Amber Archive Nov 2010: by subject

[AMBER] "excluded atoms" declaration
- Yokota_Akihiro.takeda.co.jp (Tue Nov 09 2010 - 16:55:58 PST)
- Yokota_Akihiro.takeda.co.jp (Tue Nov 09 2010 - 16:37:44 PST)
- Jason Swails (Tue Nov 09 2010 - 09:11:10 PST)
- Carlos Simmerling (Tue Nov 09 2010 - 04:03:37 PST)
- Yokota_Akihiro.takeda.co.jp (Tue Nov 09 2010 - 01:24:23 PST)
[AMBER] (no subject)
- Nilmeier, Jerome P. (Tue Nov 30 2010 - 14:35:29 PST)
- Jason Swails (Tue Nov 09 2010 - 08:26:41 PST)
- Yokota_Akihiro.takeda.co.jp (Tue Nov 09 2010 - 01:19:08 PST)
- Bill Ross (Sat Nov 06 2010 - 19:15:41 PDT)
- kanon gemini (Sat Nov 06 2010 - 03:09:27 PDT)
[AMBER] about dihedralcluster
- Balazs Jojart (Wed Nov 10 2010 - 11:36:52 PST)
- Daniel Roe (Wed Nov 10 2010 - 09:04:36 PST)
- Balazs Jojart (Wed Nov 10 2010 - 04:56:49 PST)
[AMBER] about MMPBSA
- Dwight McGee (Sun Nov 14 2010 - 15:19:07 PST)
- xuemeiwang1103 (Sat Nov 13 2010 - 19:59:42 PST)
- xuemeiwang1103 (Fri Nov 12 2010 - 00:07:21 PST)
[AMBER] About NEB calculation form amber 11
- Carlos Simmerling (Mon Nov 08 2010 - 11:42:01 PST)
- Buddhadev Maiti (Mon Nov 08 2010 - 11:26:46 PST)
[AMBER] About NEB calculation from amber 11
- Carlos Simmerling (Mon Nov 08 2010 - 16:52:44 PST)
- Buddhadev Maiti (Mon Nov 08 2010 - 14:41:14 PST)
- Buddhadev Maiti (Mon Nov 08 2010 - 12:12:12 PST)
[AMBER] About NEB calculation in NPT ensemble
- Carlos Simmerling (Wed Nov 10 2010 - 08:08:00 PST)
- Buddhadev Maiti (Wed Nov 10 2010 - 08:06:28 PST)
[AMBER] about velocity output
- hong-bin Xie (Thu Nov 18 2010 - 10:32:09 PST)
- George Madalin Giambasu (Thu Nov 18 2010 - 05:33:12 PST)
- M. L. Dodson (Wed Nov 17 2010 - 19:17:01 PST)
- hong-bin Xie (Wed Nov 17 2010 - 16:43:46 PST)
- Jason Swails (Wed Nov 17 2010 - 16:28:05 PST)
- hong-bin Xie (Wed Nov 17 2010 - 16:06:34 PST)
- Jason Swails (Wed Nov 17 2010 - 15:21:22 PST)
- hong-bin Xie (Wed Nov 17 2010 - 14:59:39 PST)
[AMBER] Amber 11 installation problems
- Scott Brozell (Wed Nov 17 2010 - 19:37:08 PST)
- Jason Swails (Wed Nov 17 2010 - 15:17:28 PST)
- Linus Johannissen (Wed Nov 17 2010 - 14:34:53 PST)
- Tru Huynh (Wed Nov 17 2010 - 10:40:54 PST)
- case (Wed Nov 17 2010 - 10:36:00 PST)
- Linus Johannissen (Wed Nov 17 2010 - 09:44:21 PST)
- Jason Swails (Wed Nov 17 2010 - 08:47:27 PST)
- Linus Johannissen (Wed Nov 17 2010 - 08:39:47 PST)
[AMBER] Amber 11 single and multiple GPU question
- Ross Walker (Mon Nov 08 2010 - 16:50:51 PST)
- Scott Le Grand (Mon Nov 08 2010 - 15:52:44 PST)
- Frank X. Vázquez (Mon Nov 08 2010 - 15:17:15 PST)
[AMBER] Amber force-field compatibility
- Carlos Simmerling (Mon Nov 08 2010 - 14:06:43 PST)
- Ross Walker (Mon Nov 08 2010 - 13:32:50 PST)
[AMBER] AMBER QMMM MPI scaling
- Ross Walker (Thu Nov 04 2010 - 10:38:23 PDT)
- Xiaohu Li (Thu Nov 04 2010 - 09:10:11 PDT)
[AMBER] amber tool 1.4 Install error
- Tru Huynh (Sun Nov 07 2010 - 16:33:44 PST)
- case (Fri Nov 05 2010 - 06:43:27 PDT)
- David Watson (Thu Nov 04 2010 - 21:21:26 PDT)
- Alice Wang (Thu Nov 04 2010 - 21:15:03 PDT)
- Alice Wang (Thu Nov 04 2010 - 21:08:51 PDT)
- David Watson (Thu Nov 04 2010 - 21:04:57 PDT)
- Alice Wang (Thu Nov 04 2010 - 20:58:38 PDT)
[AMBER] AMBER, tanya singh has invited you to open a Gmail account
- tanya singh (Sat Nov 20 2010 - 04:32:23 PST)
[AMBER] Amber10 installation problem
- case (Wed Nov 24 2010 - 07:29:03 PST)
- Shaandar Nyamtulga (Tue Nov 23 2010 - 19:43:57 PST)
[AMBER] Amber10 installation problem on MPICH1
- case (Thu Nov 18 2010 - 04:51:17 PST)
- Shaandar Nyamtulga (Thu Nov 18 2010 - 00:32:37 PST)
- Jason Swails (Tue Nov 16 2010 - 20:04:12 PST)
- Shaandar Nyamtulga (Tue Nov 16 2010 - 18:38:52 PST)
- Shaandar Nyamtulga (Tue Nov 16 2010 - 18:21:24 PST)
- case (Tue Nov 16 2010 - 04:29:34 PST)
- Shaandar Nyamtulga (Mon Nov 15 2010 - 21:33:13 PST)
- Ye MEI (Mon Nov 15 2010 - 20:59:29 PST)
- Shaandar Nyamtulga (Mon Nov 15 2010 - 20:45:34 PST)
- Ye MEI (Mon Nov 15 2010 - 20:24:19 PST)
- Shaandar Nyamtulga (Mon Nov 15 2010 - 20:02:14 PST)
[AMBER] Amber10 segmentation fault with AIX
- Andrew Emerson (Thu Nov 04 2010 - 02:45:50 PDT)
- Ross Walker (Tue Nov 02 2010 - 09:07:13 PDT)
- Andrew Emerson (Tue Nov 02 2010 - 04:22:00 PDT)
[AMBER] AMBER: molsurf.c error
- Jason Swails (Tue Nov 02 2010 - 06:18:33 PDT)
- 王亚茹 (Tue Nov 02 2010 - 03:10:05 PDT)
[AMBER] Any Force field parameters for Zn, Mg and Mn in AMBER?
- Catein Catherine (Tue Nov 23 2010 - 07:56:31 PST)
[AMBER] Atom type assignment using GAFF
- abc def (Thu Nov 11 2010 - 18:02:43 PST)
[AMBER] average structure
- Carlos Simmerling (Mon Nov 22 2010 - 08:41:00 PST)
- aneesh cna (Mon Nov 22 2010 - 08:31:11 PST)
[AMBER] Benzene Stacking in AMBER
- Thomas Cheatham (Tue Nov 30 2010 - 18:00:54 PST)
- Ross Walker (Tue Nov 30 2010 - 17:55:47 PST)
- Adrian Roitberg (Tue Nov 30 2010 - 09:21:35 PST)
- Eliac Brown (Tue Nov 30 2010 - 09:17:41 PST)
- Adrian Roitberg (Tue Nov 30 2010 - 09:12:53 PST)
- Eliac Brown (Tue Nov 30 2010 - 09:04:33 PST)
[AMBER] Binding energy and conformation
- Jason Swails (Thu Nov 04 2010 - 09:22:35 PDT)
- John S (Thu Nov 04 2010 - 08:54:13 PDT)
[AMBER] binding free energy by MM_PBSA
- Carlos Simmerling (Mon Nov 22 2010 - 13:16:22 PST)
- Shuang Ding (Mon Nov 22 2010 - 13:02:33 PST)
[AMBER] can mmpbsa calculation be restarted by the file "restrt"?
- Jason Swails (Sat Nov 13 2010 - 22:02:56 PST)
- Alice Wang (Sat Nov 13 2010 - 19:17:13 PST)
[AMBER] Can we run sanders on GPU ?
- setyanto md (Thu Nov 25 2010 - 07:06:22 PST)
- Jason Swails (Tue Nov 23 2010 - 05:52:11 PST)
- setyanto md (Mon Nov 22 2010 - 19:25:44 PST)
[AMBER] Citation of Amber
- Marek Maly (Mon Nov 15 2010 - 07:08:08 PST)
- Giorgos Lamprinidis (Mon Nov 15 2010 - 06:59:16 PST)
[AMBER] Clarification in HBond analysis
- kureeckal ramesh (Mon Nov 22 2010 - 19:13:29 PST)
- kureeckal ramesh (Wed Nov 17 2010 - 22:35:00 PST)
[AMBER] Cluster PairwiseDistances
- Beale, John (Tue Nov 02 2010 - 06:29:58 PDT)
[AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4
- Dean Cuebas (Fri Nov 12 2010 - 14:28:52 PST)
- Jason Swails (Fri Nov 12 2010 - 12:42:22 PST)
- Dean Cuebas (Fri Nov 12 2010 - 12:16:06 PST)
- Bill Ross (Thu Nov 11 2010 - 09:42:00 PST)
- Jason Swails (Thu Nov 11 2010 - 09:23:50 PST)
- Jason Swails (Thu Nov 11 2010 - 09:18:54 PST)
- Daniel Roe (Thu Nov 11 2010 - 08:42:11 PST)
- David Watson (Thu Nov 11 2010 - 08:37:20 PST)
- Jason Swails (Thu Nov 11 2010 - 08:36:37 PST)
- Dean Cuebas (Thu Nov 11 2010 - 08:19:03 PST)
[AMBER] Could not read velocities from amin.crd
- Bill Ross (Sat Nov 27 2010 - 13:34:12 PST)
- case (Sat Nov 27 2010 - 06:48:52 PST)
- case (Sat Nov 27 2010 - 05:16:16 PST)
- Ashutosh Shandilya (Fri Nov 26 2010 - 22:50:13 PST)
[AMBER] Counting water molecules
- aneesh cna (Tue Nov 09 2010 - 21:36:39 PST)
[AMBER] D2O
- Bill Ross (Mon Nov 22 2010 - 09:36:05 PST)
- case (Sun Nov 21 2010 - 18:27:30 PST)
- Jason Swails (Sun Nov 21 2010 - 15:20:18 PST)
- setyanto md (Sun Nov 21 2010 - 15:04:40 PST)
- Adrian Roitberg (Wed Nov 17 2010 - 06:00:19 PST)
- Philippe Pinard (Wed Nov 17 2010 - 05:56:37 PST)
[AMBER] decomposition problems
- fancy2012 (Sat Nov 13 2010 - 17:46:31 PST)
- fancy2012 (Sat Nov 13 2010 - 01:34:44 PST)
- Bill Miller III (Thu Nov 11 2010 - 18:18:53 PST)
- fancy2012 (Thu Nov 11 2010 - 18:13:42 PST)
[AMBER] Difference of internal energy
- Jason Swails (Mon Nov 22 2010 - 06:33:41 PST)
- Kshatresh Dutta Dubey (Mon Nov 22 2010 - 06:06:30 PST)
[AMBER] distance restraint, recenter
- Niel Henriksen (Thu Nov 18 2010 - 06:51:47 PST)
- case (Thu Nov 18 2010 - 06:04:30 PST)
- Nadine Utz (Thu Nov 18 2010 - 05:35:29 PST)
[AMBER] does the "set UNIT box { X Y Z }" command create a periodic box?
- Jose Borreguero (Tue Nov 23 2010 - 07:27:40 PST)
- case (Tue Nov 23 2010 - 07:25:31 PST)
- Jose Borreguero (Tue Nov 23 2010 - 07:09:09 PST)
[AMBER] Error Compiling NAB o AMBER Tools 1.2
- case (Wed Nov 24 2010 - 09:36:48 PST)
- Janusz Mordarski (Wed Nov 24 2010 - 04:49:01 PST)
[AMBER] Error message from binding_energy.mmpbsa
- bin wang (Thu Nov 04 2010 - 11:53:52 PDT)
- Jason Swails (Thu Nov 04 2010 - 06:52:30 PDT)
- bin wang (Thu Nov 04 2010 - 06:49:36 PDT)
- Jason Swails (Thu Nov 04 2010 - 04:49:21 PDT)
[AMBER] Error message in AMBER when running protein-protein complexes.
- Jason Swails (Thu Nov 18 2010 - 07:02:06 PST)
- Catein Catherine (Wed Nov 17 2010 - 20:34:08 PST)
[AMBER] Error when running MMPBSA.py
- Bill Miller III (Wed Nov 24 2010 - 11:09:12 PST)
- bin wang (Wed Nov 24 2010 - 09:20:51 PST)
[AMBER] Excluded atoms list
- Ross Walker (Wed Nov 24 2010 - 16:24:57 PST)
- Bill Ross (Wed Nov 24 2010 - 14:56:12 PST)
- Jason S Grosch (Wed Nov 24 2010 - 14:41:57 PST)
[AMBER] Extra points
- case (Mon Nov 08 2010 - 05:58:55 PST)
- Jason S Grosch (Sun Nov 07 2010 - 19:05:15 PST)
[AMBER] extract distribution from PairwiseDistances
- Bill Ross (Tue Nov 02 2010 - 10:14:48 PDT)
- Yannick SPILL (Tue Nov 02 2010 - 06:12:14 PDT)
[AMBER] force field searching
- case (Sat Nov 27 2010 - 19:03:56 PST)
- Eliac Brown (Sat Nov 27 2010 - 17:02:12 PST)
[AMBER] Forward: Sander file name length bug
- case (Mon Nov 01 2010 - 09:49:33 PDT)
- Don.Bashford.stjude.org (Mon Nov 01 2010 - 09:10:58 PDT)
[AMBER] freezing bonds in parallel version
- case (Mon Nov 22 2010 - 08:30:20 PST)
- Stefano Pieraccini (Fri Nov 19 2010 - 06:57:23 PST)
[AMBER] Fwd: Atom type assignment using GAFF
- abc def (Fri Nov 12 2010 - 06:55:37 PST)
[AMBER] gaff-parametrisation - how many conformation for a flexible molecule
- FyD (Wed Nov 17 2010 - 00:18:27 PST)
- Schlesier, Thomas (Tue Nov 16 2010 - 14:14:40 PST)
[AMBER] GLYCAM with FF99SB
- Lachele Foley (Lists) (Tue Nov 30 2010 - 19:31:41 PST)
- Emmanuel Baribefe Naziga (Tue Nov 30 2010 - 18:06:21 PST)
[AMBER] GPU high temperature unfolding simulation
- andy ng (Tue Nov 02 2010 - 17:29:27 PDT)
- Ross Walker (Tue Nov 02 2010 - 09:07:13 PDT)
- Ye MEI (Sun Oct 31 2010 - 09:29:04 PDT)
[AMBER] GPU related issues
- Scott Le Grand (Fri Nov 19 2010 - 09:38:12 PST)
- Ross Walker (Fri Nov 19 2010 - 09:23:48 PST)
- case (Mon Nov 15 2010 - 04:48:03 PST)
- Ye MEI (Sun Nov 14 2010 - 19:45:11 PST)
[AMBER] GPU related issues/GTX400 series
- tanya singh (Sat Nov 20 2010 - 04:32:04 PST)
- Gould, Ian R (Sat Nov 20 2010 - 02:44:08 PST)
- Scott Le Grand (Fri Nov 19 2010 - 20:23:13 PST)
- Sergio R Aragon (Fri Nov 19 2010 - 10:16:56 PST)
[AMBER] GPU related issues/GTX400 series and GTX580
- Gould, Ian R (Wed Nov 24 2010 - 03:23:55 PST)
[AMBER] How the box info is used
- Ilyas Yildirim (Wed Nov 03 2010 - 21:48:21 PDT)
- Bill Ross (Wed Nov 03 2010 - 19:44:53 PDT)
- Ilyas Yildirim (Wed Nov 03 2010 - 18:00:56 PDT)
- Ilyas Yildirim (Wed Nov 03 2010 - 17:39:38 PDT)
- Bill Ross (Wed Nov 03 2010 - 15:34:27 PDT)
- Thomas Cheatham III (Wed Nov 03 2010 - 15:30:48 PDT)
- Ilyas Yildirim (Wed Nov 03 2010 - 15:22:24 PDT)
- Bill Ross (Wed Nov 03 2010 - 15:01:28 PDT)
- Ilyas Yildirim (Wed Nov 03 2010 - 14:54:24 PDT)
[AMBER] how to change the charge in all_amino94.lib
- Bill Ross (Wed Nov 03 2010 - 13:58:14 PDT)
- zhihong ke (Wed Nov 03 2010 - 13:42:56 PDT)
- Bill Ross (Wed Nov 03 2010 - 13:32:10 PDT)
- Bill Ross (Wed Nov 03 2010 - 13:29:25 PDT)
- FyD (Wed Nov 03 2010 - 13:18:32 PDT)
- zhihong ke (Wed Nov 03 2010 - 12:53:54 PDT)
[AMBER] how to configure/compile to get sander.RISM?
- Tyler Luchko (Fri Nov 12 2010 - 11:29:24 PST)
- Jason Swails (Fri Nov 12 2010 - 11:12:13 PST)
- Magdalena Gruziel (Fri Nov 12 2010 - 10:40:11 PST)
[AMBER] How to define trivalent Sulphur ligand atom
- Jason Swails (Mon Nov 08 2010 - 08:18:42 PST)
- Mannan (Mon Nov 08 2010 - 00:00:39 PST)
[AMBER] How to prepare the MMPBSA file?
- Jason Swails (Mon Nov 08 2010 - 08:07:21 PST)
- Bill Miller III (Mon Nov 08 2010 - 03:45:12 PST)
- xuemeiwang1103 (Mon Nov 08 2010 - 01:24:23 PST)
- xuemeiwang1103 (Mon Nov 08 2010 - 00:03:46 PST)
[AMBER] How to study the dissociation pathway for two proteins with AMBER10?
- Jason Swails (Fri Nov 19 2010 - 07:47:42 PST)
- Catein Catherine (Thu Nov 18 2010 - 18:59:54 PST)
[AMBER] I can unzip Amber 9 in Linux Ubuntu. But when i follow the install instruction g95 i have some problems
- case (Thu Nov 25 2010 - 19:43:21 PST)
- Tiefeng Peng (Thu Nov 25 2010 - 16:16:05 PST)
- case (Thu Nov 25 2010 - 05:15:29 PST)
- Tiefeng Peng (Wed Nov 24 2010 - 16:56:22 PST)
- Tiefeng Peng (Wed Nov 24 2010 - 16:16:58 PST)
[AMBER] Inquire about AMBER10 ?
- Jason Swails (Tue Nov 09 2010 - 15:10:01 PST)
- Jason Swails (Tue Nov 09 2010 - 15:06:15 PST)
- Xingqing Xiao (Tue Nov 09 2010 - 14:15:24 PST)
[AMBER] Interaction energy calculation
- Alessandro Nascimento (Mon Nov 01 2010 - 09:39:19 PDT)
- aneesh cna (Sun Oct 31 2010 - 22:04:46 PDT)
[AMBER] j-restrained peptide
- Rossella Noschese (Mon Nov 22 2010 - 03:23:54 PST)
- case (Wed Nov 03 2010 - 18:01:17 PDT)
- Rossella Noschese (Wed Nov 03 2010 - 09:01:55 PDT)
- case (Wed Nov 03 2010 - 07:36:23 PDT)
- Rossella Noschese (Wed Nov 03 2010 - 06:07:23 PDT)
[AMBER] Leap adding an extra incorrect hydrogen
- case (Fri Nov 26 2010 - 05:29:21 PST)
- Almus (Fri Nov 26 2010 - 03:07:12 PST)
- Jason Swails (Thu Nov 25 2010 - 08:12:05 PST)
- Almus (Thu Nov 25 2010 - 06:49:03 PST)
[AMBER] lib and frcmod files for sucrose?
- Jose Borreguero (Tue Nov 23 2010 - 18:20:40 PST)
- Lachele Foley (Lists) (Tue Nov 23 2010 - 17:48:18 PST)
- Jose Borreguero (Tue Nov 23 2010 - 17:27:41 PST)
- Lachele Foley (Lists) (Tue Nov 23 2010 - 17:07:37 PST)
- Jose Borreguero (Tue Nov 23 2010 - 14:56:53 PST)
[AMBER] LJ interactions and cutoff
- case (Thu Nov 18 2010 - 04:45:54 PST)
- manoj singh (Wed Nov 17 2010 - 22:45:49 PST)
[AMBER] metadynamics
- fancy2012 (Tue Nov 16 2010 - 03:10:00 PST)
- Davide Branduardi (Mon Nov 15 2010 - 07:21:51 PST)
- Marek Maly (Mon Nov 15 2010 - 06:46:58 PST)
- Jason Swails (Mon Nov 15 2010 - 06:25:18 PST)
- fancy2012 (Mon Nov 15 2010 - 05:31:16 PST)
[AMBER] mm_pbsa.pl and MMPBSA.py issues in Amber-11
- Jason Swails (Thu Nov 11 2010 - 12:50:12 PST)
- Jemmy Hu (Thu Nov 11 2010 - 11:46:35 PST)
- Jason Swails (Thu Nov 11 2010 - 10:59:06 PST)
- Jemmy Hu (Thu Nov 11 2010 - 10:52:18 PST)
[AMBER] mm_pbsa.pl doesn't work after the bugfixes
- bin wang (Thu Nov 04 2010 - 06:58:25 PDT)
[AMBER] MMPBSA
- Jason Swails (Wed Nov 24 2010 - 11:15:19 PST)
- John S (Wed Nov 24 2010 - 07:57:10 PST)
- Roman Osman (Tue Nov 23 2010 - 21:09:09 PST)
- Jason Swails (Tue Nov 23 2010 - 21:02:20 PST)
- John S (Tue Nov 23 2010 - 20:26:22 PST)
[AMBER] mmpbsa error
- Alice Wang (Mon Nov 08 2010 - 16:15:19 PST)
- Alice Wang (Mon Nov 08 2010 - 15:39:47 PST)
- Ray Luo, Ph.D. (Mon Nov 08 2010 - 10:05:22 PST)
- Alice Wang (Mon Nov 08 2010 - 06:26:43 PST)
- Alice Wang (Mon Nov 08 2010 - 00:46:29 PST)
[AMBER] MMPBSA ligand/receptor selections
- mirage . (Fri Nov 05 2010 - 04:52:35 PDT)
[AMBER] MMPBSA parameters
- Jason Swails (Wed Nov 03 2010 - 16:09:19 PDT)
- Michael Petersen (Wed Nov 03 2010 - 14:58:30 PDT)
[AMBER] mmpbsa with rigid bonds ?
- Jose Borreguero (Mon Nov 15 2010 - 08:20:40 PST)
- Jason Swails (Mon Nov 15 2010 - 07:47:54 PST)
- Jose Borreguero (Mon Nov 15 2010 - 07:40:41 PST)
- Adrian Roitberg (Mon Nov 15 2010 - 06:37:45 PST)
- Bill Miller III (Mon Nov 15 2010 - 06:14:41 PST)
- Jose Borreguero (Mon Nov 15 2010 - 06:01:25 PST)
[AMBER] mmpbsa.py - weird nmode results
- Jason Swails (Wed Nov 10 2010 - 07:01:35 PST)
- Bill Miller III (Tue Nov 09 2010 - 18:03:16 PST)
- Khaled Barakat (Tue Nov 09 2010 - 16:08:45 PST)
[AMBER] MMPBSA.py Error: Unknown block, '&decomp'. Check input!
- Jason Swails (Wed Nov 10 2010 - 13:44:40 PST)
- Bill Miller III (Wed Nov 10 2010 - 12:18:09 PST)
- kbarakat.ualberta.ca (Wed Nov 10 2010 - 12:09:19 PST)
[AMBER] MMPBSA.py patch failed
- bin wang (Thu Nov 18 2010 - 13:08:32 PST)
- Jason Swails (Thu Nov 18 2010 - 08:33:16 PST)
- bin wang (Thu Nov 18 2010 - 07:38:19 PST)
[AMBER] Monte Carlo
- case (Mon Nov 29 2010 - 19:21:23 PST)
- Alok Juneja (Mon Nov 29 2010 - 12:52:51 PST)
[AMBER] nmode error
- Jason Swails (Thu Nov 18 2010 - 07:21:45 PST)
- xuemeiwang1103 (Thu Nov 18 2010 - 03:43:23 PST)
- xuemeiwang1103 (Wed Nov 17 2010 - 04:37:20 PST)
[AMBER] nmode problem with mm-pbsa.pl
- case (Sun Nov 21 2010 - 05:20:39 PST)
- Khaled Barakat (Fri Nov 19 2010 - 18:05:04 PST)
[AMBER] nmode: dihedral angle error
- case (Fri Nov 26 2010 - 06:46:12 PST)
- Michael Petersen (Mon Nov 22 2010 - 10:53:08 PST)
[AMBER] non-bonding parameters
- Jason Swails (Fri Nov 19 2010 - 17:03:38 PST)
- Bill Ross (Fri Nov 19 2010 - 16:32:33 PST)
- Eliac Brown (Fri Nov 19 2010 - 16:24:44 PST)
- Eliac Brown (Fri Nov 19 2010 - 16:09:03 PST)
- Bill Ross (Fri Nov 19 2010 - 09:49:15 PST)
- Jason Swails (Fri Nov 19 2010 - 07:02:21 PST)
- Eliac Brown (Fri Nov 19 2010 - 05:59:32 PST)
- Jason Swails (Thu Nov 18 2010 - 14:09:41 PST)
- Eliac Brown (Thu Nov 18 2010 - 12:32:15 PST)
[AMBER] nonpolar term in MM-PBSA
- Chanchal (Fri Nov 12 2010 - 08:14:52 PST)
- Jason Swails (Fri Nov 12 2010 - 08:02:11 PST)
- Chanchal (Fri Nov 12 2010 - 07:50:17 PST)
[AMBER] Parameterization of ffamber99sb for octane box
- YUVRAJ UBOVEJA (Tue Nov 23 2010 - 11:09:06 PST)
[AMBER] Plumed
- David Beveridge (Tue Nov 02 2010 - 07:42:03 PDT)
- David Beveridge (Tue Nov 02 2010 - 07:13:06 PDT)
[AMBER] possible bug: problem with defining per-residue energies using RRES & LRES
- Jason Swails (Fri Nov 05 2010 - 14:20:33 PDT)
- case (Fri Nov 05 2010 - 12:53:23 PDT)
- g t (Fri Nov 05 2010 - 11:05:42 PDT)
- Jason Swails (Fri Nov 05 2010 - 11:03:45 PDT)
- g t (Fri Nov 05 2010 - 10:43:25 PDT)
- Jason Swails (Mon Nov 01 2010 - 13:06:12 PDT)
- g t (Mon Nov 01 2010 - 12:54:26 PDT)
[AMBER] Problem in MD simulations of DNA using ABC protocol
- Thomas Cheatham III (Tue Nov 09 2010 - 10:35:29 PST)
- abc def (Tue Nov 09 2010 - 09:54:25 PST)
[AMBER] Problem of RMSd plotting using merged tarjectories
- Bill Ross (Tue Nov 02 2010 - 12:21:43 PDT)
- Hoshin Kim (Tue Nov 02 2010 - 22:48:32 PDT)
[AMBER] problem with TMD
- Su Qiu (Tue Nov 30 2010 - 01:22:59 PST)
[AMBER] Proj into RMSD Space
- David Beveridge (Tue Nov 02 2010 - 07:15:50 PDT)
[AMBER] protonate a non standard residu
- Philippe Pinard (Fri Nov 12 2010 - 08:41:46 PST)
- Jason Swails (Fri Nov 12 2010 - 08:34:55 PST)
- Philippe Pinard (Fri Nov 12 2010 - 08:19:22 PST)
[AMBER] ptraj and ambpdb problem in Amber Tools 1.4
- Thomas Cheatham III (Mon Nov 22 2010 - 11:34:20 PST)
- Michael F. Bruist (Mon Nov 22 2010 - 11:16:09 PST)
[AMBER] ptraj distance
- mirage . (Mon Nov 15 2010 - 00:19:51 PST)
[AMBER] ptraj-area per lipid and order parameter
- colvin (Thu Nov 04 2010 - 05:34:33 PDT)
[AMBER] QM/MM energy terms
- Andreas Goetz (Sun Nov 07 2010 - 16:56:59 PST)
- Davide Branduardi (Sun Nov 07 2010 - 16:04:44 PST)
[AMBER] Question about FEP and GPU
- Jason Swails (Fri Nov 05 2010 - 20:20:09 PDT)
- TJ Mustard (Fri Nov 05 2010 - 15:26:54 PDT)
[AMBER] R.E.D.III.x tutorial1 question
- FyD (Tue Nov 02 2010 - 23:53:31 PDT)
- Jason Swails (Tue Nov 02 2010 - 14:47:52 PDT)
- Computational Chemist (Tue Nov 02 2010 - 13:12:42 PDT)
[AMBER] regarding hierarchical clustering
- jani vinod (Tue Nov 23 2010 - 21:05:05 PST)
- Jianyin Shao (Mon Nov 22 2010 - 11:56:34 PST)
- jani vinod (Mon Nov 22 2010 - 00:22:02 PST)
[AMBER] Regarding Hydrogen Bonds
- Ashish Runthala (Fri Nov 12 2010 - 01:11:42 PST)
[AMBER] relaxation of the density correlation functions of a molecule
- Philippe Pinard (Fri Nov 12 2010 - 08:20:30 PST)
- Philippe Pinard (Wed Nov 10 2010 - 14:06:57 PST)
[AMBER] Release of R.E.D. Server 2.0
- FyD (Thu Nov 04 2010 - 02:50:36 PDT)
[AMBER] REMD replicas blowing up
- Adrian Roitberg (Tue Nov 30 2010 - 06:04:31 PST)
- Carlos Simmerling (Tue Nov 30 2010 - 05:59:03 PST)
- Janzsó Gábor (Mon Nov 29 2010 - 11:19:16 PST)
- Carlos Simmerling (Tue Nov 23 2010 - 16:09:49 PST)
- Janzsó Gábor (Tue Nov 23 2010 - 10:07:30 PST)
- Carlos Simmerling (Tue Nov 23 2010 - 09:10:58 PST)
- Janzsó Gábor (Tue Nov 23 2010 - 07:21:08 PST)
[AMBER] Remove solvent molecules from the rst files
- Jason Swails (Tue Nov 02 2010 - 08:59:33 PDT)
- Lekpa Duukori (Tue Nov 02 2010 - 08:28:39 PDT)
- Baptiste Legrand (Tue Nov 02 2010 - 08:21:33 PDT)
[AMBER] RESP at antechamber
- juan roman (Sat Nov 06 2010 - 15:50:46 PDT)
- juan roman (Sat Nov 06 2010 - 15:49:08 PDT)
- Jason Swails (Tue Nov 02 2010 - 06:13:53 PDT)
- juan roman (Mon Nov 01 2010 - 21:16:55 PDT)
[AMBER] Restraints questions
- Mickey Richards (Mon Nov 22 2010 - 10:41:48 PST)
- case (Mon Nov 22 2010 - 08:39:27 PST)
- Mickey Richards (Mon Nov 15 2010 - 15:17:41 PST)
[AMBER] RMSD vs reference substructure
- Thomas Cheatham (Tue Nov 09 2010 - 06:45:14 PST)
- Kasprzak, Wojciech (NIH/NCI) [C] (Tue Nov 09 2010 - 06:29:19 PST)
[AMBER] Sander with restrained atoms
- case (Tue Nov 16 2010 - 04:13:48 PST)
- Dian Jiao (Mon Nov 15 2010 - 20:37:48 PST)
- case (Mon Nov 15 2010 - 18:52:16 PST)
- Dian Jiao (Mon Nov 15 2010 - 14:04:31 PST)
[AMBER] sander: Cannot match namelist object name scee
- Scott Brozell (Thu Nov 25 2010 - 19:11:26 PST)
- Andre Serobian (Thu Nov 25 2010 - 18:34:00 PST)
[AMBER] SASA
- Jason Swails (Thu Nov 04 2010 - 06:13:02 PDT)
- Beale, John (Thu Nov 04 2010 - 04:33:43 PDT)
[AMBER] SASA and Molecular Volume
- Hopkins, Robert (Mon Nov 22 2010 - 14:35:47 PST)
[AMBER] SCC-DFT orbitals
- Gustavo Seabra (Mon Nov 01 2010 - 11:28:58 PDT)
- arikcohen (Mon Nov 01 2010 - 11:20:39 PDT)
- Gustavo Seabra (Mon Nov 01 2010 - 04:30:06 PDT)
[AMBER] Serious problem at specific time point
- Bill Ross (Thu Nov 11 2010 - 13:35:27 PST)
- Hoshin Kim (Wed Nov 10 2010 - 23:31:01 PST)
- Jason Swails (Thu Nov 11 2010 - 05:46:40 PST)
- Thomas Cheatham III (Wed Nov 10 2010 - 16:09:37 PST)
- Jason Swails (Wed Nov 10 2010 - 15:53:24 PST)
- Bill Ross (Wed Nov 10 2010 - 15:48:47 PST)
- Hoshin Kim (Wed Nov 10 2010 - 00:39:34 PST)
[AMBER] small organic molecule
- case (Tue Nov 23 2010 - 10:34:41 PST)
- Rossella Noschese (Tue Nov 23 2010 - 07:36:36 PST)
[AMBER] solute in TIP4P box
- case (Fri Nov 26 2010 - 05:32:53 PST)
- Aiko Matsumoto (Fri Nov 26 2010 - 03:26:28 PST)
- Aiko Matsumoto (Wed Nov 24 2010 - 16:20:19 PST)
[AMBER] solvatebox
- M. L. Dodson (Sat Nov 06 2010 - 20:56:58 PDT)
- Bill Ross (Sat Nov 06 2010 - 19:22:09 PDT)
- case (Sat Nov 06 2010 - 19:14:33 PDT)
- John S (Sat Nov 06 2010 - 15:17:44 PDT)
[AMBER] STOP no longer optional in mm_pbsa.pl
- Don.Bashford.stjude.org (Tue Nov 16 2010 - 04:01:28 PST)
[AMBER] Targeted MD
- Jordan, Brad (Wed Nov 03 2010 - 10:09:31 PDT)
- Carlos Simmerling (Wed Nov 03 2010 - 10:03:13 PDT)
- Jordan, Brad (Wed Nov 03 2010 - 09:55:46 PDT)
[AMBER] Targeted MD - minimization problem
- Jordan, Brad (Wed Nov 03 2010 - 11:05:31 PDT)
[AMBER] Thanks - xray_interface.f verified to work with PGI7.1-1
- Rathbone, Dan L (Thu Nov 18 2010 - 09:04:39 PST)
[AMBER] The problems with constant pH
- Jason Swails (Fri Nov 19 2010 - 07:13:50 PST)
- cwt (Thu Nov 18 2010 - 23:36:47 PST)
[AMBER] TI +- variance is coming out to be very high
- sunita gupta (Mon Nov 08 2010 - 22:20:30 PST)
[AMBER] To All - Consider Switching to NetCDF
- Daniel Roe (Thu Nov 11 2010 - 05:58:30 PST)
[AMBER] To continue the job-Reg.......
- Mark Williamson (Tue Nov 23 2010 - 05:17:28 PST)
- parasu raman (Mon Nov 22 2010 - 22:18:09 PST)
[AMBER] top and crd-reg..............
- Ross Walker (Tue Nov 30 2010 - 20:20:35 PST)
[AMBER] Trajectory
- Carlos Simmerling (Wed Nov 24 2010 - 03:22:18 PST)
- John S (Tue Nov 23 2010 - 18:13:15 PST)
- Carlos Simmerling (Tue Nov 23 2010 - 15:42:49 PST)
- John S (Tue Nov 23 2010 - 15:04:31 PST)
- Thomas Cheatham III (Tue Nov 23 2010 - 13:40:21 PST)
- John S (Tue Nov 23 2010 - 11:18:40 PST)
- Carlos Simmerling (Tue Nov 23 2010 - 05:43:26 PST)
- John S (Mon Nov 22 2010 - 22:27:12 PST)
[AMBER] Truncated Octahedron Box in Amber9
- Alexander Metz (Thu Nov 18 2010 - 00:53:50 PST)
- Bertrand Russell (Wed Nov 17 2010 - 23:44:07 PST)
[AMBER] using MM-PBSA with Zn ions.
- Roman Osman (Mon Nov 08 2010 - 20:05:29 PST)
- Roman Osman (Wed Nov 03 2010 - 11:09:44 PDT)
- Bill Miller III (Wed Nov 03 2010 - 10:02:37 PDT)
- Roman Osman (Wed Nov 03 2010 - 09:17:13 PDT)
[AMBER] vlimit exceeded for step Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large
- case (Fri Nov 26 2010 - 06:31:47 PST)
- sunita gupta (Wed Nov 24 2010 - 22:06:38 PST)
[AMBER] Watershell
- fernando (Mon Nov 15 2010 - 01:18:23 PST)
[AMBER] where to check output restraint-wt (ntr=1) decleared with restraintmask
- case (Fri Nov 26 2010 - 05:38:55 PST)
- xueqin pang (Fri Nov 26 2010 - 00:41:42 PST)
- Jason Swails (Thu Nov 25 2010 - 07:54:57 PST)
- xueqin pang (Thu Nov 25 2010 - 06:52:18 PST)
[AMBER] xray_interface.f verified to work with PGI7.1-1
- case (Thu Nov 18 2010 - 07:36:16 PST)
- Rathbone, Dan L (Thu Nov 18 2010 - 06:52:51 PST)

Amber Archive Nov 2010 by subject