Amber Archive Jan 2009: by subject

[AMBER] "bad atom type"
- Akansha Saxena (Fri Jan 09 2009 - 09:15:11 PST)
[AMBER] "Could not find bond parameter"
- Ross Walker (Fri Jan 23 2009 - 10:29:46 PST)
- George Tzotzos (Fri Jan 23 2009 - 10:16:34 PST)
[AMBER] (no subject)
- Ross Walker (Thu Jan 22 2009 - 07:46:56 PST)
- Lake, Thomas (Thu Jan 22 2009 - 05:43:59 PST)
- Jenny Iskrenova (Mon Jan 19 2009 - 10:54:39 PST)
- Ross Walker (Sun Jan 18 2009 - 10:07:24 PST)
- Carlos Simmerling (Sun Jan 18 2009 - 05:08:41 PST)
- David A. Case (Sat Jan 17 2009 - 18:48:25 PST)
- Jenny Iskrenova (Fri Jan 16 2009 - 15:20:46 PST)
- David A. Case (Fri Jan 16 2009 - 11:10:33 PST)
- Carlos Simmerling (Fri Jan 16 2009 - 10:46:11 PST)
- Jenny Iskrenova (Fri Jan 16 2009 - 10:42:08 PST)
- Carlos Simmerling (Fri Jan 16 2009 - 09:43:26 PST)
- Lake, Thomas (Fri Jan 16 2009 - 09:38:09 PST)
[AMBER] adding MG2 problem
- balaji nagarajan (Fri Jan 30 2009 - 01:45:58 PST)
[AMBER] Alpha helix plot
- Carlos Simmerling (Fri Jan 30 2009 - 14:11:10 PST)
- Beale, John (Thu Jan 29 2009 - 12:10:11 PST)
[AMBER] Amber 9 installation problem on Ubuntu
- David A. Case (Mon Jan 12 2009 - 04:01:31 PST)
- drugdesign (Sun Jan 11 2009 - 22:26:34 PST)
[AMBER] AMBER efficiency: Intel vs. AMD
- Ross Walker (Mon Jan 19 2009 - 07:39:33 PST)
- Ye MEI (Sun Jan 18 2009 - 18:20:47 PST)
- Swarup Gupta (Sun Jan 18 2009 - 17:43:32 PST)
[AMBER] AMBER External keyword
- Gustavo Seabra (Sat Jan 24 2009 - 18:32:10 PST)
- Mahmoud A. A. Ibrahim (Wed Jan 21 2009 - 07:59:33 PST)
[AMBER] Amber Parameters for Iron Heme covalently boud to carbon monoxide
- Osmar Norberto de Souza (Wed Jan 07 2009 - 10:23:06 PST)
[AMBER] Amber top file to Charmm top file
- sarvin moghaddam (Fri Jan 30 2009 - 06:48:44 PST)
[AMBER] amber.ambermd.org open for business
- Ross Walker (Tue Jan 06 2009 - 15:34:31 PST)
[AMBER] amber9 in fedora10
- Eric (Tue Jan 13 2009 - 10:28:33 PST)
- Bala subramanian (Tue Jan 13 2009 - 10:16:19 PST)
- Ross Walker (Tue Jan 13 2009 - 10:00:33 PST)
- Mark Williamson (Tue Jan 13 2009 - 09:56:31 PST)
- Bala subramanian (Tue Jan 13 2009 - 09:51:49 PST)
[AMBER] AMBER: Problems in solvation with xleap
- vallespardojl.chem.leidenuniv.nl (Wed Jan 07 2009 - 05:39:56 PST)
[AMBER] AmberTools 1.2
- David A. Case (Fri Jan 30 2009 - 04:04:41 PST)
- James W. Caldwell (Thu Jan 29 2009 - 16:04:36 PST)
[AMBER] AmberTools and ptraj clustering on Mac OS X
- David Watson (Sat Jan 24 2009 - 13:41:04 PST)
[AMBER] ambpdb is changing atom names, a feature or bug?
- David A. Case (Sat Jan 10 2009 - 08:02:53 PST)
- Ye Mei (Sat Jan 10 2009 - 00:03:10 PST)
- David A. Case (Fri Jan 09 2009 - 10:58:20 PST)
- Bill Ross (Fri Jan 09 2009 - 09:53:23 PST)
- David A. Case (Fri Jan 09 2009 - 05:01:54 PST)
- Markus Kaukonen (Fri Jan 09 2009 - 04:55:41 PST)
[AMBER] analysis
- Adrien Delmont (Tue Jan 20 2009 - 09:03:16 PST)
[AMBER] antechamber : missed atoms
- David A. Case (Tue Jan 27 2009 - 07:23:27 PST)
- Khaled Barakat (Mon Jan 26 2009 - 12:22:14 PST)
- Sean Johnston (Mon Jan 26 2009 - 11:40:59 PST)
- Khaled Barakat (Mon Jan 26 2009 - 11:20:52 PST)
- Khaled Barakat (Mon Jan 26 2009 - 11:15:33 PST)
- Khaled Barakat (Mon Jan 26 2009 - 10:54:07 PST)
[AMBER] antechamber cation failure
- Ross Walker (Wed Jan 14 2009 - 09:45:43 PST)
- Rausch, Felix (Wed Jan 14 2009 - 05:32:04 PST)
[AMBER] Antechamber Connectivity
- David Watson (Mon Jan 26 2009 - 11:59:58 PST)
- George Tzotzos (Mon Jan 26 2009 - 10:23:58 PST)
[AMBER] Antechamber ligand prep
- George Tzotzos (Tue Jan 27 2009 - 08:44:06 PST)
- George Tzotzos (Tue Jan 27 2009 - 07:43:19 PST)
- David Watson (Tue Jan 27 2009 - 07:34:25 PST)
- David A. Case (Tue Jan 27 2009 - 07:33:57 PST)
- George Tzotzos (Tue Jan 27 2009 - 07:24:30 PST)
- David A. Case (Tue Jan 27 2009 - 06:59:47 PST)
- George Tzotzos (Tue Jan 27 2009 - 06:48:11 PST)
[AMBER] atom types
- David A. Case (Tue Jan 27 2009 - 07:13:30 PST)
- deepti nayar (Tue Jan 27 2009 - 01:47:12 PST)
- George Tzotzos (Mon Jan 19 2009 - 10:02:42 PST)
- Ross Walker (Mon Jan 19 2009 - 07:46:10 PST)
- George Tzotzos (Mon Jan 19 2009 - 06:04:09 PST)
[AMBER] Atome Type
- David A. Case (Thu Jan 29 2009 - 05:08:09 PST)
- Mahmoud A. A. Ibrahim (Thu Jan 29 2009 - 02:59:42 PST)
[AMBER] atomic charge
- Barbault Florent (Thu Jan 29 2009 - 00:24:48 PST)
- m m (Thu Jan 29 2009 - 00:08:47 PST)
[AMBER] bad energy??!!
- Ross Walker (Wed Jan 14 2009 - 11:40:24 PST)
- momo momo (Wed Jan 14 2009 - 11:19:20 PST)
[AMBER] Building atom and angle parameters
- George Tzotzos (Tue Jan 27 2009 - 10:24:52 PST)
[AMBER] Can we use AMBER?
- Ross Walker (Thu Jan 08 2009 - 10:47:18 PST)
- Casey,Richard (Thu Jan 08 2009 - 09:25:57 PST)
- Casey,Richard (Thu Jan 08 2009 - 09:16:50 PST)
[AMBER] Can't reproduce RESP charges
- FyD (Tue Jan 13 2009 - 03:52:13 PST)
- Sanghwa Han (Sun Jan 11 2009 - 21:57:15 PST)
[AMBER] charge derivation for ATP molecule using antechamber
- David A. Case (Fri Jan 23 2009 - 08:51:49 PST)
- prachi munjal (Fri Jan 23 2009 - 05:19:27 PST)
[AMBER] charges in topology file
- Carlos Simmerling (Wed Jan 14 2009 - 03:24:52 PST)
- vallespardojl.chem.leidenuniv.nl (Wed Jan 14 2009 - 02:33:35 PST)
[AMBER] Compilation and usage of NAB in parallel ?
- Marek Malý (Fri Jan 30 2009 - 08:01:06 PST)
- David A. Case (Fri Jan 30 2009 - 07:51:31 PST)
- Marek Malý (Fri Jan 30 2009 - 06:59:07 PST)
- David A. Case (Thu Jan 29 2009 - 05:22:08 PST)
- Marek Malý (Wed Jan 28 2009 - 14:25:24 PST)
[AMBER] crystal waters
- steinbrt.rci.rutgers.edu (Mon Jan 12 2009 - 12:37:34 PST)
- Carmen Domene (Mon Jan 12 2009 - 12:32:28 PST)
- steinbrt.rci.rutgers.edu (Mon Jan 12 2009 - 12:16:25 PST)
- Carmen Domene (Mon Jan 12 2009 - 12:04:24 PST)
[AMBER] deduce correlation from covariance matrix
- Yi Mao (Sun Jan 25 2009 - 13:01:05 PST)
[AMBER] Dipole command in ptraj
- musa özboyacı (Wed Jan 14 2009 - 15:15:26 PST)
- musa özboyacı (Wed Jan 14 2009 - 07:41:07 PST)
[AMBER] distance restraint and SHAKE
- Thomas Cheatham III (Tue Jan 27 2009 - 10:16:30 PST)
- Michael J Yonkunas (Tue Jan 27 2009 - 09:39:56 PST)
[AMBER] Divcon or Mopac
- Martin Peters (Wed Jan 14 2009 - 01:01:12 PST)
- Cen Gao (Tue Jan 13 2009 - 15:54:33 PST)
[AMBER] Dr. Ramesh here
- David A. Case (Fri Jan 30 2009 - 08:08:43 PST)
- kureeckal ramesh (Thu Jan 29 2009 - 19:18:33 PST)
- kureeckal ramesh (Thu Jan 29 2009 - 17:41:17 PST)
- rpaduri.chem.wayne.edu (Thu Jan 29 2009 - 09:22:20 PST)
- kureeckal ramesh (Thu Jan 29 2009 - 02:41:10 PST)
[AMBER] Duplicate residues
- Bill Ross (Mon Jan 19 2009 - 11:20:01 PST)
- David A. Case (Mon Jan 19 2009 - 05:16:28 PST)
- George Tzotzos (Mon Jan 19 2009 - 04:54:37 PST)
[AMBER] error in sander (Amber10)
- archana sonawani (Tue Jan 13 2009 - 00:21:09 PST)
[AMBER] Error in xleap
- Ross Walker (Thu Jan 15 2009 - 08:01:20 PST)
- archana sonawani (Wed Jan 14 2009 - 23:39:16 PST)
[AMBER] error on open distatance restraint
- xiaonan zhang (Sat Jan 24 2009 - 19:56:02 PST)
- David A. Case (Fri Jan 23 2009 - 19:18:17 PST)
- gmail (Fri Jan 23 2009 - 18:58:27 PST)
[AMBER] errorin sander---Amber10
- David A. Case (Tue Jan 13 2009 - 05:22:36 PST)
- archana sonawani (Tue Jan 13 2009 - 01:27:43 PST)
[AMBER] errors on REMD
- Carlos Simmerling (Mon Jan 26 2009 - 09:38:39 PST)
- z g (Thu Jan 22 2009 - 17:02:08 PST)
- Carlos Simmerling (Tue Jan 20 2009 - 06:29:07 PST)
- z g (Tue Jan 20 2009 - 05:39:12 PST)
- Carlos Simmerling (Tue Jan 20 2009 - 03:02:06 PST)
- z g (Mon Jan 19 2009 - 18:41:35 PST)
[AMBER] failure to run antechamber with amber 10
- Francesco Pietra (Fri Jan 30 2009 - 00:04:33 PST)
- George Tzotzos (Thu Jan 29 2009 - 14:48:50 PST)
- David A. Case (Thu Jan 29 2009 - 14:45:53 PST)
- Francesco Pietra (Thu Jan 29 2009 - 14:29:18 PST)
[AMBER] force-field for cyclic oligosaccharide using leap
- Madhurima Jana (Sun Jan 11 2009 - 20:21:23 PST)
- Madhurima Jana (Thu Jan 08 2009 - 20:50:18 PST)
[AMBER] four prepin/frcmod files be read simultaneously by leap
- David A. Case (Wed Jan 07 2009 - 10:39:56 PST)
- Yi Mao (Wed Jan 07 2009 - 08:38:52 PST)
- rpaduri.chem.wayne.edu (Wed Jan 07 2009 - 08:05:09 PST)
- Yi Mao (Wed Jan 07 2009 - 06:46:05 PST)
[AMBER] GAFF conjugated ring system dihedrals
- David A. Case (Thu Jan 29 2009 - 10:37:24 PST)
- Floris Buelens (Wed Jan 28 2009 - 04:04:55 PST)
[AMBER] generating top file using antechmaber
- Wei Zhang (Thu Jan 29 2009 - 08:26:22 PST)
- sarvin moghaddam (Thu Jan 29 2009 - 07:24:50 PST)
- David A. Case (Thu Jan 29 2009 - 04:51:56 PST)
- sarvin moghaddam (Wed Jan 28 2009 - 12:33:00 PST)
- Wei Zhang (Wed Jan 28 2009 - 12:23:21 PST)
- Wei Zhang (Wed Jan 28 2009 - 12:12:20 PST)
- sarvin moghaddam (Wed Jan 28 2009 - 11:49:20 PST)
[AMBER] Heat and Equilibrate Hybrid GB solvent?
- Carlos Simmerling (Fri Jan 16 2009 - 13:21:27 PST)
- Jason A. Ford-Green (Fri Jan 16 2009 - 13:14:41 PST)
[AMBER] help
- Ross Walker (Fri Jan 30 2009 - 05:42:33 PST)
- momo momo (Fri Jan 30 2009 - 04:35:22 PST)
[AMBER] how many processors for parallel test
- michael bane (Thu Jan 08 2009 - 05:56:59 PST)
- David A. Case (Thu Jan 08 2009 - 05:44:52 PST)
- michael bane (Thu Jan 08 2009 - 05:31:31 PST)
- David A. Case (Thu Jan 08 2009 - 04:08:06 PST)
- michael (Thu Jan 08 2009 - 03:01:41 PST)
[AMBER] How to calculate cavity volume from MD structures?
- Jason A. Ford-Green (Wed Jan 21 2009 - 07:39:57 PST)
- ben rodriguez (Tue Jan 20 2009 - 14:21:43 PST)
[AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent"
- Carlos Simmerling (Tue Jan 20 2009 - 06:33:55 PST)
- Jagadeesh, M.N., Ph.D. (Mon Jan 19 2009 - 01:03:39 PST)
[AMBER] how to use those water models off the list in amber?
- GZ Zhang (Thu Jan 22 2009 - 12:47:02 PST)
- David A. Case (Thu Jan 22 2009 - 05:29:41 PST)
- Lauren Wickstrom (Wed Jan 21 2009 - 15:58:22 PST)
- GZ Zhang (Wed Jan 21 2009 - 13:39:50 PST)
[AMBER] implicit and explicit simulation: salt effect
- David A. Case (Sat Jan 10 2009 - 08:26:45 PST)
- David A. Case (Sat Jan 10 2009 - 08:23:08 PST)
- David LeBard (Fri Jan 09 2009 - 20:23:24 PST)
- David Watson (Fri Jan 09 2009 - 19:49:48 PST)
- Catein Catherine (Fri Jan 09 2009 - 19:03:35 PST)
[AMBER] Installation error - Amber10
- David A. Case (Thu Jan 29 2009 - 10:33:33 PST)
- Andreas Svrcek-Seiler (Thu Jan 29 2009 - 03:52:44 PST)
- Ananda Rama Krishnan Selvaraj (Thu Jan 29 2009 - 03:47:44 PST)
[AMBER] large resp charges for non-natural amino acid
- Arturas Ziemys (Sat Jan 31 2009 - 09:03:44 PST)
- Arturas Ziemys (Sat Jan 31 2009 - 09:03:09 PST)
- FyD (Thu Jan 29 2009 - 13:58:34 PST)
- Arturas Ziemys (Thu Jan 29 2009 - 13:38:12 PST)
- FyD (Thu Jan 29 2009 - 12:57:51 PST)
- Arturas Ziemys (Thu Jan 29 2009 - 07:10:50 PST)
- FyD (Wed Jan 28 2009 - 20:04:11 PST)
- Arturas Ziemys (Tue Jan 27 2009 - 14:40:49 PST)
[AMBER] Ligand Diffusion Studies?
- Jason A. Ford-Green (Thu Jan 15 2009 - 09:42:03 PST)
[AMBER] lone pairs on CYX and MET
- Ross Walker (Thu Jan 08 2009 - 10:17:52 PST)
- Beale, John (Thu Jan 08 2009 - 10:08:42 PST)
[AMBER] mairun
- wl2290.columbia.edu (Thu Jan 08 2009 - 15:11:56 PST)
- Ross Walker (Thu Jan 08 2009 - 14:51:49 PST)
- wl2290.columbia.edu (Thu Jan 08 2009 - 14:33:52 PST)
- Ross Walker (Thu Jan 08 2009 - 10:25:26 PST)
- wl2290.columbia.edu (Thu Jan 08 2009 - 09:30:05 PST)
[AMBER] MD
- Ross Walker (Wed Jan 07 2009 - 16:33:46 PST)
- Beale, John (Wed Jan 07 2009 - 06:40:07 PST)
[AMBER] MD vs scattering
- Chih-Ying Lin (Tue Jan 20 2009 - 13:26:49 PST)
- Ross Walker (Tue Jan 20 2009 - 13:18:26 PST)
- Chih-Ying Lin (Tue Jan 20 2009 - 13:10:47 PST)
[AMBER] MM - PBSA problem
- musa özboyacı (Mon Jan 26 2009 - 08:32:40 PST)
- Cenk \(Jenk\) Andac (Mon Jan 26 2009 - 08:20:25 PST)
- musa özboyacı (Mon Jan 26 2009 - 04:43:33 PST)
- Cenk \(Jenk\) Andac (Mon Jan 26 2009 - 04:14:52 PST)
- musa özboyacı (Mon Jan 26 2009 - 03:15:13 PST)
- Cenk \(Jenk\) Andac (Sun Jan 25 2009 - 12:38:16 PST)
- David A. Case (Sun Jan 25 2009 - 06:26:07 PST)
- David A. Case (Sun Jan 25 2009 - 06:21:33 PST)
- musa özboyacı (Sun Jan 25 2009 - 05:12:05 PST)
- Cenk \(Jenk\) Andac (Fri Jan 23 2009 - 06:34:46 PST)
- musa özboyacı (Fri Jan 23 2009 - 05:14:05 PST)
- Niel Henriksen (Thu Jan 22 2009 - 16:52:09 PST)
- Cenk \(Jenk\) Andac (Thu Jan 22 2009 - 14:00:13 PST)
- musa özboyacı (Thu Jan 22 2009 - 11:52:10 PST)
- Ray Luo (Thu Jan 22 2009 - 09:31:53 PST)
- musa özboyacı (Thu Jan 22 2009 - 09:06:54 PST)
[AMBER] mm-GBSA from implicit
- Carlos Simmerling (Sat Jan 10 2009 - 05:25:10 PST)
- Catein Catherine (Fri Jan 09 2009 - 19:13:28 PST)
[AMBER] molecular mechanic minimisation with amber
- Ross Walker (Wed Jan 14 2009 - 09:56:23 PST)
- momo momo (Wed Jan 14 2009 - 06:58:47 PST)
[AMBER] mpirun
- Ross Walker (Thu Jan 08 2009 - 15:28:12 PST)
[AMBER] multisander error
- Justine Condo (Mon Jan 12 2009 - 15:01:41 PST)
- Ross Walker (Mon Jan 12 2009 - 14:51:48 PST)
- Justine Condo (Mon Jan 12 2009 - 14:39:44 PST)
- Justine Condo (Mon Jan 12 2009 - 14:32:31 PST)
- Ross Walker (Mon Jan 12 2009 - 14:20:06 PST)
- David Watson (Mon Jan 12 2009 - 14:15:26 PST)
- Justine Condo (Mon Jan 12 2009 - 14:03:37 PST)
[AMBER] nab conjgrad min problem
- Jeremy Harris (Mon Jan 19 2009 - 07:00:30 PST)
- David A. Case (Fri Jan 16 2009 - 07:33:01 PST)
- Jeremy Harris (Fri Jan 16 2009 - 07:11:12 PST)
[AMBER] NAB entropy calcualtion
- David A. Case (Fri Jan 09 2009 - 05:13:32 PST)
- Andreas Svrcek-Seiler (Fri Jan 09 2009 - 01:28:48 PST)
- chaitanya koppisetty (Fri Jan 09 2009 - 01:01:13 PST)
[AMBER] Need help with point to plane distance calculation in nab
- M. L. Dodson (Thu Jan 08 2009 - 11:54:15 PST)
- IN SUK JOUNG (Thu Jan 08 2009 - 11:41:09 PST)
- M. L. Dodson (Thu Jan 08 2009 - 11:16:51 PST)
- IN SUK JOUNG (Thu Jan 08 2009 - 11:00:20 PST)
- M. L. Dodson (Thu Jan 08 2009 - 10:39:16 PST)
[AMBER] non-natural amino acids
- FyD (Thu Jan 22 2009 - 15:25:31 PST)
- Arturas Ziemys (Thu Jan 22 2009 - 09:32:11 PST)
[AMBER] Non-planarity of amide atoms after optimization
- Sanghwa Han (Wed Jan 07 2009 - 19:17:18 PST)
[AMBER] NOTICE: File size limits on AMBER reflector
- Ross Walker (Tue Jan 27 2009 - 08:35:50 PST)
[AMBER] NPT md with PME method for a water box
- Ross Walker (Wed Jan 14 2009 - 10:07:13 PST)
- Jeffrey (Wed Jan 14 2009 - 06:41:24 PST)
[AMBER] number-of-EPS-exceeds-MAXESP
- Karol Kaszuba (Sat Jan 17 2009 - 02:41:22 PST)
- Karol Kaszuba (Sun Jan 11 2009 - 23:57:50 PST)
- FyD (Sun Jan 11 2009 - 23:43:48 PST)
- Karol Kaszuba (Sun Jan 11 2009 - 00:01:07 PST)
- FyD (Sat Jan 10 2009 - 23:00:40 PST)
- Karol Kaszuba (Sat Jan 10 2009 - 07:27:08 PST)
- FyD (Sat Jan 10 2009 - 00:26:13 PST)
- Karol Kaszuba (Fri Jan 09 2009 - 13:07:13 PST)
[AMBER] Off topic. Hardware problem
- Francesco Pietra (Sat Jan 10 2009 - 00:26:55 PST)
[AMBER] Parallelepiped periodic box
- David A. Case (Fri Jan 16 2009 - 11:50:32 PST)
- Ian Streeter (Mon Jan 12 2009 - 07:57:55 PST)
[AMBER] PBSA: PB bomb in pb_setgrd()
- Ray Luo (Wed Jan 07 2009 - 10:24:15 PST)
- Larry Layne (Wed Jan 07 2009 - 07:33:57 PST)
[AMBER] PhD position in Computational Structural Biology at Cambridge, UK
- Swanand Gore (Wed Jan 28 2009 - 02:31:16 PST)
[AMBER] PHOSPHOTHREONINE
- David A. Case (Wed Jan 07 2009 - 11:29:35 PST)
- Khaled Barakat (Wed Jan 07 2009 - 11:11:43 PST)
[AMBER] pmemd | Compilation problem with ifort and mvapich environment
- Ross Walker (Wed Jan 14 2009 - 09:53:20 PST)
- fohm fohm (Wed Jan 14 2009 - 09:23:50 PST)
[AMBER] Postdoc Position Available at SDSC/UCSD
- Ross Walker (Wed Jan 14 2009 - 12:35:52 PST)
[AMBER] principal component vector onto C-alpha
- S.Sundar Raman (Tue Jan 13 2009 - 14:46:20 PST)
- Carra, Claudio (JSC-SK)[USRA] (Tue Jan 13 2009 - 12:52:31 PST)
[AMBER] problem building AmberTools/sleap on AIX
- Shan-ho Tsai (Wed Jan 21 2009 - 13:53:00 PST)
- Wei Zhang (Fri Jan 16 2009 - 13:19:42 PST)
- Shan-ho Tsai (Fri Jan 16 2009 - 12:58:53 PST)
- Shan-ho Tsai (Mon Jan 12 2009 - 07:31:51 PST)
- Wei Zhang (Fri Jan 09 2009 - 14:28:08 PST)
- Shan-ho Tsai (Fri Jan 09 2009 - 13:49:17 PST)
- Bill Ross (Fri Jan 09 2009 - 09:45:55 PST)
- Shan-ho Tsai (Fri Jan 09 2009 - 08:46:59 PST)
- Wei Zhang (Fri Jan 09 2009 - 08:37:43 PST)
- Shan-ho Tsai (Fri Jan 09 2009 - 08:27:56 PST)
[AMBER] Problem in pb simulation, PB_Bomb
- Waqas Nasir (Thu Jan 29 2009 - 01:08:22 PST)
[AMBER] Problem in watercap simulation, PB_Bomb
- Ray Luo (Thu Jan 29 2009 - 09:45:33 PST)
- Waqas Nasir (Thu Jan 29 2009 - 06:21:20 PST)
[AMBER] Problem with entropy calculation of bigger system using NMODE and NAB.
- David A. Case (Sat Jan 24 2009 - 06:37:31 PST)
- Marek Malý (Wed Jan 21 2009 - 14:48:58 PST)
- David A. Case (Wed Jan 21 2009 - 06:52:33 PST)
- Marek Malý (Tue Jan 20 2009 - 18:48:03 PST)
- David A. Case (Tue Jan 20 2009 - 12:53:48 PST)
- Niel Henriksen (Tue Jan 20 2009 - 12:49:38 PST)
- Marek Malý (Tue Jan 20 2009 - 10:24:55 PST)
[AMBER] prot-DNA simulation
- Thomas Cheatham III (Wed Jan 21 2009 - 13:55:52 PST)
- deepti nayar (Wed Jan 21 2009 - 03:16:09 PST)
[AMBER] ptraj, CHARMM PSF and CMAP
- Ross Walker (Wed Jan 14 2009 - 08:46:17 PST)
- Hannes Loeffler (Wed Jan 14 2009 - 01:45:07 PST)
[AMBER] PTRAJ: solvent accessible surface area
- Carlos Simmerling (Wed Jan 14 2009 - 07:00:59 PST)
- steinbrt.rci.rutgers.edu (Wed Jan 14 2009 - 06:59:19 PST)
- Catein Catherine (Tue Jan 13 2009 - 23:32:15 PST)
[AMBER] Question on heating for homology based model.
- drugdesign (Sat Jan 31 2009 - 10:43:06 PST)
[AMBER] reaction coordinates
- Catein Catherine (Wed Jan 14 2009 - 21:25:31 PST)
- David A. Case (Wed Jan 14 2009 - 05:00:59 PST)
- Rausch, Felix (Wed Jan 14 2009 - 03:54:57 PST)
[AMBER] reg . parallel run
- Ross Walker (Thu Jan 22 2009 - 07:52:55 PST)
- balaji nagarajan (Wed Jan 21 2009 - 21:34:03 PST)
[AMBER] reg.error in parallel run
- Ross Walker (Fri Jan 23 2009 - 07:52:20 PST)
- balaji nagarajan (Fri Jan 23 2009 - 02:05:21 PST)
[AMBER] reg.parallel run error
- Ross Walker (Thu Jan 22 2009 - 12:06:33 PST)
- balaji nagarajan (Thu Jan 22 2009 - 10:41:25 PST)
[AMBER] reg.parallel.run error
- Ross Walker (Fri Jan 23 2009 - 22:05:50 PST)
- balaji nagarajan (Fri Jan 23 2009 - 17:59:21 PST)
[AMBER] reg.parallel.run.error
- balaji nagarajan (Sat Jan 24 2009 - 07:09:49 PST)
[AMBER] reg.Targeted molecular dynamics
- Carlos Simmerling (Wed Jan 28 2009 - 10:01:43 PST)
- balaji nagarajan (Tue Jan 27 2009 - 05:57:01 PST)
- balaji nagarajan (Tue Jan 27 2009 - 05:56:54 PST)
[AMBER] reg: targeted molecular dynamics
- Carlos Simmerling (Tue Jan 27 2009 - 05:04:57 PST)
- balaji nagarajan (Tue Jan 27 2009 - 05:02:03 PST)
[AMBER] Release of the R.E.D.-III.1 tools
- FyD (Mon Jan 12 2009 - 03:59:14 PST)
[AMBER] REM_hybrid test fails on AIX
- Shan-ho Tsai (Thu Jan 22 2009 - 12:28:04 PST)
[AMBER] REMD fixed atoms
- Maxime Louet (Fri Jan 30 2009 - 09:26:08 PST)
[AMBER] RESP charges for Fe in heme
- Carina Backtorp (Mon Jan 19 2009 - 05:48:11 PST)
[AMBER] restraining atoms
- Carlos Simmerling (Thu Jan 22 2009 - 06:55:35 PST)
- neville forlemu (Thu Jan 22 2009 - 06:53:48 PST)
[AMBER] restraint of REMD
- Carlos Simmerling (Fri Jan 16 2009 - 03:57:29 PST)
- z g (Thu Jan 15 2009 - 18:51:46 PST)
[AMBER] Rosetta Academic Training Workshop
- Nir London (Tue Jan 27 2009 - 05:07:24 PST)
[AMBER] sander not working
- Carlos Simmerling (Fri Jan 16 2009 - 07:01:34 PST)
- David A. Case (Fri Jan 16 2009 - 06:58:50 PST)
- archana sonawani (Thu Jan 15 2009 - 21:52:48 PST)
[AMBER] solvent mixture
- Gustavo Seabra (Sat Jan 24 2009 - 18:44:31 PST)
- iccy liu (Tue Jan 20 2009 - 14:08:34 PST)
[AMBER] TEST Message - please ignore.
- Ross Walker (Tue Jan 06 2009 - 17:00:39 PST)
[AMBER] Test run on Solaris 10 X 86
- David A. Case (Sat Jan 31 2009 - 18:49:22 PST)
- Manikandan Chandrasekaran (Sat Jan 31 2009 - 10:39:14 PST)
[AMBER] thermo, entropy by quasiharmonic method
- David A. Case (Fri Jan 30 2009 - 15:40:38 PST)
- Carra, Claudio (JSC-SK)[USRA] (Fri Jan 30 2009 - 13:35:37 PST)
[AMBER] thioglycoside
- Lachele Foley (Lists) (Mon Jan 26 2009 - 07:36:26 PST)
- FyD (Mon Jan 26 2009 - 07:07:37 PST)
- Alexander Schierholt (Mon Jan 26 2009 - 06:46:28 PST)
[AMBER] to remove AMBER list
- Ross Walker (Sat Jan 17 2009 - 13:32:19 PST)
- Furia Gargano (Sat Jan 17 2009 - 10:02:26 PST)
[AMBER] To stop the AMBER's list
- Furia Gargano (Sat Jan 17 2009 - 09:59:48 PST)
[AMBER] topology file for GLY with amino and carboxyl group?
- FyD (Tue Jan 27 2009 - 12:02:14 PST)
- Jose Borreguero (Tue Jan 27 2009 - 10:57:45 PST)
[AMBER] Use of Amber in distributed calculations
- M. L. Dodson (Sat Jan 17 2009 - 06:01:36 PST)
- M. L. Dodson (Sat Jan 17 2009 - 05:48:42 PST)
- drugdesign (Fri Jan 16 2009 - 23:33:55 PST)
[AMBER] Using a restart file
- Ross Walker (Thu Jan 15 2009 - 08:52:44 PST)
- Carlos Simmerling (Thu Jan 15 2009 - 08:45:27 PST)
- Simone Swift (Thu Jan 15 2009 - 08:40:38 PST)
[AMBER] using binary trajectories from NAMD in PTRAJ
- karthik s (Mon Jan 26 2009 - 22:49:13 PST)
- Wei Huang (Mon Jan 26 2009 - 06:41:22 PST)
- karthik s (Sun Jan 25 2009 - 23:11:29 PST)
[AMBER] Using GAFF with a covalently bound ligand or label
- FyD (Fri Jan 16 2009 - 01:13:43 PST)
- Markus Kaukonen (Thu Jan 15 2009 - 22:31:53 PST)
- David A. Case (Wed Jan 07 2009 - 18:42:27 PST)
- Sale, Kenneth L (Wed Jan 07 2009 - 17:30:10 PST)
[AMBER] Very weird topology problem
- Peter Gannett (Sat Jan 24 2009 - 15:17:26 PST)
- ranqi zhu (Sat Jan 24 2009 - 13:14:24 PST)
[AMBER] Watercap... some querries
- Robert Duke (Wed Jan 28 2009 - 10:46:02 PST)
- Waqas Nasir (Wed Jan 28 2009 - 07:10:48 PST)
- David A. Case (Wed Jan 28 2009 - 07:01:46 PST)
- Waqas Nasir (Wed Jan 28 2009 - 06:54:00 PST)
[AMBER] Writing out trajectory in NAB
- David A. Case (Mon Jan 12 2009 - 09:22:58 PST)
- xxxzzzyyy xxxzzzyyy (Mon Jan 12 2009 - 08:43:33 PST)
[AMBER] Xleap - solvatebox - counterions
- amirhossein taghavi (Sat Jan 31 2009 - 09:34:10 PST)
- Bill Ross (Fri Jan 30 2009 - 10:40:07 PST)
- David A. Case (Fri Jan 30 2009 - 08:04:23 PST)
- Arnaud (Fri Jan 30 2009 - 02:44:58 PST)
[AMBER] xleap problem
- David A. Case (Sun Jan 25 2009 - 15:30:47 PST)
- oguz gurbulak (Sun Jan 25 2009 - 03:49:28 PST)
- oguz gurbulak (Sun Jan 25 2009 - 08:34:39 PST)
- oguz gurbulak (Sun Jan 25 2009 - 08:27:48 PST)
- oguz gurbulak (Sun Jan 25 2009 - 08:02:50 PST)
- David A. Case (Sun Jan 25 2009 - 05:57:41 PST)
- oguz gurbulak (Sun Jan 25 2009 - 03:56:12 PST)
[AMBER] xmgrace and plotting time evolution of a defined variable
- Mark Williamson (Wed Jan 14 2009 - 16:38:17 PST)
- Naser Alijabbari (Wed Jan 14 2009 - 16:20:31 PST)
amber force filed for RNA
- Ross Walker (Wed Jan 07 2009 - 08:49:41 PST)
AMBER: a question about ff03ua
- FyD (Fri Jan 02 2009 - 12:20:37 PST)
- David A. Case (Fri Jan 02 2009 - 08:35:15 PST)
- oguz gurbulak (Fri Jan 02 2009 - 07:30:46 PST)
AMBER: apparent error in closest function in ptraj 10
- Roman Osman (Fri Jan 02 2009 - 09:37:09 PST)
- D.J. Cole (Fri Jan 02 2009 - 08:06:01 PST)
- Roman Osman (Fri Jan 02 2009 - 07:54:48 PST)
AMBER: bug of the mm_pbsa module in ambertools 1.2
- Scott Brozell (Tue Jan 06 2009 - 10:59:15 PST)
- Ye Mei (Mon Jan 05 2009 - 07:28:02 PST)
AMBER: CHCl3 solvent box
- WJ Ding (Mon Jan 05 2009 - 13:21:32 PST)
- David A. Case (Mon Jan 05 2009 - 05:48:44 PST)
- WJ Ding (Sun Jan 04 2009 - 14:24:48 PST)
AMBER: Dielectric constant
- musa özboyacı (Sat Jan 03 2009 - 10:54:06 PST)
AMBER: energy jumps during molecule minimization
- David A. Case (Fri Jan 02 2009 - 04:48:23 PST)
- Paul Ledbetter (Thu Jan 01 2009 - 19:33:30 PST)
AMBER: error in amber 10
- David A. Case (Tue Jan 06 2009 - 04:28:54 PST)
- David A. Case (Tue Jan 06 2009 - 04:18:23 PST)
- archana sonawani (Mon Jan 05 2009 - 23:19:03 PST)
AMBER: IMPORTANT Information regarding AMBER Mailing List - please read.
- Ross Walker (Tue Jan 06 2009 - 12:40:00 PST)
AMBER: IMPORTANT INFORMATION: Notice regarding transition of AMBER mailing list to new address.
- Ross Walker (Sat Jan 03 2009 - 14:12:19 PST)
AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64)
- Scott Brozell (Tue Jan 06 2009 - 11:23:29 PST)
AMBER: install amber10
- Scott Brozell (Tue Jan 06 2009 - 11:33:21 PST)
- wl2290.columbia.edu (Tue Jan 06 2009 - 09:23:01 PST)
AMBER: ligand parameter
- Yu Chen (Sun Jan 11 2009 - 17:25:41 PST)
- Bo Baker (Sun Jan 11 2009 - 16:52:19 PST)
- David Watson (Sun Jan 11 2009 - 16:39:02 PST)
- Bo Baker (Sun Jan 11 2009 - 16:20:08 PST)
- Ross Walker (Wed Jan 07 2009 - 20:10:20 PST)
- Bo Baker (Wed Jan 07 2009 - 18:18:02 PST)
- David A. Case (Wed Jan 07 2009 - 05:08:27 PST)
- Bo Baker (Tue Jan 06 2009 - 21:05:00 PST)
- Ross Walker (Tue Jan 06 2009 - 20:25:20 PST)
- Bo Baker (Tue Jan 06 2009 - 19:59:19 PST)
- Ross Walker (Mon Jan 05 2009 - 21:48:13 PST)
- Bo Baker (Mon Jan 05 2009 - 14:05:18 PST)
AMBER: mail list
- M. L. Dodson (Wed Jan 07 2009 - 08:04:02 PST)
- James W. Caldwell (Tue Jan 06 2009 - 17:24:12 PST)
- Ross Walker (Tue Jan 06 2009 - 15:47:08 PST)
- Mark M Huntress (Tue Jan 06 2009 - 15:06:57 PST)
AMBER: problem with ptraj image command in Amber 10?
- Carlos Simmerling (Tue Jan 06 2009 - 09:37:51 PST)
- Ryan Pavlovicz (Tue Jan 06 2009 - 09:28:27 PST)
AMBER: questions about equilibram
- wei zhang (Tue Jan 13 2009 - 04:58:51 PST)
- David A. Case (Wed Jan 07 2009 - 04:54:10 PST)
- wei zhang (Tue Jan 06 2009 - 03:18:47 PST)
AMBER: reg sander crashing on more than 32 cores over IB
- David A. Case (Mon Jan 05 2009 - 04:47:01 PST)
- Amit Bajaj (Sun Jan 04 2009 - 22:33:15 PST)
AMBER: RMS plot
- Carlos Simmerling (Tue Jan 06 2009 - 11:57:50 PST)
- Duggan, Brendan M. (Tue Jan 06 2009 - 11:54:04 PST)
- Carlos Simmerling (Fri Jan 02 2009 - 06:08:44 PST)
AMBER: SMD-related questions
- Gustavo Seabra (Fri Jan 02 2009 - 05:21:53 PST)
AMBER: xleap problem
- Bala subramanian (Wed Jan 07 2009 - 06:54:44 PST)
- David A. Case (Wed Jan 07 2009 - 05:43:16 PST)
- Bala subramanian (Wed Jan 07 2009 - 05:34:43 PST)
- David A. Case (Wed Jan 07 2009 - 05:06:19 PST)
- Bala subramanian (Wed Jan 07 2009 - 02:53:24 PST)
- Ross Walker (Tue Jan 06 2009 - 19:58:26 PST)
- Bala subramanian (Tue Jan 06 2009 - 11:43:00 PST)
- Carlos Simmerling (Tue Jan 06 2009 - 11:05:31 PST)
- Bala subramanian (Tue Jan 06 2009 - 10:57:53 PST)
errors on remd
- Ross Walker (Fri Jan 23 2009 - 08:38:06 PST)
nmode error: bad nonbon (amber 10)
- David A. Case (Wed Jan 14 2009 - 05:13:18 PST)
- Jeremy Harris (Tue Jan 13 2009 - 13:58:36 PST)
- David A. Case (Tue Jan 06 2009 - 06:32:48 PST)
- Jeremy Harris (Tue Jan 06 2009 - 05:37:21 PST)
same result
- zgong.hust (Thu Jan 08 2009 - 00:49:29 PST)
- Ross Walker (Wed Jan 07 2009 - 08:59:39 PST)
Tutorial 5
- Ross Walker (Fri Jan 30 2009 - 17:32:03 PST)
- George Tzotzos (Fri Jan 16 2009 - 12:31:11 PST)
- Ross Walker (Fri Jan 16 2009 - 09:10:51 PST)
xleap problem
- M. L. Dodson (Thu Jan 29 2009 - 08:22:22 PST)
- oguz gurbulak (Thu Jan 29 2009 - 07:53:30 PST)
- David A. Case (Tue Jan 27 2009 - 07:18:53 PST)
- oguz gurbulak (Mon Jan 26 2009 - 13:40:22 PST)
- M. L. Dodson (Mon Jan 26 2009 - 12:47:26 PST)
- oguz gurbulak (Mon Jan 26 2009 - 11:48:11 PST)
- oguz gurbulak (Sun Jan 25 2009 - 08:08:26 PST)

Amber Archive Jan 2009 by subject