AMBER Archive (2004) - Dec 2004 By Subject

214 messages sorted by: [ author ] [ date ] [ thread ]
About this archive

Starting: Wed Dec 01 2004 - 02:46:54 CST
Ending: Fri Dec 31 2004 - 10:49:58 CST

AMBER:
- David A. Case (Wed Dec 08 2004 - 13:49:41 CST)
- Wanxin Sun (Mon Dec 06 2004 - 09:06:25 CST)
AMBER: (no subject)
- David A. Case (Tue Dec 07 2004 - 07:00:49 CST)
- Andrew Box (Mon Dec 06 2004 - 21:32:52 CST)
AMBER: 1-4 EEL
- David A. Case (Wed Dec 08 2004 - 12:13:08 CST)
- tang kwa (Tue Dec 07 2004 - 11:12:54 CST)
AMBER: a question
- David A. Case (Tue Dec 21 2004 - 16:07:51 CST)
- Germán Sciaini (Tue Dec 21 2004 - 08:10:14 CST)
AMBER: About MM/PBSA, PB Calculation
- nlxc (Thu Dec 16 2004 - 16:31:13 CST)
- David A. Case (Thu Dec 16 2004 - 11:38:32 CST)
- nlxc (Wed Dec 15 2004 - 17:11:29 CST)
AMBER: amber7 on digital unix
- David A. Case (Thu Dec 23 2004 - 12:26:55 CST)
- anshul_at_imtech.res.in (Thu Dec 23 2004 - 21:15:47 CST)
- David A. Case (Thu Dec 23 2004 - 10:18:46 CST)
- anshul_at_imtech.res.in (Thu Dec 23 2004 - 16:23:15 CST)
AMBER: Binding free energy from separate/single trajectory
- yuann (Sun Dec 12 2004 - 23:01:17 CST)
AMBER: calculate ligand's rmsd
- Ross Walker (Thu Dec 09 2004 - 00:00:30 CST)
- Yong Xu (Thu Dec 09 2004 - 00:11:15 CST)
AMBER: cluster analysis with ptraj in amber 8.0
- David Smith (Tue Dec 21 2004 - 02:47:46 CST)
- Eric Hu (Mon Dec 20 2004 - 20:01:26 CST)
AMBER: cobalt parameters
- Peter Gannett (Mon Dec 13 2004 - 19:21:50 CST)
AMBER: Compiling Antechamber/Amber8 with ia64_ifort
- Jack Lei (Mon Dec 06 2004 - 09:11:05 CST)
- Andreas Svrcek-Seiler (Mon Dec 06 2004 - 02:56:34 CST)
- Toru Yagi (Mon Dec 06 2004 - 00:25:02 CST)
AMBER: Compiling question
- Yanze Zhang (Tue Dec 14 2004 - 14:11:07 CST)
- James W. Caldwell (Tue Dec 14 2004 - 14:10:19 CST)
- Robert Duke (Tue Dec 14 2004 - 13:51:20 CST)
- Ross Walker (Tue Dec 14 2004 - 13:44:27 CST)
- David A. Case (Tue Dec 14 2004 - 13:33:34 CST)
- Yanze Zhang (Tue Dec 14 2004 - 13:27:53 CST)
AMBER: constraints on atoms
- David A. Case (Tue Dec 21 2004 - 11:12:55 CST)
- cailliez (Mon Dec 20 2004 - 05:06:19 CST)
AMBER: converting from NAMD trajectory format
- Thomas E. Cheatham, III (Wed Dec 08 2004 - 18:53:50 CST)
- Stern, Julie (Mon Dec 06 2004 - 17:02:49 CST)
AMBER: cut-off & MD
- Ross Walker (Mon Dec 06 2004 - 15:17:30 CST)
- bybaker_at_itsa.ucsf.edu (Mon Dec 06 2004 - 14:49:04 CST)
AMBER: Dielectric Constant
- David A. Case (Sat Dec 04 2004 - 17:15:10 CST)
- Bill Ross (Sat Dec 04 2004 - 14:22:33 CST)
- Marsita M (Sat Dec 04 2004 - 05:42:36 CST)
AMBER: Dummy Atoms: How to create them?
- David A. Case (Thu Dec 30 2004 - 21:55:59 CST)
- Ilyas Yildirim (Thu Dec 30 2004 - 19:23:02 CST)
AMBER: Dummy torsion paramters for thermodynamic integration
- David A. Case (Tue Dec 21 2004 - 09:49:29 CST)
- Thomas Steinbrecher (Tue Dec 21 2004 - 02:25:31 CST)
AMBER: energy unit
- Harianto (Thu Dec 23 2004 - 10:25:32 CST)
- Chen Song (Wed Dec 22 2004 - 23:20:00 CST)
AMBER: entropy implementation in ptraj
- David A. Case (Fri Dec 17 2004 - 10:11:29 CST)
- Raik Grünberg (Fri Dec 17 2004 - 08:44:13 CST)
- David A. Case (Wed Dec 15 2004 - 12:07:50 CST)
- Raik Grünberg (Tue Dec 14 2004 - 11:37:18 CST)
AMBER: Ewald
- David A. Case (Wed Dec 15 2004 - 12:17:04 CST)
- tang kwa (Wed Dec 15 2004 - 10:31:41 CST)
AMBER: extracting energy from trajector?
- David Smith (Thu Dec 02 2004 - 15:30:59 CST)
- MURAT CETINKAYA (Thu Dec 02 2004 - 14:56:47 CST)
AMBER: FEP along a reaction coordinate in sander
- David A. Case (Wed Dec 01 2004 - 11:38:45 CST)
- Masataka Nagaoka (Wed Dec 01 2004 - 06:05:01 CST)
- Tomasz Borowski (Wed Dec 01 2004 - 02:46:54 CST)
AMBER: Free Energy Perturbation using Sander (TI Method)
- Ilyas Yildirim (Wed Dec 15 2004 - 20:43:09 CST)
AMBER: General Question about AMBER's Free Energy Perturbation Method
- David A. Case (Fri Dec 17 2004 - 17:26:34 CST)
- Ilyas Yildirim (Fri Dec 17 2004 - 15:53:07 CST)
- David A. Case (Thu Dec 16 2004 - 01:03:18 CST)
- Ilyas Yildirim (Wed Dec 15 2004 - 22:13:07 CST)
AMBER: Gigabit Ethernet Switch/Opteron 246
- Ross Walker (Tue Dec 07 2004 - 12:11:24 CST)
- jianhui wu (Tue Dec 07 2004 - 11:09:11 CST)
AMBER: How is optimization done during energy minimization of the force field?
- myang (Fri Dec 31 2004 - 10:49:58 CST)
- fangyu liang (Thu Dec 30 2004 - 23:11:28 CST)
AMBER: how to prepare Zn.lib
- Ross Walker (Fri Dec 10 2004 - 12:29:24 CST)
- Yong Xu (Fri Dec 10 2004 - 01:50:16 CST)
AMBER: Ideal bonds and angles
- David A. Case (Tue Dec 21 2004 - 12:52:15 CST)
- Nhat-hang Duong (Tue Dec 21 2004 - 11:49:38 CST)
AMBER: imin=5 in sander
- Asim Okur (Tue Dec 07 2004 - 14:44:52 CST)
- Asim Okur (Tue Dec 07 2004 - 14:47:38 CST)
- Carlos Simmerling (Mon Dec 06 2004 - 19:52:14 CST)
- MURAT CETINKAYA (Tue Dec 07 2004 - 13:07:34 CST)
AMBER: Implicit 4r md
- David A. Case (Fri Dec 03 2004 - 10:48:00 CST)
- yen li (Thu Dec 02 2004 - 23:14:06 CST)
- Stefano.Pieraccini_at_unimi.it (Wed Dec 01 2004 - 02:52:27 CST)
AMBER: Implicit Solvent Models
- David A. Case (Fri Dec 10 2004 - 10:51:12 CST)
- Nelson Fonseca (Thu Dec 09 2004 - 06:02:10 CST)
AMBER: increasing the maximum value of NPHB parameter
- Alena Shmygelska (Thu Dec 02 2004 - 01:42:44 CST)
AMBER: input conversion error [Amber8]
- Bimo Ario Tejo (Tue Dec 28 2004 - 23:15:58 CST)
AMBER: install problem
- David A. Case (Tue Dec 07 2004 - 07:03:12 CST)
- Kevin Murphy (Tue Dec 07 2004 - 04:23:11 CST)
AMBER: Kinetics energy
- Andreas Svrcek-Seiler (Mon Dec 20 2004 - 04:11:10 CST)
- Carlos Simmerling (Sat Dec 18 2004 - 13:07:11 CST)
- Germán Sciaini (Sat Dec 18 2004 - 11:54:04 CST)
AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem)
- Tru Huynh (Thu Dec 02 2004 - 14:00:17 CST)
- David A. Case (Wed Dec 01 2004 - 11:44:12 CST)
AMBER: MD simulations on heparin and heparin sulfate
- Harald Lanig (Thu Dec 30 2004 - 10:23:24 CST)
AMBER: md's
- yen li (Mon Dec 06 2004 - 10:08:07 CST)
AMBER: MD: Water network analysis + visualization
- Sanjeev B.S. (Fri Dec 17 2004 - 12:23:22 CST)
AMBER: mm_gbsa results for charged ligands
- Holger Gohlke (Fri Dec 24 2004 - 04:31:22 CST)
- Cenk Andac (Fri Dec 24 2004 - 03:50:10 CST)
AMBER: mm_pbsa
- Carsten Detering (Wed Dec 15 2004 - 15:57:13 CST)
AMBER: mm_pbsa +fillratio
- Jiten (Fri Dec 31 2004 - 03:31:57 CST)
AMBER: MM_PBSA calculation error
- Jiten (Thu Dec 30 2004 - 04:57:30 CST)
AMBER: MM_PBSA calculations
- Jiten (Thu Dec 30 2004 - 01:22:25 CST)
AMBER: Molecular modelling.
- David A. Case (Thu Dec 23 2004 - 20:03:50 CST)
- Osman Gani (Thu Dec 23 2004 - 08:44:05 CST)
AMBER: nanotube parameters
- Andreas Svrcek-Seiler (Mon Dec 20 2004 - 04:02:56 CST)
- David A. Case (Fri Dec 17 2004 - 17:34:31 CST)
- Bill Ross (Fri Dec 17 2004 - 15:52:13 CST)
- MURAT CETINKAYA (Fri Dec 17 2004 - 14:28:24 CST)
AMBER: nmode & mm-pbsa
- Shekter, Lee (Thu Dec 02 2004 - 20:50:45 CST)
AMBER: nmode problem
- Yong Xu (Thu Dec 16 2004 - 22:16:23 CST)
AMBER: NMR constraint problem
- John Bushnell (Wed Dec 08 2004 - 14:39:32 CST)
- David A. Case (Wed Dec 08 2004 - 12:08:11 CST)
- Andrew Box (Tue Dec 07 2004 - 21:06:02 CST)
AMBER: No radius found for 2412 Zn Zn
- Yong Xu (Fri Dec 10 2004 - 23:53:18 CST)
- Jack Lei (Fri Dec 10 2004 - 08:49:53 CST)
- Holger Gohlke (Fri Dec 10 2004 - 04:22:19 CST)
- Yong Xu (Fri Dec 10 2004 - 03:15:14 CST)
- Holger Gohlke (Fri Dec 10 2004 - 02:21:45 CST)
- Yong Xu (Fri Dec 10 2004 - 01:13:37 CST)
AMBER: nrespa=2
- Carlos Simmerling (Tue Dec 21 2004 - 09:54:15 CST)
- David A. Case (Tue Dec 21 2004 - 09:52:53 CST)
- Marsita M (Tue Dec 21 2004 - 09:19:58 CST)
AMBER: NSCM
- Alberto p (Wed Dec 29 2004 - 06:07:48 CST)
AMBER: ntt parameter
- Ross Walker (Fri Dec 03 2004 - 01:11:31 CST)
- David Smith (Thu Dec 02 2004 - 04:30:01 CST)
- David A. Case (Wed Dec 01 2004 - 18:14:30 CST)
- tang kwa (Wed Dec 01 2004 - 15:32:22 CST)
AMBER: one question about dielectric dependent model
- Xiaowei (David) Li (Sun Dec 05 2004 - 11:42:56 CST)
AMBER: Output of sander
- David A. Case (Thu Dec 23 2004 - 15:35:49 CST)
- Harianto (Thu Dec 23 2004 - 14:36:27 CST)
- David A. Case (Wed Dec 22 2004 - 11:35:27 CST)
- Harianto (Wed Dec 22 2004 - 10:09:37 CST)
AMBER: parameter development
- David A. Case (Tue Dec 21 2004 - 10:53:19 CST)
- Sebastian Fernandez Alberti (Mon Dec 20 2004 - 13:34:42 CST)
AMBER: pbsa error in mm_pbsa amber 8
- Ray Luo (Thu Dec 16 2004 - 17:58:29 CST)
- Ben Cossins (Wed Dec 15 2004 - 06:04:50 CST)
- Ray Luo (Wed Dec 15 2004 - 00:17:01 CST)
- david.evans_at_ulsop.ac.uk (Tue Dec 14 2004 - 09:28:24 CST)
- Ben Cossins (Tue Dec 14 2004 - 07:41:08 CST)
- Ray Luo (Fri Dec 10 2004 - 15:36:53 CST)
- Ray Luo (Fri Dec 10 2004 - 12:17:07 CST)
- Ben Cossins (Fri Dec 10 2004 - 07:05:33 CST)
- david.evans_at_ulsop.ac.uk (Thu Dec 09 2004 - 10:15:52 CST)
- Ben Cossins (Thu Dec 09 2004 - 09:19:20 CST)
- Ben Cossins (Thu Dec 09 2004 - 08:58:19 CST)
AMBER: Problem with computing Resp charges using RED
- Cenk Andac (Thu Dec 30 2004 - 11:30:34 CST)
- FyD (Wed Dec 29 2004 - 14:54:05 CST)
- Cenk Andac (Sat Dec 25 2004 - 09:54:54 CST)
AMBER: ptraj hbond memory allocation on opteron
- Fabian Boes (Tue Dec 14 2004 - 08:33:42 CST)
- Andreas Svrcek-Seiler (Mon Dec 13 2004 - 10:07:25 CST)
- Fabian Boes (Mon Dec 13 2004 - 06:07:11 CST)
AMBER: ptraj questions
- Oliver Hucke (Wed Dec 01 2004 - 11:59:06 CST)
AMBER: question about md's
- yen li (Fri Dec 10 2004 - 09:27:39 CST)
AMBER: question about MGB and PB
- xhu1_at_memphis.edu (Fri Dec 10 2004 - 16:12:30 CST)
AMBER: question about mmpbsa
- xhu1_at_memphis.edu (Wed Dec 08 2004 - 16:23:27 CST)
- cailliez (Wed Dec 08 2004 - 12:23:01 CST)
- xhu1_at_memphis.edu (Tue Dec 07 2004 - 19:20:19 CST)
AMBER: question about parallel simulation
- Ross Walker (Thu Dec 02 2004 - 16:37:12 CST)
- qlu_at_notes.cc.sunysb.edu (Thu Dec 02 2004 - 15:28:43 CST)
- qlu_at_notes.cc.sunysb.edu (Thu Dec 02 2004 - 14:30:28 CST)
- Ross Walker (Wed Dec 01 2004 - 19:00:33 CST)
- qlu_at_notes.cc.sunysb.edu (Wed Dec 01 2004 - 17:38:01 CST)
- Ross Walker (Wed Dec 01 2004 - 14:40:19 CST)
- qlu_at_notes.cc.sunysb.edu (Wed Dec 01 2004 - 13:17:43 CST)
AMBER: Question concerning ANAL total energy calculation
- David A. Case (Mon Dec 20 2004 - 16:10:08 CST)
- Daniel Wetzler (Mon Dec 20 2004 - 15:15:12 CST)
- David A. Case (Sat Dec 18 2004 - 10:50:01 CST)
- Daniel Wetzler (Sat Dec 18 2004 - 03:33:26 CST)
- David A. Case (Fri Dec 17 2004 - 09:58:49 CST)
- Daniel Wetzler (Fri Dec 17 2004 - 06:04:05 CST)
AMBER: Question on tleap of amber8
- David A. Case (Mon Dec 20 2004 - 11:27:07 CST)
- Okimoto Noriaki (Mon Dec 20 2004 - 03:00:38 CST)
AMBER: Residue Loading Problem
- David A. Case (Thu Dec 16 2004 - 20:10:43 CST)
- david.evans_at_ulsop.ac.uk (Fri Dec 03 2004 - 03:41:13 CST)
- Furse, Kristina Elisabet (Fri Dec 03 2004 - 01:23:05 CST)
- Garhan Attebury (Fri Dec 03 2004 - 00:20:51 CST)
AMBER: restrainted torsion
- David A. Case (Thu Dec 02 2004 - 13:12:19 CST)
- tang kwa (Thu Dec 02 2004 - 07:18:43 CST)
AMBER: RMSD of ligand
- Yong Xu (Thu Dec 23 2004 - 18:26:14 CST)
AMBER: sander imin=5
- MURAT CETINKAYA (Thu Dec 16 2004 - 02:01:45 CST)
AMBER: Sander TI
- David A. Case (Tue Dec 21 2004 - 10:15:50 CST)
- Cai, Yufeng (Mon Dec 20 2004 - 12:11:29 CST)
AMBER: some questions....
- David A. Case (Wed Dec 08 2004 - 12:04:13 CST)
- Germán Sciaini (Wed Dec 08 2004 - 10:49:55 CST)
AMBER: strange bond energies
- Carlos Simmerling (Mon Dec 06 2004 - 08:22:10 CST)
- Magne Olufsen (Mon Dec 06 2004 - 07:42:16 CST)
AMBER: SUSE 9.1 and AMBER 8
- Cenk Andac (Wed Dec 01 2004 - 21:04:31 CST)
- Ilyas Yildirim (Wed Dec 01 2004 - 15:12:49 CST)
AMBER: TFE parameters
- Adrian E. Roitberg (Tue Dec 21 2004 - 14:34:29 CST)
AMBER: unknown elements
- David A. Case (Wed Dec 15 2004 - 12:00:32 CST)
- Youyi Peng (Wed Dec 15 2004 - 10:33:54 CST)
AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules
- David A. Case (Wed Dec 22 2004 - 18:39:57 CST)
- Jianwen Jiang (Wed Dec 22 2004 - 15:59:47 CST)
- David A. Case (Wed Dec 22 2004 - 15:50:00 CST)
- Jianwen Jiang (Wed Dec 22 2004 - 14:01:40 CST)
- Ross Walker (Tue Dec 21 2004 - 23:26:48 CST)
- Jianwen Jiang (Tue Dec 21 2004 - 20:22:00 CST)
- Bill Ross (Tue Dec 21 2004 - 16:57:13 CST)
- Jianwen Jiang (Tue Dec 21 2004 - 16:30:47 CST)
- Ross Walker (Mon Dec 20 2004 - 18:55:17 CST)
- Ilyas Yildirim (Mon Dec 20 2004 - 18:42:29 CST)
- Jianwen Jiang (Mon Dec 20 2004 - 18:18:52 CST)
AMBER: Why the charge is not an integer?
- John Mongan (Tue Dec 14 2004 - 21:10:49 CST)
- Annette Höglund (Tue Dec 14 2004 - 01:39:11 CST)
- Ross Walker (Mon Dec 13 2004 - 12:15:13 CST)
- David A. Case (Sun Dec 12 2004 - 15:05:57 CST)
- FyD (Sun Dec 12 2004 - 13:47:02 CST)
- Guanglei Cui (Sun Dec 12 2004 - 10:21:32 CST)
- mmv (Sun Dec 12 2004 - 03:44:36 CST)
AMBER: Why the surface calculations sometimes fail?
- David A. Case (Thu Dec 16 2004 - 11:32:29 CST)
- hj zou (Wed Dec 15 2004 - 22:12:59 CST)
- David A. Case (Mon Dec 13 2004 - 20:29:17 CST)
- hj zou (Wed Dec 08 2004 - 19:58:19 CST)
- David A. Case (Wed Dec 08 2004 - 13:52:29 CST)
- hj zou (Wed Dec 08 2004 - 00:53:09 CST)
AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation
- Ilyas Yildirim (Wed Dec 15 2004 - 18:47:05 CST)
- Ross Walker (Tue Dec 14 2004 - 11:53:58 CST)
- Ilyas Yildirim (Mon Dec 13 2004 - 22:34:34 CST)
two processor amd 64 bit pc
- Ross Walker (Mon Dec 06 2004 - 21:17:41 CST)
- Spero Manolatos (Mon Dec 06 2004 - 19:36:33 CST)

Last message date: Thu May 05 2005 - 14:26:38 CDT
Archived on: Thu May 05 2005 - 14:30:04 CDT

214 messages sorted by: [ author ] [ date ] [ thread ]
About this archive