14:43 PST)
- Jason Swails (Mon Mar 07 2011 - 09:07:43 PST)
- Bill Miller III (Mon Mar 07 2011 - 05:41:02 PST)
- hari krishna (Mon Mar 07 2011 - 05:33:14 PST)
- Bill Miller III (Mon Mar 07 2011 - 04:57:26 PST)
- hari krishna (Thu Mar 03 2011 - 08:47:54 PST)
- Jason Swails (Thu Mar 03 2011 - 04:26:35 PST)
- hari krishna (Thu Mar 03 2011 - 03:07:36 PST)
[AMBER] Nab PB focusing error
- Ray Luo, Ph.D. (Wed Mar 09 2011 - 12:23:12 PST)
- Bill Miller III (Wed Mar 09 2011 - 12:07:22 PST)
[AMBER] NCSU
- David Cantu (Tue Mar 15 2011 - 20:44:00 PDT)
[AMBER] Neutral Lysine (LYN) not calculated in MM_PBSA
- Jason Swails (Tue Mar 29 2011 - 08:16:53 PDT)
- Rubben Torella (Tue Mar 29 2011 - 03:50:57 PDT)
- Jason Swails (Fri Mar 25 2011 - 14:01:19 PDT)
- Rubben Torella (Fri Mar 25 2011 - 10:34:17 PDT)
[AMBER] new residue with amoeba
- Daniel Chipman (Wed Mar 30 2011 - 12:54:11 PDT)
[AMBER] Nitu Bansal wants to chat
- Nitu Bansal (Fri Mar 11 2011 - 09:17:44 PST)
[AMBER] nmode calculations
- Bill Miller III (Fri Mar 25 2011 - 12:00:42 PDT)
- amit dong (Fri Mar 25 2011 - 11:39:40 PDT)
- Bill Miller III (Fri Mar 25 2011 - 11:23:33 PDT)
- amit dong (Fri Mar 25 2011 - 11:12:24 PDT)
[AMBER] Nmode error of MMPBSA.py
- Dwight McGee (Wed Mar 23 2011 - 06:17:03 PDT)
- 陳昭同 (Wed Mar 23 2011 - 02:30:36 PDT)
[AMBER] nmode memory issue
- Dima A Sabbah (Mon Mar 21 2011 - 10:50:34 PDT)
- Sushil Mishra (Mon Mar 21 2011 - 10:14:52 PDT)
- amit dong (Mon Mar 21 2011 - 10:01:05 PDT)
[AMBER] nmropt modes for GPU accelerated pmemd 11
- Andre Serobian (Wed Mar 30 2011 - 13:09:43 PDT)
- Jason Swails (Wed Mar 30 2011 - 12:59:03 PDT)
- Andre Serobian (Wed Mar 30 2011 - 12:43:10 PDT)
- Ross Walker (Wed Mar 30 2011 - 11:27:10 PDT)
- Andre Serobian (Wed Mar 30 2011 - 00:24:04 PDT)
[AMBER] no answer so far - free energy profile for water slab
- Jojart_Balazs (Wed Mar 16 2011 - 07:38:35 PDT)
- Martina Roeselova (Tue Mar 15 2011 - 07:57:16 PDT)
- Carlos Simmerling (Tue Mar 15 2011 - 04:02:44 PDT)
- Martina Roeselova (Tue Mar 15 2011 - 02:20:09 PDT)
[AMBER] non standard Alanine
- Anselm Horn (Fri Mar 04 2011 - 07:55:01 PST)
- FyD (Fri Mar 04 2011 - 07:50:50 PST)
- Massimiliano Porrini (Fri Mar 04 2011 - 06:41:59 PST)
[AMBER] NPT simulation crash using a GPU CARD for a simulation carried out in a organic explicit solvent
- Antje Wolf (Tue Mar 01 2011 - 23:44:39 PST)
[AMBER] number of frames read in mmpbsa.py
- Jason Swails (Wed Mar 23 2011 - 11:55:04 PDT)
- Dwight McGee (Wed Mar 23 2011 - 10:29:09 PDT)
- Bill Miller III (Wed Mar 23 2011 - 09:59:00 PDT)
- Bill Miller III (Wed Mar 23 2011 - 09:52:44 PDT)
- Chris Chris (Wed Mar 23 2011 - 09:44:41 PDT)
[AMBER] NVT Vs NPT
- Marek Maly (Thu Mar 17 2011 - 10:03:08 PDT)
- Ross Walker (Thu Mar 17 2011 - 09:31:23 PDT)
- Marek Maly (Thu Mar 17 2011 - 09:10:17 PDT)
- Jason Swails (Thu Mar 17 2011 - 08:49:57 PDT)
- Marek Maly (Thu Mar 17 2011 - 06:25:27 PDT)
- Mahmoud Soliman (Wed Mar 16 2011 - 12:36:43 PDT)
- Jason Swails (Wed Mar 16 2011 - 09:49:39 PDT)
- Mahmoud Soliman (Wed Mar 16 2011 - 00:31:07 PDT)
[AMBER] NVT Vs NPT MD simulations
- Mahmoud Soliman (Wed Mar 16 2011 - 08:00:46 PDT)
[AMBER] odd output from rms measurement
- Jason Swails (Thu Mar 24 2011 - 08:41:54 PDT)
- Sangita Kachhap (Thu Mar 24 2011 - 02:54:29 PDT)
- 姜笑楠 (Thu Mar 24 2011 - 00:31:34 PDT)
- Daniel Roe (Thu Mar 24 2011 - 00:02:13 PDT)
- Jason Swails (Wed Mar 23 2011 - 18:43:12 PDT)
- Chris Chris (Wed Mar 23 2011 - 18:33:52 PDT)
- Jason Swails (Wed Mar 23 2011 - 17:35:00 PDT)
- Carlos Simmerling (Wed Mar 23 2011 - 17:24:58 PDT)
- Chris Chris (Wed Mar 23 2011 - 16:50:11 PDT)
- Carlos Simmerling (Wed Mar 23 2011 - 15:15:58 PDT)
- Chris Chris (Wed Mar 23 2011 - 14:55:44 PDT)
[AMBER] ODP: Segmentation fault
- MASLYK, MACIEJ MARCIN (Tue Mar 22 2011 - 04:10:55 PDT)
[AMBER] Parallel amber11 Installation FAIL
- David Cantu (Mon Mar 21 2011 - 19:07:21 PDT)
- Jason Swails (Mon Mar 21 2011 - 18:13:12 PDT)
- David Cantu (Mon Mar 21 2011 - 16:49:23 PDT)
[AMBER] parameter for CNTs
- Jason Swails (Thu Mar 31 2011 - 16:54:03 PDT)
- Jagur Lambix (Thu Mar 31 2011 - 16:02:14 PDT)
[AMBER] parameters for metal site
- FyD (Thu Mar 17 2011 - 11:30:37 PDT)
- Jorgen Simonsen (Thu Mar 17 2011 - 07:39:14 PDT)
- FyD (Thu Mar 17 2011 - 07:03:21 PDT)
- Jorgen Simonsen (Thu Mar 17 2011 - 02:24:16 PDT)
[AMBER] Partial Charges for Atom Types
- Bill Ross (Wed Mar 09 2011 - 09:51:45 PST)
- David A Case (Wed Mar 09 2011 - 08:44:52 PST)
- Per Jr. Greisen (Wed Mar 09 2011 - 08:42:07 PST)
- Naveen Samala (Wed Mar 09 2011 - 08:17:37 PST)
[AMBER] PB Bomb in pb_aaradi ?
- Ray Luo, Ph.D. (Thu Mar 17 2011 - 10:33:54 PDT)
- Marek Maly (Thu Mar 17 2011 - 03:43:28 PDT)
- Ray Luo, Ph.D. (Tue Mar 15 2011 - 21:43:46 PDT)
- Marek Maly (Tue Mar 15 2011 - 20:49:14 PDT)
- Marek Maly (Tue Mar 15 2011 - 18:45:06 PDT)
[AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE
- steinbrt.rci.rutgers.edu (Thu Mar 10 2011 - 00:03:05 PST)
- hari krishna (Wed Mar 09 2011 - 20:20:11 PST)
- David A Case (Wed Mar 09 2011 - 07:35:32 PST)
- hari krishna (Wed Mar 09 2011 - 06:28:55 PST)
[AMBER] Perl Vs Python in MMPBSA calculations in Amber 10
- Mahmoud Soliman (Wed Mar 23 2011 - 07:23:49 PDT)
- Bill Miller III (Wed Mar 23 2011 - 06:53:43 PDT)
- Mahmoud Soliman (Wed Mar 23 2011 - 06:52:04 PDT)
[AMBER] pmemd and generalized NMR torsional restraints in AMBER10
- Ilyas Yildirim (Wed Mar 23 2011 - 17:24:11 PDT)
- Jason Swails (Wed Mar 23 2011 - 17:18:52 PDT)
- Jason Swails (Wed Mar 23 2011 - 17:08:15 PDT)
- Ilyas Yildirim (Wed Mar 23 2011 - 17:16:04 PDT)
- Ilyas Yildirim (Wed Mar 23 2011 - 17:14:03 PDT)
- Jason Swails (Wed Mar 23 2011 - 17:10:28 PDT)
- Ilyas Yildirim (Wed Mar 23 2011 - 16:48:27 PDT)
[AMBER] pmemd and nmr restraint
- marc gueroult (Thu Mar 31 2011 - 08:56:16 PDT)
- David A Case (Fri Mar 25 2011 - 12:18:16 PDT)
- marc gueroult (Fri Mar 25 2011 - 10:53:21 PDT)
[AMBER] PMEMD on the Open Science Grid
- Steven Cox (Thu Mar 31 2011 - 07:19:42 PDT)
[AMBER] pmemd.cuda issues on Tesla S2050
- Sasha Buzko (Wed Mar 02 2011 - 09:54:08 PST)
[AMBER] PMF calculations in Amber 10
- Dmitry Nilov (Wed Mar 23 2011 - 22:11:02 PDT)
- Jason Swails (Wed Mar 23 2011 - 16:32:03 PDT)
- Mahmoud Soliman (Wed Mar 23 2011 - 16:17:28 PDT)
[AMBER] positional restraint on crystal water
- g t (Wed Mar 30 2011 - 09:35:18 PDT)
- Sangita Kachhap (Wed Mar 30 2011 - 03:14:44 PDT)
- Dmitry Nilov (Wed Mar 30 2011 - 02:56:27 PDT)
- Sangita Kachhap (Wed Mar 30 2011 - 02:40:00 PDT)
- Sangita Kachhap (Wed Mar 30 2011 - 02:31:53 PDT)
- Dmitry Nilov (Wed Mar 30 2011 - 02:18:17 PDT)
- Dmitry Nilov (Wed Mar 30 2011 - 02:03:18 PDT)
- Sangita Kachhap (Wed Mar 30 2011 - 01:45:42 PDT)
- Dmitry Nilov (Wed Mar 30 2011 - 01:26:37 PDT)
- Sangita Kachhap (Wed Mar 30 2011 - 00:30:16 PDT)
[AMBER] positive GBtot value
- Jason Swails (Thu Mar 24 2011 - 18:33:23 PDT)
- Hoshin Kim (Thu Mar 24 2011 - 18:02:30 PDT)
[AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file
- Hopkins, Robert (Mon Mar 28 2011 - 12:16:33 PDT)
[AMBER] Pressure regulation and position restraints
- Andrew Jewett (Thu Mar 10 2011 - 18:51:55 PST)
- David A Case (Wed Mar 09 2011 - 08:57:49 PST)
- Andrew Jewett (Mon Mar 07 2011 - 04:33:36 PST)
[AMBER] Problem installing Amber11/Ambertools1.4 on Ubuntu10.10
- Ben Roberts (Tue Mar 08 2011 - 10:09:15 PST)
- John Khan (Tue Mar 08 2011 - 10:01:59 PST)
[AMBER] problem with gas-phase MD simulation in Amber8.
- marta wiśniewska. (Fri Mar 18 2011 - 12:20:17 PDT)
- Jason Swails (Fri Mar 18 2011 - 12:12:54 PDT)
- marta wiśniewska. (Fri Mar 18 2011 - 12:08:36 PDT)
- Ross Walker (Fri Mar 18 2011 - 10:54:00 PDT)
- marta wiśniewska. (Fri Mar 18 2011 - 10:13:03 PDT)
- steinbrt.rci.rutgers.edu (Fri Mar 18 2011 - 05:22:50 PDT)
- Mengjuei Hsieh (Fri Mar 18 2011 - 05:19:49 PDT)
- marta wiśniewska. (Fri Mar 18 2011 - 04:37:09 PDT)
[AMBER] Problem with link atom in QM/MM
- Wook Lee (Thu Mar 17 2011 - 06:29:45 PDT)
- Wook Lee (Thu Mar 17 2011 - 01:39:47 PDT)
- Ross Walker (Wed Mar 16 2011 - 09:39:41 PDT)
- Wook Lee (Wed Mar 16 2011 - 08:01:31 PDT)
[AMBER] problem with peptide simulations
- Jason Swails (Mon Mar 28 2011 - 13:27:15 PDT)
- David A Case (Mon Mar 28 2011 - 13:04:33 PDT)
- Hashem Taha (Mon Mar 28 2011 - 13:00:58 PDT)
- Jason Swails (Mon Mar 28 2011 - 12:29:07 PDT)
- Hashem Taha (Mon Mar 28 2011 - 12:05:55 PDT)
[AMBER] probleme with "reference" using ptraj
- Muriel Jourdan (Mon Mar 21 2011 - 08:48:59 PDT)
- Rahul Banerjee (Mon Mar 21 2011 - 07:30:27 PDT)
- Muriel Jourdan (Mon Mar 21 2011 - 07:28:09 PDT)
[AMBER] Problems with tleap
- Pegado Luis (Tue Mar 08 2011 - 02:04:34 PST)
- case (Mon Mar 07 2011 - 10:56:58 PST)
- Pegado Luis (Mon Mar 07 2011 - 10:42:55 PST)
[AMBER] protein charge
- Astrid Maaß (Mon Mar 21 2011 - 07:23:04 PDT)
- Ouaray Z. (Mon Mar 21 2011 - 06:52:23 PDT)
[AMBER] ptraj / water-mediated hydrogen bonds
- leila karami (Thu Mar 03 2011 - 05:11:39 PST)
[AMBER] ptraj / water-medited hydrogen bonds
- leila karami (Thu Mar 03 2011 - 04:26:41 PST)
[AMBER] Ptraj analyze crankshaft
- Mariano Rech (Thu Mar 10 2011 - 08:12:25 PST)
[AMBER] Ptraj crashes and Hbond analysis
- Kamali Sripathi (Thu Mar 24 2011 - 06:36:28 PDT)
- Kamali Sripathi (Wed Mar 23 2011 - 11:44:45 PDT)
- Kamali Sripathi (Wed Mar 23 2011 - 11:16:15 PDT)
- Daniel Roe (Wed Mar 23 2011 - 06:45:14 PDT)
- Kamali Sripathi (Wed Mar 23 2011 - 06:01:05 PDT)
- Thomas Cheatham III (Tue Mar 22 2011 - 16:33:37 PDT)
- Kamali Sripathi (Tue Mar 22 2011 - 09:43:37 PDT)
[AMBER] ptraj minimum rmsd in presence of homotopic atoms
- Alexander Metz (Tue Mar 29 2011 - 02:21:21 PDT)
[AMBER] ptraj problems
- Jason Swails (Thu Mar 24 2011 - 08:35:14 PDT)
- Christoph Malisi (Thu Mar 24 2011 - 07:05:42 PDT)
[AMBER] ptraj: box information for truncated octahedron
- thomas.fox.boehringer-ingelheim.com (Thu Mar 24 2011 - 11:25:24 PDT)
- Ignacio J. General (Thu Mar 24 2011 - 10:24:08 PDT)
- thomas.fox.boehringer-ingelheim.com (Thu Mar 24 2011 - 10:10:35 PDT)
[AMBER] Ptraj: Hbond and Bfactor analyses
- Kamali Sripathi (Thu Mar 17 2011 - 18:49:21 PDT)
[AMBER] QM/MM error in amber 10
- Mahmoud Soliman (Sun Mar 27 2011 - 22:46:47 PDT)
- Jason Swails (Fri Mar 25 2011 - 15:32:25 PDT)
- Yuan Yao (Fri Mar 25 2011 - 15:20:04 PDT)
- Yuan Yao (Fri Mar 25 2011 - 15:16:29 PDT)
- Mahmoud Soliman (Fri Mar 25 2011 - 15:21:16 PDT)
[AMBER] Query regarding mmpbsa output file
- Bill Miller III (Sat Mar 12 2011 - 04:26:48 PST)
- Hirdesh Kumar (Fri Mar 11 2011 - 21:58:04 PST)
- Bill Miller III (Fri Mar 11 2011 - 06:44:32 PST)
- Hirdesh Kumar (Fri Mar 11 2011 - 06:24:33 PST)
[AMBER] Query regarding mmpbsa run
- Hirdesh Kumar (Mon Mar 14 2011 - 03:59:38 PDT)
[AMBER] question about the distance of pronton transfer and acetylation
- Dmitry Nilov (Wed Mar 09 2011 - 02:06:46 PST)
- asakiayumikio.gmail.com (Tue Mar 08 2011 - 18:19:42 PST)
[AMBER] questions about the input file of MD process
- Francesco Oteri (Sun Mar 13 2011 - 08:09:23 PDT)
- asakiayumikio.gmail.com (Sun Mar 13 2011 - 08:07:19 PDT)
- asakiayumikio.gmail.com (Sun Mar 13 2011 - 08:04:28 PDT)
- Francesco Oteri (Sun Mar 13 2011 - 07:41:04 PDT)
- Carlos Simmerling (Sun Mar 13 2011 - 07:38:53 PDT)
- asakiayumikio.gmail.com (Sun Mar 13 2011 - 07:34:15 PDT)
- Francesco Oteri (Sun Mar 13 2011 - 07:27:39 PDT)
- asakiayumikio.gmail.com (Sun Mar 13 2011 - 00:45:44 PST)
[AMBER] R: Exchange Acceptance Ratio
- Carlos Simmerling (Wed Mar 30 2011 - 06:44:25 PDT)
- Alessio Atzori (Wed Mar 30 2011 - 06:21:48 PDT)
[AMBER] R: Flags of secstruct
- Alessio Atzori (Thu Mar 24 2011 - 17:21:59 PDT)
[AMBER] randomly place counterions
- Bill Ross (Wed Mar 02 2011 - 12:02:27 PST)
- Kevin Hauser (Wed Mar 02 2011 - 08:52:10 PST)
- thomas.fox.boehringer-ingelheim.com (Wed Mar 02 2011 - 08:25:48 PST)
- thomas.fox.boehringer-ingelheim.com (Wed Mar 02 2011 - 08:07:02 PST)
- Hugh Heldenbrand (Wed Mar 02 2011 - 07:16:29 PST)
- Kevin Hauser (Wed Mar 02 2011 - 06:59:18 PST)
- Hugh Heldenbrand (Wed Mar 02 2011 - 04:56:01 PST)
- steinbrt.rci.rutgers.edu (Wed Mar 02 2011 - 04:42:17 PST)
- thomas.fox.boehringer-ingelheim.com (Wed Mar 02 2011 - 02:55:55 PST)
[AMBER] rdf plot
- subrata paul (Fri Mar 11 2011 - 19:54:29 PST)
[AMBER] reference for per-residue decomposition using TI Calculation
- g t (Thu Mar 24 2011 - 09:54:12 PDT)
- g t (Sat Mar 19 2011 - 11:49:00 PDT)
[AMBER] regarding anal function
- dhilip kumar ramalingam (Fri Mar 25 2011 - 04:08:02 PDT)
[AMBER] Regarding: Adding New Multi-atom Residue (Ligand) including partial charges
- FyD (Mon Mar 14 2011 - 23:55:22 PDT)
- Naveen Samala (Mon Mar 14 2011 - 11:30:32 PDT)
[AMBER] regrding the anal working
- dhilip kumar ramalingam (Thu Mar 24 2011 - 22:28:32 PDT)
[AMBER] Reimaging Problem
- chandan patel (Thu Mar 17 2011 - 02:40:02 PDT)
- manikanthan bhavaraju (Wed Mar 16 2011 - 09:34:05 PDT)
- chandan patel (Wed Mar 16 2011 - 03:43:39 PDT)
[AMBER] Request for a quotation of AMBER
- David A Case (Tue Mar 08 2011 - 05:06:22 PST)
- aseal.klyuniv.ac.in (Mon Mar 07 2011 - 23:38:14 PST)
[AMBER] Residuegen Usage
- Seungyeul Yoo (Tue Mar 22 2011 - 15:26:03 PDT)
[AMBER] RESP: optimized charges not reasonable
- FyD (Tue Mar 29 2011 - 04:54:03 PDT)
- Ignacio Faustino Plo (Tue Mar 29 2011 - 03:46:12 PDT)
- FyD (Tue Mar 29 2011 - 01:36:54 PDT)
- Ignacio Faustino Plo (Mon Mar 28 2011 - 09:59:52 PDT)
[AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal!
- case (Tue Mar 01 2011 - 04:47:41 PST)
- Ali M. Naserian-Nik (Tue Mar 01 2011 - 00:42:52 PST)
[AMBER] Restraints on equilibration of solvated complexes
- Dmitry Nilov (Wed Mar 16 2011 - 12:05:22 PDT)
- George Tzotzos (Wed Mar 16 2011 - 10:52:00 PDT)
- Dmitry Nilov (Wed Mar 16 2011 - 08:47:28 PDT)
- George Tzotzos (Wed Mar 16 2011 - 08:25:28 PDT)
- Dmitry Nilov (Wed Mar 16 2011 - 08:10:32 PDT)
- George Tzotzos (Wed Mar 16 2011 - 07:37:17 PDT)
[AMBER] RMSD Calculation
- abc def (Fri Mar 18 2011 - 09:47:41 PDT)
[AMBER] Sander was terminating in the midddle
- Sangita Kachhap (Fri Mar 25 2011 - 07:05:56 PDT)
- vani panguluri (Thu Mar 24 2011 - 23:08:39 PDT)
- Sangita Kachhap (Thu Mar 24 2011 - 11:28:15 PDT)
- vani panguluri (Thu Mar 24 2011 - 11:09:13 PDT)
- vani panguluri (Thu Mar 24 2011 - 11:02:06 PDT)
- Jason Swails (Thu Mar 24 2011 - 10:56:05 PDT)
- Ben Roberts (Thu Mar 24 2011 - 10:54:56 PDT)
- vani panguluri (Thu Mar 24 2011 - 10:47:10 PDT)
[AMBER] sander.MPI running on 8 nodes or 1??
- colvin (Tue Mar 08 2011 - 22:13:57 PST)
- Jason Swails (Tue Mar 08 2011 - 11:27:13 PST)
- colvin (Tue Mar 08 2011 - 01:11:03 PST)
[AMBER] scientific question on decomposition analysis in pbsa calculation
- Mahmoud Soliman (Wed Mar 23 2011 - 08:11:47 PDT)
- Bill Miller III (Wed Mar 23 2011 - 07:37:59 PDT)
- Mahmoud Soliman (Wed Mar 23 2011 - 07:38:56 PDT)
- Ray Luo, Ph.D. (Wed Mar 23 2011 - 07:24:52 PDT)
- Mahmoud Soliman (Wed Mar 23 2011 - 07:20:37 PDT)
[AMBER] script problem
- Mahmoud Soliman (Tue Mar 29 2011 - 14:44:46 PDT)
- Jason Swails (Tue Mar 29 2011 - 14:15:22 PDT)
- Mahmoud Soliman (Tue Mar 29 2011 - 14:16:15 PDT)
[AMBER] Segmentation fault
- Jason Swails (Thu Mar 17 2011 - 09:55:19 PDT)
- Jason Swails (Thu Mar 17 2011 - 09:53:44 PDT)
- MASLYK, MACIEJ MARCIN (Wed Mar 16 2011 - 08:50:36 PDT)
[AMBER] segmentation fault when using mmpbsa.py
- Jason Swails (Wed Mar 30 2011 - 16:23:43 PDT)
- Chris Chris (Wed Mar 30 2011 - 15:03:46 PDT)
[AMBER] Showing torsion energy as a function of angle
- Carlos Simmerling (Sun Mar 06 2011 - 15:23:11 PST)
- david condon (Sun Mar 06 2011 - 14:46:50 PST)
[AMBER] solvatecap
- Lucio Ferella (Fri Mar 25 2011 - 11:07:51 PDT)
[AMBER] solvation free energy
- David A Case (Tue Mar 22 2011 - 11:42:32 PDT)
- Jorgen Simonsen (Tue Mar 22 2011 - 11:08:57 PDT)
[AMBER] Spatial distribution function
- Ganesh Kamath (Fri Mar 25 2011 - 11:19:24 PDT)
[AMBER] Specially For You
- ros (Thu Mar 10 2011 - 05:55:29 PST)
[AMBER] Splitting the interaction energy
- Bill Miller III (Wed Mar 09 2011 - 06:44:06 PST)
- Eliac Brown (Wed Mar 09 2011 - 06:26:58 PST)
[AMBER] stacking energy calculation
- Jiri Sponer (Wed Mar 16 2011 - 04:02:39 PDT)
- hari krishna (Wed Mar 16 2011 - 03:06:36 PDT)
[AMBER] strip command usage in ptraj
- asakiayumikio.gmail.com (Sun Mar 13 2011 - 18:48:41 PDT)
- asakiayumikio.gmail.com (Sun Mar 13 2011 - 09:05:00 PDT)
- Adrian Roitberg (Sun Mar 13 2011 - 08:57:31 PDT)
- asakiayumikio.gmail.com (Sun Mar 13 2011 - 08:47:13 PDT)
- Adrian Roitberg (Sun Mar 13 2011 - 08:41:44 PDT)
- asakiayumikio.gmail.com (Sun Mar 13 2011 - 08:30:26 PDT)
- Adrian Roitberg (Sun Mar 13 2011 - 08:23:26 PDT)
- asakiayumikio.gmail.com (Sun Mar 13 2011 - 08:14:46 PDT)
[AMBER] symmetry corrected RMSD calculation
- Pooja Khurana (Sat Mar 19 2011 - 19:38:21 PDT)
[AMBER] the charge of NPRO in FF03 is equal to 0.9.
- Mengjuei Hsieh (Thu Mar 10 2011 - 11:47:15 PST)
- Ray Luo, Ph.D. (Thu Mar 10 2011 - 10:26:02 PST)
- zhihong ke (Thu Mar 10 2011 - 10:06:29 PST)
- zhihong ke (Thu Mar 10 2011 - 09:48:11 PST)
- Ray Luo, Ph.D. (Thu Mar 10 2011 - 09:48:43 PST)
- David A Case (Thu Mar 10 2011 - 09:43:47 PST)
- Ray Luo, Ph.D. (Thu Mar 10 2011 - 09:16:05 PST)
- zhihong ke (Thu Mar 10 2011 - 09:13:02 PST)
- cieplak.cgl.ucsf.edu (Wed Mar 09 2011 - 23:32:56 PST)
- zhihong ke (Wed Mar 09 2011 - 12:46:40 PST)
[AMBER] the output of REMD simulations
- Carlos Simmerling (Fri Mar 11 2011 - 09:42:42 PST)
- zhihong ke (Fri Mar 11 2011 - 09:39:59 PST)
- Carlos Simmerling (Fri Mar 11 2011 - 09:36:09 PST)
- zhihong ke (Fri Mar 11 2011 - 09:35:00 PST)
[AMBER] The validity of a per-residue decomposition in amber
- David A Case (Thu Mar 31 2011 - 05:53:02 PDT)
- g t (Wed Mar 30 2011 - 08:13:26 PDT)
- Carlos Simmerling (Wed Mar 30 2011 - 06:47:34 PDT)
- g t (Wed Mar 30 2011 - 06:36:33 PDT)
[AMBER] Thermodynamic Integration
- steinbrt.rci.rutgers.edu (Fri Mar 18 2011 - 02:11:50 PDT)
- Ignacio J. General (Thu Mar 17 2011 - 08:22:56 PDT)
- steinbrt.rci.rutgers.edu (Thu Mar 17 2011 - 08:06:03 PDT)
- Ignacio J. General (Thu Mar 17 2011 - 07:09:19 PDT)
- steinbrt.rci.rutgers.edu (Thu Mar 17 2011 - 02:10:20 PDT)
- Ignacio J. General (Wed Mar 16 2011 - 14:22:07 PDT)
[AMBER] Thermostat
- Daniel Sindhikara (Thu Mar 17 2011 - 00:27:17 PDT)
- Jason Swails (Thu Mar 17 2011 - 00:05:01 PDT)
- Diego Javier Alonso de Armiño (Wed Mar 16 2011 - 19:50:05 PDT)
[AMBER] TI minimizations cannot be performed with > 2 CPUs
- case (Sun Mar 20 2011 - 06:26:04 PDT)
- g t (Sat Mar 19 2011 - 11:56:38 PDT)
- Dian Jiao (Fri Mar 18 2011 - 22:43:29 PDT)
[AMBER] tleap strange behavior
- Ignacio J. General (Wed Mar 23 2011 - 08:45:29 PDT)
[AMBER] To fix dihedral angles during a simulation.
- case (Wed Mar 02 2011 - 06:39:37 PST)
- Baptiste Legrand (Wed Mar 02 2011 - 02:08:37 PST)
[AMBER] Tools to calculate free energies landscape from the MD simulation without doing PMF?
- Gustavo Seabra (Fri Mar 25 2011 - 05:33:18 PDT)
- steinbrt.rci.rutgers.edu (Fri Mar 25 2011 - 01:25:37 PDT)
- Catein Catherine (Fri Mar 25 2011 - 01:13:33 PDT)
[AMBER] total charge of NPRO in amber03 force field
- Ray Luo, Ph.D. (Thu Mar 03 2011 - 08:20:59 PST)
- Ye MEI (Thu Mar 03 2011 - 03:00:21 PST)
- Ye MEI (Thu Mar 03 2011 - 02:52:23 PST)
[AMBER] trouble with mmpbsa.py
- Jason Swails (Fri Mar 18 2011 - 10:47:20 PDT)
- Chris Chris (Fri Mar 18 2011 - 10:30:59 PDT)
- Bill Miller III (Fri Mar 18 2011 - 09:50:17 PDT)
- Chris Chris (Fri Mar 18 2011 - 09:44:08 PDT)
[AMBER] Umbrella sampling coordinate question
- Rajesh Raju (Thu Mar 10 2011 - 09:59:19 PST)
- Carlos Simmerling (Thu Mar 10 2011 - 09:47:45 PST)
- Rajesh Raju (Thu Mar 10 2011 - 09:45:22 PST)
- Carlos Simmerling (Thu Mar 10 2011 - 06:45:41 PST)
- Rajesh Raju (Wed Mar 09 2011 - 10:55:38 PST)
- Carlos Simmerling (Wed Mar 09 2011 - 04:04:24 PST)
- Rajesh Raju (Tue Mar 08 2011 - 15:21:36 PST)
[AMBER] Unresolved problem about MM/PBSA
- Ray Luo, Ph.D. (Thu Mar 03 2011 - 19:04:02 PST)
- ÏéÇ« ¿× (Thu Mar 03 2011 - 17:25:17 PST)
- Ray Luo, Ph.D. (Thu Mar 03 2011 - 08:09:06 PST)
- 祥谦孔 (Thu Mar 03 2011 - 08:01:07 PST)
[AMBER] unsubscribe
- Jack Lei (Wed Mar 23 2011 - 22:29:20 PDT)
[AMBER] usage of 2drms
- John S (Thu Mar 24 2011 - 10:12:36 PDT)
[AMBER] Using Intel compilers on AMD CPU
- Ross Walker (Fri Mar 18 2011 - 09:09:43 PDT)
- Bongkeun Kim (Thu Mar 17 2011 - 20:10:48 PDT)
[AMBER] using NMR restraints within LMOD
- Wong, Sergio E. (Wed Mar 09 2011 - 10:52:59 PST)
- case (Mon Mar 07 2011 - 05:06:45 PST)
- Wong, Sergio E. (Fri Mar 04 2011 - 13:45:12 PST)
[AMBER] using thermodynamic integration, how to deal with absolute pka and conformation change
- Junjian Miao (Thu Mar 17 2011 - 20:32:55 PDT)
- David Case (Wed Mar 16 2011 - 06:25:26 PDT)
- Junjian Miao (Wed Mar 16 2011 - 05:58:58 PDT)
[AMBER] water box deforms during MD
- Mahmoud Soliman (Mon Mar 28 2011 - 08:49:06 PDT)
- Dmitry Nilov (Mon Mar 28 2011 - 07:17:22 PDT)
- steinbrt.rci.rutgers.edu (Mon Mar 28 2011 - 07:05:23 PDT)
- Mahmoud Soliman (Mon Mar 28 2011 - 07:02:20 PDT)
[AMBER] water mediated H-Bond
- Sangita Kachhap (Wed Mar 02 2011 - 19:56:52 PST)
- Bill Ross (Wed Mar 02 2011 - 11:45:34 PST)
- Sangita Kachhap (Wed Mar 02 2011 - 01:52:31 PST)
- Hirdesh Kumar (Wed Mar 02 2011 - 01:25:31 PST)
- Sangita Kachhap (Wed Mar 02 2011 - 00:41:36 PST)
- Bill Ross (Tue Mar 01 2011 - 12:02:28 PST)
- Sangita Kachhap (Tue Mar 01 2011 - 10:17:14 PST)
- Bill Ross (Tue Mar 01 2011 - 10:09:20 PST)
- Sangita Kachhap (Tue Mar 01 2011 - 09:37:31 PST)
[AMBER] Will no implementation of feupdateenv cause serious problems?
- kurisaki.ncube.human.nagoya-u.ac.jp (Tue Mar 01 2011 - 22:29:52 PST)
- Ross Walker (Tue Mar 01 2011 - 22:18:00 PST)
- kurisaki.ncube.human.nagoya-u.ac.jp (Tue Mar 01 2011 - 21:55:51 PST)
[AMBER] Would liek to plot GBTOT vs Time
- Jason Swails (Mon Mar 14 2011 - 00:02:28 PDT)
- Daniel Sindhikara (Sun Mar 13 2011 - 23:40:13 PDT)
- Mannan (Sun Mar 13 2011 - 22:59:39 PDT)
[AMBER] xleap not installed
- Ben Roberts (Tue Mar 08 2011 - 09:13:47 PST)
- sonali dhindwal (Tue Mar 08 2011 - 04:00:31 PST)
- sonali dhindwal (Sun Mar 06 2011 - 22:15:04 PST)
- Mengjuei Hsieh (Sat Mar 05 2011 - 07:29:29 PST)
- Jason Swails (Sat Mar 05 2011 - 07:02:28 PST)
- sonali dhindwal (Sat Mar 05 2011 - 04:54:59 PST)
- case (Thu Mar 03 2011 - 04:20:26 PST)
- sonali dhindwal (Thu Mar 03 2011 - 02:19:48 PST)
- Jason Swails (Wed Mar 02 2011 - 22:49:13 PST)
- sonali dhindwal (Wed Mar 02 2011 - 20:26:17 PST)
- sonali dhindwal (Tue Mar 01 2011 - 20:54:11 PST)
- Jason Swails (Tue Mar 01 2011 - 06:36:42 PST)
- sonali dhindwal (Tue Mar 01 2011 - 06:24:57 PST)
- Bill Miller III (Tue Mar 01 2011 - 06:12:09 PST)
- sonali dhindwal (Tue Mar 01 2011 - 05:56:24 PST)
[AMBER] Zn active site parameterization
- Per Jr. Greisen (Mon Mar 07 2011 - 05:12:30 PST)
- kala (Sun Mar 06 2011 - 11:59:04 PST)
[AMBER] Zn Bond Length solvatebox
- Lowe, Ben (Ext) (Fri Mar 04 2011 - 04:58:37 PST)
- case (Fri Mar 04 2011 - 04:40:29 PST)
- Lowe, Ben (Ext) (Fri Mar 04 2011 - 02:25:53 PST)

Amber Archive Mar 2011 by subject