Amber Archive Jan 2008: by subject

AMBER vs Gaussian : zero VDW parameters?
- Ross Walker (Fri Jan 04 2008 - 09:01:14 PST)
AMBER:
- Chris Moth (Wed Jan 16 2008 - 07:11:07 PST)
- Reena ..... (Wed Jan 16 2008 - 01:07:30 PST)
- DawsonSean (Wed Jan 16 2008 - 00:52:07 PST)
AMBER: (no subject)
- Syed Tarique Moin (Wed Jan 30 2008 - 21:31:24 PST)
AMBER: A problem about antechamber
- Junmei Wang (Tue Jan 08 2008 - 14:19:15 PST)
- 捞毛渔 (Tue Jan 08 2008 - 08:03:49 PST)
AMBER: A problem to loadup the molecular in the xleap
- Yong Duan (Sat Jan 19 2008 - 12:44:25 PST)
- David A. Case (Sat Jan 19 2008 - 10:17:16 PST)
- 捞毛渔 (Sat Jan 19 2008 - 08:31:05 PST)
- Yong Duan (Fri Jan 18 2008 - 22:17:35 PST)
- 捞毛渔 (Fri Jan 18 2008 - 21:28:02 PST)
AMBER: a question of ptraj
- WANG,YING (Wed Jan 02 2008 - 10:04:24 PST)
AMBER: about AM1-BCC in antechamber
- Shun Zhu (Tue Jan 22 2008 - 10:09:49 PST)
- Junmei Wang (Tue Jan 22 2008 - 09:56:55 PST)
- Shun Zhu (Tue Jan 22 2008 - 09:38:01 PST)
- Junmei Wang (Fri Jan 18 2008 - 21:31:06 PST)
- David Mobley (Fri Jan 18 2008 - 14:21:44 PST)
- Shun Zhu (Fri Jan 18 2008 - 14:06:30 PST)
AMBER: About RAMD
- Yong Duan (Sat Jan 05 2008 - 11:24:53 PST)
- Adrian Roitberg (Sat Jan 05 2008 - 09:47:33 PST)
- Robert Duke (Sat Jan 05 2008 - 09:05:55 PST)
- Carlos Simmerling (Sat Jan 05 2008 - 08:46:32 PST)
- Francesco Pietra (Sat Jan 05 2008 - 08:26:01 PST)
- Carlos Simmerling (Sat Jan 05 2008 - 08:12:40 PST)
- Francesco Pietra (Sat Jan 05 2008 - 02:39:44 PST)
AMBER: Amber 9: Question regarding Test Failures and Compilers
- David A. Case (Wed Jan 23 2008 - 08:22:04 PST)
- Jan Schulze (Wed Jan 23 2008 - 02:01:04 PST)
AMBER: Amber : neutralizing without adding ions
- Lars Skjærven (Mon Jan 14 2008 - 07:41:55 PST)
- jani sahil (Mon Jan 14 2008 - 03:43:01 PST)
AMBER: amber :antechamber problem
- Florian Haberl (Mon Jan 07 2008 - 08:33:02 PST)
- Wei Chen (Mon Jan 07 2008 - 08:14:53 PST)
- jani sahil (Fri Jan 04 2008 - 19:51:56 PST)
AMBER: Amber DNA Model for X-ray Crystallography
- Hopkins, Robert (Fri Jan 11 2008 - 15:32:00 PST)
AMBER: AMBER installation problem
- David A. Case (Mon Jan 28 2008 - 08:06:54 PST)
- Sampath Koppole (Mon Jan 28 2008 - 00:36:27 PST)
- Bertrand P. S. Russell (Sat Jan 26 2008 - 07:53:43 PST)
- Jun Liu (Fri Jan 25 2008 - 10:59:29 PST)
AMBER: Amber parallel version on CPU power of 2 only
- fatima.chami.durham.ac.uk (Tue Jan 29 2008 - 13:04:56 PST)
- Robert Duke (Tue Jan 29 2008 - 10:43:03 PST)
- fatima.chami.durham.ac.uk (Tue Jan 29 2008 - 10:19:22 PST)
- Ross Walker (Tue Jan 29 2008 - 06:39:21 PST)
- fatima.chami.durham.ac.uk (Tue Jan 29 2008 - 05:38:34 PST)
AMBER: AMBER-8 parallel installation - test run failure
- Ming Lei (Thu Jan 03 2008 - 06:08:46 PST)
- brmeher.iitg.ernet.in (Thu Jan 03 2008 - 02:10:58 PST)
AMBER: Amber9 fails test.parallel
- Mark Williamson (Wed Jan 30 2008 - 12:04:31 PST)
- Marc Cozzi (Wed Jan 30 2008 - 10:58:41 PST)
AMBER: ANTECHAMBER NAMING
- FyD (Thu Jan 10 2008 - 23:53:04 PST)
- David A. Case (Thu Jan 10 2008 - 19:32:30 PST)
- Shozeb Haider (Thu Jan 10 2008 - 13:19:18 PST)
AMBER: antechamber problem
- gurpreet singh (Thu Jan 10 2008 - 20:05:38 PST)
- Junmei Wang (Thu Jan 10 2008 - 10:29:23 PST)
- gurpreet singh (Thu Jan 10 2008 - 09:49:15 PST)
AMBER: antechamber problems
- Junmei Wang (Sat Jan 05 2008 - 21:35:04 PST)
- jani sahil (Fri Jan 04 2008 - 19:49:10 PST)
AMBER: antechamber run on charged system
- snoze pa (Wed Jan 23 2008 - 11:34:04 PST)
- David A. Case (Wed Jan 23 2008 - 10:37:06 PST)
- san_amber roy (Wed Jan 23 2008 - 10:09:34 PST)
AMBER: Atomic restraints
- Marie Brut (Mon Jan 21 2008 - 05:34:42 PST)
AMBER: Back on track
- David A. Case (Wed Jan 30 2008 - 17:33:46 PST)
- Mike Summers (Mon Jan 28 2008 - 17:39:32 PST)
AMBER: BCC charges
- Thomas Exner (Wed Jan 23 2008 - 02:11:36 PST)
- Ross Walker (Tue Jan 22 2008 - 09:16:05 PST)
- Thomas Exner (Tue Jan 22 2008 - 07:47:20 PST)
AMBER: benchmark walltime to ps/day calculation
- Andrew Ring (Thu Jan 31 2008 - 13:16:22 PST)
- Steven Winfield (Thu Jan 31 2008 - 12:34:49 PST)
- Andrew Ring (Thu Jan 31 2008 - 12:11:05 PST)
AMBER: build RNA by nucgen
- David A. Case (Sun Jan 13 2008 - 09:56:32 PST)
- 欧阳德方 (Sat Jan 12 2008 - 18:26:44 PST)
AMBER: check COM velocity
- Lars Skjærven (Fri Jan 04 2008 - 08:36:53 PST)
- David A. Case (Fri Jan 04 2008 - 08:29:09 PST)
- Pankaj R. Daga (Fri Jan 04 2008 - 08:06:26 PST)
AMBER: chromophore parameters for Molecular Dynamics
- FyD (Wed Jan 16 2008 - 06:59:31 PST)
- Anthony Cruz (Wed Jan 16 2008 - 05:47:42 PST)
- FyD (Fri Jan 11 2008 - 12:57:19 PST)
- Anthony Cruz (Fri Jan 11 2008 - 07:32:31 PST)
AMBER: Cluster analysis
- Carlos Simmerling (Mon Jan 07 2008 - 08:18:22 PST)
- Francesco Pietra (Mon Jan 07 2008 - 08:00:40 PST)
AMBER: collision with surface
- Z Insepov (Tue Jan 22 2008 - 16:25:55 PST)
AMBER: Combine mdcrd
- Francesco Pietra (Fri Jan 04 2008 - 13:26:32 PST)
- Carlos Simmerling (Fri Jan 04 2008 - 09:56:04 PST)
- Francesco Pietra (Fri Jan 04 2008 - 09:36:49 PST)
- Carlos Simmerling (Fri Jan 04 2008 - 09:30:31 PST)
- Francesco Pietra (Fri Jan 04 2008 - 09:23:45 PST)
- Francesco Pietra (Fri Jan 04 2008 - 09:07:15 PST)
- Carlos Simmerling (Fri Jan 04 2008 - 08:44:55 PST)
- Francesco Pietra (Fri Jan 04 2008 - 08:37:07 PST)
AMBER: Combine mdcrd files
- Ross Walker (Fri Jan 04 2008 - 08:35:23 PST)
- Carlos Simmerling (Thu Jan 03 2008 - 15:09:23 PST)
- Francesco Pietra (Thu Jan 03 2008 - 15:01:47 PST)
AMBER: Combining multiple structures into single pdb
- Seth Lilavivat (Fri Jan 04 2008 - 12:21:58 PST)
AMBER: connectivity lose during the minimizations
- David A. Case (Sat Jan 12 2008 - 12:28:37 PST)
- rams rams (Sat Jan 12 2008 - 03:40:21 PST)
AMBER: connectivity problem
- Junmei Wang (Thu Jan 10 2008 - 07:27:07 PST)
- rams rams (Wed Jan 09 2008 - 21:04:41 PST)
- Junmei Wang (Wed Jan 09 2008 - 07:51:05 PST)
- rams rams (Wed Jan 09 2008 - 06:53:55 PST)
AMBER: convergence of free energy calculations
- David Mobley (Thu Jan 24 2008 - 10:20:35 PST)
- saurabh agrawal (Tue Jan 22 2008 - 03:54:28 PST)
AMBER: diblock copolymer
- Z Insepov (Tue Jan 22 2008 - 21:23:39 PST)
- Jed W Pitera (Tue Jan 22 2008 - 17:01:03 PST)
- Z Insepov (Thu Jan 17 2008 - 07:27:47 PST)
AMBER: Distorsion in protein and ligand during MD
- Francesco Pietra (Sun Jan 13 2008 - 01:46:23 PST)
AMBER: distorted aromatic rings
- David A. Case (Wed Jan 23 2008 - 08:24:15 PST)
- Marc Lindner (Wed Jan 23 2008 - 02:40:20 PST)
AMBER: Disturb you for help !?=
- 捞毛渔 (Thu Jan 17 2008 - 07:33:28 PST)
- Yong Duan (Wed Jan 16 2008 - 08:13:15 PST)
- 捞毛渔 (Wed Jan 16 2008 - 06:55:37 PST)
- Yong Duan (Tue Jan 15 2008 - 20:16:10 PST)
- 捞毛渔 (Tue Jan 15 2008 - 17:24:30 PST)
- Yong Duan (Mon Jan 14 2008 - 23:40:39 PST)
- 捞毛渔 (Mon Jan 14 2008 - 21:33:49 PST)
- Yong Duan (Mon Jan 14 2008 - 20:14:26 PST)
- 捞毛渔 (Mon Jan 14 2008 - 16:12:27 PST)
AMBER: Disturb you for help!
- Yong Duan (Mon Jan 14 2008 - 12:06:11 PST)
- 捞毛渔 (Mon Jan 14 2008 - 08:16:37 PST)
AMBER: disulfide bridge with ff03ua FF
- Marcin Krol (Thu Jan 31 2008 - 10:30:56 PST)
AMBER: ELAN_EXCEPTION . --: 6 (Initialisation error) ELAN_EXCEPTION . --: 6 (Initialisation error)
- Neko Maryam. (Sun Jan 13 2008 - 22:54:28 PST)
- Neko Maryam. (Sun Jan 13 2008 - 22:23:58 PST)
- David A. Case (Sun Jan 13 2008 - 22:16:31 PST)
- Neko Maryam. (Sun Jan 13 2008 - 21:44:10 PST)
AMBER: Entropy calculation
- nag raj (Thu Jan 31 2008 - 04:47:51 PST)
- nag raj (Wed Jan 30 2008 - 01:51:26 PST)
AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine
- FyD (Fri Jan 04 2008 - 02:34:00 PST)
- FyD (Wed Jan 02 2008 - 00:52:15 PST)
- John Chodera (Tue Jan 01 2008 - 17:44:34 PST)
AMBER: flexible molecule parameterization
- FyD (Sun Jan 27 2008 - 06:09:37 PST)
- Zhenwei Lu (Fri Jan 25 2008 - 07:36:46 PST)
AMBER: Fwd: Distorsion in protein and ligand during MD
- Francesco Pietra (Sun Jan 13 2008 - 01:57:43 PST)
AMBER: GAFF atom types for flavin (again)
- Junmei Wang (Thu Jan 17 2008 - 21:21:21 PST)
- Hans Martin Senn (Thu Jan 17 2008 - 12:47:54 PST)
AMBER: graphite
- Boutheina Kerkeni (Fri Jan 11 2008 - 03:26:58 PST)
AMBER: Has anyone seen a protein fall apart due to PBCs?
- Yong Duan (Tue Jan 22 2008 - 19:20:41 PST)
- David Cerutti (Tue Jan 22 2008 - 11:13:42 PST)
- Melinda Layten (Tue Jan 22 2008 - 10:43:23 PST)
- Irene Newhouse (Tue Jan 22 2008 - 09:28:44 PST)
- Thomas Cheatham III (Tue Jan 22 2008 - 08:37:03 PST)
- David Cerutti (Tue Jan 22 2008 - 08:10:10 PST)
AMBER: Help in radii
- FyD (Wed Jan 16 2008 - 12:31:07 PST)
- snoze pa (Wed Jan 16 2008 - 09:45:20 PST)
- snoze pa (Wed Jan 16 2008 - 09:08:59 PST)
AMBER: Help needed to analyze DNA Holliday Junction - Drug Binding MD simulations.
- Subramanian Arun Kumar (Thu Jan 24 2008 - 09:14:56 PST)
AMBER: Help reg. input file
- FyD (Wed Jan 02 2008 - 12:21:03 PST)
- snoze pa (Wed Jan 02 2008 - 11:50:50 PST)
- FyD (Wed Jan 02 2008 - 11:34:40 PST)
- snoze pa (Wed Jan 02 2008 - 10:34:56 PST)
AMBER: How to build a dimer using amber
- David A. Case (Tue Jan 15 2008 - 09:18:14 PST)
- Reena ..... (Tue Jan 15 2008 - 01:31:24 PST)
- Reena ..... (Tue Jan 15 2008 - 01:29:03 PST)
- David A. Case (Mon Jan 14 2008 - 23:51:50 PST)
- Reena ..... (Mon Jan 14 2008 - 23:19:45 PST)
AMBER: How to determine the basic parameters of a Replica Exchange Molecular Dynamics(REMD?
- Carlos Simmerling (Tue Jan 29 2008 - 04:21:37 PST)
- d90223013.ntu.edu.tw (Mon Jan 28 2008 - 23:35:08 PST)
AMBER: input options for replica exchange simulations
- Carlos Simmerling (Thu Jan 10 2008 - 12:50:18 PST)
- rebeca.mmb.pcb.ub.es (Thu Jan 10 2008 - 10:00:10 PST)
- Adrian Roitberg (Thu Jan 10 2008 - 09:28:50 PST)
- Carlos Simmerling (Thu Jan 10 2008 - 08:57:12 PST)
- rebeca.mmb.pcb.ub.es (Thu Jan 10 2008 - 08:46:42 PST)
AMBER: Installing OpenMPI
- Hopkins, Robert (Wed Jan 23 2008 - 16:40:22 PST)
- Francesco Pietra (Wed Jan 23 2008 - 10:18:44 PST)
- David A. Case (Wed Jan 23 2008 - 09:07:46 PST)
- Hopkins, Robert (Tue Jan 22 2008 - 15:57:49 PST)
AMBER: LEAP: solute concentration
- fatima.chami.durham.ac.uk (Thu Jan 31 2008 - 07:12:24 PST)
AMBER: MD of protein-ligand comlex
- Chris Moth (Mon Jan 07 2008 - 04:10:23 PST)
- Syed Tarique Moin (Sun Jan 06 2008 - 22:18:20 PST)
- umbrita itl (Sun Jan 06 2008 - 12:54:47 PST)
AMBER: MM-PBSA problem
- David A. Case (Fri Jan 04 2008 - 18:07:07 PST)
- Jack Lei (Fri Jan 04 2008 - 17:31:05 PST)
- stephane acoca (Thu Jan 03 2008 - 19:45:10 PST)
AMBER: mm/pbsa and saltcon effect
- Christopher Gaughan (Fri Jan 04 2008 - 13:40:17 PST)
AMBER: mmpbsa binding energy
- Marc Lindner (Thu Jan 24 2008 - 02:16:23 PST)
AMBER: NMR refinement
- David A. Case (Thu Jan 24 2008 - 18:18:48 PST)
- Seth Lilavivat (Thu Jan 24 2008 - 09:39:08 PST)
- David A. Case (Sat Jan 19 2008 - 10:39:08 PST)
- Wenyong Tong (Fri Jan 18 2008 - 20:18:18 PST)
- David A. Case (Fri Jan 18 2008 - 09:35:37 PST)
- David A. Case (Fri Jan 18 2008 - 09:11:54 PST)
- Wenyong Tong (Thu Jan 17 2008 - 18:54:04 PST)
AMBER: NMROPT=1 in minimisation
- David A. Case (Sun Jan 06 2008 - 12:59:03 PST)
- Binbin Liu (Sat Jan 05 2008 - 15:38:51 PST)
AMBER: NPT to NVT
- Age.Skjevik.student.uib.no (Tue Jan 15 2008 - 05:58:22 PST)
AMBER: Nudged Elastic Band initial heating problem
- Ross Walker (Tue Jan 08 2008 - 15:00:59 PST)
- Keith Van Nostrand (Tue Jan 08 2008 - 05:32:31 PST)
- Mike Wykes (Tue Jan 08 2008 - 02:42:09 PST)
AMBER: Number of Hydrogen Bonds?
- Jack Lei (Fri Jan 25 2008 - 05:20:53 PST)
- Jiapu.Zhang.csiro.au (Thu Jan 24 2008 - 17:35:04 PST)
- d90223013.ntu.edu.tw (Thu Jan 24 2008 - 17:07:39 PST)
AMBER: offset residue numbering
- David A. Case (Fri Jan 11 2008 - 23:10:08 PST)
- Brendan Duggan (Mon Jan 07 2008 - 12:14:30 PST)
AMBER: PEO-PLA/PCE
- FyD (Fri Jan 18 2008 - 12:42:06 PST)
- Z Insepov (Thu Jan 17 2008 - 12:19:47 PST)
AMBER: pmemd 9.0 compilation error
- Robert Duke (Mon Jan 14 2008 - 07:19:51 PST)
- Raphael Chaleil (Mon Jan 14 2008 - 06:38:12 PST)
AMBER: Problem about antechamber
- 捞毛渔 (Tue Jan 08 2008 - 08:09:03 PST)
AMBER: problem in neturalization
- jani sahil (Sat Jan 12 2008 - 19:27:31 PST)
AMBER: problem to compile PMEMD?
- Robert Duke (Tue Jan 29 2008 - 18:11:57 PST)
- Robert Duke (Tue Jan 29 2008 - 18:10:49 PST)
- fatima.chami.durham.ac.uk (Tue Jan 29 2008 - 16:10:48 PST)
- Robert Duke (Tue Jan 29 2008 - 15:09:05 PST)
- fatima.chami.durham.ac.uk (Tue Jan 29 2008 - 14:45:41 PST)
AMBER: problem with group input
- anna.schrey.gmx.de (Mon Jan 21 2008 - 06:22:48 PST)
- Ed Pate (Sun Jan 20 2008 - 22:53:28 PST)
AMBER: Problem with: Increase lastrst in the &cntrl namelist
- rdauria.uci.edu (Wed Jan 16 2008 - 10:19:27 PST)
- David A. Case (Wed Jan 16 2008 - 08:46:35 PST)
- rdauria.uci.edu (Tue Jan 15 2008 - 20:46:04 PST)
AMBER: problem:capping
- David A. Case (Sun Jan 13 2008 - 09:10:55 PST)
- jani sahil (Sat Jan 12 2008 - 18:53:24 PST)
AMBER: Problems in execution of Replica Exchange calculations Amber 9.0
- David A. Case (Thu Jan 24 2008 - 09:25:09 PST)
- rebeca.mmb.pcb.ub.es (Thu Jan 24 2008 - 08:50:22 PST)
AMBER: problems of antechamber
- JunJun Liu (Tue Jan 22 2008 - 06:45:26 PST)
- liu junjun (Sun Jan 20 2008 - 07:21:49 PST)
- Junmei Wang (Thu Jan 17 2008 - 21:24:52 PST)
- liu junjun (Thu Jan 17 2008 - 18:15:54 PST)
AMBER: problems with restart of MD
- Yong Duan (Mon Jan 14 2008 - 10:16:24 PST)
- Vijay Singh (Sun Jan 13 2008 - 11:53:11 PST)
- Yong Duan (Sun Jan 13 2008 - 10:08:52 PST)
- Vijay Singh (Sun Jan 13 2008 - 07:45:25 PST)
- Ross Walker (Sat Jan 12 2008 - 18:58:20 PST)
- Vijay Singh (Sat Jan 12 2008 - 01:48:39 PST)
- Vijay Singh (Fri Jan 11 2008 - 12:04:39 PST)
- Ross Walker (Fri Jan 11 2008 - 11:56:16 PST)
- Pankaj R. Daga (Fri Jan 11 2008 - 10:34:13 PST)
- Age.Skjevik.student.uib.no (Fri Jan 11 2008 - 10:16:00 PST)
- Vijay Singh (Fri Jan 11 2008 - 09:29:31 PST)
AMBER: ptraj: new mask parser
- Vlad Cojocaru (Thu Jan 24 2008 - 10:19:25 PST)
- Jianyin Shao (Thu Jan 24 2008 - 09:23:53 PST)
- Vlad Cojocaru (Wed Jan 23 2008 - 03:59:24 PST)
AMBER: QM/MM Heating
- Ross Walker (Tue Jan 29 2008 - 06:49:48 PST)
- Steven Winfield (Wed Jan 23 2008 - 04:30:11 PST)
- Ross Walker (Mon Jan 21 2008 - 08:41:31 PST)
- Adrian Roitberg (Mon Jan 21 2008 - 08:13:18 PST)
- Steven Winfield (Mon Jan 21 2008 - 05:48:22 PST)
- Steven Winfield (Mon Jan 14 2008 - 07:22:27 PST)
AMBER: QM/MM: input conversion error
- David A. Case (Fri Jan 25 2008 - 14:59:35 PST)
- Ross Walker (Fri Jan 25 2008 - 14:48:49 PST)
- Pankaj R. Daga (Fri Jan 25 2008 - 14:02:47 PST)
- M. L. Dodson (Fri Jan 25 2008 - 12:56:38 PST)
- Pankaj R. Daga (Fri Jan 25 2008 - 12:11:24 PST)
- Ross Walker (Thu Jan 24 2008 - 16:01:43 PST)
- M. L. Dodson (Thu Jan 24 2008 - 11:25:03 PST)
- Pankaj R. Daga (Thu Jan 24 2008 - 11:05:31 PST)
- M. L. Dodson (Thu Jan 24 2008 - 10:31:44 PST)
- Pankaj R. Daga (Thu Jan 24 2008 - 10:11:36 PST)
AMBER: question about antechamber
- Junmei Wang (Thu Jan 03 2008 - 07:18:34 PST)
- Lynn (Thu Jan 03 2008 - 06:32:56 PST)
AMBER: radial distribution function in ptraj
- Lili Peng (Tue Jan 29 2008 - 01:36:37 PST)
AMBER: Reference for rmsd
- Francesco Pietra (Mon Jan 28 2008 - 09:51:02 PST)
AMBER: Reg cysteine protonaitons states in pH constant MD
- D.Usharani (Sun Jan 27 2008 - 21:15:58 PST)
AMBER: Reg cysteine protonation states
- D.Usharani (Tue Jan 29 2008 - 19:58:22 PST)
AMBER: regarding :scee
- jani sahil (Wed Jan 23 2008 - 20:37:48 PST)
- David A. Case (Wed Jan 23 2008 - 08:45:07 PST)
- jani sahil (Wed Jan 23 2008 - 07:50:45 PST)
AMBER: Regarding neutral Arginine unit
- Carlos Simmerling (Tue Jan 15 2008 - 08:28:21 PST)
- jani sahil (Tue Jan 15 2008 - 08:19:00 PST)
AMBER: RESP
- FyD (Wed Jan 30 2008 - 21:47:38 PST)
- Syed Tarique Moin (Thu Jan 10 2008 - 01:15:15 PST)
- FyD (Wed Jan 09 2008 - 23:39:01 PST)
- Syed Tarique Moin (Wed Jan 09 2008 - 22:36:05 PST)
- FyD (Tue Jan 08 2008 - 11:49:31 PST)
- Syed Tarique Moin (Tue Jan 08 2008 - 04:40:21 PST)
- Syed Tarique Moin (Tue Jan 08 2008 - 04:41:56 PST)
- Syed Tarique Moin (Tue Jan 08 2008 - 04:41:06 PST)
- Syed Tarique Moin (Tue Jan 08 2008 - 04:40:03 PST)
AMBER: RMSD calculation using AMBER7
- Carlos Simmerling (Sat Jan 19 2008 - 06:19:45 PST)
- Biman Jana (Sat Jan 19 2008 - 05:16:46 PST)
AMBER: running AMBER in NAMD Trucated Octahedron
- Jojart Balazs (Mon Jan 14 2008 - 14:31:05 PST)
- Seth Lilavivat (Mon Jan 14 2008 - 14:19:05 PST)
AMBER: SANDER BOMB in subroutine nonbond_list
- Ross Walker (Wed Jan 30 2008 - 08:20:51 PST)
- Pankaj R. Daga (Wed Jan 30 2008 - 07:13:45 PST)
AMBER: setting periodic box
- Vijay Manickam Achari (Tue Jan 29 2008 - 20:22:05 PST)
AMBER: solvateBox/solvateDontClip
- darkcz.tlen.pl (Tue Jan 08 2008 - 08:02:19 PST)
AMBER: Structure comparison-NMR and X-ray structure using AMBER9
- Carlos Simmerling (Mon Jan 07 2008 - 08:16:16 PST)
- Prem Prakash Pathak (Mon Jan 07 2008 - 08:11:22 PST)
AMBER: Systematic drift
- Francesco Pietra (Tue Jan 22 2008 - 14:06:46 PST)
AMBER: temperature spikes
- Adrian Roitberg (Sun Jan 06 2008 - 08:41:50 PST)
- Sally Pias (Sat Jan 05 2008 - 22:26:55 PST)
AMBER: The energy minimization of SIngle RNA chain
- backy (Thu Jan 10 2008 - 00:33:20 PST)
AMBER: Thermodynamic integration with positional restraint?
- David A. Case (Thu Jan 03 2008 - 09:31:19 PST)
- Cen Gao (Thu Jan 03 2008 - 08:43:32 PST)
AMBER: Tinker 4.3
- David A. Case (Fri Jan 18 2008 - 09:07:50 PST)
- Paulo Couto (Fri Jan 18 2008 - 07:22:25 PST)
AMBER: Torsional Forcing to generate PES?
- Chris Moth (Tue Jan 08 2008 - 09:08:12 PST)
- Praveena Gopal (Mon Jan 07 2008 - 20:42:04 PST)
AMBER: Tough time with antechamber
- David A. Case (Thu Jan 24 2008 - 18:25:33 PST)
- Junmei Wang (Thu Jan 24 2008 - 15:49:51 PST)
- David Cerutti (Thu Jan 24 2008 - 10:55:48 PST)
- David A. Case (Thu Jan 24 2008 - 10:42:56 PST)
- David Mobley (Thu Jan 24 2008 - 10:14:42 PST)
- Junmei Wang (Thu Jan 24 2008 - 07:23:08 PST)
- David Cerutti (Wed Jan 23 2008 - 23:29:38 PST)
AMBER: Tough time with antechamber (UPDATE, still need help)
- David Cerutti (Thu Jan 24 2008 - 00:09:42 PST)
AMBER: tutorial_8_section_6
- Urszula Uciechowska (Wed Jan 23 2008 - 09:04:38 PST)
AMBER: Unable to create the top & crd files for a protein+ligand pdb structure
- Jiten (Sat Jan 12 2008 - 00:21:01 PST)
- abiram abiram (Fri Jan 11 2008 - 23:54:01 PST)
AMBER: Units of atomicfluct
- Lili Peng (Wed Jan 23 2008 - 16:27:16 PST)
AMBER: using hydrogen bond facility to monitor ion pair interaction
- Zhenwei Lu (Thu Jan 10 2008 - 10:16:57 PST)
- Thomas Cheatham III (Thu Jan 10 2008 - 09:21:10 PST)
- Zhenwei Lu (Thu Jan 10 2008 - 09:09:09 PST)
AMBER: Using VMD to calculate end-to-end distance?
- Keith Van Nostrand (Mon Jan 14 2008 - 19:35:42 PST)
- Lili Peng (Mon Jan 14 2008 - 14:41:55 PST)
AMBER: Visualizing Electrostatic Potential
- Seth Lilavivat (Fri Jan 11 2008 - 11:57:31 PST)
AMBER: vlimit exceeded error
- David A. Case (Wed Jan 23 2008 - 08:29:18 PST)
- priya priya (Wed Jan 23 2008 - 03:27:37 PST)
AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file?
- David A. Case (Mon Jan 28 2008 - 08:11:02 PST)
- Jack Lei (Mon Jan 28 2008 - 06:35:06 PST)
- Steve Spronk (Mon Jan 28 2008 - 05:47:39 PST)
- Jack Lei (Mon Jan 28 2008 - 04:59:38 PST)
Systematic drift
- Francesco Pietra (Tue Jan 22 2008 - 23:23:07 PST)
timestep problem
- David A. Case (Thu Jan 17 2008 - 12:27:56 PST)
- Andrey Semichaevsky (Thu Jan 17 2008 - 10:24:00 PST)

Amber Archive Jan 2008 by subject