Amber Archive May 2007: by subject

[AMBER] defining the mixed 1-4 scaling in amber 11 and sleap
- Toshifumi Yui (Thu May 03 2007 - 18:25:51 PDT)
- Toshifumi Yui (Thu May 03 2007 - 05:18:52 PDT)
AMBER:
- Steve Seibold (Thu May 24 2007 - 12:00:09 PDT)
AMBER: (no subject)
- M. L. Dodson (Wed May 30 2007 - 10:54:04 PDT)
- Catein Catherine (Wed May 30 2007 - 08:16:19 PDT)
- Catein Catherine (Tue May 22 2007 - 22:00:36 PDT)
- David A. Case (Thu May 10 2007 - 13:37:21 PDT)
- Dingguo Xu (Wed May 09 2007 - 14:29:58 PDT)
AMBER: 64-bit pgf90 revisited
- Ingvar Lagerstedt (Tue May 29 2007 - 01:39:07 PDT)
AMBER: [AMBER] QM/MM-DFTB
- 박민희 (Sun May 20 2007 - 18:55:42 PDT)
AMBER: adding polar hydrogens
- j j (Thu May 24 2007 - 06:00:12 PDT)
- j j (Thu May 24 2007 - 04:09:04 PDT)
AMBER: Amber 9 compile on OS X
- David A. Case (Thu May 10 2007 - 16:48:49 PDT)
- Knut Langsetmo (Wed May 09 2007 - 14:29:44 PDT)
AMBER: Amber 9 install on Debian Linux amd64
- Francesco Pietra (Mon May 28 2007 - 00:14:49 PDT)
AMBER: AMBER8 compiler with intel 9.1 compiler
- Scott Brozell (Fri May 25 2007 - 10:45:55 PDT)
- Peter Z. Qin (Fri May 25 2007 - 09:49:13 PDT)
- Peter Z. Qin (Tue May 22 2007 - 22:39:18 PDT)
- Scott Brozell (Tue May 22 2007 - 19:20:26 PDT)
- Peter Z. Qin (Fri May 18 2007 - 17:53:29 PDT)
- Mark Williamson (Fri May 18 2007 - 05:19:37 PDT)
- David A. Case (Thu May 17 2007 - 18:38:00 PDT)
- David A. Case (Thu May 17 2007 - 18:32:55 PDT)
- Peter Z. Qin (Thu May 17 2007 - 16:17:29 PDT)
- Peter Z. Qin (Thu May 17 2007 - 15:49:39 PDT)
- David A. Case (Wed May 16 2007 - 14:01:21 PDT)
- Peter Z. Qin (Wed May 16 2007 - 13:37:53 PDT)
- Scott Brozell (Wed May 16 2007 - 11:42:06 PDT)
- Peter Z. Qin (Tue May 15 2007 - 18:37:22 PDT)
AMBER: ambpdb gives empty cpin
- tri nam Vo (Tue May 22 2007 - 07:01:42 PDT)
- Achuth Prabhu (Mon May 21 2007 - 01:27:16 PDT)
AMBER: Antechamber
- Francesco Pietra (Mon May 28 2007 - 00:20:55 PDT)
- Cenk Andac (Sun May 27 2007 - 23:56:57 PDT)
- Catein Catherine (Sun May 27 2007 - 17:45:42 PDT)
- David A. Case (Sat May 12 2007 - 10:13:39 PDT)
- Santanu Roy (Fri May 11 2007 - 22:50:13 PDT)
- Scott Brozell (Fri May 11 2007 - 15:46:24 PDT)
- Santanu Roy (Fri May 11 2007 - 06:40:24 PDT)
AMBER: antechamber question
- Junmei Wang (Tue May 22 2007 - 08:08:18 PDT)
- Yao Xin (Tue May 22 2007 - 06:39:41 PDT)
- Francesco Pietra (Sun May 20 2007 - 08:36:28 PDT)
- David A. Case (Sun May 20 2007 - 07:44:18 PDT)
- Francesco Pietra (Sun May 20 2007 - 00:05:59 PDT)
AMBER: assigning of head atom as null.
- SHARAD gupta (Tue May 15 2007 - 00:26:23 PDT)
AMBER: Atomic positional Fluctuations
- Sandeep Kaushik (Wed May 30 2007 - 06:08:09 PDT)
AMBER: Atoms closer to 2 angstroms to each other
- Ross Walker (Mon May 07 2007 - 08:30:29 PDT)
- David A. Case (Mon May 07 2007 - 07:55:30 PDT)
- Christopher Gaughan (Mon May 07 2007 - 07:38:06 PDT)
AMBER: Average PDB - Unusual Bonds
- Ross Walker (Fri May 04 2007 - 08:29:36 PDT)
- Hayden Eastwood (Fri May 04 2007 - 07:45:01 PDT)
- Seth Lilavivat (Fri May 04 2007 - 07:12:25 PDT)
AMBER: Average structure
- Thomas Cheatham (Thu May 17 2007 - 07:57:12 PDT)
- Steve Seibold (Thu May 17 2007 - 07:33:41 PDT)
AMBER: B or E Dihedral Labels in RDPARM output
- Thomas Cheatham III (Fri May 04 2007 - 08:24:07 PDT)
- Mark Williamson (Fri May 04 2007 - 07:04:17 PDT)
AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8
- kkirschn.hamilton.edu (Wed May 30 2007 - 13:28:55 PDT)
- Carlos Simmerling (Wed May 30 2007 - 10:50:05 PDT)
- Andrew Borgert (Wed May 30 2007 - 10:35:51 PDT)
AMBER: binding energy_decomposition per residue
- Srinivas Odde (Fri May 11 2007 - 14:39:50 PDT)
AMBER: bug in reprocessing with PB?
- Ray Luo (Thu May 10 2007 - 14:04:42 PDT)
- David Mobley (Thu May 10 2007 - 12:20:26 PDT)
- David Mobley (Thu May 10 2007 - 12:18:23 PDT)
- David A. Case (Thu May 10 2007 - 11:24:20 PDT)
- Ray Luo (Thu May 10 2007 - 11:52:37 PDT)
- Carlos Simmerling (Thu May 10 2007 - 11:14:08 PDT)
- David Mobley (Thu May 10 2007 - 11:08:10 PDT)
AMBER: Calculating RMS for each residue?
- tri nam Vo (Sun May 27 2007 - 09:01:38 PDT)
AMBER: Chemical shift: simulation vs. experiment
- Mingfeng Yang (Fri May 04 2007 - 00:52:48 PDT)
- Mingfeng Yang (Fri May 04 2007 - 00:17:04 PDT)
- Adrian Roitberg (Thu May 03 2007 - 23:42:55 PDT)
- Mingfeng Yang (Thu May 03 2007 - 22:16:30 PDT)
- Mingfeng Yang (Thu May 03 2007 - 18:07:05 PDT)
AMBER: command line alternatives for teLeap
- David A. Case (Thu May 03 2007 - 07:30:00 PDT)
- Neelanjana Sengupta (Wed May 02 2007 - 21:21:07 PDT)
AMBER: Compiling parallel Amber9 on Linux cluster
- Ross Walker (Wed May 09 2007 - 08:27:36 PDT)
- Jesus Angulo (Wed May 09 2007 - 03:27:23 PDT)
AMBER: Complexes
- M. L. Dodson (Tue May 08 2007 - 12:26:11 PDT)
- M. L. Dodson (Tue May 08 2007 - 12:14:59 PDT)
- Beale, John (Tue May 08 2007 - 11:54:34 PDT)
AMBER: constant pH with 25 titrable sites
- tri nam Vo (Tue May 15 2007 - 10:44:22 PDT)
AMBER: correlation between PBTOT and GBTOT values in a MD trajectory
- Ray Luo (Fri May 11 2007 - 09:54:21 PDT)
- Giulio Rastelli (Fri May 11 2007 - 07:47:39 PDT)
AMBER: Covert NOEs form Xplor to Amber
- saccenti.cerm.unifi.it (Wed May 09 2007 - 07:09:12 PDT)
AMBER: cutoff & speed-up of GBSA
- Julien Michel (Thu May 31 2007 - 14:24:11 PDT)
- Wei Chen (Thu May 31 2007 - 13:50:54 PDT)
- David A. Case (Thu May 31 2007 - 13:31:42 PDT)
- Carlos Simmerling (Thu May 31 2007 - 13:30:00 PDT)
- Wei Chen (Thu May 31 2007 - 13:18:09 PDT)
- Carlos Simmerling (Wed May 30 2007 - 14:59:41 PDT)
- Wei Chen (Wed May 30 2007 - 13:27:53 PDT)
AMBER: deeper problem with the energetics
- Carlos Simmerling (Mon May 21 2007 - 07:11:58 PDT)
- Pankaj R. Daga (Thu May 17 2007 - 09:50:11 PDT)
- Carlos Simmerling (Thu May 17 2007 - 06:56:43 PDT)
- Pankaj R. Daga (Thu May 17 2007 - 06:46:33 PDT)
AMBER: dielectric constant in GB/SA
- Shuting Wei (Mon May 21 2007 - 13:25:12 PDT)
AMBER: distance.restraint for two groups of atoms (center of mass)
- David A. Case (Sat May 12 2007 - 10:18:59 PDT)
- Catein Catherine (Fri May 11 2007 - 19:30:36 PDT)
AMBER: DivCon calculation in Amber9
- Wang, Xuelin (Thu May 03 2007 - 12:51:35 PDT)
AMBER: divcon missing in Antechamber 1.27
- David A. Case (Tue May 29 2007 - 07:24:20 PDT)
- Neelanjana Sengupta (Mon May 28 2007 - 19:18:08 PDT)
- David A. Case (Mon May 28 2007 - 18:33:52 PDT)
- Neelanjana Sengupta (Mon May 28 2007 - 17:54:18 PDT)
AMBER: Docking with AMber
- David A. Case (Mon May 21 2007 - 21:26:07 PDT)
- Urszula Uciechowska (Mon May 21 2007 - 00:13:01 PDT)
AMBER: electric field calculation
- David A. Case (Thu May 31 2007 - 09:44:34 PDT)
- lishan yao (Thu May 31 2007 - 06:33:20 PDT)
- David A. Case (Wed May 30 2007 - 16:14:37 PDT)
- lishan yao (Wed May 30 2007 - 05:25:16 PDT)
AMBER: Electrostatic Energy in MD Simulation (GB)
- David A. Case (Thu May 10 2007 - 10:45:45 PDT)
- adelene.Stanford.EDU (Thu May 10 2007 - 10:20:32 PDT)
AMBER: Energy Spread using GB & Langevin Dynamics (NAB)
- David A. Case (Tue May 15 2007 - 09:03:52 PDT)
- Andreas Svrcek-Seiler (Tue May 15 2007 - 02:20:16 PDT)
- David A. Case (Mon May 14 2007 - 14:40:50 PDT)
- adelene.Stanford.EDU (Mon May 14 2007 - 13:17:28 PDT)
AMBER: error in running sander
- devrani mitra (Wed May 30 2007 - 16:39:47 PDT)
- devrani mitra (Wed May 30 2007 - 16:34:41 PDT)
- Ross Walker (Tue May 29 2007 - 19:49:37 PDT)
- Thomas Cheatham (Tue May 29 2007 - 20:03:36 PDT)
- devrani mitra (Tue May 29 2007 - 18:12:59 PDT)
- devrani mitra (Tue May 29 2007 - 17:41:57 PDT)
- Ross Walker (Tue May 29 2007 - 15:08:30 PDT)
- Carlos Simmerling (Tue May 29 2007 - 15:06:29 PDT)
- devrani mitra (Tue May 29 2007 - 15:01:40 PDT)
- Carlos Simmerling (Tue May 29 2007 - 14:33:42 PDT)
- devrani mitra (Tue May 29 2007 - 14:27:09 PDT)
- Carlos Simmerling (Tue May 29 2007 - 13:47:24 PDT)
- devrani mitra (Tue May 29 2007 - 13:22:35 PDT)
AMBER: Finding x-displacement
- Ben Tan (Tue May 15 2007 - 02:23:11 PDT)
AMBER: GB Energy Spreads for MD Structures
- David A. Case (Mon May 07 2007 - 14:13:41 PDT)
- adelene.Stanford.EDU (Mon May 07 2007 - 12:19:47 PDT)
AMBER: grid output: bulk water density
- mathew k varghese (Fri May 25 2007 - 03:19:30 PDT)
AMBER: Group declaration question
- Bill Ross (Wed May 02 2007 - 12:10:23 PDT)
- cristian obiol (Wed May 02 2007 - 02:28:19 PDT)
AMBER: hbond ptraj
- Thomas Cheatham (Thu May 17 2007 - 07:32:15 PDT)
- Chris Moth (Thu May 17 2007 - 05:14:31 PDT)
- Catein Catherine (Wed May 16 2007 - 23:33:31 PDT)
- Thomas Cheatham (Wed May 16 2007 - 20:57:46 PDT)
- Catein Catherine (Wed May 16 2007 - 20:39:02 PDT)
AMBER: hbond ptraj pls help.
- Kateryna Miroshnychenko (Wed May 23 2007 - 04:22:18 PDT)
- Catein Catherine (Wed May 23 2007 - 03:17:27 PDT)
- Kateryna Miroshnychenko (Wed May 23 2007 - 02:01:03 PDT)
- Catein Catherine (Tue May 22 2007 - 21:56:50 PDT)
AMBER: Heat of Vaporization
- Rita Cassia (Wed May 16 2007 - 04:55:49 PDT)
- David A. Case (Tue May 15 2007 - 13:14:24 PDT)
- Falck da Silva Eirik (Tue May 15 2007 - 13:00:31 PDT)
- David A. Case (Tue May 15 2007 - 09:51:36 PDT)
- Thomas Cheatham III (Tue May 15 2007 - 09:37:01 PDT)
- David A. Case (Tue May 15 2007 - 09:09:27 PDT)
- Rita Cassia (Tue May 15 2007 - 05:35:49 PDT)
AMBER: high energy with mm_gbsa igb=5
- AYTUG TUNCEL (Thu May 17 2007 - 23:39:43 PDT)
- AYTUG TUNCEL (Thu May 17 2007 - 02:53:07 PDT)
AMBER: how to solvate the protein with different solvents
- Rachel (Fri May 11 2007 - 06:01:07 PDT)
AMBER: hybrid remd
- Geoff Wood (Thu May 10 2007 - 12:24:55 PDT)
- Carlos Simmerling (Thu May 10 2007 - 06:39:43 PDT)
- Geoff Wood (Thu May 10 2007 - 04:49:59 PDT)
- Carlos Simmerling (Thu May 10 2007 - 04:20:14 PDT)
- Geoff Wood (Wed May 09 2007 - 14:30:50 PDT)
- Carlos Simmerling (Wed May 09 2007 - 14:18:05 PDT)
- Geoff Wood (Wed May 09 2007 - 14:13:32 PDT)
- Carlos Simmerling (Wed May 09 2007 - 13:52:03 PDT)
- Geoff Wood (Wed May 09 2007 - 13:38:45 PDT)
- Asim Okur (Wed May 09 2007 - 12:07:59 PDT)
- Geoff Wood (Wed May 09 2007 - 04:22:09 PDT)
- Geoff Wood (Wed May 09 2007 - 03:15:16 PDT)
AMBER: Hydration points
- Cenk Andac (Wed May 30 2007 - 14:23:33 PDT)
- Carlos Simmerling (Tue May 29 2007 - 14:34:54 PDT)
- Cenk Andac (Tue May 29 2007 - 14:31:24 PDT)
AMBER: Ignore my reply to Amber protonate!
- saccenti.cerm.unifi.it (Wed May 16 2007 - 09:24:12 PDT)
AMBER: inconsistency between PBSA and GBSA
- AYTUG TUNCEL (Wed May 23 2007 - 06:26:32 PDT)
- AYTUG TUNCEL (Wed May 23 2007 - 10:30:11 PDT)
AMBER: inconsistency between PBSA and GBSA - help
- AYTUG TUNCEL (Sat May 26 2007 - 02:35:36 PDT)
AMBER: Ionic strength in pbsa
- Hu, Shaowen (JSC-SK)[USRA] (Tue May 22 2007 - 13:29:02 PDT)
- Qizhi Cui (Tue May 22 2007 - 13:21:27 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Tue May 22 2007 - 07:59:01 PDT)
AMBER: Is the simulation reasonable ? (SMD : dissocation antibody-antigen)
- Adrian Roitberg (Thu May 17 2007 - 08:06:49 PDT)
- wang (Wed May 16 2007 - 23:41:39 PDT)
AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj
- j j (Wed May 16 2007 - 04:39:48 PDT)
- Carlos Simmerling (Wed May 16 2007 - 04:11:15 PDT)
- Carlos Simmerling (Wed May 16 2007 - 04:09:01 PDT)
- j j (Wed May 16 2007 - 01:56:54 PDT)
- j j (Wed May 16 2007 - 02:01:24 PDT)
- Carlos Simmerling (Tue May 15 2007 - 12:55:54 PDT)
- Gustavo Seabra (Tue May 15 2007 - 12:11:21 PDT)
- j j (Tue May 15 2007 - 11:32:30 PDT)
- Carlos Simmerling (Tue May 15 2007 - 11:11:57 PDT)
- j j (Tue May 15 2007 - 10:55:40 PDT)
AMBER: junk in `Noshake mask` output section
- Ben Sattelle (Wed May 30 2007 - 15:05:20 PDT)
- David A. Case (Wed May 30 2007 - 14:47:51 PDT)
- Ben Sattelle (Wed May 30 2007 - 14:23:49 PDT)
AMBER: Keq computations
- Carlos Simmerling (Mon May 07 2007 - 15:43:53 PDT)
- Sean Rathlef (Mon May 07 2007 - 16:10:09 PDT)
AMBER: Langevin dynamics in NAB
- David A. Case (Sun May 20 2007 - 18:39:42 PDT)
AMBER: leap problem
- David A. Case (Thu May 10 2007 - 13:51:13 PDT)
- Achuth Prabhu (Wed May 09 2007 - 05:48:33 PDT)
- Achuth Prabhu (Wed May 09 2007 - 05:28:01 PDT)
- Achuth Prabhu (Wed May 09 2007 - 05:03:51 PDT)
AMBER: LES
- Carlos Simmerling (Thu May 31 2007 - 06:35:57 PDT)
- Urszula Uciechowska (Thu May 31 2007 - 06:29:27 PDT)
- Carlos Simmerling (Thu May 31 2007 - 06:17:02 PDT)
- Urszula Uciechowska (Thu May 31 2007 - 05:57:26 PDT)
AMBER: Les analyse
- Wei Zhang (Tue May 29 2007 - 07:26:28 PDT)
- Carlos Simmerling (Tue May 29 2007 - 04:16:22 PDT)
- Urszula Uciechowska (Tue May 29 2007 - 02:12:07 PDT)
AMBER: les/nudged elastic band
- Ross Walker (Thu May 31 2007 - 16:59:25 PDT)
- Tamara Rogers (Thu May 31 2007 - 16:20:21 PDT)
AMBER: Less error
- Carlos Simmerling (Fri May 25 2007 - 03:42:48 PDT)
- Urszula Uciechowska (Fri May 25 2007 - 03:32:56 PDT)
AMBER: md output file
- Gustavo Seabra (Thu May 03 2007 - 04:32:56 PDT)
- deepti nayar (Thu May 03 2007 - 02:06:24 PDT)
AMBER: Minimization increases energy
- saccenti.cerm.unifi.it (Wed May 23 2007 - 10:22:33 PDT)
- Hayden Eastwood (Wed May 23 2007 - 09:21:35 PDT)
- Hayden Eastwood (Wed May 23 2007 - 09:24:15 PDT)
AMBER: Minimization with heme group
- saccenti.cerm.unifi.it (Wed May 16 2007 - 09:25:23 PDT)
AMBER: Missing BELE for MM in 1 (residue 47)
- AYTUG TUNCEL (Thu May 10 2007 - 00:32:26 PDT)
AMBER: missing impropers for nitros?
- Junmei Wang (Mon May 21 2007 - 10:48:58 PDT)
- David Mobley (Mon May 14 2007 - 06:28:34 PDT)
- David A. Case (Sat May 12 2007 - 10:37:27 PDT)
- David Mobley (Fri May 11 2007 - 17:03:55 PDT)
AMBER: MM-PBSA calculation with GB dynamic
- Carlos Simmerling (Wed May 16 2007 - 07:03:01 PDT)
- Andrea - Tisacali (Wed May 16 2007 - 06:56:15 PDT)
AMBER: mm-pbsa error with nm = 1
- Cenk Andac (Wed May 02 2007 - 05:55:55 PDT)
- Hayden Eastwood (Wed May 02 2007 - 04:10:10 PDT)
- Cenk Andac (Wed May 02 2007 - 03:50:47 PDT)
- Hayden Eastwood (Wed May 02 2007 - 03:36:55 PDT)
- Cenk Andac (Tue May 01 2007 - 16:58:17 PDT)
- Urszula Uciechowska (Tue May 01 2007 - 10:43:28 PDT)
- Hayden Eastwood (Tue May 01 2007 - 10:21:22 PDT)
AMBER: MM/GBSA error message
- Catein Catherine (Tue May 22 2007 - 22:09:51 PDT)
AMBER: multiple excecution of sander
- Carlos Simmerling (Mon May 21 2007 - 07:12:59 PDT)
- Achuth Prabhu (Thu May 17 2007 - 23:03:23 PDT)
- Carlos Simmerling (Thu May 17 2007 - 09:03:23 PDT)
- Achuth Prabhu (Thu May 17 2007 - 08:55:47 PDT)
AMBER: NAB Average Structure
- David A. Case (Thu May 17 2007 - 14:13:10 PDT)
- Andreas Svrcek-Seiler (Thu May 17 2007 - 12:40:26 PDT)
- adelene.Stanford.EDU (Thu May 17 2007 - 11:59:42 PDT)
- David A. Case (Thu May 17 2007 - 09:32:59 PDT)
- adelene.Stanford.EDU (Thu May 17 2007 - 09:12:47 PDT)
AMBER: NAB MD Output
- Andreas Svrcek-Seiler (Tue May 08 2007 - 03:09:18 PDT)
- Russell Brown (Mon May 07 2007 - 16:06:27 PDT)
- adelene.Stanford.EDU (Mon May 07 2007 - 15:30:51 PDT)
AMBER: NAB normal mode output
- Andreas Svrcek-Seiler (Fri May 25 2007 - 02:15:46 PDT)
- David A. Case (Thu May 24 2007 - 21:17:04 PDT)
- nadiav.soton.ac.uk (Thu May 24 2007 - 10:27:59 PDT)
AMBER: need help to calculate IR spectra from amber trajectory
- Adrian Roitberg (Thu May 10 2007 - 12:16:59 PDT)
- S.Sundar Raman (Thu May 10 2007 - 10:53:16 PDT)
AMBER: NOC 3.0 is released
- mchen2.mailer.fsu.edu (Wed May 16 2007 - 13:03:30 PDT)
AMBER: parameter file for Fe-S cluster
- devrani mitra (Thu May 24 2007 - 15:26:05 PDT)
AMBER: pi-pi interactions
- Sara Alexandra Moura (Fri May 25 2007 - 03:36:05 PDT)
- Jiri Sponer (Tue May 22 2007 - 03:14:36 PDT)
- Roberto Veiga (Tue May 22 2007 - 02:27:22 PDT)
- Jiri Sponer (Mon May 21 2007 - 08:34:37 PDT)
- Roberto Veiga (Mon May 21 2007 - 08:03:16 PDT)
- Adrian Roitberg (Mon May 21 2007 - 06:56:51 PDT)
- Jiri Sponer (Mon May 21 2007 - 06:28:22 PDT)
- David Cerutti (Mon May 21 2007 - 06:13:16 PDT)
- Jiri Sponer (Mon May 21 2007 - 06:09:08 PDT)
- Roberto Veiga (Mon May 21 2007 - 05:33:32 PDT)
AMBER: PME memory requirement
- Robert Duke (Mon May 07 2007 - 19:05:48 PDT)
- Russell Brown (Mon May 07 2007 - 15:36:45 PDT)
AMBER: PMEMD and restart files
- Robert Duke (Sat May 12 2007 - 15:01:38 PDT)
- Austin B. Yongye (Sat May 12 2007 - 11:21:30 PDT)
AMBER: pmemd source issues
- Thomas Zeiser (Thu May 10 2007 - 04:55:16 PDT)
- Robert Duke (Wed May 09 2007 - 08:43:36 PDT)
- Thomas Zeiser (Wed May 09 2007 - 08:00:00 PDT)
- Robert Duke (Wed May 09 2007 - 06:37:59 PDT)
- Thomas Zeiser (Wed May 09 2007 - 04:33:11 PDT)
AMBER: PMF along 1D axis or every axis
- Catein Catherine (Fri May 11 2007 - 20:05:57 PDT)
AMBER: PMF define dehedral angel and distance restrainst for center of mass of domains.
- Carlos Simmerling (Tue May 08 2007 - 04:11:42 PDT)
- Catein Catherine (Mon May 07 2007 - 23:28:14 PDT)
AMBER: PMF for DG calculation.
- David A. Case (Mon May 14 2007 - 08:01:41 PDT)
- David Mobley (Mon May 14 2007 - 07:06:46 PDT)
- Catein Catherine (Fri May 11 2007 - 19:45:30 PDT)
AMBER: PMF: WHAM result
- Catein Catherine (Fri May 11 2007 - 20:28:30 PDT)
AMBER: polarizable water models.
- David A. Case (Sun May 06 2007 - 14:31:50 PDT)
- Karen Callahan (Fri May 04 2007 - 23:38:34 PDT)
AMBER: polymer
- Achuth Prabhu (Mon May 14 2007 - 05:55:12 PDT)
AMBER: Potential of mean force, how to calculate rate of dissociation?
- Gustavo Seabra (Mon May 07 2007 - 05:26:55 PDT)
- wang (Sun May 06 2007 - 23:20:41 PDT)
- Catein Catherine (Fri May 04 2007 - 18:55:26 PDT)
- David Mobley (Fri May 04 2007 - 14:09:36 PDT)
- Thomas Steinbrecher (Fri May 04 2007 - 11:05:09 PDT)
- David Mobley (Fri May 04 2007 - 10:39:34 PDT)
- Thomas Steinbrecher (Fri May 04 2007 - 08:49:03 PDT)
- Jerome.GOLEBIOWSKI.unice.fr (Fri May 04 2007 - 01:06:17 PDT)
- Catein Catherine (Thu May 03 2007 - 19:13:55 PDT)
- David Mobley (Thu May 03 2007 - 15:17:31 PDT)
- Jerome.GOLEBIOWSKI.unice.fr (Thu May 03 2007 - 06:57:32 PDT)
- Catein Catherine (Thu May 03 2007 - 02:46:27 PDT)
AMBER: problem about the coordinates out the box
- Shaoqing.Zhang.mail.uh.edu (Sat May 12 2007 - 20:26:45 PDT)
AMBER: Problem with calcpka.pl and constant pH
- David A. Case (Thu May 03 2007 - 10:13:50 PDT)
AMBER: Problem with SCC-DFTB parameter files
- 한재범 (Fri May 04 2007 - 21:25:29 PDT)
- Gustavo Seabra (Wed May 02 2007 - 08:27:00 PDT)
- M. L. Dodson (Wed May 02 2007 - 07:59:02 PDT)
- Ross Walker (Wed May 02 2007 - 07:45:07 PDT)
- Gustavo Seabra (Wed May 02 2007 - 04:46:58 PDT)
- 한재범 (Tue May 01 2007 - 21:55:03 PDT)
AMBER: protonate
- David A. Case (Wed May 16 2007 - 09:33:20 PDT)
- David A. Case (Wed May 16 2007 - 09:32:37 PDT)
- saccenti.cerm.unifi.it (Wed May 16 2007 - 09:22:20 PDT)
- Christopher Gaughan (Wed May 16 2007 - 08:56:37 PDT)
AMBER: QM/MM-DRFTB
- Gustavo Seabra (Mon May 21 2007 - 12:18:10 PDT)
- Gustavo Seabra (Mon May 21 2007 - 08:43:43 PDT)
- 박민희 (Sun May 20 2007 - 18:57:56 PDT)
AMBER: query regarding parameter files for manganese
- neetu.imtech.res.in (Thu May 10 2007 - 05:43:44 PDT)
AMBER: query regarding parameter files for manganese and mercuric ions
- neetu.imtech.res.in (Tue May 08 2007 - 04:40:56 PDT)
AMBER: Question about determination of hydration points in binding sites
- Cenk Andac (Sun May 27 2007 - 01:51:27 PDT)
AMBER: Rate of Dissociation
- wang (Sun May 06 2007 - 18:44:36 PDT)
- Catein Catherine (Fri May 04 2007 - 19:10:02 PDT)
- Sean Rathlef (Fri May 04 2007 - 12:15:03 PDT)
- David Mobley (Fri May 04 2007 - 10:41:51 PDT)
- Catein Catherine (Fri May 04 2007 - 02:37:46 PDT)
AMBER: REF file problem
- Ross Walker (Mon May 07 2007 - 08:13:58 PDT)
- Gustavo Seabra (Mon May 07 2007 - 05:20:10 PDT)
- deepti nayar (Sun May 06 2007 - 23:49:53 PDT)
AMBER: Reg restraint value obtained during umbrella sampling
- David A. Case (Thu May 31 2007 - 13:39:39 PDT)
- David A. Case (Thu May 31 2007 - 12:17:53 PDT)
- D.Usharani (Thu May 31 2007 - 11:28:50 PDT)
- Jerome.GOLEBIOWSKI.unice.fr (Thu May 31 2007 - 11:02:45 PDT)
- D.Usharani (Thu May 31 2007 - 10:22:21 PDT)
AMBER: REMD error
- Carlos Simmerling (Thu May 24 2007 - 10:23:02 PDT)
- Carlos Simmerling (Thu May 24 2007 - 08:41:04 PDT)
- Jason K (Thu May 24 2007 - 08:31:17 PDT)
- Carlos Simmerling (Tue May 22 2007 - 14:15:43 PDT)
- Jason K (Tue May 22 2007 - 12:02:22 PDT)
- Carlos Simmerling (Mon May 21 2007 - 08:41:53 PDT)
- Jason K (Mon May 21 2007 - 08:20:12 PDT)
AMBER: restraining atoms
- Thomas Cheatham III (Mon May 14 2007 - 10:27:01 PDT)
- deepti nayar (Sun May 13 2007 - 21:39:15 PDT)
AMBER: restraint_wt and fixing chi
- Thomas Cheatham III (Thu May 10 2007 - 10:09:59 PDT)
- deepti nayar (Thu May 10 2007 - 03:44:40 PDT)
AMBER: RESTRAINTMASK
- David A. Case (Thu May 31 2007 - 08:59:42 PDT)
- Roberto Veiga (Thu May 31 2007 - 07:29:26 PDT)
AMBER: rfree: Error input file
- Steve Seibold (Thu May 24 2007 - 12:22:39 PDT)
- Carlos Simmerling (Thu May 24 2007 - 11:56:51 PDT)
- Steve Seibold (Thu May 24 2007 - 11:43:02 PDT)
AMBER: Rotations about center of mass of an isolated system
- David A. Case (Mon May 14 2007 - 17:06:24 PDT)
- Jennie Thomas (Mon May 14 2007 - 16:55:44 PDT)
- David A. Case (Mon May 14 2007 - 14:37:09 PDT)
- Jennie Thomas (Mon May 14 2007 - 12:50:30 PDT)
- David A. Case (Mon May 14 2007 - 09:19:20 PDT)
- Jennie Thomas (Thu May 10 2007 - 18:08:06 PDT)
AMBER: Sander (Amber 9) crash on cortex
- Robert Duke (Thu May 10 2007 - 21:46:28 PDT)
- Thomas Cheatham (Thu May 10 2007 - 19:56:19 PDT)
- Evan Kelly (Thu May 10 2007 - 18:10:46 PDT)
- Ross Walker (Thu May 10 2007 - 13:09:19 PDT)
- David A. Case (Thu May 10 2007 - 12:55:16 PDT)
- Evan Kelly (Thu May 10 2007 - 11:57:20 PDT)
AMBER: Simulated Annealing - Best way to create randomness
- Seth Lilavivat (Fri May 04 2007 - 13:42:18 PDT)
AMBER: Simulated Annealing - Start with Poor Structure
- Carlos Simmerling (Tue May 22 2007 - 14:08:28 PDT)
- Seth Lilavivat (Tue May 22 2007 - 12:28:54 PDT)
AMBER: simulations stops in half way
- Robert Duke (Wed May 09 2007 - 05:51:17 PDT)
- Vijay Manickam Achari (Tue May 08 2007 - 22:01:21 PDT)
AMBER: single phospholipid molecule in vacuo
- David A. Case (Thu May 10 2007 - 16:51:39 PDT)
- Kliman, Michal (Thu May 10 2007 - 13:02:55 PDT)
AMBER: Small scale compute environments
- M. L. Dodson (Mon May 14 2007 - 11:32:36 PDT)
- Robert Duke (Mon May 14 2007 - 08:59:50 PDT)
- M. L. Dodson (Sat May 12 2007 - 12:13:59 PDT)
AMBER: software to extract data from the output file??
- Gustavo Seabra (Sat May 26 2007 - 07:09:08 PDT)
- Steven Winfield (Sat May 26 2007 - 02:15:52 PDT)
- Avinash Kumar (Sat May 26 2007 - 01:49:37 PDT)
AMBER: Solvent models
- FyD (Thu May 31 2007 - 13:41:24 PDT)
- Francesco Pietra (Thu May 31 2007 - 08:23:56 PDT)
AMBER: Some questions on mm_pbsa
- Hu, Shaowen (JSC-SK)[USRA] (Fri May 18 2007 - 07:53:35 PDT)
AMBER: Statictical significance of differences in energy mean values between different simulations
- Mostafa Sadighi (Sat May 19 2007 - 08:54:40 PDT)
AMBER: Steered MD & Jarzynski's equality
- wang (Thu May 03 2007 - 01:06:43 PDT)
- David Mobley (Wed May 02 2007 - 07:39:23 PDT)
- Gustavo Seabra (Wed May 02 2007 - 04:37:51 PDT)
- James W (Wed May 02 2007 - 02:44:28 PDT)
- Adrian Roitberg (Wed May 02 2007 - 00:26:30 PDT)
- James W (Tue May 01 2007 - 23:44:20 PDT)
AMBER: Steered MD & Jarzynski's equality]
- Gustavo Seabra (Thu May 03 2007 - 04:53:33 PDT)
AMBER: Temperature Drift in MD (NAB)
- David A. Case (Sat May 19 2007 - 21:03:24 PDT)
- adelene.Stanford.EDU (Fri May 18 2007 - 16:56:39 PDT)
- David A. Case (Fri May 18 2007 - 16:07:09 PDT)
- adelene.Stanford.EDU (Fri May 18 2007 - 15:49:25 PDT)
AMBER: thermodynamic integration
- Servaas Michielssens (Fri May 25 2007 - 00:23:21 PDT)
- David A. Case (Thu May 24 2007 - 21:14:43 PDT)
- Servaas Michielssens (Thu May 24 2007 - 08:50:48 PDT)
AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set"
- David A. Case (Wed May 16 2007 - 09:04:57 PDT)
- Thomas Steinbrecher (Wed May 16 2007 - 08:48:20 PDT)
- Carlos Simmerling (Wed May 16 2007 - 06:29:35 PDT)
- S. Jamal Rahi (Wed May 16 2007 - 06:22:47 PDT)
AMBER: total energies during MM-PBSA
- Hu, Shaowen (JSC-SK)[USRA] (Wed May 16 2007 - 06:57:26 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Tue May 15 2007 - 14:01:11 PDT)
AMBER: Tutorial 3: MM-PBSA.....implicit solvent for MD calculations?
- Catein Catherine (Fri May 04 2007 - 01:13:44 PDT)
AMBER: Umbrella Sampling for the twist angle of a DNA base pairs
- Catein Catherine (Wed May 30 2007 - 08:11:36 PDT)
- Catein Catherine (Wed May 30 2007 - 01:33:18 PDT)
AMBER: umbrella sampling: distance restraint
- Jerome.GOLEBIOWSKI.unice.fr (Thu May 10 2007 - 05:19:35 PDT)
- Catein Catherine (Thu May 10 2007 - 03:25:46 PDT)
AMBER: use of pucker function in ptraj
- Thomas Cheatham III (Thu May 10 2007 - 09:48:58 PDT)
- Ben Tan (Thu May 10 2007 - 04:00:41 PDT)
AMBER: water count
- Carlos Simmerling (Mon May 28 2007 - 05:20:30 PDT)
- mathew k varghese (Sun May 27 2007 - 23:41:50 PDT)
AMBER: work with constant pH on amber8
- David A. Case (Wed May 16 2007 - 11:40:42 PDT)
- tri nam Vo (Wed May 16 2007 - 11:13:43 PDT)
- tri nam Vo (Wed May 16 2007 - 10:52:47 PDT)
divcon missing in Antechamber 1.27
- Neelanjana Sengupta (Mon May 28 2007 - 17:56:55 PDT)
Fwd: AMBER: missing impropers for nitros?
- David Mobley (Mon May 21 2007 - 08:47:04 PDT)
Fwd: AMBER: MM-PBSA: Can't finish the binding energy process
- jitrayut jitonnom (Wed May 09 2007 - 21:12:55 PDT)
Minimization with heme group
- saccenti.cerm.unifi.it (Wed May 16 2007 - 10:11:43 PDT)
missing impropers for nitros?
- David Mobley (Fri May 11 2007 - 17:15:11 PDT)
Query regarding using tleap for preparing carbohydrate molecule
- Ross Walker (Mon May 07 2007 - 08:11:12 PDT)
- Gustavo Seabra (Mon May 07 2007 - 05:36:15 PDT)
- Ross Walker (Sun May 06 2007 - 18:31:24 PDT)

Amber Archive May 2007 by subject