Amber Archive Nov 2008: by subject

About restart amber
- Robert Duke (Tue Nov 25 2008 - 13:55:15 PST)
- Francesco Pietra (Tue Nov 25 2008 - 13:47:35 PST)
- Robert Duke (Tue Nov 25 2008 - 13:23:09 PST)
- Francesco Pietra (Tue Nov 25 2008 - 12:59:35 PST)
- Robert Duke (Tue Nov 25 2008 - 06:27:16 PST)
- Francesco Pietra (Tue Nov 25 2008 - 00:00:38 PST)
- Francesco Pietra (Mon Nov 24 2008 - 13:22:44 PST)
- Ross Walker (Sat Nov 22 2008 - 09:18:57 PST)
- Francesco Pietra (Sat Nov 22 2008 - 08:03:02 PST)
- Ross Walker (Fri Nov 21 2008 - 13:45:16 PST)
AMBER:
- Chin, Keith B (Tue Nov 18 2008 - 15:39:26 PST)
- Prem Prakash Pathak (Mon Nov 03 2008 - 19:20:09 PST)
AMBER: About antechamber and GAFF
- Stephane Abel (Wed Nov 26 2008 - 03:02:00 PST)
AMBER: About antechamber and GAFF [UPDATED]
- Stephane Abel (Thu Nov 27 2008 - 03:33:56 PST)
- Wenyong Tong (Wed Nov 26 2008 - 09:13:34 PST)
- Ross Walker (Wed Nov 26 2008 - 08:39:30 PST)
- Navnit Kumar Mishra (Wed Nov 26 2008 - 05:04:20 PST)
- Stephane Abel (Wed Nov 26 2008 - 03:21:52 PST)
AMBER: AdoMet parameterization with antechamber
- Jeffrey (Thu Nov 27 2008 - 07:30:33 PST)
- Ross Walker (Wed Nov 26 2008 - 09:28:51 PST)
- Jeffrey (Wed Nov 26 2008 - 06:44:27 PST)
- Jeffrey (Tue Nov 25 2008 - 08:14:44 PST)
- David A. Case (Mon Nov 24 2008 - 09:19:54 PST)
- Wei Huang (Mon Nov 24 2008 - 08:41:12 PST)
- Jeffrey (Mon Nov 24 2008 - 08:19:41 PST)
- Alan (Mon Nov 24 2008 - 02:46:52 PST)
- David A. Case (Sun Nov 23 2008 - 13:13:23 PST)
- Jeffrey (Sun Nov 23 2008 - 07:55:30 PST)
AMBER: Amber 9 installation problems
- drugdesign (Thu Nov 13 2008 - 08:25:34 PST)
- Ross Walker (Wed Nov 12 2008 - 13:16:03 PST)
- drugdesign (Wed Nov 12 2008 - 11:09:47 PST)
- Ross Walker (Wed Nov 12 2008 - 07:21:59 PST)
- drugdesign (Tue Nov 11 2008 - 23:36:51 PST)
- David A. Case (Tue Nov 11 2008 - 15:22:54 PST)
- drugdesign (Tue Nov 11 2008 - 06:13:32 PST)
- David A. Case (Mon Nov 10 2008 - 09:32:39 PST)
- Shozeb Haider (Mon Nov 10 2008 - 08:37:54 PST)
- drugdesign (Mon Nov 10 2008 - 03:27:39 PST)
AMBER: AMBER : Inconsistent MD length and no of angles after ptraj
- David A. Case (Fri Nov 07 2008 - 21:33:48 PST)
- parul sharma (Fri Nov 07 2008 - 01:52:07 PST)
AMBER: AMBER forfield choose
- Carlos Simmerling (Thu Nov 20 2008 - 08:21:51 PST)
- Barbault Florent (Thu Nov 20 2008 - 08:21:17 PST)
- Carlos Simmerling (Thu Nov 20 2008 - 07:51:18 PST)
- Wang,Ying (Thu Nov 20 2008 - 07:17:45 PST)
- mori.cerm.unifi.it (Thu Nov 20 2008 - 07:09:28 PST)
- Wang,Ying (Thu Nov 20 2008 - 07:05:28 PST)
- Barbault Florent (Thu Nov 20 2008 - 06:45:20 PST)
- Wang,Ying (Thu Nov 20 2008 - 06:32:24 PST)
AMBER: Amber on linux
- steinbrt.rci.rutgers.edu (Wed Nov 19 2008 - 11:47:45 PST)
- Marudachalam S (Wed Nov 19 2008 - 09:58:10 PST)
AMBER: AMBER question: perturbed charge twice the unperturbed
- David A. Case (Thu Nov 13 2008 - 12:39:41 PST)
- E.M. (Sun Nov 09 2008 - 15:08:05 PST)
- David A. Case (Sun Nov 09 2008 - 09:16:52 PST)
- Edward M (Sat Nov 08 2008 - 21:36:54 PST)
AMBER: AMBER10 compiling SANDER parallel problem
- David A. Case (Tue Nov 18 2008 - 13:25:23 PST)
- Hazard, E. Starr (Tue Nov 18 2008 - 12:48:31 PST)
AMBER: AMBER10 failing to compile PMEMD
- Robert Duke (Sat Nov 22 2008 - 14:42:50 PST)
- Hazard, E. Starr (Sat Nov 22 2008 - 14:06:03 PST)
AMBER: AMBER10 installation question
- Jeffrey (Wed Nov 19 2008 - 05:27:13 PST)
- David A. Case (Tue Nov 18 2008 - 04:05:07 PST)
- Jeffrey (Mon Nov 17 2008 - 19:20:14 PST)
AMBER: AMBER10: QMMM parallel test error
- Ross Walker (Wed Nov 05 2008 - 17:41:27 PST)
- Yang, Ping (Wed Nov 05 2008 - 19:57:29 PST)
- Yang, Ping (Wed Nov 05 2008 - 15:44:27 PST)
AMBER: antechamber and gaff for a homodimer
- FyD (Thu Nov 27 2008 - 08:02:55 PST)
- rebeca (Thu Nov 27 2008 - 05:33:19 PST)
- Alan (Thu Nov 27 2008 - 04:27:31 PST)
- rebeca (Thu Nov 27 2008 - 03:12:23 PST)
AMBER: Br - ion defined ?
- Chih-Ying Lin (Wed Nov 05 2008 - 09:20:36 PST)
AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters
- Lachele Foley (Lists) (Fri Nov 07 2008 - 13:25:18 PST)
- Francois Theillet (Fri Nov 07 2008 - 07:24:36 PST)
AMBER: CG and HC atoms partial charges in AMBER
- Stephane Abel (Thu Nov 20 2008 - 09:07:07 PST)
- Matthew Tessier (Thu Nov 20 2008 - 09:09:16 PST)
- Stephane Abel (Thu Nov 20 2008 - 08:51:25 PST)
- Matthew Tessier (Thu Nov 20 2008 - 08:40:43 PST)
- Stephane Abel (Thu Nov 20 2008 - 08:26:10 PST)
- Matthew Tessier (Thu Nov 20 2008 - 08:15:56 PST)
- David A. Case (Thu Nov 20 2008 - 07:56:15 PST)
- Stephane Abel (Thu Nov 20 2008 - 07:40:17 PST)
AMBER: changing pdb structure
- Taufik Al-Sarraj (Mon Nov 24 2008 - 15:37:24 PST)
- Carlos Simmerling (Tue Nov 11 2008 - 03:35:42 PST)
- Taufik Al-Sarraj (Mon Nov 10 2008 - 13:10:23 PST)
- Carlos Simmerling (Mon Nov 10 2008 - 12:37:32 PST)
- Taufik Al-Sarraj (Mon Nov 10 2008 - 12:31:39 PST)
AMBER: Chloride anion ligands leave the protein during MD
- Francesco Pietra (Sun Nov 16 2008 - 03:17:00 PST)
- Jiri Sponer (Fri Nov 14 2008 - 06:19:33 PST)
- Adrian Roitberg (Fri Nov 14 2008 - 06:00:33 PST)
- Gustavo Seabra (Fri Nov 14 2008 - 05:40:45 PST)
- Francesco Pietra (Thu Nov 13 2008 - 07:06:06 PST)
AMBER: Choline chloride salt
- CHAMI F. (Wed Nov 26 2008 - 06:49:45 PST)
AMBER: cis - trans isomerization
- Nina Fischer (Thu Nov 27 2008 - 06:39:21 PST)
AMBER: compiling amber 10
- David A. Case (Sat Nov 22 2008 - 12:33:54 PST)
- Andrei Neamtu (Fri Nov 21 2008 - 23:26:58 PST)
AMBER: compiling ambertools with intel compilers
- David A. Case (Fri Nov 21 2008 - 09:44:58 PST)
- Thomas Patko (Thu Nov 20 2008 - 14:15:58 PST)
- David A. Case (Thu Nov 20 2008 - 12:50:27 PST)
- Francesco Pietra (Thu Nov 20 2008 - 10:44:21 PST)
- Francesco Pietra (Thu Nov 20 2008 - 08:38:29 PST)
- Alan (Thu Nov 20 2008 - 04:10:58 PST)
- David A. Case (Thu Nov 20 2008 - 04:04:22 PST)
- Alan (Thu Nov 20 2008 - 02:27:26 PST)
AMBER: coot mutation
- Taufik Al-Sarraj (Thu Nov 06 2008 - 12:19:00 PST)
AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
- David A. Case (Thu Nov 20 2008 - 05:38:37 PST)
- David A. Case (Thu Nov 20 2008 - 05:36:48 PST)
- Alan (Thu Nov 20 2008 - 04:13:09 PST)
- Alan (Thu Nov 20 2008 - 03:48:56 PST)
- David A. Case (Wed Nov 19 2008 - 06:35:45 PST)
- John Chodera (Tue Nov 18 2008 - 11:58:22 PST)
AMBER: Electrostatic Energy Components
- Balazs JOJART (Mon Nov 24 2008 - 04:19:42 PST)
- David A. Case (Mon Nov 24 2008 - 04:14:13 PST)
- Junmei Wang (Sun Nov 23 2008 - 19:36:38 PST)
- Jojart Balazs (Sun Nov 23 2008 - 00:34:01 PST)
- David A. Case (Sat Nov 22 2008 - 12:37:51 PST)
- Carlos Simmerling (Sat Nov 22 2008 - 09:42:53 PST)
- Carlos Simmerling (Sat Nov 22 2008 - 09:41:48 PST)
- Ross Walker (Sat Nov 22 2008 - 09:21:22 PST)
- Jojart Balazs (Fri Nov 21 2008 - 23:53:46 PST)
- Ross Walker (Fri Nov 21 2008 - 16:20:56 PST)
- Ilyas Yildirim (Fri Nov 21 2008 - 16:12:44 PST)
- Carlos Simmerling (Fri Nov 21 2008 - 15:46:10 PST)
- Ross Walker (Fri Nov 21 2008 - 14:33:30 PST)
- Ilyas Yildirim (Fri Nov 21 2008 - 14:11:14 PST)
- Ross Walker (Fri Nov 21 2008 - 13:36:20 PST)
- guardiani.fi.infn.it (Fri Nov 21 2008 - 11:29:08 PST)
AMBER: Equilibration protocol for large protein
- Dmitri Nilov (Tue Nov 18 2008 - 08:33:26 PST)
AMBER: error message of xleap
- Ross Walker (Mon Nov 03 2008 - 09:05:54 PST)
- Catein Catherine (Mon Nov 03 2008 - 01:52:24 PST)
AMBER: Ewald troubles when running very big boxes
- Robert Duke (Mon Nov 24 2008 - 18:09:23 PST)
- steinbrt.rci.rutgers.edu (Mon Nov 24 2008 - 12:50:50 PST)
AMBER: Extracting periodic box size deviation
- Bill Ross (Thu Nov 06 2008 - 17:42:35 PST)
- CJ Dickson (Thu Nov 06 2008 - 15:29:20 PST)
AMBER: ff02 in nmode gives error "too many dihedrals" ?
- David A. Case (Wed Nov 12 2008 - 07:13:45 PST)
- Jacob Kongsted (Mon Nov 10 2008 - 01:16:36 PST)
AMBER: Force field for Gd (gadolinium)?
- Lili Peng (Thu Nov 06 2008 - 01:05:26 PST)
AMBER: Force field for Gd3+ (metal ion)?
- Lili Peng (Thu Nov 20 2008 - 16:00:29 PST)
AMBER: Fully QM periodic runs
- Ross Walker (Tue Nov 25 2008 - 08:54:24 PST)
- David A. Case (Tue Nov 25 2008 - 03:56:51 PST)
- hfox1.nd.edu (Mon Nov 24 2008 - 13:28:36 PST)
AMBER: GB versus explicit medium
- M. L. Dodson (Mon Nov 24 2008 - 07:43:52 PST)
- Francesco Pietra (Mon Nov 24 2008 - 07:33:43 PST)
- Carlos Simmerling (Mon Nov 24 2008 - 03:08:40 PST)
- Francesco Pietra (Mon Nov 24 2008 - 01:39:58 PST)
AMBER: gigabit ethernet cards and switches
- Mengjuei Hsieh (Thu Nov 06 2008 - 18:39:23 PST)
- Alessandro Nascimento (Thu Nov 06 2008 - 11:28:46 PST)
- Ross Walker (Thu Nov 06 2008 - 10:37:04 PST)
- Alessandro Nascimento (Thu Nov 06 2008 - 08:51:43 PST)
AMBER: Glycam
- Lachele Foley (Lists) (Thu Nov 06 2008 - 07:01:48 PST)
- Neha Gandhi (Wed Nov 05 2008 - 20:02:01 PST)
AMBER: Gradual releasing of position restraints
- David A. Case (Wed Nov 26 2008 - 09:00:41 PST)
- Ross Walker (Tue Nov 25 2008 - 08:48:13 PST)
- Dmitri Nilov (Tue Nov 25 2008 - 06:23:02 PST)
AMBER: Heating up
- Francesco Pietra (Fri Nov 28 2008 - 07:57:49 PST)
- Carlos Simmerling (Fri Nov 28 2008 - 04:30:29 PST)
- Francesco Pietra (Thu Nov 27 2008 - 10:29:30 PST)
AMBER: High ESURF
- Andreas Svrcek-Seiler (Mon Nov 17 2008 - 00:24:02 PST)
- Siddharth Rastogi (Mon Nov 17 2008 - 00:07:57 PST)
AMBER: How to create *.top & *.crd file with hexagonal lattice
- David A. Case (Tue Nov 18 2008 - 06:05:12 PST)
- Chin, Keith B (Sun Nov 16 2008 - 17:02:05 PST)
AMBER: How to manually adjust periodic boundary conditions (PBC)
- David A. Case (Thu Nov 20 2008 - 12:52:57 PST)
- Chin, Keith B (Wed Nov 19 2008 - 17:15:17 PST)
- David A. Case (Wed Nov 19 2008 - 15:35:33 PST)
- Chin, Keith B (Wed Nov 19 2008 - 11:58:41 PST)
AMBER: how to remove counter ions ( K+ / Cl- ions) using rdparm?
- Siddharth Rastogi (Fri Nov 14 2008 - 06:02:34 PST)
AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms
- Ye Mei (Thu Nov 27 2008 - 07:12:51 PST)
AMBER: load opls force field
- Bill Ross (Thu Nov 13 2008 - 12:32:19 PST)
- David A. Case (Thu Nov 13 2008 - 04:06:40 PST)
- oguz gurbulak (Thu Nov 13 2008 - 02:38:11 PST)
AMBER: looks like I have problem with "make clean" command
- David A. Case (Mon Nov 10 2008 - 04:39:26 PST)
- drugdesign (Sun Nov 09 2008 - 23:27:22 PST)
AMBER: Minimisation and heating under GB conditions
- Francesco Pietra (Mon Nov 03 2008 - 23:27:55 PST)
- Carlos Simmerling (Mon Nov 03 2008 - 10:52:23 PST)
- Francesco Pietra (Mon Nov 03 2008 - 10:07:14 PST)
- Carlos Simmerling (Mon Nov 03 2008 - 06:45:22 PST)
- Francesco Pietra (Mon Nov 03 2008 - 06:17:34 PST)
- Francesco Pietra (Mon Nov 03 2008 - 06:08:42 PST)
- David A. Case (Mon Nov 03 2008 - 06:01:59 PST)
- Carlos Simmerling (Mon Nov 03 2008 - 03:29:25 PST)
- Francesco Pietra (Mon Nov 03 2008 - 00:58:58 PST)
AMBER: MM-PBSA and trajectory input
- Arturas Ziemys (Thu Nov 13 2008 - 09:22:36 PST)
AMBER: MM_PBSA binding error
- Ray Luo (Tue Nov 04 2008 - 11:18:54 PST)
- Larry Layne (Tue Nov 04 2008 - 05:51:22 PST)
AMBER: mm_pbsa.pl and Amber10
- Holger Gohlke (Mon Nov 10 2008 - 09:12:16 PST)
- Stephan.Reiling.sanofi-aventis.com (Mon Nov 10 2008 - 08:05:27 PST)
AMBER: molsurf fails
- David A. Case (Tue Nov 25 2008 - 11:26:14 PST)
- Arturas Ziemys (Tue Nov 25 2008 - 07:27:27 PST)
AMBER: MOLYBDENUM
- Joachim Reichelt (Wed Nov 19 2008 - 06:14:31 PST)
AMBER: N(CN2)- ion
- babak minoofar (Fri Nov 28 2008 - 05:12:26 PST)
AMBER: Newbie question: partial minimization in implicit solvent
- Ross Walker (Wed Nov 12 2008 - 13:00:39 PST)
- Carlos Simmerling (Wed Nov 12 2008 - 12:47:56 PST)
- Jochen Heil (Wed Nov 12 2008 - 09:48:38 PST)
AMBER: NMR optimization with group averages (IGR1 / IGR2)
- Ryan Pavlovicz (Fri Nov 14 2008 - 07:59:36 PST)
AMBER: nonbonded parameters for titanium
- saurabh agrawal (Mon Nov 24 2008 - 08:57:56 PST)
AMBER: normal-vector of a plane with 'corrplane'
- Gert Kiss (Thu Nov 27 2008 - 12:28:46 PST)
AMBER: Optimal compiling of amber on XT3
- Patrick McCarren (Sat Nov 01 2008 - 00:13:08 PDT)
AMBER: organic solvents
- FyD (Fri Nov 14 2008 - 23:56:30 PST)
- Mark Williamson (Fri Nov 14 2008 - 15:28:10 PST)
- Marcelo Puiatti (Fri Nov 14 2008 - 15:20:30 PST)
AMBER: PB Radii
- Carlos Simmerling (Mon Nov 17 2008 - 03:30:41 PST)
- Swarup Gupta (Mon Nov 17 2008 - 03:24:42 PST)
- Swarup Gupta (Sat Nov 15 2008 - 19:44:25 PST)
- David A. Case (Thu Nov 13 2008 - 04:01:57 PST)
- Swarup Gupta (Wed Nov 12 2008 - 23:06:34 PST)
AMBER: pmemd
- Robert Duke (Thu Nov 20 2008 - 08:40:36 PST)
- Ross Walker (Thu Nov 20 2008 - 08:36:51 PST)
- Jeremy Harris (Thu Nov 20 2008 - 08:27:14 PST)
AMBER: PMEMD with AMOEBA parms including a lone pair site
- Robert Duke (Tue Nov 18 2008 - 18:50:14 PST)
- Margaret Johnson (Tue Nov 18 2008 - 18:29:04 PST)
AMBER: problem
- Arturas Ziemys (Tue Nov 18 2008 - 07:07:19 PST)
- David A. Case (Tue Nov 18 2008 - 04:15:57 PST)
- Arturas Ziemys (Mon Nov 17 2008 - 20:36:25 PST)
- FyD (Sun Nov 16 2008 - 23:40:33 PST)
- Arturas Ziemys (Sun Nov 16 2008 - 21:07:38 PST)
AMBER: Problem running NEB in AMBER10
- Ross Walker (Wed Nov 26 2008 - 11:04:55 PST)
- Chris C. (Wed Nov 26 2008 - 10:38:17 PST)
AMBER: problem with AMOEBA
- j00323240.students.jsums.edu (Wed Nov 26 2008 - 11:07:13 PST)
AMBER: problem with cartesian restraints with NTP simulations
- David A. Case (Wed Nov 19 2008 - 07:02:56 PST)
- Barbault Florent (Wed Nov 19 2008 - 06:50:13 PST)
AMBER: Problem with evaporating water over longer simulation times
- Adrian Roitberg (Wed Nov 12 2008 - 17:06:38 PST)
- Sasha Buzko (Wed Nov 12 2008 - 16:53:06 PST)
- Sasha Buzko (Wed Nov 12 2008 - 12:56:16 PST)
- steinbrt.rci.rutgers.edu (Wed Nov 12 2008 - 11:57:33 PST)
- Gustavo Seabra (Wed Nov 12 2008 - 11:48:01 PST)
- Sasha Buzko (Wed Nov 12 2008 - 11:14:00 PST)
AMBER: problem with group input and NMR restaints
- Carlos Simmerling (Wed Nov 05 2008 - 12:39:29 PST)
- priya priya (Wed Nov 05 2008 - 12:00:48 PST)
- Carlos Simmerling (Wed Nov 05 2008 - 10:13:29 PST)
- priya priya (Wed Nov 05 2008 - 09:22:33 PST)
- Carlos Simmerling (Wed Nov 05 2008 - 08:53:09 PST)
- priya priya (Wed Nov 05 2008 - 08:05:05 PST)
- Carlos Simmerling (Tue Nov 04 2008 - 09:53:48 PST)
- priya priya (Tue Nov 04 2008 - 09:38:37 PST)
- Carlos Simmerling (Tue Nov 04 2008 - 08:41:22 PST)
- priya priya (Tue Nov 04 2008 - 08:16:34 PST)
- Ross Walker (Tue Nov 04 2008 - 07:46:17 PST)
- Carlos Simmerling (Tue Nov 04 2008 - 07:35:46 PST)
- priya priya (Tue Nov 04 2008 - 07:20:09 PST)
AMBER: problem with zMatrix in tleap
- David A. Case (Sun Nov 09 2008 - 09:17:02 PST)
AMBER: Problems compiling leap on Altix Cluster
- Ross Walker (Mon Nov 03 2008 - 16:06:07 PST)
- John Finke (Mon Nov 03 2008 - 15:43:09 PST)
- Ross Walker (Mon Nov 03 2008 - 13:47:06 PST)
- John Finke (Mon Nov 03 2008 - 12:51:54 PST)
AMBER: Problems for use manganese molecules
- David A. Case (Fri Nov 21 2008 - 04:46:22 PST)
- vallespardojl.chem.leidenuniv.nl (Fri Nov 21 2008 - 01:06:37 PST)
AMBER: Problems of MM/MM-GBSA calculations
- Sergey Samsonov (Thu Nov 27 2008 - 02:53:53 PST)
AMBER: process_mdout modify
- Ross Walker (Tue Nov 04 2008 - 07:41:33 PST)
- Naser Alijabbari (Mon Nov 03 2008 - 22:20:07 PST)
AMBER: ptraj and netcdf with AmberTools1.2 ?
- David A. Case (Thu Nov 06 2008 - 04:08:00 PST)
- Dave Rogers (Wed Nov 05 2008 - 13:34:21 PST)
AMBER: ptraj center problem
- robaldo.dna.uba.ar (Fri Nov 21 2008 - 12:04:56 PST)
- Carlos Simmerling (Fri Nov 21 2008 - 10:42:17 PST)
- robaldo.dna.uba.ar (Fri Nov 21 2008 - 09:31:27 PST)
AMBER: ptraj closest command
- Gustavo Seabra (Mon Nov 17 2008 - 08:51:42 PST)
- steinbrt.rci.rutgers.edu (Mon Nov 17 2008 - 08:14:11 PST)
AMBER: ptraj new mask parser: differences from ambmask and core dumps
- M. L. Dodson (Mon Nov 10 2008 - 10:23:17 PST)
- M. L. Dodson (Fri Nov 07 2008 - 15:15:06 PST)
- Jianyin Shao (Fri Nov 07 2008 - 08:24:03 PST)
- M. L. Dodson (Thu Nov 06 2008 - 15:49:49 PST)
- Jianyin Shao (Thu Nov 06 2008 - 14:48:47 PST)
- M. L. Dodson (Thu Nov 06 2008 - 10:31:07 PST)
AMBER: Ptraj Normal Mode Analysis
- Jesse Jun (Fri Nov 14 2008 - 13:19:31 PST)
AMBER: QM/MM simulation
- Gustavo Seabra (Sat Nov 22 2008 - 11:19:22 PST)
- Ross Walker (Sat Nov 22 2008 - 08:59:49 PST)
- Syed Tarique Moin (Sat Nov 22 2008 - 07:11:12 PST)
- David A. Case (Sat Nov 22 2008 - 06:53:50 PST)
- Syed Tarique Moin (Sat Nov 22 2008 - 00:00:36 PST)
AMBER: question - gaff and leaprc.ff03ua
- David A. Case (Sun Nov 23 2008 - 13:49:37 PST)
- oguz gurbulak (Sun Nov 23 2008 - 08:43:48 PST)
- David A. Case (Wed Nov 19 2008 - 07:08:02 PST)
- oguz gurbulak (Wed Nov 19 2008 - 05:56:17 PST)
AMBER: question about ptraj
- rai001.student.ucr.edu (Thu Nov 13 2008 - 15:56:49 PST)
- Jianyin Shao (Thu Nov 13 2008 - 15:38:44 PST)
- rai001.student.ucr.edu (Wed Nov 12 2008 - 22:30:48 PST)
AMBER: Question fot Amber 10 Benchmarks
- sychen (Thu Nov 27 2008 - 18:18:00 PST)
- Ross Walker (Thu Nov 27 2008 - 08:57:06 PST)
- Robert Duke (Thu Nov 27 2008 - 06:37:20 PST)
- sychen (Wed Nov 26 2008 - 23:50:11 PST)
AMBER: Question on AMBER MD Implications
- Campbell, Patrick (Sat Nov 01 2008 - 03:01:17 PDT)
AMBER: Questions on TIP4P model?
- Chin, Keith B (Sat Nov 29 2008 - 15:43:21 PST)
- David A. Case (Sat Nov 29 2008 - 11:21:01 PST)
- Carlos Simmerling (Fri Nov 28 2008 - 12:03:14 PST)
- Chin, Keith B (Fri Nov 28 2008 - 11:20:38 PST)
AMBER: RED vIII-lack of charges in mol2
- FyD (Sat Nov 29 2008 - 08:23:34 PST)
- Neha Gandhi (Sat Nov 29 2008 - 06:24:30 PST)
AMBER: Referencing AMBER
- David A. Case (Wed Nov 26 2008 - 08:25:20 PST)
- Joseph Nachman (Wed Nov 26 2008 - 08:01:57 PST)
AMBER: resp charges in parameterization
- steinbrt.rci.rutgers.edu (Wed Nov 12 2008 - 08:44:17 PST)
- Mark M Huntress (Wed Nov 12 2008 - 08:24:55 PST)
AMBER: Restraints
- Ross Walker (Thu Nov 13 2008 - 11:11:53 PST)
- Ashish Sangwai (Thu Nov 13 2008 - 11:11:45 PST)
- Joseph Nachman (Thu Nov 13 2008 - 10:59:23 PST)
AMBER: RESTRAINTS: no valid redirection found
- Francesco Pietra (Mon Nov 17 2008 - 13:30:54 PST)
- Robert Duke (Mon Nov 17 2008 - 11:58:18 PST)
- Francesco Pietra (Mon Nov 17 2008 - 11:21:01 PST)
- Francesco Pietra (Mon Nov 17 2008 - 10:00:25 PST)
- Robert Duke (Mon Nov 17 2008 - 09:34:50 PST)
- Francesco Pietra (Mon Nov 17 2008 - 09:15:17 PST)
AMBER: Running Amber8 - Sander
- tri nam Vo (Sun Nov 23 2008 - 22:28:31 PST)
AMBER: Sander *.top and *.crd file from PDB file
- Carlos Simmerling (Fri Nov 14 2008 - 13:00:30 PST)
- Chin, Keith B (Fri Nov 14 2008 - 12:55:57 PST)
- Gustavo Seabra (Fri Nov 14 2008 - 12:30:21 PST)
- Chin, Keith B (Fri Nov 14 2008 - 11:43:41 PST)
AMBER: seeking help regrading Zinc protein GBSA minimization
- Carlos Simmerling (Fri Nov 28 2008 - 04:33:16 PST)
- S.Sundar Raman (Thu Nov 27 2008 - 04:32:08 PST)
AMBER: segmentation fault when restarting periodic structure
- David A. Case (Tue Nov 18 2008 - 06:20:41 PST)
- Diddo Diddens (Fri Nov 14 2008 - 04:47:23 PST)
AMBER: Setting GROUP for pmemd
- Francesco Pietra (Fri Nov 28 2008 - 02:12:07 PST)
AMBER: SPCFW temperature oscillations
- Robert Duke (Tue Nov 18 2008 - 05:16:27 PST)
- David A. Case (Tue Nov 18 2008 - 04:13:16 PST)
- Naser Alijabbari (Mon Nov 17 2008 - 20:19:12 PST)
AMBER: Steered MD and Jarzynski in pulling simulations
- Gustavo Seabra (Sun Nov 09 2008 - 18:36:38 PST)
- M. L. Dodson (Wed Nov 05 2008 - 07:04:23 PST)
- Samuel Genheden (Wed Nov 05 2008 - 06:48:33 PST)
AMBER: subroutine for torsional potential
- steinbrt.rci.rutgers.edu (Fri Nov 14 2008 - 06:49:25 PST)
- CHAMI F. (Fri Nov 14 2008 - 06:16:37 PST)
AMBER: subroutine Work : Jarynski work theorem
- CHAMI F. (Wed Nov 26 2008 - 04:21:07 PST)
AMBER: temperature error in md calculation
- David A. Case (Wed Nov 05 2008 - 06:10:41 PST)
- Catein Catherine (Wed Nov 05 2008 - 00:11:41 PST)
AMBER: Test failure with Amber 10
- Robert Duke (Wed Nov 26 2008 - 09:28:14 PST)
- Ross Walker (Wed Nov 26 2008 - 08:30:42 PST)
- Kevin Parkes (Wed Nov 26 2008 - 06:36:36 PST)
- David A. Case (Wed Nov 26 2008 - 04:46:41 PST)
- Kevin Parkes (Wed Nov 26 2008 - 02:33:35 PST)
AMBER: test sander error in amber7
- David A. Case (Tue Nov 11 2008 - 04:15:51 PST)
- Saiful Islam (Mon Nov 10 2008 - 23:36:30 PST)
- Saiful Islam (Mon Nov 10 2008 - 05:43:45 PST)
AMBER: Trajectory file ended and unit 24 error on open inptraj
- Gustavo Seabra (Sun Nov 16 2008 - 08:05:42 PST)
- Carlos Simmerling (Sun Nov 16 2008 - 04:42:22 PST)
- Siddharth Rastogi (Sat Nov 15 2008 - 22:18:59 PST)
- Carlos Simmerling (Sat Nov 15 2008 - 07:44:32 PST)
- Siddharth Rastogi (Sat Nov 15 2008 - 07:33:10 PST)
AMBER: unsubscribe amber
- Su Nwe (Mon Nov 24 2008 - 23:12:02 PST)
AMBER: using "EP" for dummy atom
- Ross Walker (Thu Nov 06 2008 - 18:05:22 PST)
- Ashish Sangwai (Thu Nov 06 2008 - 17:24:23 PST)
AMBER: using packmol file in Amber
- David A. Case (Tue Nov 25 2008 - 11:45:29 PST)
- oguz gurbulak (Tue Nov 25 2008 - 07:49:19 PST)
AMBER: velocity units?
- David A. Case (Mon Nov 17 2008 - 08:53:19 PST)
- Jose Borreguero (Mon Nov 17 2008 - 08:14:35 PST)
AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?
- FyD (Fri Nov 28 2008 - 23:30:19 PST)
- Ross Walker (Fri Nov 28 2008 - 18:11:49 PST)
- jitrayut jitonnom (Fri Nov 28 2008 - 15:34:43 PST)
- Guillermo Mulliert Carlín (Thu Nov 27 2008 - 23:20:30 PST)
- jitrayut jitonnom (Thu Nov 27 2008 - 17:26:54 PST)
AMBER: xLeap error
- Mark Williamson (Mon Nov 10 2008 - 13:58:27 PST)
- Lili Peng (Mon Nov 10 2008 - 13:49:53 PST)
- Lili Peng (Mon Nov 10 2008 - 12:45:58 PST)
AMBER: Your "bellymask-patch"
- Ross Walker (Thu Nov 13 2008 - 10:17:58 PST)
- Jochen Heil (Thu Nov 13 2008 - 05:45:30 PST)
Fwd: AMBER: RESTRAINTS: no valid redirection found
- Francesco Pietra (Mon Nov 17 2008 - 09:35:04 PST)
Poly(A)-Poly(T) DNA Tutorial Query
- Ross Walker (Thu Nov 06 2008 - 10:37:04 PST)
- Ross Walker (Thu Nov 06 2008 - 00:18:22 PST)
Problem with the NEB tutorial
- Ross Walker (Thu Nov 06 2008 - 11:24:30 PST)
problems about TMD in your tutorial
- Ross Walker (Mon Nov 10 2008 - 00:20:18 PST)
- Ross Walker (Thu Nov 06 2008 - 11:32:58 PST)
QUERRY?
- Ross Walker (Thu Nov 06 2008 - 10:37:04 PST)

Amber Archive Nov 2008 by subject