AMBER Archive (2008) - Nov 2008 By DateMost recent messages
356 messages sorted by:
[ author ]
[ thread ]
[ subject ]
About this archive
Starting: Sat Nov 01 2008 - 02:13:08 CDT
Ending: Sat Nov 29 2008 - 17:43:21 CST
- Re: AMBER: Optimal compiling of amber on XT3 Patrick McCarren (Sat Nov 01 2008 - 02:13:08 CDT)
- AMBER: Question on AMBER MD Implications Campbell, Patrick (Sat Nov 01 2008 - 05:01:17 CDT)
- AMBER: Minimisation and heating under GB conditions Francesco Pietra (Mon Nov 03 2008 - 02:58:58 CST)
- RE: AMBER: error message of xleap Catein Catherine (Mon Nov 03 2008 - 03:52:24 CST)
- Re: AMBER: Minimisation and heating under GB conditions Carlos Simmerling (Mon Nov 03 2008 - 05:29:25 CST)
- Re: AMBER: Minimisation and heating under GB conditions David A. Case (Mon Nov 03 2008 - 08:01:59 CST)
- Re: AMBER: Minimisation and heating under GB conditions Francesco Pietra (Mon Nov 03 2008 - 08:08:42 CST)
- Re: AMBER: Minimisation and heating under GB conditions Francesco Pietra (Mon Nov 03 2008 - 08:17:34 CST)
- Re: AMBER: Minimisation and heating under GB conditions Carlos Simmerling (Mon Nov 03 2008 - 08:45:22 CST)
- RE: AMBER: error message of xleap Ross Walker (Mon Nov 03 2008 - 11:05:54 CST)
- Re: AMBER: Minimisation and heating under GB conditions Francesco Pietra (Mon Nov 03 2008 - 12:07:14 CST)
- Re: AMBER: Minimisation and heating under GB conditions Carlos Simmerling (Mon Nov 03 2008 - 12:52:23 CST)
- AMBER: Problems compiling leap on Altix Cluster John Finke (Mon Nov 03 2008 - 14:51:54 CST)
- RE: AMBER: Problems compiling leap on Altix Cluster Ross Walker (Mon Nov 03 2008 - 15:47:06 CST)
- Re: AMBER: Problems compiling leap on Altix Cluster John Finke (Mon Nov 03 2008 - 17:43:09 CST)
- RE: AMBER: Problems compiling leap on Altix Cluster Ross Walker (Mon Nov 03 2008 - 18:06:07 CST)
- AMBER: Prem Prakash Pathak (Mon Nov 03 2008 - 21:20:09 CST)
- AMBER: process_mdout modify Naser Alijabbari (Tue Nov 04 2008 - 00:20:07 CST)
- Re: AMBER: Minimisation and heating under GB conditions Francesco Pietra (Tue Nov 04 2008 - 01:27:55 CST)
- Re: AMBER: MM_PBSA binding error Larry Layne (Tue Nov 04 2008 - 07:51:22 CST)
- AMBER: problem with group input and NMR restaints priya priya (Tue Nov 04 2008 - 09:20:09 CST)
- Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Tue Nov 04 2008 - 09:35:46 CST)
- RE: AMBER: process_mdout modify Ross Walker (Tue Nov 04 2008 - 09:41:33 CST)
- RE: AMBER: problem with group input and NMR restaints Ross Walker (Tue Nov 04 2008 - 09:46:17 CST)
- RE: AMBER: problem with group input and NMR restaints priya priya (Tue Nov 04 2008 - 10:16:34 CST)
- Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Tue Nov 04 2008 - 10:41:22 CST)
- Re: AMBER: problem with group input and NMR restaints priya priya (Tue Nov 04 2008 - 11:38:37 CST)
- Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Tue Nov 04 2008 - 11:53:48 CST)
- RE: AMBER: MM_PBSA binding error Ray Luo (Tue Nov 04 2008 - 13:18:54 CST)
- AMBER: temperature error in md calculation Catein Catherine (Wed Nov 05 2008 - 02:11:41 CST)
- Re: AMBER: temperature error in md calculation David A. Case (Wed Nov 05 2008 - 08:10:41 CST)
- AMBER: Steered MD and Jarzynski in pulling simulations Samuel Genheden (Wed Nov 05 2008 - 08:48:33 CST)
- Re: AMBER: Steered MD and Jarzynski in pulling simulations M. L. Dodson (Wed Nov 05 2008 - 09:04:23 CST)
- Re: AMBER: problem with group input and NMR restaints priya priya (Wed Nov 05 2008 - 10:05:05 CST)
- Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Wed Nov 05 2008 - 10:53:09 CST)
- AMBER: Br - ion defined ? Chih-Ying Lin (Wed Nov 05 2008 - 11:20:36 CST)
- Re: AMBER: problem with group input and NMR restaints priya priya (Wed Nov 05 2008 - 11:22:33 CST)
- Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Wed Nov 05 2008 - 12:13:29 CST)
- Re: AMBER: problem with group input and NMR restaints priya priya (Wed Nov 05 2008 - 14:00:48 CST)
- Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Wed Nov 05 2008 - 14:39:29 CST)
- Re: AMBER: ptraj and netcdf with AmberTools1.2 ? Dave Rogers (Wed Nov 05 2008 - 15:34:21 CST)
- AMBER: AMBER10: QMMM parallel test error Yang, Ping (Wed Nov 05 2008 - 17:44:27 CST)
- RE: AMBER: AMBER10: QMMM parallel test error Ross Walker (Wed Nov 05 2008 - 19:41:27 CST)
- RE: AMBER: AMBER10: QMMM parallel test error Yang, Ping (Wed Nov 05 2008 - 21:57:29 CST)
- AMBER: Glycam Neha Gandhi (Wed Nov 05 2008 - 22:02:01 CST)
- AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query Ross Walker (Thu Nov 06 2008 - 02:18:22 CST)
- AMBER: Force field for Gd (gadolinium)? Lili Peng (Thu Nov 06 2008 - 03:05:26 CST)
- Re: AMBER: ptraj and netcdf with AmberTools1.2 ? David A. Case (Thu Nov 06 2008 - 06:08:00 CST)
- Re: AMBER: Glycam Lachele Foley (Lists) (Thu Nov 06 2008 - 09:01:48 CST)
- AMBER: gigabit ethernet cards and switches Alessandro Nascimento (Thu Nov 06 2008 - 10:51:43 CST)
- AMBER: ptraj new mask parser: differences from ambmask and core dumps M. L. Dodson (Thu Nov 06 2008 - 12:31:07 CST)
- AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query Ross Walker (Thu Nov 06 2008 - 12:37:04 CST)
- AMBER: RE: QUERRY? Ross Walker (Thu Nov 06 2008 - 12:37:04 CST)
- RE: AMBER: gigabit ethernet cards and switches Ross Walker (Thu Nov 06 2008 - 12:37:04 CST)
- AMBER: RE: Problem with the NEB tutorial Ross Walker (Thu Nov 06 2008 - 13:24:30 CST)
- Re: AMBER: gigabit ethernet cards and switches Alessandro Nascimento (Thu Nov 06 2008 - 13:28:46 CST)
- AMBER: RE: problems about TMD in your tutorial Ross Walker (Thu Nov 06 2008 - 13:32:58 CST)
- AMBER: coot mutation Taufik Al-Sarraj (Thu Nov 06 2008 - 14:19:00 CST)
- Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps Jianyin Shao (Thu Nov 06 2008 - 16:48:47 CST)
- AMBER: Extracting periodic box size deviation CJ Dickson (Thu Nov 06 2008 - 17:29:20 CST)
- Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps M. L. Dodson (Thu Nov 06 2008 - 17:49:49 CST)
- AMBER: using "EP" for dummy atom Ashish Sangwai (Thu Nov 06 2008 - 19:24:23 CST)
- Re: AMBER: Extracting periodic box size deviation Bill Ross (Thu Nov 06 2008 - 19:42:35 CST)
- RE: AMBER: using "EP" for dummy atom Ross Walker (Thu Nov 06 2008 - 20:05:22 CST)
- Re: AMBER: gigabit ethernet cards and switches Mengjuei Hsieh (Thu Nov 06 2008 - 20:39:23 CST)
- AMBER: AMBER : Inconsistent MD length and no of angles after ptraj parul sharma (Fri Nov 07 2008 - 03:52:07 CST)
- AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters Francois Theillet (Fri Nov 07 2008 - 09:24:36 CST)
- Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps Jianyin Shao (Fri Nov 07 2008 - 10:24:03 CST)
- Re: AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters Lachele Foley (Lists) (Fri Nov 07 2008 - 15:25:18 CST)
- Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps M. L. Dodson (Fri Nov 07 2008 - 17:15:06 CST)
- Re: AMBER: AMBER : Inconsistent MD length and no of angles after ptraj David A. Case (Fri Nov 07 2008 - 23:33:48 CST)
- AMBER: AMBER question: perturbed charge twice the unperturbed Edward M (Sat Nov 08 2008 - 23:36:54 CST)
- Re: AMBER: problem with zMatrix in tleap David A. Case (Sun Nov 09 2008 - 11:17:02 CST)
- Re: AMBER: AMBER question: perturbed charge twice the unperturbed David A. Case (Sun Nov 09 2008 - 11:16:52 CST)
- Re: AMBER: AMBER question: perturbed charge twice the unperturbed E.M. (Sun Nov 09 2008 - 17:08:05 CST)
- Re: AMBER: Steered MD and Jarzynski in pulling simulations Gustavo Seabra (Sun Nov 09 2008 - 20:36:38 CST)
- AMBER: looks like I have problem with "make clean" command drugdesign (Mon Nov 10 2008 - 01:27:22 CST)
- AMBER: RE: problems about TMD in your tutorial Ross Walker (Mon Nov 10 2008 - 02:20:18 CST)
- AMBER: ff02 in nmode gives error "too many dihedrals" ? Jacob Kongsted (Mon Nov 10 2008 - 03:16:36 CST)
- Re: AMBER: looks like I have problem with "make clean" command David A. Case (Mon Nov 10 2008 - 06:39:26 CST)
- AMBER: test sander error in amber7 Saiful Islam (Mon Nov 10 2008 - 07:43:45 CST)
- AMBER: mm_pbsa.pl and Amber10 Stephan.Reiling_at_sanofi-aventis.com (Mon Nov 10 2008 - 10:05:27 CST)
- AMBER: Amber 9 installation problems drugdesign (Mon Nov 10 2008 - 05:27:39 CST)
- Re: AMBER: Amber 9 installation problems Shozeb Haider (Mon Nov 10 2008 - 10:37:54 CST)
- Re: AMBER: mm_pbsa.pl and Amber10 Holger Gohlke (Mon Nov 10 2008 - 11:12:16 CST)
- Re: AMBER: Amber 9 installation problems David A. Case (Mon Nov 10 2008 - 11:32:39 CST)
- Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps M. L. Dodson (Mon Nov 10 2008 - 12:23:17 CST)
- Re: AMBER: changing pdb structure Taufik Al-Sarraj (Mon Nov 10 2008 - 14:31:39 CST)
- Re: AMBER: changing pdb structure Carlos Simmerling (Mon Nov 10 2008 - 14:37:32 CST)
- AMBER: xLeap error Lili Peng (Mon Nov 10 2008 - 14:45:58 CST)
- Re: AMBER: changing pdb structure Taufik Al-Sarraj (Mon Nov 10 2008 - 15:10:23 CST)
- Re: AMBER: xLeap error Lili Peng (Mon Nov 10 2008 - 15:49:53 CST)
- Re: AMBER: xLeap error Mark Williamson (Mon Nov 10 2008 - 15:58:27 CST)
- Re: AMBER: test sander error in amber7 Saiful Islam (Tue Nov 11 2008 - 01:36:30 CST)
- Re: AMBER: changing pdb structure Carlos Simmerling (Tue Nov 11 2008 - 05:35:42 CST)
- Re: AMBER: test sander error in amber7 David A. Case (Tue Nov 11 2008 - 06:15:51 CST)
- Re: AMBER: Amber 9 installation problems drugdesign (Tue Nov 11 2008 - 08:13:32 CST)
- Re: AMBER: Amber 9 installation problems David A. Case (Tue Nov 11 2008 - 17:22:54 CST)
- Re: AMBER: Amber 9 installation problems drugdesign (Wed Nov 12 2008 - 01:36:51 CST)
- Re: AMBER: ff02 in nmode gives error "too many dihedrals" ? David A. Case (Wed Nov 12 2008 - 09:13:45 CST)
- RE: AMBER: Amber 9 installation problems Ross Walker (Wed Nov 12 2008 - 09:21:59 CST)
- AMBER: resp charges in parameterization Mark M Huntress (Wed Nov 12 2008 - 10:24:55 CST)
- Re: AMBER: resp charges in parameterization steinbrt_at_rci.rutgers.edu (Wed Nov 12 2008 - 10:44:17 CST)
- AMBER: Newbie question: partial minimization in implicit solvent Jochen Heil (Wed Nov 12 2008 - 11:48:38 CST)
- Re: AMBER: Amber 9 installation problems drugdesign (Wed Nov 12 2008 - 13:09:47 CST)
- AMBER: Problem with evaporating water over longer simulation times Sasha Buzko (Wed Nov 12 2008 - 13:14:00 CST)
- Re: AMBER: Problem with evaporating water over longer simulation times Gustavo Seabra (Wed Nov 12 2008 - 13:48:01 CST)
- Re: AMBER: Problem with evaporating water over longer simulation times steinbrt_at_rci.rutgers.edu (Wed Nov 12 2008 - 13:57:33 CST)
- Re: AMBER: Problem with evaporating water over longer simulation times steinbrt_at_rci.rutgers.edu (Wed Nov 12 2008 - 13:57:33 CST)
- Re: AMBER: Newbie question: partial minimization in implicit solvent Carlos Simmerling (Wed Nov 12 2008 - 14:47:56 CST)
- Re: AMBER: Problem with evaporating water over longer simulation times Sasha Buzko (Wed Nov 12 2008 - 14:56:16 CST)
- RE: AMBER: Newbie question: partial minimization in implicit solvent Ross Walker (Wed Nov 12 2008 - 15:00:39 CST)
- RE: AMBER: Amber 9 installation problems Ross Walker (Wed Nov 12 2008 - 15:16:03 CST)
- Re: AMBER: Problem with evaporating water over longer simulation times Sasha Buzko (Wed Nov 12 2008 - 18:53:06 CST)
- Re: AMBER: Problem with evaporating water over longer simulation times Adrian Roitberg (Wed Nov 12 2008 - 19:06:38 CST)
- AMBER: question about ptraj rai001_at_student.ucr.edu (Thu Nov 13 2008 - 00:30:48 CST)
- AMBER: PB Radii Swarup Gupta (Thu Nov 13 2008 - 01:06:34 CST)
- AMBER: load opls force field oguz gurbulak (Thu Nov 13 2008 - 04:38:11 CST)
- Re: AMBER: PB Radii David A. Case (Thu Nov 13 2008 - 06:01:57 CST)
- Re: AMBER: load opls force field David A. Case (Thu Nov 13 2008 - 06:06:40 CST)
- AMBER: Your "bellymask-patch" Jochen Heil (Thu Nov 13 2008 - 07:45:30 CST)
- AMBER: Chloride anion ligands leave the protein during MD Francesco Pietra (Thu Nov 13 2008 - 09:06:06 CST)
- AMBER: MM-PBSA and trajectory input Arturas Ziemys (Thu Nov 13 2008 - 11:22:36 CST)
- RE: AMBER: Your "bellymask-patch" Ross Walker (Thu Nov 13 2008 - 12:17:58 CST)
- AMBER: Restraints Joseph Nachman (Thu Nov 13 2008 - 12:59:23 CST)
- Re: AMBER: Restraints Ashish Sangwai (Thu Nov 13 2008 - 13:11:45 CST)
- RE: AMBER: Restraints Ross Walker (Thu Nov 13 2008 - 13:11:53 CST)
- Re: AMBER: Amber 9 installation problems drugdesign (Thu Nov 13 2008 - 10:25:34 CST)
- Re: AMBER: load opls force field Bill Ross (Thu Nov 13 2008 - 14:32:19 CST)
- Re: AMBER: AMBER question: perturbed charge twice the unperturbed David A. Case (Thu Nov 13 2008 - 14:39:41 CST)
- Re: AMBER: question about ptraj Jianyin Shao (Thu Nov 13 2008 - 17:38:44 CST)
- Re: AMBER: question about ptraj rai001_at_student.ucr.edu (Thu Nov 13 2008 - 17:56:49 CST)
- AMBER: segmentation fault when restarting periodic structure Diddo Diddens (Fri Nov 14 2008 - 06:47:23 CST)
- Re: AMBER: Chloride anion ligands leave the protein during MD Gustavo Seabra (Fri Nov 14 2008 - 07:40:45 CST)
- Re: AMBER: Chloride anion ligands leave the protein during MD Adrian Roitberg (Fri Nov 14 2008 - 08:00:33 CST)
- AMBER: how to remove counter ions ( K+ / Cl- ions) using rdparm? Siddharth Rastogi (Fri Nov 14 2008 - 08:02:34 CST)
- Re: AMBER: Chloride anion ligands leave the protein during MD Jiri Sponer (Fri Nov 14 2008 - 08:19:33 CST)
- AMBER: subroutine for torsional potential CHAMI F. (Fri Nov 14 2008 - 08:16:37 CST)
- Re: AMBER: subroutine for torsional potential steinbrt_at_rci.rutgers.edu (Fri Nov 14 2008 - 08:49:25 CST)
- AMBER: NMR optimization with group averages (IGR1 / IGR2) Ryan Pavlovicz (Fri Nov 14 2008 - 09:59:36 CST)
- AMBER: Sander *.top and *.crd file from PDB file Chin, Keith B (Fri Nov 14 2008 - 13:43:41 CST)
- Re: AMBER: Sander *.top and *.crd file from PDB file Gustavo Seabra (Fri Nov 14 2008 - 14:30:21 CST)
- RE: AMBER: Sander *.top and *.crd file from PDB file Chin, Keith B (Fri Nov 14 2008 - 14:55:57 CST)
- Re: AMBER: Sander *.top and *.crd file from PDB file Carlos Simmerling (Fri Nov 14 2008 - 15:00:30 CST)
- AMBER: Ptraj Normal Mode Analysis Jesse Jun (Fri Nov 14 2008 - 15:19:31 CST)
- AMBER: organic solvents Marcelo Puiatti (Fri Nov 14 2008 - 17:20:30 CST)
- Re: AMBER: organic solvents Mark Williamson (Fri Nov 14 2008 - 17:28:10 CST)
- Re: AMBER: organic solvents FyD (Sat Nov 15 2008 - 01:56:30 CST)
- AMBER: Trajectory file ended and unit 24 error on open inptraj Siddharth Rastogi (Sat Nov 15 2008 - 09:33:10 CST)
- Re: AMBER: Trajectory file ended and unit 24 error on open inptraj Carlos Simmerling (Sat Nov 15 2008 - 09:44:32 CST)
- Re: AMBER: PB Radii Swarup Gupta (Sat Nov 15 2008 - 21:44:25 CST)
- Re: AMBER: Trajectory file ended and unit 24 error on open inptraj Siddharth Rastogi (Sun Nov 16 2008 - 00:18:59 CST)
- Re: AMBER: Chloride anion ligands leave the protein during MD Francesco Pietra (Sun Nov 16 2008 - 05:17:00 CST)
- Re: AMBER: Trajectory file ended and unit 24 error on open inptraj Carlos Simmerling (Sun Nov 16 2008 - 06:42:22 CST)
- Re: AMBER: Trajectory file ended and unit 24 error on open inptraj Gustavo Seabra (Sun Nov 16 2008 - 10:05:42 CST)
- AMBER: How to create *.top & *.crd file with hexagonal lattice Chin, Keith B (Sun Nov 16 2008 - 19:02:05 CST)
- AMBER: problem Arturas Ziemys (Sun Nov 16 2008 - 23:07:38 CST)
- Re: AMBER: problem FyD (Mon Nov 17 2008 - 01:40:33 CST)
- AMBER: High ESURF Siddharth Rastogi (Mon Nov 17 2008 - 02:07:57 CST)
- Re: AMBER: High ESURF Andreas Svrcek-Seiler (Mon Nov 17 2008 - 02:24:02 CST)
- Re: AMBER: PB Radii Swarup Gupta (Mon Nov 17 2008 - 05:24:42 CST)
- Re: AMBER: PB Radii Carlos Simmerling (Mon Nov 17 2008 - 05:30:41 CST)
- AMBER: velocity units? Jose Borreguero (Mon Nov 17 2008 - 10:14:35 CST)
- AMBER: ptraj closest command steinbrt_at_rci.rutgers.edu (Mon Nov 17 2008 - 10:14:11 CST)
- Re: AMBER: ptraj closest command Gustavo Seabra (Mon Nov 17 2008 - 10:51:42 CST)
- Re: AMBER: velocity units? David A. Case (Mon Nov 17 2008 - 10:53:19 CST)
- AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 11:15:17 CST)
- Re: AMBER: RESTRAINTS: no valid redirection found Robert Duke (Mon Nov 17 2008 - 11:34:50 CST)
- Fwd: AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 11:35:04 CST)
- Re: AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 12:00:25 CST)
- Re: AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 13:21:01 CST)
- Re: AMBER: RESTRAINTS: no valid redirection found Robert Duke (Mon Nov 17 2008 - 13:58:18 CST)
- Re: AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 15:30:54 CST)
- AMBER: AMBER10 installation question Jeffrey (Mon Nov 17 2008 - 21:20:14 CST)
- AMBER: SPCFW temperature oscillations Naser Alijabbari (Mon Nov 17 2008 - 22:19:12 CST)
- RE: AMBER: problem Arturas Ziemys (Mon Nov 17 2008 - 22:36:25 CST)
- Re: AMBER: AMBER10 installation question David A. Case (Tue Nov 18 2008 - 06:05:07 CST)
- Re: AMBER: SPCFW temperature oscillations David A. Case (Tue Nov 18 2008 - 06:13:16 CST)
- Re: AMBER: problem David A. Case (Tue Nov 18 2008 - 06:15:57 CST)
- Re: AMBER: SPCFW temperature oscillations Robert Duke (Tue Nov 18 2008 - 07:16:27 CST)
- Re: AMBER: How to create *.top & *.crd file with hexagonal lattice David A. Case (Tue Nov 18 2008 - 08:05:12 CST)
- Re: AMBER: segmentation fault when restarting periodic structure David A. Case (Tue Nov 18 2008 - 08:20:41 CST)
- Re: AMBER: problem Arturas Ziemys (Tue Nov 18 2008 - 09:07:19 CST)
- AMBER: Equilibration protocol for large protein Dmitri Nilov (Tue Nov 18 2008 - 10:33:26 CST)
- AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) John Chodera (Tue Nov 18 2008 - 13:58:22 CST)
- AMBER: AMBER10 compiling SANDER parallel problem Hazard, E. Starr (Tue Nov 18 2008 - 14:48:31 CST)
- Re: AMBER: AMBER10 compiling SANDER parallel problem David A. Case (Tue Nov 18 2008 - 15:25:23 CST)
- AMBER: Chin, Keith B (Tue Nov 18 2008 - 17:39:26 CST)
- AMBER: PMEMD with AMOEBA parms including a lone pair site Margaret Johnson (Tue Nov 18 2008 - 20:29:04 CST)
- Re: AMBER: PMEMD with AMOEBA parms including a lone pair site Robert Duke (Tue Nov 18 2008 - 20:50:14 CST)
- Re: Re: AMBER: AMBER10 installation question Jeffrey (Wed Nov 19 2008 - 07:27:13 CST)
- AMBER: question - gaff and leaprc.ff03ua oguz gurbulak (Wed Nov 19 2008 - 07:56:17 CST)
- AMBER: MOLYBDENUM Joachim Reichelt (Wed Nov 19 2008 - 08:14:31 CST)
- Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) David A. Case (Wed Nov 19 2008 - 08:35:45 CST)
- AMBER: problem with cartesian restraints with NTP simulations Barbault Florent (Wed Nov 19 2008 - 08:50:13 CST)
- Re: AMBER: problem with cartesian restraints with NTP simulations David A. Case (Wed Nov 19 2008 - 09:02:56 CST)
- Re: AMBER: question - gaff and leaprc.ff03ua David A. Case (Wed Nov 19 2008 - 09:08:02 CST)
- AMBER: Amber on linux Marudachalam S (Wed Nov 19 2008 - 11:58:10 CST)
- Re: AMBER: Amber on linux steinbrt_at_rci.rutgers.edu (Wed Nov 19 2008 - 13:47:45 CST)
- AMBER: How to manually adjust periodic boundary conditions (PBC) Chin, Keith B (Wed Nov 19 2008 - 13:58:41 CST)
- Re: AMBER: How to manually adjust periodic boundary conditions (PBC) David A. Case (Wed Nov 19 2008 - 17:35:33 CST)
- RE: AMBER: How to manually adjust periodic boundary conditions (PBC) Chin, Keith B (Wed Nov 19 2008 - 19:15:17 CST)
- AMBER: compiling ambertools with intel compilers Alan (Thu Nov 20 2008 - 04:27:26 CST)
- Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) Alan (Thu Nov 20 2008 - 05:48:56 CST)
- Re: AMBER: compiling ambertools with intel compilers David A. Case (Thu Nov 20 2008 - 06:04:22 CST)
- Re: AMBER: compiling ambertools with intel compilers Alan (Thu Nov 20 2008 - 06:10:58 CST)
- Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) Alan (Thu Nov 20 2008 - 06:13:09 CST)
- Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) David A. Case (Thu Nov 20 2008 - 07:36:48 CST)
- Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) David A. Case (Thu Nov 20 2008 - 07:38:37 CST)
- Re: AMBER: AMBER forfield choose Wang,Ying (Thu Nov 20 2008 - 09:05:28 CST)
- Re: AMBER: AMBER forfield choose mori_at_cerm.unifi.it (Thu Nov 20 2008 - 09:09:28 CST)
- Re: AMBER: AMBER forfield choose Wang,Ying (Thu Nov 20 2008 - 09:17:45 CST)
- AMBER: CG and HC atoms partial charges in AMBER Stephane Abel (Thu Nov 20 2008 - 09:40:17 CST)
- Re: AMBER: AMBER forfield choose Carlos Simmerling (Thu Nov 20 2008 - 09:51:18 CST)
- Re: AMBER: CG and HC atoms partial charges in AMBER David A. Case (Thu Nov 20 2008 - 09:56:15 CST)
- Re: AMBER: AMBER forfield choose Barbault Florent (Thu Nov 20 2008 - 10:21:17 CST)
- Re: AMBER: AMBER forfield choose Carlos Simmerling (Thu Nov 20 2008 - 10:21:51 CST)
- RE: AMBER: CG and HC atoms partial charges in AMBER Matthew Tessier (Thu Nov 20 2008 - 10:15:56 CST)
- AMBER: pmemd Jeremy Harris (Thu Nov 20 2008 - 10:27:14 CST)
- Re: AMBER: CG and HC atoms partial charges in AMBER Stephane Abel (Thu Nov 20 2008 - 10:26:10 CST)
- RE: AMBER: pmemd Ross Walker (Thu Nov 20 2008 - 10:36:51 CST)
- Re: AMBER: compiling ambertools with intel compilers Francesco Pietra (Thu Nov 20 2008 - 10:38:29 CST)
- Re: AMBER: pmemd Robert Duke (Thu Nov 20 2008 - 10:40:36 CST)
- RE: AMBER: CG and HC atoms partial charges in AMBER Matthew Tessier (Thu Nov 20 2008 - 10:40:43 CST)
- Re: AMBER: CG and HC atoms partial charges in AMBER Stephane Abel (Thu Nov 20 2008 - 10:51:25 CST)
- RE: AMBER: CG and HC atoms partial charges in AMBER Matthew Tessier (Thu Nov 20 2008 - 11:09:16 CST)
- Re: AMBER: CG and HC atoms partial charges in AMBER Stephane Abel (Thu Nov 20 2008 - 11:07:07 CST)
- AMBER: AMBER forfield choose Wang,Ying (Thu Nov 20 2008 - 08:32:24 CST)
- Re: AMBER: AMBER forfield choose Barbault Florent (Thu Nov 20 2008 - 08:45:20 CST)
- Re: AMBER: compiling ambertools with intel compilers Francesco Pietra (Thu Nov 20 2008 - 12:44:21 CST)
- Re: AMBER: compiling ambertools with intel compilers David A. Case (Thu Nov 20 2008 - 14:50:27 CST)
- Re: AMBER: How to manually adjust periodic boundary conditions (PBC) David A. Case (Thu Nov 20 2008 - 14:52:57 CST)
- Re: AMBER: compiling ambertools with intel compilers Thomas Patko (Thu Nov 20 2008 - 16:15:58 CST)
- Re: AMBER: Force field for Gd3+ (metal ion)? Lili Peng (Thu Nov 20 2008 - 18:00:29 CST)
- AMBER: Problems for use manganese molecules vallespardojl_at_chem.leidenuniv.nl (Fri Nov 21 2008 - 03:06:37 CST)
- Re: AMBER: Problems for use manganese molecules David A. Case (Fri Nov 21 2008 - 06:46:22 CST)
- AMBER: ptraj center problem robaldo_at_dna.uba.ar (Fri Nov 21 2008 - 11:31:27 CST)
- Re: AMBER: compiling ambertools with intel compilers David A. Case (Fri Nov 21 2008 - 11:44:58 CST)
- Re: AMBER: ptraj center problem Carlos Simmerling (Fri Nov 21 2008 - 12:42:17 CST)
- AMBER: Electrostatic Energy Components guardiani_at_fi.infn.it (Fri Nov 21 2008 - 13:29:08 CST)
- Re: AMBER: ptraj center problem robaldo_at_dna.uba.ar (Fri Nov 21 2008 - 14:04:56 CST)
- RE: AMBER: Electrostatic Energy Components Ross Walker (Fri Nov 21 2008 - 15:36:20 CST)
- AMBER: RE: About restart amber Ross Walker (Fri Nov 21 2008 - 15:45:16 CST)
- RE: AMBER: Electrostatic Energy Components Ilyas Yildirim (Fri Nov 21 2008 - 16:11:14 CST)
- RE: AMBER: Electrostatic Energy Components Ross Walker (Fri Nov 21 2008 - 16:33:30 CST)
- Re: AMBER: Electrostatic Energy Components Carlos Simmerling (Fri Nov 21 2008 - 17:46:10 CST)
- RE: AMBER: Electrostatic Energy Components Ilyas Yildirim (Fri Nov 21 2008 - 18:12:44 CST)
- RE: AMBER: Electrostatic Energy Components Ross Walker (Fri Nov 21 2008 - 18:20:56 CST)
- AMBER: compiling amber 10 Andrei Neamtu (Sat Nov 22 2008 - 01:26:58 CST)
- Re: AMBER: Electrostatic Energy Components Jojart Balazs (Sat Nov 22 2008 - 01:53:46 CST)
- AMBER: QM/MM simulation Syed Tarique Moin (Sat Nov 22 2008 - 02:00:36 CST)
- Re: AMBER: QM/MM simulation David A. Case (Sat Nov 22 2008 - 08:53:50 CST)
- Re: AMBER: QM/MM simulation Syed Tarique Moin (Sat Nov 22 2008 - 09:11:12 CST)
- Re: AMBER: RE: About restart amber Francesco Pietra (Sat Nov 22 2008 - 10:03:02 CST)
- RE: AMBER: QM/MM simulation Ross Walker (Sat Nov 22 2008 - 10:59:49 CST)
- RE: AMBER: RE: About restart amber Ross Walker (Sat Nov 22 2008 - 11:18:57 CST)
- RE: AMBER: Electrostatic Energy Components Ross Walker (Sat Nov 22 2008 - 11:21:22 CST)
- Re: AMBER: Electrostatic Energy Components Carlos Simmerling (Sat Nov 22 2008 - 11:41:48 CST)
- Re: AMBER: Electrostatic Energy Components Carlos Simmerling (Sat Nov 22 2008 - 11:42:53 CST)
- Re: AMBER: QM/MM simulation Gustavo Seabra (Sat Nov 22 2008 - 13:19:22 CST)
- Re: AMBER: compiling amber 10 David A. Case (Sat Nov 22 2008 - 14:33:54 CST)
- Re: AMBER: Electrostatic Energy Components David A. Case (Sat Nov 22 2008 - 14:37:51 CST)
- AMBER: AMBER10 failing to compile PMEMD Hazard, E. Starr (Sat Nov 22 2008 - 16:06:03 CST)
- Re: AMBER: AMBER10 failing to compile PMEMD Robert Duke (Sat Nov 22 2008 - 16:42:50 CST)
- Re: AMBER: Electrostatic Energy Components Jojart Balazs (Sun Nov 23 2008 - 02:34:01 CST)
- AMBER: AdoMet parameterization with antechamber Jeffrey (Sun Nov 23 2008 - 09:55:30 CST)
- Re: AMBER: question - gaff and leaprc.ff03ua oguz gurbulak (Sun Nov 23 2008 - 10:43:48 CST)
- Re: AMBER: AdoMet parameterization with antechamber David A. Case (Sun Nov 23 2008 - 15:13:23 CST)
- Re: AMBER: question - gaff and leaprc.ff03ua David A. Case (Sun Nov 23 2008 - 15:49:37 CST)
- Re: AMBER: Electrostatic Energy Components Junmei Wang (Sun Nov 23 2008 - 21:36:38 CST)
- AMBER: Running Amber8 - Sander tri nam Vo (Mon Nov 24 2008 - 00:28:31 CST)
- AMBER: GB versus explicit medium Francesco Pietra (Mon Nov 24 2008 - 03:39:58 CST)
- Re: AMBER: AdoMet parameterization with antechamber Alan (Mon Nov 24 2008 - 04:46:52 CST)
- Re: AMBER: GB versus explicit medium Carlos Simmerling (Mon Nov 24 2008 - 05:08:40 CST)
- Re: AMBER: Electrostatic Energy Components David A. Case (Mon Nov 24 2008 - 06:14:13 CST)
- Re: AMBER: Electrostatic Energy Components Balazs JOJART (Mon Nov 24 2008 - 06:19:42 CST)
- Re: AMBER: GB versus explicit medium Francesco Pietra (Mon Nov 24 2008 - 09:33:43 CST)
- Re: AMBER: GB versus explicit medium M. L. Dodson (Mon Nov 24 2008 - 09:43:52 CST)
- Re: Re: AMBER: AdoMet parameterization with antechamber Jeffrey (Mon Nov 24 2008 - 10:19:41 CST)
- AMBER: nonbonded parameters for titanium saurabh agrawal (Mon Nov 24 2008 - 10:57:56 CST)
- Re: Re: AMBER: AdoMet parameterization with antechamber Wei Huang (Mon Nov 24 2008 - 10:41:12 CST)
- Re: Re: AMBER: AdoMet parameterization with antechamber David A. Case (Mon Nov 24 2008 - 11:19:54 CST)
- AMBER: Ewald troubles when running very big boxes steinbrt_at_rci.rutgers.edu (Mon Nov 24 2008 - 14:50:50 CST)
- Re: AMBER: RE: About restart amber Francesco Pietra (Mon Nov 24 2008 - 15:22:44 CST)
- RE: AMBER: Fully QM periodic runs hfox1_at_nd.edu (Mon Nov 24 2008 - 15:28:36 CST)
- Re: AMBER: changing pdb structure Taufik Al-Sarraj (Mon Nov 24 2008 - 17:37:24 CST)
- Re: AMBER: Ewald troubles when running very big boxes Robert Duke (Mon Nov 24 2008 - 20:09:23 CST)
- AMBER: unsubscribe amber Su Nwe (Tue Nov 25 2008 - 01:12:02 CST)
- Re: AMBER: RE: About restart amber Francesco Pietra (Tue Nov 25 2008 - 02:00:38 CST)
- Re: AMBER: Fully QM periodic runs David A. Case (Tue Nov 25 2008 - 05:56:51 CST)
- AMBER: Gradual releasing of position restraints Dmitri Nilov (Tue Nov 25 2008 - 08:23:02 CST)
- Re: AMBER: RE: About restart amber Robert Duke (Tue Nov 25 2008 - 08:27:16 CST)
- AMBER: molsurf fails Arturas Ziemys (Tue Nov 25 2008 - 09:27:27 CST)
- AMBER: using packmol file in Amber oguz gurbulak (Tue Nov 25 2008 - 09:49:19 CST)
- Re: Re: Re: AMBER: AdoMet parameterization with antechamber Jeffrey (Tue Nov 25 2008 - 10:14:44 CST)
- RE: AMBER: Gradual releasing of position restraints Ross Walker (Tue Nov 25 2008 - 10:48:13 CST)
- RE: AMBER: Fully QM periodic runs Ross Walker (Tue Nov 25 2008 - 10:54:24 CST)
- Re: AMBER: molsurf fails David A. Case (Tue Nov 25 2008 - 13:26:14 CST)
- Re: AMBER: using packmol file in Amber David A. Case (Tue Nov 25 2008 - 13:45:29 CST)
- Re: AMBER: RE: About restart amber Francesco Pietra (Tue Nov 25 2008 - 14:59:35 CST)
- Re: AMBER: RE: About restart amber Robert Duke (Tue Nov 25 2008 - 15:23:09 CST)
- Re: AMBER: RE: About restart amber Francesco Pietra (Tue Nov 25 2008 - 15:47:35 CST)
- Re: AMBER: RE: About restart amber Robert Duke (Tue Nov 25 2008 - 15:55:15 CST)
- AMBER: Test failure with Amber 10 Kevin Parkes (Wed Nov 26 2008 - 04:33:35 CST)
- AMBER: About antechamber and GAFF Stephane Abel (Wed Nov 26 2008 - 05:02:00 CST)
- AMBER: About antechamber and GAFF [UPDATED] Stephane Abel (Wed Nov 26 2008 - 05:21:52 CST)
- AMBER: subroutine Work : Jarynski work theorem CHAMI F. (Wed Nov 26 2008 - 06:21:07 CST)
- Re: AMBER: Test failure with Amber 10 David A. Case (Wed Nov 26 2008 - 06:46:41 CST)
- Re: AMBER: About antechamber and GAFF [UPDATED] Navnit Kumar Mishra (Wed Nov 26 2008 - 07:04:20 CST)
- RE: AMBER: Test failure with Amber 10 Kevin Parkes (Wed Nov 26 2008 - 08:36:36 CST)
- Re: Re: Re: Re: AMBER: AdoMet parameterization with antechamber Jeffrey (Wed Nov 26 2008 - 08:44:27 CST)
- AMBER: Choline chloride salt CHAMI F. (Wed Nov 26 2008 - 08:49:45 CST)
- AMBER: Referencing AMBER Joseph Nachman (Wed Nov 26 2008 - 10:01:57 CST)
- Re: AMBER: Referencing AMBER David A. Case (Wed Nov 26 2008 - 10:25:20 CST)
- RE: AMBER: Test failure with Amber 10 Ross Walker (Wed Nov 26 2008 - 10:30:42 CST)
- RE: AMBER: About antechamber and GAFF [UPDATED] Ross Walker (Wed Nov 26 2008 - 10:39:30 CST)
- Re: AMBER: Gradual releasing of position restraints David A. Case (Wed Nov 26 2008 - 11:00:41 CST)
- Re: AMBER: About antechamber and GAFF [UPDATED] Wenyong Tong (Wed Nov 26 2008 - 11:13:34 CST)
- Re: AMBER: Test failure with Amber 10 Robert Duke (Wed Nov 26 2008 - 11:28:14 CST)
- RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber Ross Walker (Wed Nov 26 2008 - 11:28:51 CST)
- AMBER: Problem running NEB in AMBER10 Chris C. (Wed Nov 26 2008 - 12:38:17 CST)
- RE: AMBER: Problem running NEB in AMBER10 Ross Walker (Wed Nov 26 2008 - 13:04:55 CST)
- AMBER: problem with AMOEBA j00323240_at_students.jsums.edu (Wed Nov 26 2008 - 13:07:13 CST)
- AMBER: Question fot Amber 10 Benchmarks sychen (Thu Nov 27 2008 - 01:50:11 CST)
- AMBER: Problems of MM/MM-GBSA calculations Sergey Samsonov (Thu Nov 27 2008 - 04:53:53 CST)
- AMBER: antechamber and gaff for a homodimer rebeca (Thu Nov 27 2008 - 05:12:23 CST)
- Re: AMBER: About antechamber and GAFF [UPDATED] Stephane Abel (Thu Nov 27 2008 - 05:33:56 CST)
- Re: AMBER: antechamber and gaff for a homodimer Alan (Thu Nov 27 2008 - 06:27:31 CST)
- AMBER: seeking help regrading Zinc protein GBSA minimization S.Sundar Raman (Thu Nov 27 2008 - 06:32:08 CST)
- Re: AMBER: antechamber and gaff for a homodimer rebeca (Thu Nov 27 2008 - 07:33:19 CST)
- Re: AMBER: Question fot Amber 10 Benchmarks Robert Duke (Thu Nov 27 2008 - 08:37:20 CST)
- AMBER: cis - trans isomerization Nina Fischer (Thu Nov 27 2008 - 08:39:21 CST)
- 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 - 09:12:51 CST)
- Re: RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber Jeffrey (Thu Nov 27 2008 - 09:30:33 CST)
- Re: AMBER: antechamber and gaff for a homodimer FyD (Thu Nov 27 2008 - 10:02:55 CST)
- RE: AMBER: Question fot Amber 10 Benchmarks Ross Walker (Thu Nov 27 2008 - 10:57:06 CST)
- AMBER: Heating up Francesco Pietra (Thu Nov 27 2008 - 12:29:30 CST)
- AMBER: normal-vector of a plane with 'corrplane' Gert Kiss (Thu Nov 27 2008 - 14:28:46 CST)
- AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? jitrayut jitonnom (Thu Nov 27 2008 - 19:26:54 CST)
- Re[2]: AMBER: Question fot Amber 10 Benchmarks sychen (Thu Nov 27 2008 - 20:18:00 CST)
- Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? Guillermo Mulliert Carlín (Fri Nov 28 2008 - 01:20:30 CST)
- Re: AMBER: Setting GROUP for pmemd Francesco Pietra (Fri Nov 28 2008 - 04:12:07 CST)
- Re: AMBER: Setting GROUP for pmemd Francesco Pietra (Fri Nov 28 2008 - 04:12:07 CST)
- Re: AMBER: Heating up Carlos Simmerling (Fri Nov 28 2008 - 06:30:29 CST)
- Re: AMBER: seeking help regrading Zinc protein GBSA minimization Carlos Simmerling (Fri Nov 28 2008 - 06:33:16 CST)
- AMBER: N(CN2)- ion babak minoofar (Fri Nov 28 2008 - 07:12:26 CST)
- Re: AMBER: Heating up Francesco Pietra (Fri Nov 28 2008 - 09:57:49 CST)
- AMBER: Questions on TIP4P model? Chin, Keith B (Fri Nov 28 2008 - 13:20:38 CST)
- Re: AMBER: Questions on TIP4P model? Carlos Simmerling (Fri Nov 28 2008 - 14:03:14 CST)
- Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? jitrayut jitonnom (Fri Nov 28 2008 - 17:34:43 CST)
- RE: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? Ross Walker (Fri Nov 28 2008 - 20:11:49 CST)
- Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? FyD (Sat Nov 29 2008 - 01:30:19 CST)
- AMBER: RED vIII-lack of charges in mol2 Neha Gandhi (Sat Nov 29 2008 - 08:24:30 CST)
- Re: AMBER: RED vIII-lack of charges in mol2 FyD (Sat Nov 29 2008 - 10:23:34 CST)
- Re: AMBER: Questions on TIP4P model? David A. Case (Sat Nov 29 2008 - 13:21:01 CST)
- RE: AMBER: Questions on TIP4P model? Chin, Keith B (Sat Nov 29 2008 - 17:43:21 CST)
Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:50 CST
356 messages sorted by:
[ author ]
[ thread ]
[ subject ]
About this archive
|