Amber Archive May 2004: by subject

AMBER:
- David A. Case (Thu May 20 2004 - 10:14:13 PDT)
- Gustavo Pierdominici Sottile (Mon May 17 2004 - 11:38:53 PDT)
AMBER: A parm file suit for half beta and half alpha structure
- Qiang Lu (Mon May 10 2004 - 11:51:57 PDT)
AMBER: A problem for compiling amber8 parallel version
- David A. Case (Wed May 26 2004 - 10:08:43 PDT)
- Chen Yongzhi (Tue May 25 2004 - 13:58:37 PDT)
AMBER: a question about Van der waals radius
- Ye Mei (Sun May 23 2004 - 23:54:30 PDT)
- Xiao He (Sat May 22 2004 - 08:01:28 PDT)
- Jiri Sponer (Sat May 22 2004 - 07:42:27 PDT)
- Xiao He (Sat May 22 2004 - 07:29:56 PDT)
- Jiri Sponer (Sat May 22 2004 - 07:09:46 PDT)
- Xiao He (Sat May 22 2004 - 06:55:05 PDT)
- Jiri Sponer (Sat May 22 2004 - 05:41:12 PDT)
- Xiao He (Sat May 22 2004 - 05:07:05 PDT)
AMBER: about amber8, replica exchange
- J. Zhang, Dr (Sun May 30 2004 - 17:09:24 PDT)
- Carlos Simmerling (Fri May 28 2004 - 20:55:34 PDT)
- Guanglei Cui (Fri May 28 2004 - 21:04:33 PDT)
- J. Zhang, Dr (Fri May 28 2004 - 20:45:49 PDT)
AMBER: address error
- Carsten Detering (Wed May 19 2004 - 10:09:12 PDT)
AMBER: Amber 7 (sander) use of PME
- Carlos Simmerling (Thu May 27 2004 - 12:47:50 PDT)
- Linda Prengaman (Thu May 27 2004 - 12:42:13 PDT)
AMBER: Amber 8 compilation
- Viktor Hornak (Wed May 26 2004 - 10:08:08 PDT)
- A. Hungie (Wed May 26 2004 - 09:23:07 PDT)
AMBER: amber 8 under windows XP
- David A. Case (Thu May 27 2004 - 08:34:50 PDT)
- Adrian E. Roitberg (Thu May 27 2004 - 06:09:51 PDT)
- Piotr Cieplak (Wed May 26 2004 - 15:08:38 PDT)
- David A. Case (Wed May 26 2004 - 13:07:05 PDT)
- Ross Walker (Wed May 26 2004 - 12:03:54 PDT)
- Adrian E. Roitberg (Wed May 26 2004 - 11:50:02 PDT)
AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D
- Piotr Cieplak (Wed May 12 2004 - 11:57:20 PDT)
- FyD (Wed May 12 2004 - 11:01:31 PDT)
- FyD (Wed May 12 2004 - 09:42:31 PDT)
- Mikyung Seo (Tue May 11 2004 - 15:51:01 PDT)
AMBER: amber on AMD 64
- xhu1.memphis.edu (Fri May 28 2004 - 11:56:02 PDT)
AMBER: amber7, namelist, xlf and osx
- Knut Langsetmo (Tue May 25 2004 - 06:17:26 PDT)
- Mengjuei Hsieh (Wed May 19 2004 - 17:56:23 PDT)
- Knut Langsetmo (Wed May 19 2004 - 15:47:26 PDT)
AMBER: Amber8 compilation error
- Arvind (Fri Apr 30 2004 - 12:50:38 PDT)
AMBER: Amber8 on Tru64 UNIX on Alpha systems
- Jiten (Mon May 24 2004 - 20:54:40 PDT)
- James W. Caldwell (Thu May 20 2004 - 20:02:01 PDT)
- David A. Case (Thu May 20 2004 - 18:33:14 PDT)
- Jiten (Thu May 20 2004 - 17:49:42 PDT)
- David A. Case (Thu May 20 2004 - 08:22:26 PDT)
- Jiten (Wed May 19 2004 - 18:28:50 PDT)
AMBER: Ammonia
- Lishan Yao (Thu May 20 2004 - 14:11:43 PDT)
AMBER: antechamber
- David A. Case (Sat May 15 2004 - 09:02:30 PDT)
- anshul.imtech.res.in (Sat May 15 2004 - 09:43:48 PDT)
- Scott Brozell (Wed May 05 2004 - 14:30:17 PDT)
- Amber admin (Wed May 05 2004 - 13:51:22 PDT)
- Guanglei Cui (Tue May 04 2004 - 19:49:28 PDT)
AMBER: antechamber gives GDP 0 charge
- Oliver Hucke (Wed May 05 2004 - 13:46:06 PDT)
- Raik Grünberg (Wed May 05 2004 - 13:17:53 PDT)
AMBER: antechamber/Mopac: strange GTP charges
- David A. Case (Mon May 17 2004 - 12:31:38 PDT)
- Raik Grünberg (Mon May 17 2004 - 08:38:17 PDT)
- David A. Case (Fri May 14 2004 - 12:20:24 PDT)
- Raik Grünberg (Fri May 14 2004 - 03:35:13 PDT)
- David A. Case (Thu May 13 2004 - 11:41:18 PDT)
- carlsonh.umich.edu (Thu May 13 2004 - 11:40:03 PDT)
- Raik Grünberg (Thu May 13 2004 - 10:57:06 PDT)
AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file
- David A. Case (Fri May 28 2004 - 14:34:45 PDT)
- Kamp, Marc vander (Thu May 27 2004 - 06:01:13 PDT)
AMBER: any program or tool
- Viktor Hornak (Mon May 03 2004 - 05:18:56 PDT)
- Andreas Svrcek-Seiler (Mon May 03 2004 - 05:11:50 PDT)
- Helios Chen (Mon May 03 2004 - 03:16:15 PDT)
AMBER: Atom type with/without POL
- Jiten (Thu May 13 2004 - 07:01:38 PDT)
AMBER: average structure from traj
- Holly Freedman (Tue May 18 2004 - 14:30:07 PDT)
AMBER: Bug in babel conversion
- FyD (Tue May 25 2004 - 11:14:55 PDT)
AMBER: Bug in babel conversion (while following the RED manual in pp.15)
- Ilyas Yildirim (Tue May 25 2004 - 11:00:39 PDT)
AMBER: Cannot read in sander
- Ross Walker (Thu May 27 2004 - 15:36:10 PDT)
- bybaker.itsa.ucsf.edu (Thu May 27 2004 - 13:56:12 PDT)
- David A. Case (Thu May 27 2004 - 08:11:03 PDT)
- Ross Walker (Wed May 26 2004 - 18:08:48 PDT)
- bybaker.itsa.ucsf.edu (Wed May 26 2004 - 17:47:30 PDT)
- David A. Case (Wed May 26 2004 - 09:14:52 PDT)
- bybaker.itsa.ucsf.edu (Tue May 25 2004 - 15:51:48 PDT)
AMBER: Cannot read in sander-again
- David A. Case (Thu May 27 2004 - 16:15:37 PDT)
- Bill Ross (Thu May 27 2004 - 15:16:56 PDT)
- bybaker.itsa.ucsf.edu (Thu May 27 2004 - 15:05:22 PDT)
- Guanglei Cui (Thu May 27 2004 - 14:28:39 PDT)
- Bill Ross (Thu May 27 2004 - 14:28:27 PDT)
- bybaker.itsa.ucsf.edu (Thu May 27 2004 - 14:22:00 PDT)
AMBER: CAP PROTOCOL SIMULATION
- David A. Case (Tue May 18 2004 - 15:47:26 PDT)
- Ray Luo (Mon May 17 2004 - 16:07:17 PDT)
- Oliver Hucke (Tue May 18 2004 - 14:07:45 PDT)
- Ray Luo (Mon May 17 2004 - 14:43:55 PDT)
- Andreas Svrcek-Seiler (Tue May 18 2004 - 05:13:56 PDT)
- Obdulia Rabal (Tue May 18 2004 - 02:32:29 PDT)
AMBER: cap waters always flexible?
- Oliver Hucke (Thu May 06 2004 - 13:41:19 PDT)
AMBER: CG maxitn exceeded
- Ray Luo (Mon May 17 2004 - 12:10:29 PDT)
- Obdulia Rabal (Tue May 18 2004 - 09:29:53 PDT)
AMBER: Charges and atom type
- anshul.imtech.res.in (Sat May 08 2004 - 14:06:25 PDT)
AMBER: choosing 3 atoms for reorientaion in R.E.D
- FyD (Thu May 06 2004 - 15:00:44 PDT)
- Mikyung Seo (Thu May 06 2004 - 14:38:19 PDT)
AMBER: Clean in RESP
- David A. Case (Tue May 18 2004 - 07:55:42 PDT)
- Gustavo Pierdominici Sottile (Tue May 18 2004 - 04:46:38 PDT)
AMBER: Compiling AMBER MPI program using GCC/G77 compiler and MPICH on AMD OPTERON 64
- Scott Brozell (Tue May 25 2004 - 12:24:23 PDT)
- Ming Lei (Tue May 25 2004 - 08:27:49 PDT)
AMBER: Compiling AMBER MPI program using GCC/G77 compiler andMPICH on AMD OPTERON 64
- Jyh-Shyong Ho (Tue May 25 2004 - 17:07:34 PDT)
AMBER: Computing psec/day using Amber 8
- David A. Case (Thu May 06 2004 - 12:27:10 PDT)
- Craig TOEPFER (Thu May 06 2004 - 12:19:01 PDT)
- David A. Case (Thu May 06 2004 - 11:42:37 PDT)
- Craig TOEPFER (Thu May 06 2004 - 11:21:53 PDT)
AMBER: Converting ORAC's topology file to AMBER's prepi file
- scopio (Fri May 14 2004 - 05:30:32 PDT)
AMBER: DEBUG and GB
- David A. Case (Thu May 20 2004 - 11:34:38 PDT)
- Jones, Garth A (Tue May 18 2004 - 05:02:32 PDT)
AMBER: Decomposition in MMPBSA
- Thomas Steinbrecher (Thu May 13 2004 - 17:15:03 PDT)
AMBER: dihedral driver
- Beale, John (Wed May 12 2004 - 06:58:35 PDT)
AMBER: Does this warning matter? (about improper torsion parameters)
- J. Zhang, Dr (Wed May 19 2004 - 18:57:35 PDT)
- David A. Case (Wed May 19 2004 - 08:00:59 PDT)
- J. Zhang, Dr (Tue May 18 2004 - 20:04:32 PDT)
AMBER: dummy atom other than H
- Carsten Detering (Wed May 12 2004 - 14:18:23 PDT)
- David A. Case (Wed May 12 2004 - 12:30:26 PDT)
- Carsten Detering (Tue May 11 2004 - 18:12:22 PDT)
AMBER: energy conservation with GB !!
- Dr. Yong Duan (Sat May 15 2004 - 23:58:25 PDT)
- Pradipta Bandyopadhyay (Sat May 15 2004 - 23:27:01 PDT)
AMBER: esp or resp for all_amino94.lib
- FyD (Fri Apr 30 2004 - 16:28:57 PDT)
AMBER: FAD cofactor.
- Osman Gani (Fri May 14 2004 - 02:34:28 PDT)
AMBER: FEP error/early termination - why?
- Carlos Simmerling (Mon May 31 2004 - 11:21:41 PDT)
- Sébastien Osborne (Mon May 31 2004 - 11:12:54 PDT)
- Carlos Simmerling (Mon May 31 2004 - 10:56:24 PDT)
- Sébastien Osborne (Mon May 31 2004 - 10:51:15 PDT)
- David A. Case (Mon May 31 2004 - 10:33:08 PDT)
- Annette Höglund (Mon May 31 2004 - 06:23:27 PDT)
AMBER: fit a 3D line to points
- myang (Thu May 27 2004 - 14:11:08 PDT)
AMBER: Free energies using Sander in Amber8
- David A. Case (Mon May 24 2004 - 21:36:22 PDT)
- Jiten (Mon May 24 2004 - 19:52:52 PDT)
AMBER: gaussian03 output in antechamber
- Stefano.Pieraccini.unimi.it (Wed May 12 2004 - 01:46:17 PDT)
- Stefano.Pieraccini.unimi.it (Tue May 11 2004 - 02:27:46 PDT)
AMBER: Gibbs and solvent caps
- Miguel de Federico (Mon May 03 2004 - 03:28:47 PDT)
- Sébastien Osborne (Sat May 01 2004 - 11:59:07 PDT)
AMBER: h bond
- Ye Mei (Sun May 23 2004 - 23:27:37 PDT)
AMBER: H Bonds
- anshul.imtech.res.in (Thu May 06 2004 - 16:01:33 PDT)
- anshul.imtech.res.in (Thu May 06 2004 - 15:51:32 PDT)
- anshul.imtech.res.in (Wed May 05 2004 - 13:07:01 PDT)
- Sanjeev B.S. (Fri May 07 2004 - 01:38:24 PDT)
- Bill Ross (Thu May 06 2004 - 11:16:11 PDT)
- Sanjeev B.S. (Wed May 05 2004 - 22:09:06 PDT)
- Bill Ross (Wed May 05 2004 - 14:18:22 PDT)
- David A. Case (Wed May 05 2004 - 09:20:26 PDT)
AMBER: hbond in ptraj
- Thomas E. Cheatham, III (Fri May 07 2004 - 12:15:15 PDT)
- Qiang Lu (Fri May 07 2004 - 11:43:33 PDT)
AMBER: HIS protonation
- scopio (Mon May 10 2004 - 04:00:19 PDT)
- Stefano.Pieraccini.unimi.it (Mon May 10 2004 - 02:50:40 PDT)
AMBER: How to choose force constant?
- David A. Case (Wed May 05 2004 - 15:00:14 PDT)
- tomjas.poczta.onet.pl (Tue May 04 2004 - 06:48:44 PDT)
AMBER: IGR1/grnam1 problem
- David A. Case (Sat May 22 2004 - 21:03:16 PDT)
- Marcin Krol (Tue May 18 2004 - 10:40:58 PDT)
AMBER: Implicit solvents
- anshul.imtech.res.in (Wed May 05 2004 - 13:10:20 PDT)
- David A. Case (Wed May 05 2004 - 08:54:56 PDT)
AMBER: instalation of RES
- David A. Case (Thu May 20 2004 - 10:15:35 PDT)
- anshul.imtech.res.in (Thu May 20 2004 - 11:22:08 PDT)
AMBER: Install Amber8 under cygwin
- Seonah Kim (Mon May 31 2004 - 18:35:16 PDT)
AMBER: install RESP
- David A. Case (Sat May 15 2004 - 09:03:57 PDT)
- Gustavo Pierdominici Sottile (Sat May 15 2004 - 04:54:41 PDT)
AMBER: Installation AMber 8: "cannot find -lU77"
- A. Hungie (Tue May 25 2004 - 06:21:09 PDT)
AMBER: installing RESP
- Gustavo Pierdominici Sottile (Sat May 15 2004 - 04:52:59 PDT)
AMBER: ions in mm_pbsa
- Thomas E. Cheatham, III (Thu May 06 2004 - 12:07:42 PDT)
- S. Frank Yan (Thu May 06 2004 - 10:23:55 PDT)
- Fang, Jianwen (Thu May 06 2004 - 08:30:12 PDT)
AMBER: IOUTFM and binary/unformatted files error
- David A. Case (Tue May 25 2004 - 08:01:28 PDT)
- Martin Mucha (Tue May 25 2004 - 00:18:44 PDT)
AMBER: Ligand from CCDC.
- Osman Gani (Thu May 06 2004 - 08:38:16 PDT)
AMBER: ligand minimization
- atobak.eden.rutgers.edu (Sat May 08 2004 - 14:13:21 PDT)
AMBER: Low frequency in quasi-harmonic analysis!!
- Pradipta Bandyopadhyay (Sun May 30 2004 - 02:23:50 PDT)
AMBER: MD with NTR + NMROPT
- anshul.imtech.res.in (Wed May 12 2004 - 08:07:49 PDT)
- David A. Case (Wed May 12 2004 - 12:09:24 PDT)
- David A. Case (Mon May 10 2004 - 08:46:06 PDT)
- Martin Fabani (Mon May 10 2004 - 01:56:28 PDT)
AMBER: methane box
- anshul.imtech.res.in (Wed May 05 2004 - 11:57:16 PDT)
- FyD (Wed May 05 2004 - 08:36:08 PDT)
AMBER: mm-pbsa:- atom charges and radii ?
- Holger Gohlke (Tue May 11 2004 - 23:40:52 PDT)
- Ray Luo (Mon May 10 2004 - 23:21:06 PDT)
- Thomas E. Cheatham, III (Tue May 11 2004 - 07:24:17 PDT)
- Jeffrey Dyason (Tue May 11 2004 - 01:07:12 PDT)
AMBER: mm_pbsa energy decomposition error
- David A. Case (Tue May 25 2004 - 08:20:13 PDT)
- Fang, Jianwen (Tue May 25 2004 - 07:40:32 PDT)
AMBER: mm_pbsa examples; delphi in mm_pbsa
- Kazuo Koyano (Fri May 14 2004 - 02:35:36 PDT)
AMBER: MMPBSA problem
- Dalmaris, John (Sun May 30 2004 - 06:22:55 PDT)
AMBER: NHE problem
- David A. Case (Sun May 23 2004 - 09:14:34 PDT)
- Ryan Ye (Sun May 23 2004 - 08:19:56 PDT)
- Mengjuei Hsieh (Sat May 22 2004 - 17:30:07 PDT)
- David A. Case (Sat May 22 2004 - 16:55:52 PDT)
- Ryan Ye (Fri May 21 2004 - 22:36:44 PDT)
AMBER: nmode analysis
- David A. Case (Mon May 03 2004 - 10:14:19 PDT)
- sebnem.mercury.chem.pitt.edu (Mon May 03 2004 - 09:31:18 PDT)
- David A. Case (Mon May 03 2004 - 08:50:44 PDT)
- sebnem (Sun May 02 2004 - 17:52:12 PDT)
AMBER: Nonplanar ring systems in nucleic acid
- Jiri Sponer (Thu May 20 2004 - 05:42:16 PDT)
- Jiri Sponer (Thu May 20 2004 - 04:46:41 PDT)
- darden (Wed May 19 2004 - 14:05:59 PDT)
- Ilyas Yildirim (Wed May 19 2004 - 13:14:14 PDT)
AMBER: Normal Mode Analysis possibility
- David A. Case (Tue May 04 2004 - 11:25:27 PDT)
- myang (Tue May 04 2004 - 08:52:05 PDT)
AMBER: NTT=4
- Joachim Reichelt (Tue May 18 2004 - 10:01:50 PDT)
- David A. Case (Tue May 18 2004 - 07:57:19 PDT)
- Joachim Reichelt (Tue May 18 2004 - 07:30:33 PDT)
AMBER: ntwprt feature in AMBER7
- Dave S Walker (Thu May 06 2004 - 19:26:51 PDT)
AMBER: Opteron PMEMD
- David A. Case (Thu May 06 2004 - 15:09:47 PDT)
- Robert Duke (Thu May 06 2004 - 13:31:46 PDT)
- Gary Waters (Thu May 06 2004 - 11:29:56 PDT)
AMBER: parallel installation problem
- Oliver Hucke (Mon May 24 2004 - 16:57:01 PDT)
- Viktor Hornak (Mon May 24 2004 - 07:38:50 PDT)
- Oliver Hucke (Sat May 22 2004 - 17:40:17 PDT)
- Guanglei Cui (Wed May 19 2004 - 18:54:21 PDT)
- Oliver Hucke (Wed May 19 2004 - 15:17:08 PDT)
AMBER: parametrizacion partial charges
- FyD (Mon May 17 2004 - 08:37:02 PDT)
- Gustavo Pierdominici Sottile (Mon May 17 2004 - 06:45:58 PDT)
AMBER: PB bomb in pb_saarc
- Ray Luo (Tue May 18 2004 - 17:54:21 PDT)
- S. Frank Yan (Tue May 18 2004 - 16:14:36 PDT)
- Ray Luo (Mon May 17 2004 - 15:58:21 PDT)
- S. Frank Yan (Tue May 18 2004 - 13:41:41 PDT)
AMBER: pbsa calculation on part of the molecule
- Ray Luo (Wed May 19 2004 - 13:31:50 PDT)
- S. Frank Yan (Thu May 20 2004 - 13:25:46 PDT)
AMBER: pbsa calculation on part of the molecule & nmode analysis
- David A. Case (Thu May 20 2004 - 18:40:10 PDT)
- S. Frank Yan (Thu May 20 2004 - 18:06:11 PDT)
AMBER: PCA prep file
- Majid moghaddam (Tue May 18 2004 - 01:19:26 PDT)
AMBER: pdb in RED
- FyD (Thu May 27 2004 - 12:16:59 PDT)
- Gustavo Pierdominici Sottile (Thu May 27 2004 - 10:29:44 PDT)
AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5.2.0GHz
- Tru Huynh (Tue May 25 2004 - 07:31:34 PDT)
- David A. Case (Mon May 24 2004 - 08:37:29 PDT)
- Tru Huynh (Mon May 24 2004 - 00:45:39 PDT)
AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz
- Mengjuei Hsieh (Mon May 24 2004 - 12:12:39 PDT)
AMBER: performance of periodic vs. non-periodic simulation
- Oliver Hucke (Thu May 13 2004 - 09:14:08 PDT)
- Ben Cossins (Thu May 13 2004 - 02:22:21 PDT)
- Oliver Hucke (Wed May 12 2004 - 13:42:50 PDT)
- Thomas E. Cheatham, III (Wed May 12 2004 - 13:17:33 PDT)
- Oliver Hucke (Wed May 12 2004 - 12:08:18 PDT)
AMBER: PF6- force field parameters
- Jiten (Thu May 20 2004 - 17:32:29 PDT)
AMBER: PMEMD Built ? Wont run..
- Amber Administration (Tue May 11 2004 - 14:15:14 PDT)
- Gary Waters (Tue May 11 2004 - 13:08:49 PDT)
- Scott Brozell (Tue May 11 2004 - 12:41:15 PDT)
- Gary Waters (Tue May 11 2004 - 10:36:16 PDT)
- Amber admin (Tue May 11 2004 - 10:25:03 PDT)
- Gary Waters (Tue May 11 2004 - 09:55:14 PDT)
- david.evans.ulsop.ac.uk (Tue May 11 2004 - 09:32:18 PDT)
- Gary Waters (Tue May 11 2004 - 09:00:33 PDT)
AMBER: PMF correction factor
- David A. Case (Tue May 04 2004 - 11:01:18 PDT)
- Harvey, David Richard (Tue May 04 2004 - 06:35:13 PDT)
AMBER: Possible amber8 antechamber PDB parsing bug
- Junmei Wang (Thu May 06 2004 - 10:09:30 PDT)
- Mark Williamson (Thu May 06 2004 - 08:16:19 PDT)
AMBER: Problem : antechamber produces no output
- Junmei Wang (Wed May 12 2004 - 07:40:00 PDT)
- Marc Perea (Tue May 11 2004 - 03:19:52 PDT)
AMBER: Problem compiling amber7
- Joachim Reichelt (Tue May 25 2004 - 05:27:59 PDT)
- Viktor Hornak (Tue May 25 2004 - 05:20:40 PDT)
- Andreas Svrcek-Seiler (Tue May 25 2004 - 05:21:40 PDT)
- scopio (Tue May 25 2004 - 05:15:28 PDT)
- Miguel (Tue May 25 2004 - 02:54:55 PDT)
- Viktor Hornak (Mon May 24 2004 - 08:19:04 PDT)
- David A. Case (Fri May 21 2004 - 08:23:09 PDT)
- Miguel (Fri May 21 2004 - 02:15:10 PDT)
AMBER: problem for compiling amber7 by ifc8
- scopio (Sun May 02 2004 - 21:18:31 PDT)
- scopio (Sun May 02 2004 - 17:15:58 PDT)
- Viktor Hornak (Sat May 01 2004 - 07:11:49 PDT)
- scopio (Sat May 01 2004 - 05:26:57 PDT)
AMBER: problem in antechamber
- Junmei Wang (Wed May 19 2004 - 15:21:43 PDT)
- Suwipa saen-oon (Wed May 19 2004 - 01:27:24 PDT)
AMBER: problem with MM/PBSA
- Holger Gohlke (Wed May 05 2004 - 03:14:47 PDT)
- Itziar Maestre Asenjo (Tue May 04 2004 - 09:38:32 PDT)
AMBER: problems with mpich
- Viktor Hornak (Fri May 28 2004 - 12:00:15 PDT)
- David A. Case (Fri May 28 2004 - 11:43:23 PDT)
- Chen Yongzhi (Fri May 28 2004 - 11:23:48 PDT)
- David A. Case (Fri May 28 2004 - 09:52:56 PDT)
- Amber admin (Fri May 28 2004 - 07:55:25 PDT)
AMBER: program compatibility
- David A. Case (Sun May 30 2004 - 22:05:15 PDT)
- hj zou (Sun May 30 2004 - 19:07:39 PDT)
AMBER: Program error in testing of Amber8
- Scott Brozell (Sun May 16 2004 - 16:17:44 PDT)
- Do Anh Tuan (Sat May 15 2004 - 21:16:44 PDT)
AMBER: protein is out of the water box
- David A. Case (Wed May 26 2004 - 09:17:00 PDT)
- Feng, Hanqiao (NIH/NCI) (Tue May 25 2004 - 15:35:01 PDT)
AMBER: ptraj
- Holly Freedman (Wed May 26 2004 - 10:30:07 PDT)
- Holly Freedman (Tue May 25 2004 - 17:45:24 PDT)
- scopio (Tue May 25 2004 - 16:49:47 PDT)
- Ross Walker (Tue May 25 2004 - 10:35:39 PDT)
- Holly Freedman (Tue May 25 2004 - 09:16:42 PDT)
AMBER: ptraj analyze matrix entropy
- David A. Case (Mon May 17 2004 - 12:36:41 PDT)
- Holger Gohlke (Mon May 17 2004 - 11:05:57 PDT)
- Holger Gohlke (Fri May 07 2004 - 05:48:51 PDT)
- Marcin Krol (Fri May 07 2004 - 01:01:23 PDT)
- David A. Case (Thu May 06 2004 - 08:29:30 PDT)
- Marcin Krol (Thu May 06 2004 - 06:48:02 PDT)
- Holger Gohlke (Wed May 05 2004 - 09:32:23 PDT)
- Marcin Krol (Wed May 05 2004 - 08:07:05 PDT)
- Holger Gohlke (Wed May 05 2004 - 03:28:57 PDT)
- Marcin Krol (Wed May 05 2004 - 02:19:32 PDT)
AMBER: ptraj and LES
- Guanglei Cui (Wed May 12 2004 - 12:34:31 PDT)
- David A. Case (Wed May 12 2004 - 08:19:00 PDT)
- Guanglei Cui (Tue May 11 2004 - 14:00:12 PDT)
AMBER: ptraj bug?
- Holger Gohlke (Wed May 19 2004 - 08:31:12 PDT)
- Ian Withers (Wed May 19 2004 - 07:33:38 PDT)
AMBER: ptraj read in matrix
- Holger Gohlke (Tue May 11 2004 - 07:45:11 PDT)
- Marcin Krol (Mon May 10 2004 - 04:57:25 PDT)
AMBER: ptraj: radius of gyration
- Bill Ross (Sun May 02 2004 - 13:12:23 PDT)
- Scott Brozell (Sun May 02 2004 - 01:09:12 PDT)
- Sichun Yang (Sat May 01 2004 - 19:50:37 PDT)
AMBER: question about mm-pbsa
- Thomas Steinbrecher (Mon May 10 2004 - 18:10:09 PDT)
- aini.UMDNJ.EDU (Mon May 10 2004 - 17:10:05 PDT)
AMBER: question about NMODE for RNA
- xhu1.memphis.edu (Sun May 30 2004 - 18:53:58 PDT)
- David A. Case (Sun May 30 2004 - 16:14:33 PDT)
- xhu1.memphis.edu (Sun May 30 2004 - 15:32:22 PDT)
AMBER: questions on mm_pbsa
- Holger Gohlke (Tue May 18 2004 - 08:18:24 PDT)
- Fang, Jianwen (Fri May 14 2004 - 11:49:54 PDT)
AMBER: reference with ptraj
- Fernandez-Carmona Juan (Thu May 06 2004 - 23:27:53 PDT)
- Thomas E. Cheatham, III (Thu May 06 2004 - 15:12:18 PDT)
- Bill Ross (Thu May 06 2004 - 15:05:55 PDT)
- Thomas E. Cheatham, III (Thu May 06 2004 - 13:11:58 PDT)
- John (Thu May 06 2004 - 12:50:48 PDT)
AMBER: Removal of rotation: Flying ice cube
- Carlos Simmerling (Tue May 18 2004 - 17:39:59 PDT)
- koby levy (Tue May 18 2004 - 17:23:54 PDT)
AMBER: reorientation in R.E.D
- FyD (Wed May 05 2004 - 10:55:51 PDT)
- Mikyung Seo (Wed May 05 2004 - 09:38:01 PDT)
AMBER: Reproducing the energy during restart in MD!
- Carlos Simmerling (Wed May 19 2004 - 06:41:17 PDT)
- Pradipta Bandyopadhyay (Tue May 18 2004 - 23:33:27 PDT)
AMBER: reproduction of RESP charges for Gly
- FyD (Tue May 04 2004 - 13:48:43 PDT)
- Bill Ross (Tue May 04 2004 - 13:35:49 PDT)
- Bill Ross (Tue May 04 2004 - 13:24:41 PDT)
- FyD (Tue May 04 2004 - 13:16:00 PDT)
- Mikyung Seo (Tue May 04 2004 - 10:51:01 PDT)
AMBER: resp demo files
- FyD (Mon May 03 2004 - 14:40:15 PDT)
- Kristy Mardis (Mon May 03 2004 - 12:29:45 PDT)
AMBER: rmsd over residues using ptraj
- Bill Ross (Wed May 19 2004 - 14:15:01 PDT)
- Qiang Lu (Wed May 19 2004 - 12:19:33 PDT)
- Bill Ross (Wed May 19 2004 - 11:34:08 PDT)
- Qiang Lu (Wed May 19 2004 - 10:19:38 PDT)
- Ty Curtis (Wed May 19 2004 - 09:23:50 PDT)
- Bill Ross (Tue May 18 2004 - 17:57:54 PDT)
- Qiang Lu (Tue May 18 2004 - 17:41:16 PDT)
AMBER: Sander klambda question
- David A. Case (Wed May 05 2004 - 16:43:44 PDT)
- Linda Prengaman (Wed May 05 2004 - 15:14:22 PDT)
AMBER: Sander went through
- bybaker.itsa.ucsf.edu (Sat May 29 2004 - 04:51:26 PDT)
- Rhonda Torres (Fri May 28 2004 - 17:49:44 PDT)
- bybaker.itsa.ucsf.edu (Fri May 28 2004 - 17:19:02 PDT)
AMBER: sander_classic for cap simulations?
- David A. Case (Mon May 17 2004 - 13:18:41 PDT)
- Oliver Hucke (Thu May 13 2004 - 15:43:36 PDT)
AMBER: Scaling nb between groups
- David A. Case (Tue May 25 2004 - 13:52:30 PDT)
- Marcin Krol (Tue May 25 2004 - 08:34:00 PDT)
AMBER: segmentation fault when running parmchk
- Chutintorn Punwong (Fri May 28 2004 - 13:08:56 PDT)
- David A. Case (Thu May 27 2004 - 16:47:49 PDT)
- Chutintorn Punwong (Thu May 27 2004 - 11:37:09 PDT)
- David A. Case (Thu May 27 2004 - 11:24:27 PDT)
- Chutintorn Punwong (Thu May 27 2004 - 11:01:16 PDT)
- David A. Case (Mon May 24 2004 - 21:41:14 PDT)
- Chutintorn Punwong (Mon May 24 2004 - 15:34:11 PDT)
AMBER: separate the longitudinal and transverse vibrations frequencies
- David A. Case (Tue May 04 2004 - 11:15:38 PDT)
- xiaowei li (Mon May 03 2004 - 21:33:11 PDT)
AMBER: SHAKE in thermodynamic integration
- David A. Case (Thu May 20 2004 - 11:01:17 PDT)
- by way of riccardo nifosi (Thu May 20 2004 - 03:38:21 PDT)
AMBER: shake option in sander
- David A. Case (Wed May 12 2004 - 12:11:53 PDT)
- Lishan Yao (Wed May 12 2004 - 06:32:48 PDT)
AMBER: simulated anealing ...vlimit exceed
- anshul.imtech.res.in (Thu May 06 2004 - 16:14:53 PDT)
- anshul.imtech.res.in (Thu May 06 2004 - 14:50:35 PDT)
- Michele Porro (Tue May 11 2004 - 00:24:56 PDT)
- Carlos Simmerling (Thu May 06 2004 - 06:24:02 PDT)
- Carlos Simmerling (Thu May 06 2004 - 04:47:48 PDT)
AMBER: Simulated annealing ...vlimit problem
- Narang Manpreet Kaur (Tue May 18 2004 - 07:09:31 PDT)
- David A. Case (Mon May 17 2004 - 12:27:30 PDT)
- Carlos Simmerling (Mon May 17 2004 - 10:08:56 PDT)
- Venkata S Koppuravuri (Mon May 17 2004 - 10:00:44 PDT)
- anshul.imtech.res.in (Sun May 16 2004 - 13:01:55 PDT)
- David A. Case (Sat May 15 2004 - 09:14:06 PDT)
- Venkata S Koppuravuri (Fri May 14 2004 - 07:22:44 PDT)
AMBER: single amino acid energy
- Holger Gohlke (Tue May 18 2004 - 08:23:26 PDT)
- Helios Chen (Tue May 18 2004 - 01:15:02 PDT)
AMBER: Solvent accessible surface area(LCPO) computation
- David A. Case (Fri May 07 2004 - 08:23:33 PDT)
- Sunil_Koovakkat.berlex.com (Wed May 05 2004 - 14:51:59 PDT)
AMBER: solvent cap and eedmeth
- David A. Case (Fri May 07 2004 - 08:20:18 PDT)
- Oliver Hucke (Thu May 06 2004 - 16:31:42 PDT)
AMBER: solvents reference.
- David A. Case (Fri May 14 2004 - 13:16:06 PDT)
- Herbert Georg (Fri May 14 2004 - 12:56:38 PDT)
AMBER: some bugfixes
- David A. Case (Mon May 10 2004 - 16:10:08 PDT)
- Junmei Wang (Tue May 04 2004 - 12:23:55 PDT)
- Oliver Hucke (Tue May 04 2004 - 11:12:53 PDT)
- Sébastien Osborne (Mon May 03 2004 - 11:14:33 PDT)
- David A. Case (Mon May 03 2004 - 11:10:47 PDT)
AMBER: Surface E&S Potential Mapping
- Ilyas Yildirim (Tue May 25 2004 - 14:14:45 PDT)
AMBER: thermodynamic integration of ring opening
- Bill Ross (Tue May 18 2004 - 12:08:13 PDT)
- M. L. Dodson (Tue May 18 2004 - 05:33:28 PDT)
- Bill Ross (Mon May 17 2004 - 17:10:36 PDT)
- M. L. Dodson (Mon May 17 2004 - 16:46:29 PDT)
- Bill Ross (Mon May 17 2004 - 16:42:25 PDT)
- David A. Case (Mon May 17 2004 - 16:21:15 PDT)
- Bill Ross (Mon May 17 2004 - 15:47:24 PDT)
- Carsten Detering (Mon May 17 2004 - 13:37:42 PDT)
AMBER: time-averaged restraints
- John (Fri May 14 2004 - 10:04:49 PDT)
AMBER: tmd questions
- Viktor Hornak (Thu May 13 2004 - 05:16:36 PDT)
- Carlos Simmerling (Thu May 13 2004 - 04:41:31 PDT)
- hj zou (Wed May 12 2004 - 19:07:36 PDT)
AMBER: torsion angles
- John (Fri May 28 2004 - 16:02:04 PDT)
AMBER: Treating atom type LP the same as EP
- Sarah Wittkopp (Mon May 17 2004 - 12:16:20 PDT)
AMBER: Troubles in the NTP simulation: "vlimit exceeded".
- Bill Ross (Tue May 04 2004 - 09:44:16 PDT)
- David A. Case (Tue May 04 2004 - 08:10:36 PDT)
- Jiten (Tue May 04 2004 - 03:58:20 PDT)
- Ülo Lille (Tue May 04 2004 - 03:16:24 PDT)
AMBER: types of water atom
- Gustavo Pierdominici Sottile (Fri May 28 2004 - 11:25:45 PDT)
- David A. Case (Thu May 27 2004 - 13:34:59 PDT)
- Gustavo Pierdominici Sottile (Thu May 27 2004 - 12:28:27 PDT)
- Piotr Cieplak (Wed May 26 2004 - 10:28:17 PDT)
- Gustavo Pierdominici Sottile (Wed May 26 2004 - 10:06:16 PDT)
AMBER: Use of RED
- FyD (Fri May 28 2004 - 13:20:42 PDT)
- Gustavo Pierdominici Sottile (Fri May 28 2004 - 11:44:26 PDT)
AMBER: what does EAMBER stand for?
- Scott Brozell (Tue May 11 2004 - 10:45:09 PDT)
- David A. Case (Tue May 11 2004 - 10:30:56 PDT)
- scopio (Mon May 10 2004 - 18:08:35 PDT)
AMBER: what is its file format ?
- scopio (Sat May 08 2004 - 07:13:21 PDT)
AMBER: why delete water molecule
- Oliver Hucke (Tue May 04 2004 - 09:23:01 PDT)
- Dr. Yong Duan (Tue May 04 2004 - 07:40:57 PDT)
- Helios Chen (Mon May 03 2004 - 21:18:49 PDT)
AMBER: why EGB = nan
- Fang, Jianwen (Mon May 17 2004 - 07:54:44 PDT)
AMBER: xleap don't recognize formaldehyde?
- anshul.imtech.res.in (Sat May 08 2004 - 12:44:33 PDT)
AMBER: xleap problem
- hj zou (Tue May 04 2004 - 19:44:43 PDT)
- David A. Case (Mon May 03 2004 - 08:45:34 PDT)
- scopio (Mon May 03 2004 - 01:51:03 PDT)
- hj zou (Mon May 03 2004 - 01:02:34 PDT)
- Oliver Hucke (Sun May 02 2004 - 15:53:42 PDT)
- David A. Case (Sun May 02 2004 - 14:07:20 PDT)
- hj zou (Sun May 02 2004 - 06:49:40 PDT)
AMBER: xleap solvatebox problem
- David A. Case (Thu May 27 2004 - 08:42:48 PDT)
- Tomas Kubar (Thu May 27 2004 - 05:33:44 PDT)
CCL:Helical parameters extraction from trajectory
- Peter Gannett (Fri May 28 2004 - 04:47:08 PDT)
Extreme Privacy Violation 4896
- Deanna Yarbro (Wed May 19 2004 - 09:48:11 PDT)
Five Fingered F'in amber Unreal Photos
- Fist Action (Fri May 14 2004 - 23:23:18 PDT)
- Fist Action (Fri May 14 2004 - 23:23:15 PDT)
Request to mailing list Ahmadis rejected
- ahmadis-bounces.imperial.ac.uk (Fri May 21 2004 - 05:31:19 PDT)

Amber Archive May 2004 by subject