AMBER Archive (2005) - By Date

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Starting: Sat Jan 01 2005 - 08:25:14 CST
Ending: Sat Dec 31 2005 - 12:51:27 CST

Re: AMBER: Problem with computing Resp charges using RED Cenk Andac (Sat Jan 01 2005 - 08:08:24 CST)
Re: AMBER: Problem with computing Resp charges using RED FyD (Sat Jan 01 2005 - 13:51:12 CST)
AMBER: Sander and NMODE energy minimization fangyu liang (Sat Jan 01 2005 - 23:53:49 CST)
Re: AMBER: NSCM David A. Case (Sun Jan 02 2005 - 16:35:54 CST)
Re: AMBER: Sander and NMODE energy minimization David A. Case (Sun Jan 02 2005 - 16:47:28 CST)
AMBER: How can i use AMBER with CHARMM forcefield parameter? ÍõÐ¡Çå (Sun Jan 02 2005 - 21:54:25 CST)
AMBER: MM_PBSA fillratio error Jiten (Mon Jan 03 2005 - 03:36:30 CST)
AMBER: Hbonds restraints OK but Dihedral restraints not applied pl (Mon Jan 03 2005 - 08:06:48 CST)
Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied David A. Case (Mon Jan 03 2005 - 10:34:09 CST)
Re: AMBER: MM_PBSA fillratio error Ray Luo (Mon Jan 03 2005 - 16:28:46 CST)
AMBER: AMBER related employment Anthony Fejes (Mon Jan 03 2005 - 19:43:24 CST)
AMBER: lipid bilayer membrane force field parameter Xiaoqing,Wang (Tue Jan 04 2005 - 03:51:47 CST)
Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied pl (Tue Jan 04 2005 - 05:27:07 CST)
Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied Carlos Simmerling (Tue Jan 04 2005 - 06:47:03 CST)
Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied pl (Tue Jan 04 2005 - 07:25:39 CST)
Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied Bill Ross (Tue Jan 04 2005 - 12:07:49 CST)
AMBER: Steered Molecular Dynamics with AMBER? Rino Ragno (Tue Jan 04 2005 - 16:33:09 CST)
Re: AMBER: Steered Molecular Dynamics with AMBER? Carlos Simmerling (Tue Jan 04 2005 - 16:47:38 CST)
Re: AMBER: Dummy Atoms: How to create them? Ilyas Yildirim (Tue Jan 04 2005 - 21:25:24 CST)
Re: AMBER: Steered Molecular Dynamics with AMBER? David E. Konerding (Tue Jan 04 2005 - 22:44:15 CST)
Re: AMBER: MM_PBSA fillratio error Jiten (Wed Jan 05 2005 - 00:54:35 CST)
Re: AMBER: Steered Molecular Dynamics with AMBER? Piotr Cieplak (Wed Jan 05 2005 - 01:29:41 CST)
Re: AMBER: Steered Molecular Dynamics with AMBER? aldo jongejan (Wed Jan 05 2005 - 01:46:44 CST)
AMBER: lipid parameter file Xiaoqing,Wang (Wed Jan 05 2005 - 02:23:07 CST)
AMBER: distance between images cailliez (Wed Jan 05 2005 - 04:34:46 CST)
AMBER: MM_PBSA arguments for MM calculations Nelson Fonseca (Wed Jan 05 2005 - 05:54:30 CST)
AMBER: Floating Exception in sander anshul_at_imtech.res.in (Wed Jan 05 2005 - 17:26:20 CST)
Re: AMBER: Floating Exception in sander Robert Duke (Wed Jan 05 2005 - 07:55:22 CST)
Re: AMBER: Steered Molecular Dynamics with AMBER? Adrian E. Roitberg (Wed Jan 05 2005 - 08:13:10 CST)
Re: AMBER: Steered Molecular Dynamics with AMBER? Anthony Fejes (Wed Jan 05 2005 - 10:26:05 CST)
Re: AMBER: distance between images Thomas E. Cheatham, III (Wed Jan 05 2005 - 11:29:19 CST)
Re: AMBER: Dummy Atoms: How to create them? David A. Case (Wed Jan 05 2005 - 11:40:11 CST)
Re: AMBER: Dummy Atoms: How to create them? Ilyas Yildirim (Wed Jan 05 2005 - 15:05:22 CST)
AMBER: General Question about AMBER's Free Energy Perturbation Method Chris Moth (Wed Jan 05 2005 - 16:06:33 CST)
Re: AMBER: How can i use AMBER with CHARMM forcefield parameter? David A. Case (Thu Jan 06 2005 - 08:23:44 CST)
AMBER: about install amber8 on windows xiaowen (Thu Jan 06 2005 - 16:56:53 CST)
AMBER: recompiling problem on IBM aix Yuuki A. Komata (Thu Jan 06 2005 - 20:35:46 CST)
Re: AMBER: Floating Exception in sander anshul_at_imtech.res.in (Fri Jan 07 2005 - 08:14:12 CST)
AMBER: Weighting of different restraint types? pl (Fri Jan 07 2005 - 07:03:15 CST)
Re: AMBER: Floating Exception in sander Robert Duke (Fri Jan 07 2005 - 07:15:44 CST)
AMBER: Questions about sander.QMMM Cenk Andac (Fri Jan 07 2005 - 09:51:56 CST)
Re: AMBER: Questions about sander.QMMM M. L. Dodson (Fri Jan 07 2005 - 10:26:25 CST)
Re: AMBER: Questions about sander.QMMM M. L. Dodson (Fri Jan 07 2005 - 10:45:45 CST)
Re: AMBER: about install amber8 on windows David A. Case (Fri Jan 07 2005 - 12:59:27 CST)
Re: AMBER: recompiling problem on IBM aix David A. Case (Fri Jan 07 2005 - 13:03:30 CST)
RE: AMBER: Questions about sander.QMMM Ross Walker (Fri Jan 07 2005 - 13:38:29 CST)
Re: AMBER: Weighting of different restraint types? David A. Case (Fri Jan 07 2005 - 18:06:37 CST)
RE: AMBER: Questions about sander.QMMM Cenk Andac (Sat Jan 08 2005 - 03:57:22 CST)
AMBER: dynamics Germán Sciaini (Sat Jan 08 2005 - 13:51:30 CST)
Re: AMBER: dynamics David A. Case (Sat Jan 08 2005 - 15:05:53 CST)
AMBER: Floating Exception and installation on Digital Unix. anshul_at_imtech.res.in (Sun Jan 09 2005 - 21:32:11 CST)
Re: AMBER: Floating Exception and installation on Digital Unix. Robert Duke (Sun Jan 09 2005 - 11:54:16 CST)
AMBER: error in parallel gsmith_at_ibab.ac.in (Mon Jan 10 2005 - 02:18:51 CST)
Re: AMBER: Weighting of different restraint types? pl (Mon Jan 10 2005 - 03:27:19 CST)
AMBER: istart2 gsmith_at_ibab.ac.in (Mon Jan 10 2005 - 07:14:15 CST)
AMBER: guanidinium chloride Monica Civera (Mon Jan 10 2005 - 09:27:38 CST)
RE: AMBER: guanidinium chloride Nagy, Peter I. (Mon Jan 10 2005 - 11:15:41 CST)
RE: AMBER: istart2 Ross Walker (Mon Jan 10 2005 - 11:18:32 CST)
AMBER: Copper library? Cenk Andac (Mon Jan 10 2005 - 12:31:51 CST)
AMBER: the DNA conformation after engery minimization using NMODE Xiaowei (David) Li (Mon Jan 10 2005 - 13:32:26 CST)
AMBER: .dat and frcmod files Ilyas Yildirim (Mon Jan 10 2005 - 16:10:36 CST)
Re: AMBER: .dat and frcmod files Anthony Fejes (Mon Jan 10 2005 - 16:47:12 CST)
AMBER: AMBER tutorial ambpdb question Kara Wald (Mon Jan 10 2005 - 19:33:44 CST)
RE: AMBER: AMBER tutorial ambpdb question Ross Walker (Mon Jan 10 2005 - 20:14:49 CST)
Re: AMBER: AMBER tutorial ambpdb question David A. Case (Mon Jan 10 2005 - 21:16:10 CST)
Re: AMBER: the DNA conformation after engery minimization using NMODE Bill Ross (Mon Jan 10 2005 - 21:56:25 CST)
Re: AMBER: Floating Exception and installation on Digital Unix. anshul_at_imtech.res.in (Tue Jan 11 2005 - 09:17:32 CST)
Re: AMBER: .dat and frcmod files Germán Sciaini (Tue Jan 11 2005 - 04:46:03 CST)
Re: AMBER: Copper library? Germán Sciaini (Tue Jan 11 2005 - 04:40:55 CST)
AMBER: parallel run gsmith_at_ibab.ac.in (Tue Jan 11 2005 - 04:27:20 CST)
Re: AMBER: Floating Exception and installation on Digital Unix. Robert Duke (Tue Jan 11 2005 - 07:18:20 CST)
Re: AMBER: Floating Exception and installation on Digital Unix. M. L. Dodson (Tue Jan 11 2005 - 09:46:45 CST)
AMBER: QM/MM with pmemd Ping Lin (Tue Jan 11 2005 - 13:08:45 CST)
AMBER: sander free energy calculation Cai, Yufeng (Tue Jan 11 2005 - 13:47:03 CST)
Re: AMBER: Dummy Atoms: How to create them? David A. Case (Tue Jan 11 2005 - 23:54:02 CST)
AMBER: PB dynamics Nelson Fonseca (Wed Jan 12 2005 - 04:06:33 CST)
AMBER: amber8 parallel sander yen li (Wed Jan 12 2005 - 04:57:19 CST)
AMBER: van der waals parameters Monica Civera (Wed Jan 12 2005 - 05:42:53 CST)
Re: AMBER: amber8 parallel sander Carlos Simmerling (Wed Jan 12 2005 - 06:38:30 CST)
Re: AMBER: van der waals parameters Carlos Simmerling (Wed Jan 12 2005 - 06:41:31 CST)
Re: AMBER: amber8 parallel sander Robert Duke (Wed Jan 12 2005 - 07:03:05 CST)
Re: AMBER: amber8 parallel sander yen li (Wed Jan 12 2005 - 07:54:48 CST)
Re: AMBER: amber8 parallel sander Carlos Simmerling (Wed Jan 12 2005 - 08:03:32 CST)
AMBER: units Monica Civera (Wed Jan 12 2005 - 09:12:19 CST)
Re: AMBER: amber8 parallel sander Robert Duke (Wed Jan 12 2005 - 09:20:40 CST)
Re: AMBER: amber8 parallel sander Carlos Simmerling (Wed Jan 12 2005 - 09:30:22 CST)
Re: AMBER: PB dynamics David A. Case (Wed Jan 12 2005 - 11:26:19 CST)
Re: AMBER: units David A. Case (Wed Jan 12 2005 - 11:22:03 CST)
Re: AMBER: amber8 parallel sander Bill Ross (Wed Jan 12 2005 - 14:12:18 CST)
AMBER: Problem with restart file Azira Muhamad (Thu Jan 13 2005 - 01:45:30 CST)
Re: AMBER: units Germán Sciaini (Thu Jan 13 2005 - 05:35:07 CST)
Re: AMBER: units Germán Sciaini (Thu Jan 13 2005 - 05:33:16 CST)
Re: AMBER: Problem with restart file Melinda Layten (Thu Jan 13 2005 - 08:53:42 CST)
Re: AMBER: Problem with restart file Guanglei Cui (Thu Jan 13 2005 - 09:40:14 CST)
AMBER: PBCAL=0. Problems in MM/PBSA Javier Perez Miron (Thu Jan 13 2005 - 14:41:29 CST)
Re: AMBER: PBCAL=0. Problems in MM/PBSA Holger Gohlke (Fri Jan 14 2005 - 01:31:45 CST)
AMBER: last call for early registrations for "Horizons2005" Vlad Cojocaru (Fri Jan 14 2005 - 07:19:00 CST)
AMBER: protonate Gustavo Pierdominici Sottile (Fri Jan 14 2005 - 12:05:49 CST)
Re: AMBER: protonate David A. Case (Fri Jan 14 2005 - 12:36:35 CST)
FW: AMBER: parametrization problem Ross Walker (Fri Jan 14 2005 - 16:39:12 CST)
RE: FW: AMBER: parametrization problem Vineet Pande (Sat Jan 15 2005 - 05:15:39 CST)
AMBER: Coordinate Superimposition in PTRAJ Vineet Pande (Sun Jan 16 2005 - 05:42:09 CST)
Re: AMBER: Coordinate Superimposition in PTRAJ Carlos Simmerling (Sun Jan 16 2005 - 08:56:30 CST)
RE: AMBER: Coordinate Superimposition in PTRAJ Ross Walker (Sun Jan 16 2005 - 12:59:48 CST)
AMBER: How to set AMBER parameter files for lipid? Xiaoqing Wang (Sun Jan 16 2005 - 19:38:49 CST)
RE: AMBER: Coordinate Superimposition in PTRAJ Vineet Pande (Mon Jan 17 2005 - 03:45:20 CST)
AMBER: Sander Replica Exchange exits with unit 6 error] Jordi Rodrigo (Mon Jan 17 2005 - 02:02:51 CST)
AMBER: distance restraint and file fort.35 Fabien Cailliez (Mon Jan 17 2005 - 05:34:00 CST)
Re: AMBER: Sander Replica Exchange exits with unit 6 error] Carlos Simmerling (Mon Jan 17 2005 - 07:58:20 CST)
AMBER: RMS fluctuations along modes obtained from PCA Majid moghaddam (Mon Jan 17 2005 - 07:47:56 CST)
AMBER: Sander Replica Exchange exits with unit 6 error Jordi Rodrigo (Mon Jan 17 2005 - 06:37:00 CST)
Re: AMBER: Sander Replica Exchange exits with unit 6 error Carlos Simmerling (Mon Jan 17 2005 - 08:45:56 CST)
Re: AMBER: distance restraint and file fort.35 Robert Duke (Mon Jan 17 2005 - 08:48:57 CST)
AMBER: Sander Replica Exchange exits with unit 6 error Jordi Rodrigo (Mon Jan 17 2005 - 07:25:14 CST)
Re: AMBER: distance restraint and file fort.35 Fabien Cailliez (Mon Jan 17 2005 - 09:58:03 CST)
Re: AMBER: Sander Replica Exchange exits with unit 6 error Guanglei Cui (Mon Jan 17 2005 - 10:09:03 CST)
AMBER: new aminoacid Gustavo Pierdominici Sottile (Mon Jan 17 2005 - 10:26:32 CST)
AMBER: Sander Replica Exchange exits with unit 6 error Jordi Rodrigo (Mon Jan 17 2005 - 08:57:53 CST)
Re: AMBER: Sander Replica Exchange exits with unit 6 error Carlos Simmerling (Mon Jan 17 2005 - 11:17:56 CST)
Re: AMBER: new aminoacid David A. Case (Mon Jan 17 2005 - 11:56:34 CST)
Re: AMBER: amber8 parallel sander yen li (Mon Jan 17 2005 - 11:55:26 CST)
Re: AMBER: amber8 parallel sander Robert Duke (Mon Jan 17 2005 - 12:13:10 CST)
RE: AMBER: new aminoacid Ross Walker (Mon Jan 17 2005 - 12:34:05 CST)
AMBER: Compiling AMBER 8 for Mac OSX (Parallel) nallen_at_unca.edu (Mon Jan 17 2005 - 11:41:06 CST)
Re: AMBER: Sander Replica Exchange exits with unit 6 error Guanglei Cui (Mon Jan 17 2005 - 13:31:07 CST)
AMBER: H-atom types attached to a carbon atom next to carbonyl group Takashi Nakamura (Mon Jan 17 2005 - 11:52:56 CST)
RE: AMBER: H-atom types attached to a carbon atom next to carbonyl group Vineet Pande (Mon Jan 17 2005 - 14:32:37 CST)
AMBER: SO4 prep file Jagdish Rai (Tue Jan 18 2005 - 06:36:42 CST)
Re: AMBER: SO4 prep file scopio (Tue Jan 18 2005 - 06:57:29 CST)
AMBER: details of new aminoacid Gustavo Pierdominici Sottile (Tue Jan 18 2005 - 07:01:15 CST)
AMBER: GB differences between AMBER7 and AMBER8 Fabien Cailliez (Tue Jan 18 2005 - 07:53:04 CST)
Re: AMBER: GB differences between AMBER7 and AMBER8 Carlos Simmerling (Tue Jan 18 2005 - 08:08:20 CST)
AMBER: problem with position restraints (refc file) pl (Tue Jan 18 2005 - 09:25:27 CST)
Re: AMBER: details of new aminoacid David A. Case (Tue Jan 18 2005 - 10:01:20 CST)
Re: AMBER: problem with position restraints (refc file) Carlos Simmerling (Tue Jan 18 2005 - 10:03:03 CST)
Re: AMBER: protonate myang (Tue Jan 18 2005 - 10:07:12 CST)
AMBER: Amber8 installation problems on Sparc/Solaris9 Joe Nolan (Tue Jan 18 2005 - 10:17:35 CST)
AMBER: Sander Replica Exchange exits with unit 6 error Jordi Rodrigo (Tue Jan 18 2005 - 08:46:27 CST)
Re: AMBER: Amber8 installation problems on Sparc/Solaris9 David A. Case (Tue Jan 18 2005 - 10:48:33 CST)
Re: AMBER: problem with position restraints (refc file) pl (Tue Jan 18 2005 - 11:13:17 CST)
Re: AMBER: problem with position restraints (refc file) Carlos Simmerling (Tue Jan 18 2005 - 11:36:55 CST)
Re: AMBER: Compiling AMBER 8 for Mac OSX (Parallel) Emmanuel Giudice (Tue Jan 18 2005 - 00:09:47 CST)
AMBER: Converting prmtop and inpcrd files Andrew Box (Tue Jan 18 2005 - 17:02:02 CST)
Re: AMBER: Converting prmtop and inpcrd files Bill Ross (Tue Jan 18 2005 - 17:43:04 CST)
Re: AMBER: problem with position restraints (refc file) pl (Wed Jan 19 2005 - 05:47:18 CST)
Re: AMBER: RMS fluctuations along modes obtained from PCA Holger Gohlke (Wed Jan 19 2005 - 08:51:10 CST)
AMBER: Scaling of charges in a polarizable simulation ! Pradipta Bandyopadhyay (Wed Jan 19 2005 - 10:02:37 CST)
AMBER: IGB parameter Javier Perez Miron (Wed Jan 19 2005 - 11:09:38 CST)
AMBER: enhanced sampling methods Vlad Cojocaru (Wed Jan 19 2005 - 12:13:58 CST)
Re: AMBER: Scaling of charges in a polarizable simulation ! Piotr Cieplak (Wed Jan 19 2005 - 12:14:05 CST)
RE: AMBER: Compiling AMBER 8 for Mac OSX (Parallel) Ross Walker (Wed Jan 19 2005 - 12:23:40 CST)
AMBER: ptraj analysis Thomas E. Cheatham, III (Wed Jan 19 2005 - 12:16:17 CST)
Re: AMBER: IGB parameter Furse, Kristina Elisabet (Wed Jan 19 2005 - 13:33:13 CST)
Re: AMBER: Scaling of charges in a polarizable simulation ! David A. Case (Wed Jan 19 2005 - 14:11:08 CST)
Re: AMBER: ptraj analysis David A. Case (Wed Jan 19 2005 - 14:24:58 CST)
Re: AMBER: enhanced sampling methods David A. Case (Wed Jan 19 2005 - 14:34:24 CST)
AMBER: AMBER8: compiling under cygwin using lahey fortran Rino Ragno (Wed Jan 19 2005 - 16:13:07 CST)
Re: AMBER: Scaling of charges in a polarizable simulation ! Pradipta Bandyopadhyay (Wed Jan 19 2005 - 22:54:13 CST)
Re: AMBER: Scaling of charges in a polarizable simulation ! Piotr Cieplak (Thu Jan 20 2005 - 00:56:04 CST)
Re: AMBER: ptraj analysis Holger Gohlke (Thu Jan 20 2005 - 01:28:27 CST)
AMBER:Hydroxy Proline S.Sundar Raman (Thu Jan 20 2005 - 03:19:42 CST)
AMBER: pmemd and distance restraint Fabien Cailliez (Thu Jan 20 2005 - 04:39:20 CST)
Re: AMBER: pmemd and distance restraint Robert Duke (Thu Jan 20 2005 - 06:41:30 CST)
AMBER: some question about MM-PBSA scopio (Thu Jan 20 2005 - 09:10:39 CST)
AMBER: Cutoff for anal Harianto (Thu Jan 20 2005 - 11:50:14 CST)
AMBER: new tutorial available David A. Case (Thu Jan 20 2005 - 13:06:30 CST)
Re: AMBER: Cutoff for anal David A. Case (Thu Jan 20 2005 - 13:17:31 CST)
AMBER: Can someone recommend a tutorial? Kara Wald (Thu Jan 20 2005 - 14:28:46 CST)
RE: AMBER: Can someone recommend a tutorial? Ross Walker (Thu Jan 20 2005 - 14:37:22 CST)
AMBER: sander failure ygao_at_phase1.unl.edu (Thu Jan 20 2005 - 15:46:56 CST)
RE: AMBER: sander failure Ross Walker (Thu Jan 20 2005 - 16:04:32 CST)
RE: AMBER: sander failure ygao_at_phase1.unl.edu (Thu Jan 20 2005 - 16:09:56 CST)
Re: AMBER: sander failure Carlos Simmerling (Thu Jan 20 2005 - 16:20:00 CST)
RE: AMBER: sander failure Ross Walker (Thu Jan 20 2005 - 16:26:58 CST)
RE: AMBER: sander failure ygao_at_phase1.unl.edu (Thu Jan 20 2005 - 16:31:37 CST)
RE: AMBER: sander failure Ross Walker (Thu Jan 20 2005 - 16:47:34 CST)
Re: AMBER: sander failure Asim Okur (Thu Jan 20 2005 - 16:50:25 CST)
AMBER: Suspended (tty input) ygao_at_phase1.unl.edu (Thu Jan 20 2005 - 17:39:48 CST)
RE: AMBER: Suspended (tty input) Ross Walker (Thu Jan 20 2005 - 17:58:13 CST)
Re: AMBER: Suspended (tty input) Thomas E. Cheatham, III (Thu Jan 20 2005 - 18:09:16 CST)
Re: AMBER: pmemd and distance restraint Robert Duke (Thu Jan 20 2005 - 21:12:17 CST)
AMBER: &dipoles in sander Cenk Andac (Fri Jan 21 2005 - 05:59:47 CST)
AMBER: mm_pbsa example doesn't run Yuuki Komata (Fri Jan 21 2005 - 06:10:48 CST)
AMBER: amber 8 installation Stern, Julie (Fri Jan 21 2005 - 11:28:17 CST)
Re: AMBER: amber 8 installation David A. Case (Fri Jan 21 2005 - 11:55:50 CST)
Re: AMBER: amber 8 installation Robert Duke (Fri Jan 21 2005 - 12:03:42 CST)
RE: AMBER: &dipoles in sander Ross Walker (Fri Jan 21 2005 - 12:26:24 CST)
AMBER: Andersen thermostat: target T? Arantxa Sanz (Fri Jan 21 2005 - 13:06:01 CST)
AMBER: carnal - water-mediated HBond Sichun Yang (Fri Jan 21 2005 - 16:36:52 CST)
Re: AMBER: Andersen thermostat: target T? David A. Case (Fri Jan 21 2005 - 18:23:17 CST)
AMBER: eedmeth=5 Lihua Wang (Fri Jan 21 2005 - 18:20:59 CST)
AMBER: problem runing parallel (REM) on tru64 Sergio E. Wong (Fri Jan 21 2005 - 18:22:26 CST)
AMBER: nmode calculation mingche Pan (Fri Jan 21 2005 - 19:43:32 CST)
RE: AMBER: &dipoles in sander Cenk Andac (Sat Jan 22 2005 - 03:47:50 CST)
Re: AMBER: eedmeth=5 David A. Case (Sat Jan 22 2005 - 12:20:22 CST)
Re: AMBER: problem runing parallel (REM) on tru64 David A. Case (Sat Jan 22 2005 - 12:25:55 CST)
RE: AMBER: &dipoles in sander Ross Walker (Sat Jan 22 2005 - 13:11:54 CST)
Re: AMBER: problem runing parallel (REM) on tru64 Sergio E. Wong (Sat Jan 22 2005 - 14:44:23 CST)
Re: AMBER: carnal - water-mediated HBond Bill Ross (Sat Jan 22 2005 - 22:49:09 CST)
AMBER: Question about TI integral method tanc_at_uci.edu (Sun Jan 23 2005 - 04:01:33 CST)
RE: AMBER: eedmeth=5 Vineet Pande (Sun Jan 23 2005 - 05:46:23 CST)
AMBER: D-amino acid prep-files(simple method) Jagdish Rai (Sun Jan 23 2005 - 08:18:45 CST)
Re: AMBER: carnal - water-mediated HBond Jiri Sponer (Sun Jan 23 2005 - 08:52:55 CST)
Re: AMBER: D-amino acid prep-files(simple method) FyD (Sun Jan 23 2005 - 14:05:38 CST)
AMBER: system size limit Guanglei Cui (Sun Jan 23 2005 - 23:54:06 CST)
Re: AMBER: Question about TI integral method David A. Case (Mon Jan 24 2005 - 00:41:26 CST)
Re: AMBER: system size limit David A. Case (Mon Jan 24 2005 - 00:56:30 CST)
AMBER: What does a crash mean while running a md simulation? shuli kang (Sun Jan 23 2005 - 23:56:00 CST)
AMBER: FW: amber 8 problem Vojtìch Klusák (Mon Jan 24 2005 - 02:13:47 CST)
RE: AMBER: Andersen thermostat: target T? Arantxa Sanz (Mon Jan 24 2005 - 04:18:05 CST)
AMBER: nmode calculation mingche Pan (Mon Jan 24 2005 - 09:34:18 CST)
AMBER: AMBER 8: Freeze AND restrain questions Guillaume Bollot (Mon Jan 24 2005 - 10:19:11 CST)
Re: AMBER: AMBER 8: Freeze AND restrain questions Viktor Hornak (Mon Jan 24 2005 - 12:02:53 CST)
RE: AMBER: nmode calculation Ross Walker (Mon Jan 24 2005 - 13:13:59 CST)
RE: AMBER: What does a crash mean while running a md simulation? Ross Walker (Mon Jan 24 2005 - 13:19:48 CST)
AMBER: test suite possible failures Stern, Julie (Mon Jan 24 2005 - 13:39:42 CST)
AMBER: amber 8 benchmarks dec alpha Sergio E. Wong (Mon Jan 24 2005 - 16:08:14 CST)
RE: AMBER: nmode calculation mingche Pan (Mon Jan 24 2005 - 16:12:13 CST)
Re: AMBER: amber 8 benchmarks dec alpha Robert Duke (Mon Jan 24 2005 - 16:27:50 CST)
Re: AMBER: test suite possible failures David A. Case (Mon Jan 24 2005 - 16:38:21 CST)
Re: AMBER: amber 8 benchmarks dec alpha Sergio E. Wong (Mon Jan 24 2005 - 17:54:41 CST)
AMBER: How to make PDB file by myself Mayumi Haga (Mon Jan 24 2005 - 22:23:32 CST)
AMBER: TI with electrostatic decoupling at sander yipinl_at_umich.edu (Mon Jan 24 2005 - 23:15:43 CST)
Re: AMBER: What does a crash mean while running a md simulation? shuli kang (Mon Jan 24 2005 - 23:58:54 CST)
RE: AMBER: What does a crash mean while running a md simulation? Ross Walker (Tue Jan 25 2005 - 00:28:32 CST)
Re: AMBER: What does a crash mean while running a md simulation? shuli kang (Tue Jan 25 2005 - 01:35:45 CST)
AMBER: calculating electrostatic potential Vlad Cojocaru (Tue Jan 25 2005 - 04:59:48 CST)
RE: AMBER: How to make PDB file by myself Vineet Pande (Tue Jan 25 2005 - 05:06:42 CST)
Re: AMBER: calculating electrostatic potential david.evans_at_ulsop.ac.uk (Tue Jan 25 2005 - 05:24:52 CST)
AMBER: PBSA residual and pairwise decompostion Jiten (Tue Jan 25 2005 - 07:43:38 CST)
AMBER: LEAP heddi (Tue Jan 25 2005 - 07:42:36 CST)
AMBER: Error while running resp. praveena moldy (Tue Jan 25 2005 - 08:24:01 CST)
AMBER: Error while running resp. praveena moldy (Tue Jan 25 2005 - 08:28:55 CST)
AMBER: Sander Replica Exchange exits with unit 6 error Jordi Rodrigo (Tue Jan 25 2005 - 08:28:13 CST)
Re: AMBER: How to make PDB file by myself David A. Case (Tue Jan 25 2005 - 10:40:21 CST)
Re: AMBER: TI with electrostatic decoupling at sander David A. Case (Tue Jan 25 2005 - 10:41:36 CST)
Re: AMBER: Error while running resp. David A. Case (Tue Jan 25 2005 - 10:43:32 CST)
AMBER: gold atoms Stern, Julie (Tue Jan 25 2005 - 10:53:09 CST)
Re: AMBER: calculating electrostatic potential Ilyas Yildirim (Tue Jan 25 2005 - 12:26:32 CST)
AMBER: collision frequency in GBSA dynamics Giulio Rastelli (Tue Jan 25 2005 - 12:33:33 CST)
AMBER: NAN errors Venkata S Koppuravuri (Tue Jan 25 2005 - 15:39:45 CST)
RE: AMBER: NAN errors Ross Walker (Tue Jan 25 2005 - 15:56:33 CST)
Re: AMBER: NAN errors David A. Case (Tue Jan 25 2005 - 16:09:11 CST)
Re: AMBER: collision frequency in GBSA dynamics David A. Case (Tue Jan 25 2005 - 16:23:34 CST)
AMBER: ANTECHAMBER & DIVCON Vineet Pande (Wed Jan 26 2005 - 04:18:17 CST)
Re: AMBER: ANTECHAMBER & DIVCON Julien Michel (Wed Jan 26 2005 - 05:09:05 CST)
Re: AMBER: new tutorial available Ilyas Yildirim (Wed Jan 26 2005 - 05:59:16 CST)
Re: AMBER: new tutorial available Julien Michel (Wed Jan 26 2005 - 07:48:55 CST)
AMBER: how to solvate in TIP5P box ygao_at_phase1.unl.edu (Wed Jan 26 2005 - 09:59:43 CST)
AMBER: pmemd and restraints Filip Lankas (Wed Jan 26 2005 - 11:01:50 CST)
Re: AMBER: TI with electrostatic decoupling at sander yipinl_at_umich.edu (Wed Jan 26 2005 - 11:19:43 CST)
Re: AMBER: new tutorial available David A. Case (Wed Jan 26 2005 - 11:27:58 CST)
Re: AMBER: pmemd and restraints Robert Duke (Wed Jan 26 2005 - 11:45:01 CST)
RE: AMBER: how to solvate in TIP5P box Ross Walker (Wed Jan 26 2005 - 12:26:22 CST)
AMBER: Increasing Volume with ntb=1 Harianto (Wed Jan 26 2005 - 14:12:29 CST)
RE: AMBER: Increasing Volume with ntb=1 Ross Walker (Wed Jan 26 2005 - 14:42:13 CST)
Re: AMBER: Increasing Volume with ntb=1 Harianto (Wed Jan 26 2005 - 17:19:59 CST)
RE: AMBER: Increasing Volume with ntb=1 Ross Walker (Wed Jan 26 2005 - 16:59:57 CST)
Re: AMBER: TI with electrostatic decoupling at sander David A. Case (Wed Jan 26 2005 - 23:51:32 CST)
Re: AMBER: pmemd and restraints Fabien Cailliez (Thu Jan 27 2005 - 03:01:31 CST)
AMBER:idecomp B (Thu Jan 27 2005 - 05:22:37 CST)
Re: AMBER: pmemd and restraints Robert Duke (Thu Jan 27 2005 - 07:15:00 CST)
AMBER: replica exchange trouble with unit 6 Yuuki Komata (Thu Jan 27 2005 - 08:39:03 CST)
AMBER: antechamber error message Yanze Zhang (Thu Jan 27 2005 - 09:02:46 CST)
Re: AMBER: replica exchange trouble with unit 6 Carlos Simmerling (Thu Jan 27 2005 - 09:10:20 CST)
Re: AMBER: Increasing Volume with ntb=1 Harianto (Thu Jan 27 2005 - 11:49:52 CST)
Re: AMBER: TI with electrostatic decoupling at sander yipinl_at_umich.edu (Thu Jan 27 2005 - 11:39:46 CST)
RE: AMBER: Increasing Volume with ntb=1 Ross Walker (Thu Jan 27 2005 - 12:13:27 CST)
AMBER: problem with pressure equilibration Cenk Andac (Thu Jan 27 2005 - 16:23:59 CST)
RE: AMBER: problem with pressure equilibration Ross Walker (Thu Jan 27 2005 - 16:45:20 CST)
Re: AMBER: ANTECHAMBER & DIVCON David A. Case (Thu Jan 27 2005 - 19:12:23 CST)
Re: AMBER: TI with electrostatic decoupling at sander David A. Case (Thu Jan 27 2005 - 19:27:10 CST)
Re: AMBER: replica exchange trouble with unit 6 Yuuki Komata (Thu Jan 27 2005 - 19:27:50 CST)
AMBER: question about xwin load pdb file xiaowen (Thu Jan 27 2005 - 23:04:57 CST)
RE: AMBER: question about xwin load pdb file Ross Walker (Thu Jan 27 2005 - 23:38:30 CST)
RE: AMBER: &dipoles in sander Cenk Andac (Fri Jan 28 2005 - 04:04:21 CST)
AMBER: sugar pucker with Carnal and ptraj Vlad Cojocaru (Fri Jan 28 2005 - 08:56:23 CST)
AMBER: pucker: deatails about pucker calculation Vlad Cojocaru (Fri Jan 28 2005 - 09:13:13 CST)
AMBER: question about xwin load pdb file xiaowen (Fri Jan 28 2005 - 10:48:28 CST)
AMBER: plane definition in ptraj Vlad Cojocaru (Fri Jan 28 2005 - 12:00:23 CST)
RE: AMBER: &dipoles in sander Ross Walker (Fri Jan 28 2005 - 12:10:21 CST)
RE: AMBER: question about xwin load pdb file Ross Walker (Fri Jan 28 2005 - 12:20:18 CST)
Re: AMBER: &dipoles in sander David A. Case (Fri Jan 28 2005 - 12:21:59 CST)
RE: AMBER: problem with pressure equilibration Cenk Andac (Fri Jan 28 2005 - 13:18:02 CST)
Re: AMBER: &dipoles in sander Cenk Andac (Fri Jan 28 2005 - 13:25:36 CST)
Re: AMBER: antechamber error message David A. Case (Fri Jan 28 2005 - 16:00:22 CST)
AMBER: Problems with xLEaP Kara Di Giorgio (Fri Jan 28 2005 - 16:04:14 CST)
RE: AMBER: Problems with xLEaP Ross Walker (Fri Jan 28 2005 - 16:19:52 CST)
Re: AMBER: Problems with xLEaP Bill Ross (Fri Jan 28 2005 - 16:26:12 CST)
AMBER: NCOPY definition Kenley Barrett (Fri Jan 28 2005 - 16:59:14 CST)
RE: AMBER: NCOPY definition Ross Walker (Fri Jan 28 2005 - 17:18:05 CST)
Re: AMBER: new tutorial available Difei Wang (Fri Jan 28 2005 - 18:08:59 CST)
Re: AMBER: Problems with xLEaP Kara Di Giorgio (Fri Jan 28 2005 - 18:14:02 CST)
Re: AMBER: Problems with xLEaP Kara Di Giorgio (Fri Jan 28 2005 - 18:18:44 CST)
RE: AMBER: Problems with xLEaP Ross Walker (Fri Jan 28 2005 - 18:29:10 CST)
Re: AMBER: Problems with xLEaP Kara Di Giorgio (Fri Jan 28 2005 - 18:48:52 CST)
Re: AMBER: new tutorial available David A. Case (Fri Jan 28 2005 - 18:57:28 CST)
AMBER: Problem in ptraj anshul_at_imtech.res.in (Mon Jan 31 2005 - 16:23:30 CST)
AMBER: amber 8 problem Vojtìch Klusák (Mon Jan 31 2005 - 07:01:35 CST)
AMBER: gaussian output file Yanze Zhang (Mon Jan 31 2005 - 11:09:40 CST)
Re: AMBER: Problem in ptraj Furse, Kristina Elisabet (Mon Jan 31 2005 - 11:22:21 CST)
Re: AMBER: FW: amber 8 problem David A. Case (Mon Jan 31 2005 - 12:37:08 CST)
AMBER: skip snapshots with ptraj in amber 8.0 Eric Hu (Mon Jan 31 2005 - 13:30:58 CST)
AMBER: Manuals need update: protonate -b and -c options gone in Amber 7 and 8 Chris Moth (Mon Jan 31 2005 - 15:39:56 CST)
Re: AMBER: skip snapshots with ptraj in amber 8.0 Guanglei Cui (Mon Jan 31 2005 - 16:19:27 CST)
Re: AMBER: Manuals need update: protonate -b and -c options gone in Amber 7 and 8 David A. Case (Mon Jan 31 2005 - 16:56:21 CST)
Re: AMBER: skip snapshots with ptraj in amber 8.0 Eric Hu (Mon Jan 31 2005 - 19:08:26 CST)
AMBER: amber8 in IBM-SP4 Jiten (Mon Jan 31 2005 - 21:32:28 CST)
AMBER: N Metyl amino acids Andrew Box (Mon Jan 31 2005 - 23:14:47 CST)
AMBER: vacuum bubbles in system equilibration Marie-Pierre Durrieu (Tue Feb 01 2005 - 04:56:21 CST)
Re: AMBER: Problem in ptraj anshul_at_imtech.res.in (Tue Feb 01 2005 - 16:26:48 CST)
Re: AMBER: N Metyl amino acids Carlos Simmerling (Tue Feb 01 2005 - 06:47:30 CST)
AMBER: Carnal in Amber8 Vlad Cojocaru (Tue Feb 01 2005 - 10:11:09 CST)
Re: AMBER: Carnal in Amber8 David A. Case (Tue Feb 01 2005 - 11:27:25 CST)
AMBER: Multiple dihedral restraints Joseph Fernandez (Tue Feb 01 2005 - 11:29:40 CST)
AMBER: Redhat Enterprise Linux Beale, John (Tue Feb 01 2005 - 11:49:20 CST)
RE: AMBER: Redhat Enterprise Linux S. Frank Yan (Tue Feb 01 2005 - 11:57:00 CST)
Re: AMBER: Problem in ptraj Furse, Kristina Elisabet (Tue Feb 01 2005 - 13:30:53 CST)
Re: AMBER: Carnal in Amber8 Bill Ross (Tue Feb 01 2005 - 13:47:15 CST)
Re: AMBER: Carnal in Amber8 Bill Ross (Tue Feb 01 2005 - 13:57:19 CST)
AMBER: doubts with a new aminoacid Gustavo Pierdominici Sottile (Tue Feb 01 2005 - 14:28:52 CST)
AMBER: External Electric Field Brandon Tefft (Tue Feb 01 2005 - 15:30:22 CST)
AMBER: sander segmentation fault Xin Wang (Tue Feb 01 2005 - 16:15:12 CST)
Re: AMBER: Multiple dihedral restraints David A. Case (Tue Feb 01 2005 - 16:54:49 CST)
RE: AMBER: gaussian output file Junmei Wang (Tue Feb 01 2005 - 17:03:22 CST)
Re: AMBER: doubts with a new aminoacid David A. Case (Tue Feb 01 2005 - 17:35:36 CST)
RE: AMBER: Redhat Enterprise Linux Andrew Box (Tue Feb 01 2005 - 17:37:55 CST)
Re: AMBER: doubts with a new aminoacid Bill Ross (Tue Feb 01 2005 - 18:36:38 CST)
AMBER: xleap: different distance results from "check" command in xleap Woojin Lee (Tue Feb 01 2005 - 23:54:14 CST)
Re: AMBER: Problem in ptraj anshul_at_imtech.res.in (Wed Feb 02 2005 - 16:04:28 CST)
AMBER: Compilation problem at dual processor linux ! Pradipta Bandyopadhyay (Wed Feb 02 2005 - 06:32:52 CST)
AMBER: change of prmtop file Gustavo Pierdominici Sottile (Wed Feb 02 2005 - 09:43:34 CST)
AMBER: xleap MOVE and .lib file Stern, Julie (Wed Feb 02 2005 - 11:01:55 CST)
RE: AMBER: Compilation problem at dual processor linux ! Ross Walker (Wed Feb 02 2005 - 11:52:10 CST)
RE: AMBER: Redhat Enterprise Linux Beale, John (Wed Feb 02 2005 - 12:01:53 CST)
Re: AMBER: change of prmtop file Guanglei Cui (Wed Feb 02 2005 - 12:03:53 CST)
Re: AMBER: External Electric Field David A. Case (Wed Feb 02 2005 - 12:08:59 CST)
AMBER: Multiple dihedral restraints (follow up) Joseph Fernandez (Wed Feb 02 2005 - 12:11:01 CST)
Re: AMBER: Problem in ptraj Furse, Kristina Elisabet (Wed Feb 02 2005 - 12:16:03 CST)
Re: AMBER: change of prmtop file David A. Case (Wed Feb 02 2005 - 12:21:34 CST)
AMBER: amber 8 system requirements dkohen_at_carleton.edu (Wed Feb 02 2005 - 12:28:48 CST)
Re: AMBER: Problem in ptraj Thomas E. Cheatham, III (Wed Feb 02 2005 - 12:34:01 CST)
RE: AMBER: amber 8 system requirements Ross Walker (Wed Feb 02 2005 - 12:47:55 CST)
Re: AMBER: Multiple dihedral restraints (follow up) David A. Case (Wed Feb 02 2005 - 13:04:47 CST)
Re: AMBER: sander segmentation fault David A. Case (Wed Feb 02 2005 - 13:28:37 CST)
Re: AMBER: sander segmentation fault Xin Wang (Wed Feb 02 2005 - 15:36:25 CST)
Re: AMBER: sander segmentation fault David A. Case (Wed Feb 02 2005 - 16:39:06 CST)
Re: AMBER: sander segmentation fault Furse, Kristina Elisabet (Wed Feb 02 2005 - 17:32:25 CST)
AMBER: gaff frcmod file for TI calculation Eric Hu (Wed Feb 02 2005 - 17:50:00 CST)
Re: AMBER: sander segmentation fault Thomas E. Cheatham, III (Wed Feb 02 2005 - 17:59:13 CST)
Re: AMBER: gaff frcmod file for TI calculation David A. Case (Wed Feb 02 2005 - 18:44:13 CST)
Re: AMBER: gaff frcmod file for TI calculation Eric Hu (Wed Feb 02 2005 - 19:47:32 CST)
RE: AMBER: sander segmentation fault Ross Walker (Wed Feb 02 2005 - 20:05:41 CST)
AMBER: question about tleap load pdb file xiaowen (Wed Feb 02 2005 - 21:19:19 CST)
AMBER: protonate and input conversion error Stern, Julie (Thu Feb 03 2005 - 10:48:20 CST)
AMBER: non-periodic condition gsciaini (Thu Feb 03 2005 - 10:40:46 CST)
Re: AMBER: protonate and input conversion error David A. Case (Thu Feb 03 2005 - 12:09:31 CST)
RE: AMBER: non-periodic condition Ross Walker (Thu Feb 03 2005 - 12:27:30 CST)
Re: AMBER: Multiple dihedral restraints (follow up) M. L. Dodson (Thu Feb 03 2005 - 14:07:11 CST)
RE: AMBER: non-periodic condition Germán Sciaini (Thu Feb 03 2005 - 14:42:34 CST)
AMBER: DNA melting free energy calculation lei jia (Thu Feb 03 2005 - 18:39:57 CST)
AMBER: unnatural ligand Eric Hu (Thu Feb 03 2005 - 21:37:41 CST)
AMBER: clusters Germán Sciaini (Fri Feb 04 2005 - 06:36:48 CST)
AMBER: tleap load pdb file xiaowen (Fri Feb 04 2005 - 09:44:17 CST)
Re: AMBER: tleap load pdb file David A. Case (Fri Feb 04 2005 - 10:35:49 CST)
AMBER: dppsv returns error code: 29 Xiaowei (David) Li (Fri Feb 04 2005 - 11:58:56 CST)
AMBER: tleap load pdb file xiaowen (Fri Feb 04 2005 - 15:18:09 CST)
Re: AMBER: dppsv returns error code: 29 David A. Case (Fri Feb 04 2005 - 16:48:38 CST)
Re: AMBER: tleap load pdb file David A. Case (Fri Feb 04 2005 - 16:45:50 CST)
Re: AMBER: unnatural ligand David A. Case (Fri Feb 04 2005 - 16:54:06 CST)
AMBER: Antechamber/formatting question Kara Di Giorgio (Fri Feb 04 2005 - 17:05:18 CST)
AMBER: huge bond distances in new residue Stern, Julie (Fri Feb 04 2005 - 17:48:14 CST)
AMBER: trajectory of minimization Stern, Julie (Fri Feb 04 2005 - 17:49:17 CST)
AMBER: Is droplet boundary condition option possible ? Soo (Sat Feb 05 2005 - 00:18:36 CST)
Re: AMBER: tleap load pdb file xiaowen (Sat Feb 05 2005 - 11:20:12 CST)
Re: AMBER: huge bond distances in new residue David A. Case (Sat Feb 05 2005 - 12:57:37 CST)
Re: AMBER: Is droplet boundary condition option possible ? David A. Case (Sat Feb 05 2005 - 12:53:53 CST)
Re: AMBER: trajectory of minimization David A. Case (Sat Feb 05 2005 - 12:54:39 CST)
Re: AMBER: Antechamber/formatting question David A. Case (Sat Feb 05 2005 - 13:17:24 CST)
AMBER: loading pdb in leap to create parmeter files mrbroad_at_ilstu.edu (Sat Feb 05 2005 - 15:24:04 CST)
Re: AMBER: loading pdb in leap to create parmeter files David A. Case (Sat Feb 05 2005 - 16:29:13 CST)
AMBER: Tutorial Request Kara Di Giorgio (Sun Feb 06 2005 - 11:01:15 CST)
Re: AMBER: Tutorial Request David A. Case (Sun Feb 06 2005 - 11:40:28 CST)
RE: AMBER: trajectory of minimization Ross Walker (Sun Feb 06 2005 - 12:36:29 CST)
RE: AMBER: tleap load pdb file Ross Walker (Sun Feb 06 2005 - 12:50:29 CST)
AMBER: inconsistent ordering in an improper dihedral of TRP Sanghyun Park (Sun Feb 06 2005 - 22:38:03 CST)
AMBER: correlation along PCA modes Vlad Cojocaru (Mon Feb 07 2005 - 05:35:44 CST)
Re: AMBER: unnatural ligand Eric Hu (Mon Feb 07 2005 - 12:28:14 CST)
AMBER: Creating an input file for GRASP using AMBER 8 Ilyas Yildirim (Mon Feb 07 2005 - 13:07:29 CST)
Re: AMBER: Creating an input file for GRASP using AMBER 8 Bill Ross (Mon Feb 07 2005 - 13:40:33 CST)
Re: AMBER: Creating an input file for GRASP using AMBER 8 FyD (Mon Feb 07 2005 - 13:52:42 CST)
AMBER: problem in writing Gustavo Pierdominici Sottile (Mon Feb 07 2005 - 13:59:49 CST)
RE: AMBER: tleap load pdb file xiaowen (Mon Feb 07 2005 - 14:58:39 CST)
Re: AMBER: Creating an input file for GRASP using AMBER 8 Ilyas Yildirim (Mon Feb 07 2005 - 16:24:24 CST)
Re: AMBER: Creating an input file for GRASP using AMBER 8 FyD (Mon Feb 07 2005 - 16:45:05 CST)
Re: AMBER: problem in writing David A. Case (Mon Feb 07 2005 - 17:22:05 CST)
RE: AMBER: tleap load pdb file xiaowen (Mon Feb 07 2005 - 21:52:36 CST)
AMBER: How to calculate RESTRAINT value Mayumi Haga (Mon Feb 07 2005 - 22:09:25 CST)
AMBER: dynamics error S.Sundar Raman (Tue Feb 08 2005 - 05:10:19 CST)
AMBER: Dynamics error S.Sundar Raman (Tue Feb 08 2005 - 05:25:07 CST)
Re: AMBER: Dynamics error Carlos Simmerling (Tue Feb 08 2005 - 06:59:04 CST)
Re: AMBER: How to calculate RESTRAINT value Carlos Simmerling (Tue Feb 08 2005 - 07:01:46 CST)
Re: AMBER: Dynamics error S.Sundar Raman (Tue Feb 08 2005 - 08:09:04 CST)
AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel Fabien Cailliez (Tue Feb 08 2005 - 11:16:51 CST)
AMBER: problem in minimization Gustavo Pierdominici Sottile (Tue Feb 08 2005 - 12:31:17 CST)
Re: AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel David A. Case (Tue Feb 08 2005 - 13:28:23 CST)
AMBER: Minimization Beale, John (Tue Feb 08 2005 - 13:30:52 CST)
AMBER: Linux Enterprise Beale, John (Tue Feb 08 2005 - 13:39:54 CST)
RE: AMBER: Linux Enterprise S. Frank Yan (Tue Feb 08 2005 - 13:45:40 CST)
Re: AMBER: tleap load pdb file David A. Case (Tue Feb 08 2005 - 13:50:08 CST)
Re: AMBER: problem in minimization David A. Case (Tue Feb 08 2005 - 13:51:42 CST)
AMBER: Amber8 installation test possible failures Joe Nolan (Tue Feb 08 2005 - 13:55:39 CST)
Re: AMBER: problem in minimization Natasja Brooijmans (Tue Feb 08 2005 - 13:56:22 CST)
Re: AMBER: Linux Enterprise David A. Case (Tue Feb 08 2005 - 13:59:15 CST)
RE: AMBER: Linux Enterprise Ross Walker (Tue Feb 08 2005 - 13:59:43 CST)
Re: AMBER: Amber8 installation test possible failures David A. Case (Tue Feb 08 2005 - 14:02:54 CST)
Re: AMBER: problem in minimization Bill Ross (Tue Feb 08 2005 - 14:16:18 CST)
RE: AMBER: Amber8 installation test possible failures Ross Walker (Tue Feb 08 2005 - 14:17:40 CST)
Re: AMBER: problem in minimization Carlos Simmerling (Tue Feb 08 2005 - 15:47:30 CST)
Re: AMBER: problem in minimization Bill Ross (Tue Feb 08 2005 - 16:16:47 CST)
Re: AMBER: problem in minimization David A. Case (Tue Feb 08 2005 - 16:23:51 CST)
AMBER: leap bond angle building Stern, Julie (Tue Feb 08 2005 - 17:44:39 CST)
Re: AMBER: leap bond angle building Bill Ross (Tue Feb 08 2005 - 18:00:12 CST)
AMBER: minimize a ptraj average pdb structure Eric Hu (Tue Feb 08 2005 - 19:48:26 CST)
RE: AMBER: minimize a ptraj average pdb structure Vineet Pande (Wed Feb 09 2005 - 04:05:14 CST)
AMBER: energy plot in minimization Gustavo Pierdominici Sottile (Wed Feb 09 2005 - 11:36:25 CST)
AMBER: stereo Filip Lankas (Wed Feb 09 2005 - 11:53:45 CST)
RE: AMBER: energy plot in minimization Ross Walker (Wed Feb 09 2005 - 12:10:13 CST)
AMBER: question about mm_gbsa output file michael chen (Wed Feb 09 2005 - 12:10:06 CST)
Re: AMBER: tleap load pdb file xiaowen (Wed Feb 09 2005 - 12:51:44 CST)
RE: AMBER: stereo Vineet Pande (Wed Feb 09 2005 - 12:51:06 CST)
AMBER: Convert to Pdb Beale, John (Wed Feb 09 2005 - 13:03:27 CST)
Re: AMBER: Convert to Pdb Peter Gannett (Wed Feb 09 2005 - 13:07:07 CST)
RE: AMBER: tleap load pdb file Ross Walker (Wed Feb 09 2005 - 13:18:31 CST)
RE: AMBER: Convert to Pdb Ross Walker (Wed Feb 09 2005 - 13:19:15 CST)
Re: AMBER: Convert to Pdb M. L. Dodson (Wed Feb 09 2005 - 13:28:22 CST)
AMBER: minimization.out Gustavo Pierdominici Sottile (Wed Feb 09 2005 - 13:32:01 CST)
RE: AMBER: minimize a ptraj average pdb structure Bill Ross (Wed Feb 09 2005 - 13:39:27 CST)
AMBER: DIVCON optimization Kara Di Giorgio (Wed Feb 09 2005 - 13:46:03 CST)
Re: AMBER: minimization.out David A. Case (Wed Feb 09 2005 - 13:53:41 CST)
Re: AMBER: stereo Chris Moth (Wed Feb 09 2005 - 14:02:13 CST)
Re: AMBER: DIVCON optimization David A. Case (Wed Feb 09 2005 - 14:22:59 CST)
AMBER: Can REM be used as multiple normal sander jobs on parallel machine qlu_at_notes.cc.sunysb.edu (Wed Feb 09 2005 - 17:15:59 CST)
Re: AMBER: DIVCON optimization Kara Wald (Wed Feb 09 2005 - 17:30:07 CST)
Re: AMBER: Can REM be used as multiple normal sander jobs on parallel machine Carlos Simmerling (Wed Feb 09 2005 - 18:03:55 CST)
AMBER: desc NEWRES and blank unit type Stern, Julie (Wed Feb 09 2005 - 20:07:00 CST)
Re: AMBER: DIVCON optimization David A. Case (Wed Feb 09 2005 - 20:22:07 CST)
AMBER: Another question about surface area calculation michael chen (Thu Feb 10 2005 - 00:26:00 CST)
AMBER: question about surface area to GBsurf calculation michael chen (Thu Feb 10 2005 - 00:20:58 CST)
Re: AMBER: question about surface area to GBsurf calculation David A. Case (Thu Feb 10 2005 - 09:55:33 CST)
AMBER: Poisson Boltzmann dynamics error Rachel Burdge (Thu Feb 10 2005 - 10:04:55 CST)
Re: AMBER: Poisson Boltzmann dynamics error David A. Case (Thu Feb 10 2005 - 10:57:51 CST)
RE: AMBER: Poisson Boltzmann dynamics error Ross Walker (Thu Feb 10 2005 - 11:03:46 CST)
Re: AMBER: Poisson Boltzmann dynamics error Ray Luo (Tue Feb 08 2005 - 06:13:58 CST)
Re: AMBER: Poisson Boltzmann dynamics error Rachel Burdge (Thu Feb 10 2005 - 12:51:05 CST)
AMBER: Protonate state of ARG and LYS. Liu, Jingyuan (Thu Feb 10 2005 - 15:56:39 CST)
AMBER: How to converts a binary mdcrd file thanyarat Udom (Fri Feb 11 2005 - 01:02:21 CST)
AMBER: How to converts a binary mdcrd file thanyarat Udom (Fri Feb 11 2005 - 02:00:10 CST)
AMBER: Cu++ and RED Cenk Andac (Fri Feb 11 2005 - 03:46:13 CST)
AMBER: too much vacuum in the box created by Leap Marie-Pierre Durrieu (Fri Feb 11 2005 - 06:53:35 CST)
Re: AMBER: too much vacuum in the box created by Leap Carlos Simmerling (Fri Feb 11 2005 - 07:21:23 CST)
AMBER: ptraj error and min problems Gustavo Pierdominici Sottile (Fri Feb 11 2005 - 08:54:23 CST)
AMBER: archive Gustavo Pierdominici Sottile (Fri Feb 11 2005 - 08:58:33 CST)
Re: AMBER: too much vacuum in the box created by Leap David A. Case (Fri Feb 11 2005 - 10:21:29 CST)
Re: AMBER: ptraj error and min problems David A. Case (Fri Feb 11 2005 - 10:29:42 CST)
Re: AMBER: Cu++ and RED FyD (Fri Feb 11 2005 - 11:23:53 CST)
Re: AMBER: desc NEWRES and blank unit type David A. Case (Fri Feb 11 2005 - 16:24:25 CST)
Re: AMBER: inconsistent ordering in an improper dihedral of TRP David A. Case (Fri Feb 11 2005 - 16:19:03 CST)
Re: AMBER: inconsistent ordering in an improper dihedral of TRP Carlos Simmerling (Fri Feb 11 2005 - 17:41:26 CST)
AMBER: nucgen problem Ilyas Yildirim (Fri Feb 11 2005 - 18:56:41 CST)
Re: AMBER: nucgen problem David A. Case (Fri Feb 11 2005 - 19:37:32 CST)
Re: AMBER: inconsistent ordering in an improper dihedral of TRP Bill Ross (Fri Feb 11 2005 - 19:56:10 CST)
AMBER: reverse TI charge perturbation Eric Hu (Fri Feb 11 2005 - 19:59:10 CST)
Re: AMBER: reverse TI charge perturbation David A. Case (Sat Feb 12 2005 - 18:14:58 CST)
AMBER: S.Sundar Raman (Mon Feb 14 2005 - 03:03:27 CST)
AMBER:how to analyse trajectory files S.Sundar Raman (Mon Feb 14 2005 - 03:17:39 CST)
RE: AMBER:how to analyse trajectory files Vineet Pande (Mon Feb 14 2005 - 05:07:21 CST)
AMBER: vlimit Gustavo Pierdominici Sottile (Mon Feb 14 2005 - 06:23:31 CST)
AMBER: AMBER 8 : Water cap problem Guillaume Bollot (Mon Feb 14 2005 - 07:14:20 CST)
AMBER: constrains Gustavo Pierdominici Sottile (Mon Feb 14 2005 - 08:53:18 CST)
RE: AMBER: constrains Vineet Pande (Mon Feb 14 2005 - 09:48:39 CST)
RE: AMBER: Ross Walker (Mon Feb 14 2005 - 11:03:52 CST)
RE: AMBER: AMBER 8 : Water cap problem Ross Walker (Mon Feb 14 2005 - 11:07:21 CST)
RE: AMBER: constrains Ross Walker (Mon Feb 14 2005 - 11:10:42 CST)
RE: AMBER: vlimit Ross Walker (Mon Feb 14 2005 - 11:14:56 CST)
AMBER: Restart Problem opitz_at_che.udel.edu (Mon Feb 14 2005 - 13:12:54 CST)
RE: AMBER: Restart Problem Ross Walker (Mon Feb 14 2005 - 14:01:16 CST)
AMBER: Mainchain example needed Kara Wald (Mon Feb 14 2005 - 15:43:06 CST)
AMBER: running shell scripts in tleap? Cenk Andac (Mon Feb 14 2005 - 16:23:44 CST)
RE: AMBER: running shell scripts in tleap? Ross Walker (Mon Feb 14 2005 - 17:31:03 CST)
Re: AMBER: running shell scripts in tleap? Lihua Wang (Mon Feb 14 2005 - 17:26:31 CST)
Re: AMBER: running shell scripts in tleap? John Bushnell (Mon Feb 14 2005 - 17:32:32 CST)
Re: AMBER: reverse TI charge perturbation Eric Hu (Mon Feb 14 2005 - 18:42:14 CST)
AMBER: Dummy Atom Types on both states Ilyas Yildirim (Mon Feb 14 2005 - 20:29:03 CST)
Re: AMBER:how to analyse trajectory files S.Sundar Raman (Mon Feb 14 2005 - 22:58:19 CST)
RE: AMBER: running shell scripts in tleap? Cenk Andac (Mon Feb 14 2005 - 23:24:44 CST)
Re: AMBER: Cu++ and RED Cenk Andac (Mon Feb 14 2005 - 23:30:47 CST)
Re: AMBER: Dummy Atom Types on both states Thomas Steinbrecher (Tue Feb 15 2005 - 03:04:06 CST)
AMBER: Topology Format Amber 8 Stuart Murdock (Tue Feb 15 2005 - 06:00:56 CST)
Re: AMBER: Topology Format Amber 8 Carlos Simmerling (Tue Feb 15 2005 - 06:42:29 CST)
Re: AMBER: Topology Format Amber 8 Ian Withers (Tue Feb 15 2005 - 07:33:15 CST)
Re: AMBER: Dummy Atom Types on both states yipinl_at_umich.edu (Tue Feb 15 2005 - 09:31:56 CST)
Re: AMBER: Dummy Atom Types on both states Julien Michel (Tue Feb 15 2005 - 10:10:34 CST)
Re: AMBER: Dummy Atom Types on both states david.evans_at_ulsop.ac.uk (Tue Feb 15 2005 - 11:29:39 CST)
Re: AMBER: Dummy Atom Types on both states david.evans_at_ulsop.ac.uk (Tue Feb 15 2005 - 12:13:57 CST)
Re: AMBER: Cu++ and RED FyD (Tue Feb 15 2005 - 12:19:16 CST)
AMBER: problems with running sander in parallel on linux Piotr Cieplak (Tue Feb 15 2005 - 12:28:02 CST)
RE: AMBER: problems with running sander in parallel on linux Ross Walker (Tue Feb 15 2005 - 12:50:53 CST)
RE: AMBER: problems with running sander in parallel on linux Piotr Cieplak (Tue Feb 15 2005 - 13:01:15 CST)
AMBER: blows up Gustavo Pierdominici Sottile (Tue Feb 15 2005 - 13:11:43 CST)
AMBER: check in leap Gustavo Pierdominici Sottile (Tue Feb 15 2005 - 13:34:21 CST)
Re: AMBER: problems with running sander in parallel on linux Scott Brozell (Tue Feb 15 2005 - 13:42:45 CST)
Re: AMBER: problems with running sander in parallel on linux Robert Duke (Tue Feb 15 2005 - 13:43:37 CST)
Re: AMBER: problems with running sander in parallel on linux David E. Konerding DSD staff (Tue Feb 15 2005 - 14:48:50 CST)
Re: AMBER: problems with running sander in parallel on linux Piotr Cieplak (Tue Feb 15 2005 - 14:55:59 CST)
Re: AMBER: problems with running sander in parallel on linux Scott Brozell (Tue Feb 15 2005 - 15:01:21 CST)
AMBER: Cyclic peptide arubin_at_unmc.edu (Tue Feb 15 2005 - 15:12:28 CST)
Re: AMBER: check in leap David A. Case (Tue Feb 15 2005 - 15:17:07 CST)
Re: AMBER: problems with running sander in parallel on linux Robert Duke (Tue Feb 15 2005 - 15:25:52 CST)
Re: AMBER: problems with running sander in parallel on linux Piotr Cieplak (Tue Feb 15 2005 - 15:58:09 CST)
Re: AMBER: problems with running sander in parallel on linux Scott Brozell (Tue Feb 15 2005 - 16:02:56 CST)
Re: AMBER: Dummy Atom Types on both states David A. Case (Tue Feb 15 2005 - 16:26:21 CST)
AMBER: soft-cores and Amber David A. Case (Tue Feb 15 2005 - 16:55:30 CST)
Re: AMBER: soft-cores and Amber Carlos Simmerling (Tue Feb 15 2005 - 17:11:14 CST)
AMBER: PDB conversion to gzmat using antechamber Scott Pendley (Tue Feb 15 2005 - 17:32:21 CST)
AMBER: EWALD and belly not strictly correct Stern, Julie (Tue Feb 15 2005 - 23:41:49 CST)
AMBER: Why I couldnt used carnal for analyzed RMSD ? thanyarat Udom (Wed Feb 16 2005 - 03:28:17 CST)
Re: AMBER: Cyclic peptide Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Wed Feb 16 2005 - 03:48:19 CST)
AMBER: Gustavo Pierdominici Sottile (Wed Feb 16 2005 - 06:22:59 CST)
Re: AMBER: Carlos Simmerling (Wed Feb 16 2005 - 06:55:57 CST)
Re: AMBER: Cyclic peptide Carlos Simmerling (Wed Feb 16 2005 - 07:00:29 CST)
AMBER: rms Gustavo Pierdominici Sottile (Wed Feb 16 2005 - 07:14:50 CST)
Re: AMBER: rms Carlos Simmerling (Wed Feb 16 2005 - 07:59:43 CST)
AMBER: Beale, John (Wed Feb 16 2005 - 07:42:26 CST)
AMBER: Phi-Psi-Energy plot L Jin (Wed Feb 16 2005 - 09:45:18 CST)
Re: AMBER: David A. Case (Wed Feb 16 2005 - 10:49:18 CST)
Re: AMBER: EWALD and belly not strictly correct David A. Case (Wed Feb 16 2005 - 10:52:20 CST)
Re: AMBER: EWALD and belly not strictly correct darden (Wed Feb 16 2005 - 11:08:31 CST)
AMBER: generate charmm paramater file from amber parm file HL Eastwood (Wed Feb 16 2005 - 11:19:56 CST)
Re: AMBER: generate charmm paramater file from amber parm file david.evans_at_ulsop.ac.uk (Wed Feb 16 2005 - 12:02:07 CST)
Re: AMBER: generate charmm paramater file from amber parm file David E. Konerding DSD staff (Wed Feb 16 2005 - 12:13:23 CST)
Re: AMBER: Why I couldnt used carnal for analyzed RMSD ? Bill Ross (Wed Feb 16 2005 - 12:19:30 CST)
AMBER: Amber7 nmropt Markus W. Germann (Wed Feb 16 2005 - 15:09:08 CST)
RE: AMBER: Amber7 nmropt Ross Walker (Wed Feb 16 2005 - 15:32:05 CST)
Re: AMBER: Amber7 nmropt Markus W. Germann (Wed Feb 16 2005 - 15:40:46 CST)
Re: AMBER: Amber7 nmropt David A. Case (Wed Feb 16 2005 - 15:53:19 CST)
RE: AMBER: Amber7 nmropt Ross Walker (Wed Feb 16 2005 - 15:55:40 CST)
Re: AMBER: Amber7 nmropt Robert Duke (Wed Feb 16 2005 - 17:05:37 CST)
AMBER: installation of amber 8 on windows anshul_at_imtech.res.in (Thu Feb 17 2005 - 14:17:11 CST)
AMBER: Re: pmemd problems Robert Duke (Thu Feb 17 2005 - 09:15:33 CST)
AMBER: rotameric populations? Cenk Andac (Thu Feb 17 2005 - 09:15:05 CST)
AMBER: moil-view Beale, John (Thu Feb 17 2005 - 09:56:30 CST)
Re: AMBER: moil-view Carlos Simmerling (Thu Feb 17 2005 - 10:28:15 CST)
Re: AMBER: installation of amber 8 on windows David Mathews (Thu Feb 17 2005 - 10:42:05 CST)
AMBER: Antechamber help needed Kara Di Giorgio (Thu Feb 17 2005 - 11:24:34 CST)
AMBER: Moil view trajectory clusters Austin B. Yongye (Thu Feb 17 2005 - 11:36:15 CST)
AMBER: problem with ptraj and randomizeions Fabien Cailliez (Thu Feb 17 2005 - 11:56:24 CST)
Re: AMBER: Moil view trajectory clusters Carlos Simmerling (Thu Feb 17 2005 - 12:19:50 CST)
Re: AMBER: problem with ptraj and randomizeions Thomas E. Cheatham, III (Thu Feb 17 2005 - 12:57:23 CST)
AMBER: PSC Summer Workshop: Modeling Proteins and Nucleic Acids with AMBER, VMD and the MMTSB Toolkit Troy Wymore (Thu Feb 17 2005 - 13:00:36 CST)
AMBER: amber8 and moil-view Lihua Wang (Thu Feb 17 2005 - 13:26:32 CST)
Re: AMBER: amber8 and moil-view Carlos Simmerling (Thu Feb 17 2005 - 13:42:13 CST)
Re: AMBER: amber8 and moil-view Lihua Wang (Thu Feb 17 2005 - 13:52:08 CST)
Re: AMBER: amber8 and moil-view Carlos Simmerling (Thu Feb 17 2005 - 14:06:42 CST)
Re: AMBER: amber8 and moil-view Lihua Wang (Thu Feb 17 2005 - 14:14:04 CST)
AMBER: Amber8 Solaris installation failure Joe Nolan (Thu Feb 17 2005 - 14:27:12 CST)
Re: AMBER: Moil view trajectory clusters Austin B. Yongye (Thu Feb 17 2005 - 15:31:37 CST)
AMBER: sander errors with atom restraints on ia64 Rachel Burdge (Thu Feb 17 2005 - 15:46:04 CST)
Re: AMBER: sander errors with atom restraints on ia64 Viktor Hornak (Thu Feb 17 2005 - 16:46:26 CST)
AMBER: leap saveamberparm chain types response Stern, Julie (Thu Feb 17 2005 - 17:16:50 CST)
AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) Greg Recine (Thu Feb 17 2005 - 18:23:01 CST)
Re: AMBER: leap saveamberparm chain types response Bill Ross (Thu Feb 17 2005 - 19:15:20 CST)
Re: AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) M. L. Dodson (Thu Feb 17 2005 - 20:21:29 CST)
Re: AMBER: Amber8 Solaris installation failure David A. Case (Thu Feb 17 2005 - 20:31:00 CST)
Re: AMBER: installation of amber 8 on windows anshul_at_imtech.res.in (Fri Feb 18 2005 - 08:33:40 CST)
AMBER: GB solvation and "boxed" environment simulation Soo (Thu Feb 17 2005 - 23:32:38 CST)
AMBER: molecule blowing apart during equilibration Stern, Julie (Fri Feb 18 2005 - 01:12:16 CST)
Re: AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) David A. Case (Fri Feb 18 2005 - 01:41:23 CST)
Re: AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) David A. Case (Fri Feb 18 2005 - 01:56:20 CST)
Re: AMBER: problem with ptraj and randomizeions Fabien Cailliez (Fri Feb 18 2005 - 02:50:00 CST)
Re: AMBER: problem with ptraj and randomizeions Marie-Pierre Durrieu (Fri Feb 18 2005 - 03:49:16 CST)
Re: AMBER: problem with ptraj and randomizeions Marie-Pierre Durrieu (Fri Feb 18 2005 - 04:19:06 CST)
Re: AMBER: problem with ptraj and randomizeions Filip Lankas (Fri Feb 18 2005 - 06:19:10 CST)
AMBER: ptraj Gustavo Pierdominici Sottile (Fri Feb 18 2005 - 08:58:37 CST)
Re: AMBER: sander errors with atom restraints on ia64 Rachel Burdge (Fri Feb 18 2005 - 10:04:17 CST)
RE: AMBER: molecule blowing apart during equilibration Ross Walker (Fri Feb 18 2005 - 10:56:30 CST)
Re: AMBER: Antechamber/formatting question Kara Di Giorgio (Fri Feb 18 2005 - 12:20:40 CST)
AMBER: XMGR Beale, John (Fri Feb 18 2005 - 12:20:44 CST)
Re: AMBER: molecule blowing apart during equilibration Carlos Simmerling (Fri Feb 18 2005 - 14:11:49 CST)
Re: AMBER: amber8 and moil-view Carlos Simmerling (Fri Feb 18 2005 - 14:13:03 CST)
Re: AMBER: XMGR Andreas Svrcek-Seiler (Fri Feb 18 2005 - 14:31:15 CST)
AMBER: DNA Tutorial Dwayne Hoobler (Fri Feb 18 2005 - 17:07:34 CST)
RE: AMBER: DNA Tutorial Ross Walker (Fri Feb 18 2005 - 19:15:31 CST)
AMBER: Amber: sander error segmentation fault. S.Sundar Raman (Sat Feb 19 2005 - 00:03:50 CST)
RE: AMBER: Amber: sander error segmentation fault. Ross Walker (Sat Feb 19 2005 - 00:34:22 CST)
Re: AMBER: installation of amber 8 on windows David Mathews (Sat Feb 19 2005 - 10:01:54 CST)
AMBER: ptraj for RDF calculations Javier Perez Miron (Sat Feb 19 2005 - 10:47:02 CST)
AMBER: simulation with explicit water molecules Ye MEI (Sat Feb 19 2005 - 21:24:48 CST)
AMBER: (no subject) yen li (Sun Feb 20 2005 - 12:16:32 CST)
AMBER: AIX problem Mayumi Haga (Sun Feb 20 2005 - 23:17:29 CST)
AMBER: ptraj for RDF calculations Javier Perez Miron (Mon Feb 21 2005 - 02:42:33 CST)
AMBER: Amber 8 with lam compilation problem m m (Mon Feb 21 2005 - 02:55:49 CST)
AMBER: problem with protein minimization yen li (Mon Feb 21 2005 - 03:12:02 CST)
Re: AMBER: ptraj for RDF calculations Carlos Jaime (Mon Feb 21 2005 - 03:11:22 CST)
RE: AMBER: Amber 8 with lam compilation problem Ross Walker (Mon Feb 21 2005 - 03:20:21 CST)
AMBER: separate solvent-solvent and solvent-solute interaction Ye MEI (Mon Feb 21 2005 - 06:44:22 CST)
Re: AMBER: Antechamber/formatting question YoungJin Cho (Mon Feb 21 2005 - 10:15:32 CST)
Re: AMBER: separate solvent-solvent and solvent-solute interaction David A. Case (Mon Feb 21 2005 - 11:07:24 CST)
AMBER: Formatting Questions Kara Di Giorgio (Mon Feb 21 2005 - 13:09:44 CST)
RE: AMBER: DNA Tutorial Dwayne Hoobler (Mon Feb 21 2005 - 14:26:37 CST)
AMBER: Free energy extimate for the same structure but different conformers claudio (Mon Feb 21 2005 - 14:56:10 CST)
Re: AMBER: DNA Tutorial David A. Case (Mon Feb 21 2005 - 17:52:21 CST)
Re: AMBER: Free energy extimate for the same structure but different conformers David A. Case (Mon Feb 21 2005 - 18:00:39 CST)
Re: AMBER: AIX problem David A. Case (Mon Feb 21 2005 - 18:05:40 CST)
Re: AMBER: problem with protein minimization David A. Case (Mon Feb 21 2005 - 18:11:37 CST)
RE: AMBER: AIX problem Mayumi Haga (Mon Feb 21 2005 - 18:45:33 CST)
Re: AMBER: Formatting Questions David A. Case (Mon Feb 21 2005 - 19:33:34 CST)
Re: AMBER: Formatting Questions Kara Di Giorgio (Mon Feb 21 2005 - 20:03:37 CST)
Re: Re: AMBER: separate solvent-solvent and solvent-solute interaction Ye MEI (Mon Feb 21 2005 - 21:21:48 CST)
Re: AMBER: problem with protein minimization yen li (Tue Feb 22 2005 - 03:26:37 CST)
AMBER: ptraj problem Mayumi Haga (Tue Feb 22 2005 - 03:38:43 CST)
Re: AMBER: ptraj problem scopio (Tue Feb 22 2005 - 04:08:28 CST)
AMBER: restraint only for Z cartegian coordinate? Jaroslav Hanus (Tue Feb 22 2005 - 09:40:58 CST)
Re: AMBER: restraint only for Z cartegian coordinate? Carlos Simmerling (Tue Feb 22 2005 - 10:02:31 CST)
AMBER: Restraint of atoms during minimization L Jin (Tue Feb 22 2005 - 10:17:05 CST)
AMBER: dihedral driver? Beale, John (Tue Feb 22 2005 - 10:26:26 CST)
Re: AMBER: Restraint of atoms during minimization Carlos Simmerling (Tue Feb 22 2005 - 10:34:06 CST)
AMBER: vlimit exceeded and temperature blow up Stern, Julie (Tue Feb 22 2005 - 10:36:05 CST)
Re: AMBER: vlimit exceeded and temperature blow up Carlos Simmerling (Tue Feb 22 2005 - 10:46:21 CST)
RE: AMBER: problem with protein minimization Ross Walker (Tue Feb 22 2005 - 10:47:56 CST)
AMBER: MPI for sander8 S. Frank Yan (Tue Feb 22 2005 - 11:04:56 CST)
Re: AMBER: Restraint of atoms during minimization L Jin (Tue Feb 22 2005 - 11:12:13 CST)
Re: AMBER: problem with protein minimization Robert Duke (Tue Feb 22 2005 - 11:10:51 CST)
Re: AMBER: MPI for sander8 Viktor Hornak (Tue Feb 22 2005 - 11:13:46 CST)
Re: AMBER: MPI for sander8 Thomas E. Cheatham, III (Tue Feb 22 2005 - 11:22:18 CST)
Re: AMBER: Restraint of atoms during minimization David A. Case (Tue Feb 22 2005 - 11:19:17 CST)
Re: AMBER: Restraint of atoms during minimization Carlos Simmerling (Tue Feb 22 2005 - 11:28:01 CST)
Re: AMBER: Restraint of atoms during minimization Thomas E. Cheatham, III (Tue Feb 22 2005 - 11:36:42 CST)
RE: AMBER: MPI for sander8 Ross Walker (Tue Feb 22 2005 - 11:54:37 CST)
AMBER: ptraj8: trajectory windows Anselm Horn (Tue Feb 22 2005 - 11:16:13 CST)
RE: AMBER: MPI for sander8 James W. Caldwell (Tue Feb 22 2005 - 13:52:56 CST)
Re: AMBER: Amber8 Solaris installation failure Joe Nolan (Tue Feb 22 2005 - 14:12:02 CST)
Re: AMBER: Amber8 Solaris installation failure Atro Tossavainen (Tue Feb 22 2005 - 14:19:31 CST)
Re: AMBER: Formatting Questions Kara Di Giorgio (Tue Feb 22 2005 - 15:48:46 CST)
AMBER: lastrst Stern, Julie (Tue Feb 22 2005 - 17:06:24 CST)
Re: AMBER: Amber8 Solaris installation failure Joe Nolan (Tue Feb 22 2005 - 17:34:50 CST)
RE: AMBER: Amber8 Solaris installation failure Ross Walker (Tue Feb 22 2005 - 17:55:17 CST)
Re: AMBER: Formatting Questions Bill Ross (Tue Feb 22 2005 - 18:03:26 CST)
RE: AMBER: Amber8 Solaris installation failure Bill Ross (Tue Feb 22 2005 - 18:08:37 CST)
Re: AMBER: Amber8 Solaris installation failure David A. Case (Tue Feb 22 2005 - 18:52:13 CST)
AMBER: minimizing structures before MM-PBSA? scopio (Tue Feb 22 2005 - 19:23:37 CST)
AMBER: lastrst Stern, Julie (Tue Feb 22 2005 - 19:21:00 CST)
AMBER: convert one functional group to another with TI Eric Hu (Tue Feb 22 2005 - 19:29:42 CST)
Re: AMBER: minimizing structures before MM-PBSA? Carlos Simmerling (Tue Feb 22 2005 - 19:37:18 CST)
Re: AMBER: lastrst Carlos Simmerling (Tue Feb 22 2005 - 19:39:37 CST)
Re: AMBER: Amber8 Solaris installation failure M. L. Dodson (Tue Feb 22 2005 - 20:33:31 CST)
Re: AMBER: lastrst Ilyas Yildirim (Tue Feb 22 2005 - 20:36:00 CST)
AMBER: total energy of solvation Holly Freedman (Tue Feb 22 2005 - 22:05:36 CST)
AMBER: size of solventbox mathew k varghese (Tue Feb 22 2005 - 22:07:00 CST)
AMBER: parallel AMBER/pmemd installation problem on Opteron Jyh-Shyong Ho (Tue Feb 22 2005 - 23:08:22 CST)
RE: AMBER: size of solventbox Ross Walker (Tue Feb 22 2005 - 23:22:03 CST)
Re: AMBER: total energy of solvation David A. Case (Tue Feb 22 2005 - 23:40:47 CST)
Re: AMBER: convert one functional group to another with TI David A. Case (Tue Feb 22 2005 - 23:44:41 CST)
Re: AMBER: lastrst David A. Case (Tue Feb 22 2005 - 23:53:28 CST)
Re: AMBER: convert one functional group to another with TI Eric Hu (Wed Feb 23 2005 - 00:36:03 CST)
AMBER: RE:Amber 8 with lam compilation problem Maciej KA (Wed Feb 23 2005 - 01:08:16 CST)
AMBER: mpirun sander8 problem S. Frank Yan (Wed Feb 23 2005 - 01:13:34 CST)
RE: AMBER: RE:Amber 8 with lam compilation problem Ross Walker (Wed Feb 23 2005 - 01:20:54 CST)
AMBER: RE:Amber 8 with lam compilation problem Maciej KA (Wed Feb 23 2005 - 02:07:37 CST)
Re: AMBER: size of solventbox Germán Sciaini (Wed Feb 23 2005 - 04:50:39 CST)
Re: AMBER: size of solventbox Fabien Cailliez (Wed Feb 23 2005 - 05:21:52 CST)
Re: AMBER: mpirun sander8 problem Carlos Simmerling (Wed Feb 23 2005 - 07:05:01 CST)
Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Robert Duke (Wed Feb 23 2005 - 07:17:54 CST)
Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Lars Packschies (Wed Feb 23 2005 - 10:22:59 CST)
RE: AMBER: mpirun sander8 problem S. Frank Yan (Wed Feb 23 2005 - 10:58:08 CST)
Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Robert Duke (Wed Feb 23 2005 - 11:27:13 CST)
RE: AMBER: RE:Amber 8 with lam compilation problem Ross Walker (Wed Feb 23 2005 - 12:02:47 CST)
Re: AMBER: RE:Amber 8 with lam compilation problem Amber admin (Wed Feb 23 2005 - 14:39:02 CST)
Re: AMBER: size of solventbox Brent Krueger (Wed Feb 23 2005 - 14:54:35 CST)
Re: AMBER: lastrst Stern, Julie (Wed Feb 23 2005 - 15:03:57 CST)
AMBER: classes Gustavo Pierdominici Sottile (Wed Feb 23 2005 - 15:00:47 CST)
Re: AMBER: lastrst Furse, Kristina Elisabet (Wed Feb 23 2005 - 15:36:08 CST)
Re: AMBER: convert one functional group to another with TI David A. Case (Wed Feb 23 2005 - 16:46:55 CST)
Re: AMBER: convert one functional group to another with TI David A. Case (Wed Feb 23 2005 - 17:01:42 CST)
Re: AMBER: convert one functional group to another with TI Eric Hu (Wed Feb 23 2005 - 17:18:29 CST)
AMBER: solvateOct method Cameron Mura (Wed Feb 23 2005 - 20:26:19 CST)
AMBER: RE:Amber 8 with lam compilation problem Maciej (Thu Feb 24 2005 - 01:43:53 CST)
FW: AMBER: mpirun sander8 problem S. Frank Yan (Thu Feb 24 2005 - 02:41:14 CST)
Re: AMBER: Use of ibelly with nmode analysis marti (Thu Feb 24 2005 - 05:47:28 CST)
AMBER: How to build dynamics input for guanine with tleap ? Maciej (Thu Feb 24 2005 - 07:44:37 CST)
Re: AMBER: RE:Amber 8 with lam compilation problem Robert Duke (Thu Feb 24 2005 - 07:54:08 CST)
RE: AMBER: classes Vineet Pande (Thu Feb 24 2005 - 08:29:19 CST)
RE: AMBER: How to build dynamics input for guanine with tleap ? Vineet Pande (Thu Feb 24 2005 - 08:35:23 CST)
AMBER: Joining residues/units Bogos Agianian (Thu Feb 24 2005 - 08:58:55 CST)
Re: FW: AMBER: mpirun sander8 problem Guanglei Cui (Thu Feb 24 2005 - 09:46:05 CST)
Re: AMBER: mpirun sander8 problem S. Frank Yan (Thu Feb 24 2005 - 10:30:23 CST)
Re: AMBER: Use of ibelly with nmode analysis David A. Case (Thu Feb 24 2005 - 10:30:31 CST)
AMBER: cross-correlation Xin Hu (Thu Feb 24 2005 - 10:40:54 CST)
AMBER: ambpdb radii Harianto (Thu Feb 24 2005 - 13:24:39 CST)
AMBER: units describing projection onto modes Vlad Cojocaru (Thu Feb 24 2005 - 12:40:18 CST)
AMBER: correlation Gustavo Pierdominici Sottile (Thu Feb 24 2005 - 13:48:50 CST)
Re: AMBER: Joining residues/units David A. Case (Thu Feb 24 2005 - 14:54:37 CST)
Re: AMBER: Joining residues/units Bogos Agianian (Thu Feb 24 2005 - 15:22:07 CST)
AMBER: pmemd + pgi 5.1 + ntr = 1 Peter Varnai (Thu Feb 24 2005 - 16:25:04 CST)
Re: AMBER: pmemd + pgi 5.1 + ntr = 1 Robert Duke (Thu Feb 24 2005 - 16:38:02 CST)
Re: AMBER: pmemd + pgi 5.1 + ntr = 1 Peter Varnai (Thu Feb 24 2005 - 16:59:16 CST)
Re: AMBER: pmemd + pgi 5.1 + ntr = 1 Robert Duke (Thu Feb 24 2005 - 17:22:37 CST)
Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Lars Packschies (Thu Feb 24 2005 - 17:58:25 CST)
Re: AMBER: ambpdb radii David A. Case (Thu Feb 24 2005 - 18:56:40 CST)
AMBER: Does delta.charge mean "final charge" for a dummy atom? Eric Hu (Thu Feb 24 2005 - 19:22:23 CST)
Re: AMBER: Does delta.charge mean "final charge" for a dummy atom? David A. Case (Thu Feb 24 2005 - 20:31:04 CST)
Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Robert Duke (Thu Feb 24 2005 - 22:06:54 CST)
AMBER: My last posting Robert Duke (Thu Feb 24 2005 - 22:15:08 CST)
AMBER: compile amber8 on RHEL4 HuiZhe Li (Fri Feb 25 2005 - 01:59:02 CST)
AMBER: nmode entropy calculations in MMPBSA Fabien Cailliez (Fri Feb 25 2005 - 04:20:23 CST)
Re: AMBER: restraint only for Z cartegian coordinate? Jaroslav Hanus (Fri Feb 25 2005 - 05:12:48 CST)
Re: AMBER: compile amber8 on RHEL4 Ye MEI (Fri Feb 25 2005 - 06:01:17 CST)
AMBER: vlimit Gustavo Pierdominici Sottile (Fri Feb 25 2005 - 06:45:35 CST)
Re: AMBER: compile amber8 on RHEL4 Tru Huynh (Fri Feb 25 2005 - 07:09:33 CST)
Re: AMBER: nmode entropy calculations in MMPBSA david.evans_at_ulsop.ac.uk (Fri Feb 25 2005 - 08:14:55 CST)
Re: AMBER: ambpdb radii Harianto (Fri Feb 25 2005 - 10:20:31 CST)
Re: AMBER: ambpdb radii David A. Case (Fri Feb 25 2005 - 10:09:53 CST)
Re: AMBER: solvateOct method David A. Case (Fri Feb 25 2005 - 10:53:19 CST)
Re: AMBER: Joining residues/units FyD (Fri Feb 25 2005 - 11:13:29 CST)
AMBER: make test.lmod error yuann (Fri Feb 25 2005 - 10:45:11 CST)
Re: AMBER: make test.lmod error David A. Case (Fri Feb 25 2005 - 11:41:32 CST)
Re: AMBER: ambpdb radii Harianto (Fri Feb 25 2005 - 12:41:59 CST)
Re: AMBER: ambpdb radii David A. Case (Fri Feb 25 2005 - 12:15:57 CST)
AMBER: setBox buffer in leap Stern, Julie (Fri Feb 25 2005 - 12:43:19 CST)
AMBER: problem with solvateBox ReichertD_at_mir.wustl.edu (Fri Feb 25 2005 - 14:38:51 CST)
Re: AMBER: problem with solvateBox David A. Case (Fri Feb 25 2005 - 15:41:38 CST)
AMBER: Austin B. Yongye (Fri Feb 25 2005 - 15:43:56 CST)
Re: AMBER: Does delta.charge mean "final charge" for a dummy atom? Eric Hu (Fri Feb 25 2005 - 18:38:05 CST)
Re: AMBER: Antechamber/formatting question Kara Di Giorgio (Fri Feb 25 2005 - 18:43:36 CST)
Re: AMBER: Antechamber/formatting question Ilyas Yildirim (Fri Feb 25 2005 - 19:31:46 CST)
AMBER: vlimit problem Ilyas Yildirim (Fri Feb 25 2005 - 19:45:03 CST)
Re: AMBER: Antechamber/formatting question Kara Di Giorgio (Fri Feb 25 2005 - 20:02:40 CST)
AMBER: ico(i)=-1? Xiao He (Fri Feb 25 2005 - 21:49:46 CST)
AMBER: Pyranose pucker parameters Austin B. Yongye (Fri Feb 25 2005 - 23:10:06 CST)
Re: AMBER: ico(i)=-1? Guanglei Cui (Sat Feb 26 2005 - 09:42:08 CST)
RE: AMBER: Pyranose pucker parameters Ross Walker (Sun Feb 27 2005 - 13:58:30 CST)
RE: AMBER: Antechamber/formatting question Ross Walker (Sun Feb 27 2005 - 13:56:18 CST)
Re: AMBER: Antechamber/formatting question Kara Di Giorgio (Sun Feb 27 2005 - 19:13:19 CST)
RE: AMBER: Pyranose pucker parameters Austin B. Yongye (Sun Feb 27 2005 - 21:08:52 CST)
Re: AMBER: Antechamber/formatting question FyD (Sun Feb 27 2005 - 22:12:37 CST)
Re: AMBER: Antechamber/formatting question FyD (Sun Feb 27 2005 - 22:43:23 CST)
AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem praveena moldy (Sun Feb 27 2005 - 23:36:36 CST)
AMBER: GBSA calculation Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon Feb 28 2005 - 04:59:23 CST)
AMBER: creating a new residue Amber admin (Mon Feb 28 2005 - 10:44:59 CST)
Re: AMBER: correlation David A. Case (Mon Feb 28 2005 - 11:32:54 CST)
Re: AMBER: vlimit problem David A. Case (Mon Feb 28 2005 - 11:40:26 CST)
Re: AMBER: GBSA calculation David A. Case (Mon Feb 28 2005 - 11:48:24 CST)
Re: AMBER: PDB conversion to gzmat using antechamber David A. Case (Mon Feb 28 2005 - 12:02:58 CST)
Re: AMBER: Amber8 Solaris installation failure Joe Nolan (Mon Feb 28 2005 - 14:24:28 CST)
Re: AMBER: Amber8 Solaris installation failure M. L. Dodson (Mon Feb 28 2005 - 14:55:47 CST)
Re: AMBER: Amber8 Solaris installation failure David A. Case (Mon Feb 28 2005 - 16:42:21 CST)
AMBER: An error during minimization using RED tomjas_at_poczta.onet.pl (Tue Mar 01 2005 - 01:18:55 CST)
AMBER: Controlling number of water residues... Pavan G (Tue Mar 01 2005 - 01:14:51 CST)
AMBER: problem with MD simulation Ye Mei (Tue Mar 01 2005 - 02:00:31 CST)
AMBER: NaNQ ilaria massarelli (Tue Mar 01 2005 - 02:45:10 CST)
Re: AMBER: creating a new residue YoungJin Cho (Tue Mar 01 2005 - 09:18:16 CST)
Re: AMBER: Amber8 Solaris installation failure Joe Nolan (Tue Mar 01 2005 - 09:23:06 CST)
Re: AMBER: Controlling number of water residues... Guanglei Cui (Tue Mar 01 2005 - 09:49:57 CST)
Re: AMBER: Controlling number of water residues... David A. Case (Tue Mar 01 2005 - 10:25:14 CST)
Re: AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem David A. Case (Tue Mar 01 2005 - 10:41:08 CST)
RE: AMBER: NaNQ Ross Walker (Tue Mar 01 2005 - 10:46:08 CST)
RE: AMBER: problem with MD simulation Ross Walker (Tue Mar 01 2005 - 10:51:40 CST)
AMBER: Dihedral Energy calculation yen li (Tue Mar 01 2005 - 12:12:56 CST)
RE: AMBER: Dihedral Energy calculation Junmei Wang (Tue Mar 01 2005 - 12:57:49 CST)
AMBER: PMEMD on Opterons; building/benchmarks/recommendations Robert Duke (Tue Mar 01 2005 - 13:14:56 CST)
AMBER: Xleap execution problems on Solaris Joe Nolan (Tue Mar 01 2005 - 14:51:26 CST)
AMBER: RESP of negatively charged molecule Rhoad, Jonathan S. (Tue Mar 01 2005 - 15:39:05 CST)
Re: AMBER: An error during minimization using RED FyD (Tue Mar 01 2005 - 15:44:33 CST)
Re: AMBER: Xleap execution problems on Solaris Scott Brozell (Tue Mar 01 2005 - 21:36:56 CST)
Re: Re: AMBER: An error during minimization using RED tomjas_at_poczta.onet.pl (Wed Mar 02 2005 - 03:15:15 CST)
AMBER: MM-GBSA Alessio Coi (Wed Mar 02 2005 - 04:00:52 CST)
RE: AMBER: Dihedral Energy calculation yen li (Wed Mar 02 2005 - 06:37:01 CST)
AMBER: Sample more conformational space Bogos Agianian (Wed Mar 02 2005 - 06:52:49 CST)
Re: AMBER: Sample more conformational space Marc Baaden (Wed Mar 02 2005 - 07:03:02 CST)
Re: Re: AMBER: An error during minimization using RED tomjas_at_poczta.onet.pl (Wed Mar 02 2005 - 07:18:00 CST)
RE: AMBER: NaNQ ilaria massarelli (Wed Mar 02 2005 - 09:01:33 CST)
Re: AMBER: MM-GBSA David A. Case (Wed Mar 02 2005 - 09:44:15 CST)
AMBER: across-correlation in ptraj Xin Hu (Wed Mar 02 2005 - 10:20:09 CST)
Re: AMBER: Sample more conformational space Carlos Simmerling (Wed Mar 02 2005 - 10:35:18 CST)
RE: AMBER: Dihedral Energy calculation Ross Walker (Wed Mar 02 2005 - 10:48:56 CST)
RE: AMBER: Dihedral Energy calculation yen li (Wed Mar 02 2005 - 12:03:24 CST)
RE: AMBER: Dihedral Energy calculation Ross Walker (Wed Mar 02 2005 - 16:37:20 CST)
AMBER: bond type for a virtual bond in a biomolecular transition state Eric Hu (Wed Mar 02 2005 - 16:54:45 CST)
Re: AMBER: bond type for a virtual bond in a biomolecular transition state David A. Case (Wed Mar 02 2005 - 17:08:38 CST)
AMBER: Installation problem S.Sundar Raman (Thu Mar 03 2005 - 00:28:29 CST)
Re: AMBER: Installation problem Maciej (Thu Mar 03 2005 - 03:26:30 CST)
AMBER: Amber 8 on cygwin install problem Maciej (Thu Mar 03 2005 - 04:49:17 CST)
AMBER: phosphorylated DNA not recognized Annette Höglund (Thu Mar 03 2005 - 08:55:18 CST)
Re: AMBER: Amber 8 on cygwin install problem David A. Case (Thu Mar 03 2005 - 10:07:52 CST)
Re: AMBER: Installation problem David A. Case (Thu Mar 03 2005 - 10:18:47 CST)
Re: AMBER: phosphorylated DNA not recognized FyD (Thu Mar 03 2005 - 12:59:27 CST)
AMBER: bond connectivity among dummy atoms Eric Hu (Thu Mar 03 2005 - 12:56:32 CST)
Re: AMBER: bond connectivity among dummy atoms Ilyas Yildirim (Thu Mar 03 2005 - 13:57:48 CST)
Re: AMBER: bond connectivity among dummy atoms Eric Hu (Thu Mar 03 2005 - 15:25:19 CST)
Re: AMBER: bond connectivity among dummy atoms Ilyas Yildirim (Thu Mar 03 2005 - 15:58:38 CST)
Re: AMBER: bond connectivity among dummy atoms Eric Hu (Thu Mar 03 2005 - 16:12:26 CST)
Re: AMBER: A problem about Gaussian FyD (Thu Mar 03 2005 - 17:27:23 CST)
AMBER: A problem about Gaussian Yanze Zhang (Thu Mar 03 2005 - 16:38:59 CST)
AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Thu Mar 03 2005 - 18:24:03 CST)
Re: AMBER: A problem about Gaussian David A. Case (Thu Mar 03 2005 - 18:55:35 CST)
AMBER: Antechamber/Divcon assigned charges Marc Christensen (Thu Mar 03 2005 - 21:38:10 CST)
Re: AMBER: Antechamber/Divcon assigned charges David A. Case (Thu Mar 03 2005 - 23:17:13 CST)
RE: AMBER: Antechamber/Divcon assigned charges Junmei Wang (Thu Mar 03 2005 - 23:20:38 CST)
Re: AMBER: Amber 8 on cygwin install problem Maciej (Fri Mar 04 2005 - 00:51:32 CST)
Re: AMBER: Dummy atoms: Changing the source code Julien Michel (Fri Mar 04 2005 - 03:44:31 CST)
RE: AMBER: Dihedral Energy calculation yen li (Fri Mar 04 2005 - 15:29:08 CST)
AMBER: atom type designation Lihua Wang (Fri Mar 04 2005 - 18:05:10 CST)
Re: RE: AMBER: problem with MD simulation Ye Mei (Fri Mar 04 2005 - 19:46:24 CST)
Re: AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Fri Mar 04 2005 - 20:56:34 CST)
AMBER: R.E.D Wai Keat Yam (Sat Mar 05 2005 - 23:14:49 CST)
Re: AMBER: Amber 8 on cygwin install problem David A. Case (Sun Mar 06 2005 - 13:23:52 CST)
Re: AMBER: R.E.D Piotr Cieplak (Sun Mar 06 2005 - 18:20:42 CST)
AMBER: Citing Generalized Born Implicit solvent Model (igb=5) Cenk Andac (Sun Mar 06 2005 - 18:57:21 CST)
Re: AMBER: Citing Generalized Born Implicit solvent Model (igb=5) Yuuki Komata (Sun Mar 06 2005 - 19:14:18 CST)
Re: AMBER: Citing Generalized Born Implicit solvent Model (igb=5) David A. Case (Sun Mar 06 2005 - 19:14:35 CST)
Re: AMBER: R.E.D FyD (Sun Mar 06 2005 - 19:42:20 CST)
AMBER: AMBER8 Compile Error on Dual Opteron Thomas Patko (Sun Mar 06 2005 - 19:53:46 CST)
Re: AMBER: R.E.D Wai Keat Yam (Sun Mar 06 2005 - 20:31:57 CST)
AMBER: amber with mpich-G2 putra abdullah (Sun Mar 06 2005 - 20:55:44 CST)
Re: AMBER: amber with mpich-G2 Robert Duke (Sun Mar 06 2005 - 22:07:21 CST)
Re: AMBER: AMBER8 Compile Error on Dual Opteron David A. Case (Sun Mar 06 2005 - 22:24:27 CST)
AMBER: A problem about removing waters and counterions by ptraj scopio (Mon Mar 07 2005 - 06:28:19 CST)
Re: AMBER: A problem about removing waters and counterions by ptraj Carlos Simmerling (Mon Mar 07 2005 - 07:29:14 CST)
Re: AMBER: A problem about removing waters and counterions by ptraj scopio (Mon Mar 07 2005 - 07:48:40 CST)
AMBER: New pmemd build utility; pathscale vs. pgi vs. ifort em64 opteron benchmarks Robert Duke (Mon Mar 07 2005 - 10:47:02 CST)
Re: AMBER: New pmemd build utility; pathscale vs. pgi vs. ifort em64 opteron benchmarks David A. Case (Mon Mar 07 2005 - 12:36:40 CST)
AMBER: What PRESS is? hj zou (Mon Mar 07 2005 - 21:08:39 CST)
Re: AMBER: What PRESS is? Mingyue Zheng (Mon Mar 07 2005 - 21:26:01 CST)
RE: AMBER: What PRESS is? Ross Walker (Mon Mar 07 2005 - 22:07:37 CST)
AMBER: global pH variation in AMBER. Osman Gani (Tue Mar 08 2005 - 04:56:06 CST)
AMBER: Error limits of TI and MM_PBSA methods Nelson Fonseca (Tue Mar 08 2005 - 10:54:42 CST)
AMBER: Energy fluctuations David.LeBard_at_asu.edu (Tue Mar 08 2005 - 11:40:46 CST)
Re: AMBER: Energy fluctuations David A. Case (Tue Mar 08 2005 - 13:36:14 CST)
AMBER: radii "leap" from which file xhu1_at_memphis.edu (Tue Mar 08 2005 - 13:34:48 CST)
Re: AMBER: global pH variation in AMBER. David A. Case (Tue Mar 08 2005 - 13:38:30 CST)
Re: AMBER: Dummy atoms: Changing the source code David A. Case (Tue Mar 08 2005 - 13:50:58 CST)
AMBER: Sander questions on dual-processor Sun with MPICH Joe Nolan (Tue Mar 08 2005 - 14:37:50 CST)
Re: AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Tue Mar 08 2005 - 14:56:48 CST)
AMBER: X Windows for LEaP on SGI Akshay Patny (Tue Mar 08 2005 - 15:07:44 CST)
AMBER: capping? Hui-Hsu Tsai (Tue Mar 08 2005 - 15:34:59 CST)
Re: AMBER: radii "leap" from which file Bill Ross (Tue Mar 08 2005 - 15:43:18 CST)
AMBER: heating Gustavo Pierdominici Sottile (Tue Mar 08 2005 - 16:20:34 CST)
Re: AMBER: heating Bill Ross (Tue Mar 08 2005 - 16:55:47 CST)
Re: AMBER: heating Ilyas Yildirim (Tue Mar 08 2005 - 17:02:17 CST)
RE: AMBER: Sander questions on dual-processor Sun with MPICH Ross Walker (Tue Mar 08 2005 - 19:50:55 CST)
AMBER: The pressure bybaker_at_itsa.ucsf.edu (Tue Mar 08 2005 - 19:54:44 CST)
RE: AMBER: X Windows for LEaP on SGI Ross Walker (Tue Mar 08 2005 - 20:05:01 CST)
RE: AMBER: capping? Ross Walker (Tue Mar 08 2005 - 20:09:44 CST)
RE: AMBER: The pressure Ross Walker (Tue Mar 08 2005 - 20:20:44 CST)
Re: AMBER: radii "leap" from which file xhu1_at_memphis.edu (Tue Mar 08 2005 - 21:06:22 CST)
AMBER: how can I deal with the puzzle? hj zou (Tue Mar 08 2005 - 21:36:39 CST)
Re: AMBER: how can I deal with the puzzle? Thomas E. Cheatham, III (Tue Mar 08 2005 - 21:53:48 CST)
AMBER: Problems Binding Protein to DNA Pieter Smith (Tue Mar 08 2005 - 23:21:30 CST)
Re: AMBER: X Windows for LEaP on SGI Thomas Patko (Tue Mar 08 2005 - 23:44:26 CST)
Re: AMBER: The pressure bybaker_at_itsa.ucsf.edu (Wed Mar 09 2005 - 00:38:14 CST)
AMBER: Priti Hansia (Wed Mar 09 2005 - 01:38:59 CST)
Re: Re: AMBER: how can I deal with the puzzle? ZhangJian (Wed Mar 09 2005 - 01:59:42 CST)
RE: AMBER: Problems Binding Protein to DNA Vineet Pande (Wed Mar 09 2005 - 05:16:44 CST)
AMBER: amber on sgi mathew k varghese (Wed Mar 09 2005 - 05:23:12 CST)
AMBER: For further question about Targeted MD ZhangJian (Wed Mar 09 2005 - 06:48:44 CST)
Re: AMBER: amber on sgi Robert Duke (Wed Mar 09 2005 - 07:32:29 CST)
Re: AMBER: amber on sgi Karol Miaskiewicz (Wed Mar 09 2005 - 07:37:31 CST)
Re: AMBER: Sander questions on dual-processor Sun with MPICH Robert Duke (Wed Mar 09 2005 - 07:41:08 CST)
AMBER: problem with running AMBER with lam-mpi though PBS script Ru-Zhen Li (Wed Mar 09 2005 - 08:01:24 CST)
Re: AMBER: problem with running AMBER with lam-mpi though PBS script Karol Miaskiewicz (Wed Mar 09 2005 - 07:57:46 CST)
AMBER: vlimit in heating Gustavo Pierdominici Sottile (Wed Mar 09 2005 - 08:13:20 CST)
Re: AMBER: amber on sgi Bill Ross (Wed Mar 09 2005 - 09:35:21 CST)
Re: AMBER: vlimit in heating Bill Ross (Wed Mar 09 2005 - 09:44:06 CST)
Re: AMBER: vlimit in heating David A. Case (Wed Mar 09 2005 - 10:10:42 CST)
AMBER: solvatebox problem in the antechamber tutorial Heiko Meyer (Wed Mar 09 2005 - 10:29:00 CST)
Re: AMBER: amber on sgi Melinda Layten (Wed Mar 09 2005 - 10:52:28 CST)
RE: AMBER: capping? FyD (Wed Mar 09 2005 - 10:51:32 CST)
Re: AMBER: capping? Heiko Meyer (Wed Mar 09 2005 - 11:17:01 CST)
AMBER: vlimit heat Gustavo Pierdominici Sottile (Wed Mar 09 2005 - 11:36:30 CST)
Re: AMBER: solvatebox problem in the antechamber tutorial David A. Case (Wed Mar 09 2005 - 18:18:19 CST)
Re: AMBER: radii "leap" from which file David A. Case (Wed Mar 09 2005 - 19:02:43 CST)
Re: AMBER: problem with running AMBER with lam-mpi though PBS script Ru-Zhen Li (Wed Mar 09 2005 - 19:48:56 CST)
AMBER: Re: Amber 8 dual-Xeon compile problem keiodai_at_shohoku.ac.jp (Wed Mar 09 2005 - 22:14:33 CST)
AMBER: how to excite a single residue ? Priti Hansia (Wed Mar 09 2005 - 22:28:24 CST)
Re: AMBER: how to excite a single residue ? Pradipta Bandyopadhyay (Wed Mar 09 2005 - 23:24:34 CST)
AMBER: PTRAJ $ Antechamber Andrew Box (Thu Mar 10 2005 - 00:47:29 CST)
AMBER: Sander error Vojtìch Klusák (Thu Mar 10 2005 - 06:03:21 CST)
Re: AMBER: Sander questions on dual-processor Sun with MPICH Joe Nolan (Thu Mar 10 2005 - 10:46:23 CST)
Re: AMBER: PTRAJ $ Antechamber Bill Ross (Thu Mar 10 2005 - 11:22:39 CST)
AMBER: expected error in mean (Amber 8 TI tutorial) Eric Hu (Thu Mar 10 2005 - 17:38:13 CST)
AMBER: Re: inconsistent ordering in an improper dihedral of TRP Sanghyun Park (Thu Mar 10 2005 - 21:08:25 CST)
AMBER: Compiling just sander Ilyas Yildirim (Thu Mar 10 2005 - 21:07:31 CST)
AMBER: IDIEL in sander sebnem (Fri Mar 11 2005 - 01:14:50 CST)
Re: AMBER: Compiling just sander david.evans_at_ulsop.ac.uk (Fri Mar 11 2005 - 03:24:24 CST)
AMBER: vlimit Gustavo Pierdominici Sottile (Fri Mar 11 2005 - 06:33:36 CST)
AMBER: Holes in water Lukasz Bielecki (Fri Mar 11 2005 - 08:13:40 CST)
AMBER: problem with nmode using ntrun=5 Phineus Markwick (Fri Mar 11 2005 - 08:38:34 CST)
Re :AMBER: Holes in water Pascal Auffinger (Fri Mar 11 2005 - 09:26:31 CST)
Re: AMBER: Re: inconsistent ordering in an improper dihedral of TRP Bill Ross (Fri Mar 11 2005 - 09:46:40 CST)
Re: Re :AMBER: Holes in water Bill Ross (Fri Mar 11 2005 - 09:59:03 CST)
AMBER: problem with nmode using ntrun=5 (2) Phineus Markwick (Fri Mar 11 2005 - 10:39:43 CST)
Re: AMBER: Sander error Viktor Hornak (Fri Mar 11 2005 - 10:36:38 CST)
Re: AMBER: David A. Case (Fri Mar 11 2005 - 13:02:40 CST)
AMBER: ptraj xueping (Fri Mar 11 2005 - 22:56:29 CST)
Re: AMBER: ptraj scopio (Fri Mar 11 2005 - 23:44:04 CST)
Re: AMBER: ptraj xueping (Sat Mar 12 2005 - 01:08:37 CST)
AMBER: Amber PBMD:Energy fluctuation Praveena Gopal (Sat Mar 12 2005 - 03:48:03 CST)
Re: AMBER: Cu++ and RED Cenk Andac (Sat Mar 12 2005 - 06:28:34 CST)
Re: Re :AMBER: Holes in water Lukasz Bielecki (Sat Mar 12 2005 - 10:52:31 CST)
Re: AMBER: Cu++ and RED FyD (Sat Mar 12 2005 - 11:35:53 CST)
Re: Re :AMBER: Holes in water Bill Ross (Sat Mar 12 2005 - 12:13:06 CST)
Re: Re :AMBER: Holes in water Carlos Simmerling (Sat Mar 12 2005 - 12:32:06 CST)
Re:Re: AMBER: Cu++ and RED Cenk Andac (Sat Mar 12 2005 - 12:39:10 CST)
Re: Re :AMBER: Holes in water Carlos Simmerling (Sat Mar 12 2005 - 12:46:24 CST)
AMBER: spherical boundary condition Hui-Hsu Tsai (Sat Mar 12 2005 - 13:05:52 CST)
Re: Re :AMBER: Holes in water Bill Ross (Sat Mar 12 2005 - 13:15:43 CST)
Re: AMBER: Cu++ and RED FyD (Sat Mar 12 2005 - 16:00:56 CST)
Re: AMBER: IDIEL in sander David A. Case (Sat Mar 12 2005 - 16:10:09 CST)
Re: AMBER: PTRAJ $ Antechamber David A. Case (Sat Mar 12 2005 - 16:17:49 CST)
Re: AMBER: expected error in mean (Amber 8 TI tutorial) David A. Case (Sat Mar 12 2005 - 16:18:40 CST)
Re: Re :AMBER: Holes in water Thomas E. Cheatham, III (Sat Mar 12 2005 - 16:20:32 CST)
Re: AMBER: spherical boundary condition David A. Case (Sat Mar 12 2005 - 20:51:58 CST)
AMBER: mesure dihedral angle during MD julien (Sun Mar 13 2005 - 10:52:01 CST)
AMBER: gyration radius julien (Sun Mar 13 2005 - 10:49:50 CST)
Re: AMBER: mesure dihedral angle during MD Guanglei Cui (Sun Mar 13 2005 - 12:10:46 CST)
Re: AMBER: gyration radius Guanglei Cui (Sun Mar 13 2005 - 12:18:18 CST)
Re: AMBER: gyration radius Bill Ross (Sun Mar 13 2005 - 13:36:15 CST)
RE: AMBER: Ross Walker (Sun Mar 13 2005 - 18:29:08 CST)
AMBER: leap warnings mathew k varghese (Mon Mar 14 2005 - 00:34:32 CST)
RE: AMBER: leap warnings Ross Walker (Mon Mar 14 2005 - 00:56:17 CST)
AMBER: surfen and surfoff Giulio Rastelli (Mon Mar 14 2005 - 10:21:22 CST)
AMBER: RDF input preparation problem Maciej (Sun Mar 13 2005 - 22:12:22 CST)
AMBER: Xserve and amber Markus W. Germann (Mon Mar 14 2005 - 10:55:53 CST)
Re: AMBER: spherical boundary condition protege_at_snu.ac.kr (Mon Mar 14 2005 - 11:43:14 CST)
Re: AMBER: spherical boundary condition protege_at_snu.ac.kr (Mon Mar 14 2005 - 11:43:14 CST)
AMBER: Geometrical distortion because of charge? peng79_at_email.unc.edu (Mon Mar 14 2005 - 12:21:28 CST)
Re: AMBER: spherical boundary condition Andreas Svrcek-Seiler (Mon Mar 14 2005 - 12:36:06 CST)
Re: AMBER: spherical boundary condition Hui-Hsu Tsai (Mon Mar 14 2005 - 12:59:01 CST)
AMBER: Question about radial command in ptraj opitz_at_che.udel.edu (Mon Mar 14 2005 - 13:19:11 CST)
Re: AMBER: Question about radial command in ptraj Bill Ross (Mon Mar 14 2005 - 13:48:17 CST)
AMBER: antechamber and multiplicity Cenk Andac (Mon Mar 14 2005 - 13:57:27 CST)
Re: AMBER: Question about radial command in ptraj opitz_at_che.udel.edu (Mon Mar 14 2005 - 14:04:55 CST)
Re: AMBER: Question about radial command in ptraj Bill Ross (Mon Mar 14 2005 - 15:09:08 CST)
AMBER: determining solvent/ion densities Joseph W.Toporowski (Mon Mar 14 2005 - 17:35:25 CST)
Re: AMBER: Xserve and amber Mengjuei Hsieh (Mon Mar 14 2005 - 19:51:12 CST)
AMBER: Hydrogen bonding question opitz_at_che.udel.edu (Tue Mar 15 2005 - 08:57:45 CST)
Re: AMBER: Hydrogen bonding question Carlos Simmerling (Tue Mar 15 2005 - 09:21:37 CST)
Re: AMBER: Hydrogen bonding question David A. Case (Tue Mar 15 2005 - 09:23:30 CST)
Re: AMBER: Hydrogen bonding question opitz_at_che.udel.edu (Tue Mar 15 2005 - 09:34:53 CST)
Re: AMBER: Hydrogen bonding question Carlos Simmerling (Tue Mar 15 2005 - 09:48:41 CST)
Re: AMBER: Hydrogen bonding question Thomas E. Cheatham, III (Tue Mar 15 2005 - 09:59:00 CST)
AMBER: Problem saving file in xleap aanzellotti_at_mail2.vcu.edu (Tue Mar 15 2005 - 11:03:12 CST)
RE: AMBER: Problem saving file in xleap Ross Walker (Tue Mar 15 2005 - 12:02:32 CST)
AMBER: Sander: idecomp lei jia (Tue Mar 15 2005 - 13:45:47 CST)
AMBER: frcmod.mod_phipsi.2 bybaker_at_itsa.ucsf.edu (Tue Mar 15 2005 - 14:04:31 CST)
RE: AMBER: frcmod.mod_phipsi.2 Junmei Wang (Tue Mar 15 2005 - 14:22:29 CST)
Re: AMBER: frcmod.mod_phipsi.2 Carlos Simmerling (Tue Mar 15 2005 - 16:52:53 CST)
AMBER: in vacuo parameters Stern, Julie (Tue Mar 15 2005 - 17:14:44 CST)
Re: AMBER: in vacuo parameters Carlos Simmerling (Tue Mar 15 2005 - 17:29:31 CST)
Re: AMBER: Sander: idecomp Jack Lei (Tue Mar 15 2005 - 17:57:21 CST)
Re: AMBER: Sander: idecomp lei jia (Tue Mar 15 2005 - 20:25:24 CST)
AMBER: Bio-Image summer school in Paris this year Marc Baaden (Wed Mar 16 2005 - 05:44:47 CST)
AMBER: restraintmask dimension Piero Altoè (Wed Mar 16 2005 - 05:42:12 CST)
Re: AMBER: restraintmask dimension Viktor Hornak (Wed Mar 16 2005 - 07:46:27 CST)
AMBER: Velocity Info Vineet Pande (Wed Mar 16 2005 - 08:08:42 CST)
Re: AMBER: Velocity Info Guanglei Cui (Wed Mar 16 2005 - 08:55:07 CST)
Re: AMBER: Velocity Info Vineet Pande (Wed Mar 16 2005 - 10:02:04 CST)
AMBER: "personality" of Amber force field Hui-Hsu Tsai (Wed Mar 16 2005 - 10:01:00 CST)
Re: AMBER: Velocity Info Guanglei Cui (Wed Mar 16 2005 - 10:29:35 CST)
AMBER: question about amber parameter file format etc. jz7_at_duke.edu (Wed Mar 16 2005 - 11:37:29 CST)
RE: AMBER: question about amber parameter file format etc. Vineet Pande (Wed Mar 16 2005 - 12:06:53 CST)
AMBER: periodicity problem Stern, Julie (Wed Mar 16 2005 - 15:02:28 CST)
Re: AMBER: periodicity problem Ilyas Yildirim (Wed Mar 16 2005 - 15:25:39 CST)
AMBER: Zn complex parametrization question Ashutosh Suhas Jogalekar (Wed Mar 16 2005 - 15:27:38 CST)
Re: AMBER: periodicity problem Bill Ross (Wed Mar 16 2005 - 16:23:03 CST)
AMBER: sander.QMMM and fcap Claudio Morgado (Thu Mar 17 2005 - 07:56:34 CST)
AMBER: van der Waals interactions (PTRAJ) Vineet Pande (Thu Mar 17 2005 - 08:07:12 CST)
AMBER: Minimization of avg structure-SANDER Bomb Vineet Pande (Thu Mar 17 2005 - 08:50:03 CST)
AMBER: Bus error - ambpdb David C. Chan (Thu Mar 17 2005 - 08:54:17 CST)
Re: AMBER: sander.QMMM and fcap David A. Case (Thu Mar 17 2005 - 10:00:04 CST)
AMBER: compiler for amber8 on opteron Marc Petitmermet (Thu Mar 17 2005 - 09:56:37 CST)
AMBER: Making topology files of big moleucles in antechamber Hwankyu Lee (Thu Mar 17 2005 - 10:09:06 CST)
RE: AMBER: Problem saving file in xleap aanzellotti_at_mail2.vcu.edu (Thu Mar 17 2005 - 10:45:07 CST)
Re: AMBER: Bus error - ambpdb David A. Case (Thu Mar 17 2005 - 10:54:28 CST)
Re: AMBER: Minimization of avg structure-SANDER Bomb David A. Case (Thu Mar 17 2005 - 10:51:59 CST)
AMBER: add waters to a system + leap problem with solvateOct command Fabien Cailliez (Thu Mar 17 2005 - 12:30:24 CST)
Re: AMBER: Minimization of avg structure-SANDER Bomb Vineet Pande (Thu Mar 17 2005 - 12:45:01 CST)
Re: AMBER: Minimization of avg structure-SANDER Bomb David A. Case (Thu Mar 17 2005 - 12:54:18 CST)
Re: AMBER: Minimization of avg structure-SANDER Bomb Thomas E. Cheatham, III (Thu Mar 17 2005 - 13:01:33 CST)
AMBER: Trajectory problems Steve Seibold (Thu Mar 17 2005 - 13:21:37 CST)
Re: AMBER: Trajectory problems Melinda Layten (Thu Mar 17 2005 - 13:34:50 CST)
Re: AMBER: Making topology files of big moleucles in antechamber Melinda Layten (Thu Mar 17 2005 - 13:48:39 CST)
Re: AMBER: Minimization of avg structure-SANDER Bomb Vineet Pande (Thu Mar 17 2005 - 14:11:10 CST)
AMBER: building helix bundle Yanze Zhang (Thu Mar 17 2005 - 15:30:54 CST)
AMBER: Trajectory problems Steve Seibold (Thu Mar 17 2005 - 15:44:23 CST)
AMBER: Separating solvent and solute energy in the microcanonical mode Mey Khalili (Thu Mar 17 2005 - 16:50:09 CST)
Re: AMBER: Separating solvent and solute energy in the microcanonical mode Carlos Simmerling (Thu Mar 17 2005 - 17:05:17 CST)
Re: AMBER: Separating solvent and solute energy in the microcanonical mode Mey Khalili (Thu Mar 17 2005 - 17:11:48 CST)
Re: AMBER: Trajectory problems Asim Okur (Thu Mar 17 2005 - 17:14:28 CST)
Re: AMBER: Separating solvent and solute energy in the microcanonical mode Carlos Simmerling (Thu Mar 17 2005 - 17:33:43 CST)
AMBER: ptraj: determining solvent/ion densities Joseph W.Toporowski (Thu Mar 17 2005 - 19:40:38 CST)
Re: AMBER: compiler for amber8 on opteron Noriyuki Yamaotsu (Thu Mar 17 2005 - 19:50:24 CST)
AMBER: re Updating Tutorials Vidana.Epa_at_csiro.au (Thu Mar 17 2005 - 21:17:50 CST)
Re: AMBER: compiler for amber8 on opteron Marc Petitmermet (Fri Mar 18 2005 - 02:22:42 CST)
AMBER: Replica Exchange crashing Hayden Eastwood (Fri Mar 18 2005 - 06:39:48 CST)
Re: AMBER: Replica Exchange crashing Viktor Hornak (Fri Mar 18 2005 - 06:51:48 CST)
Re: AMBER: Replica Exchange crashing Carlos Simmerling (Fri Mar 18 2005 - 07:11:13 CST)
Re: AMBER: compiler for amber8 on opteron Robert Duke (Fri Mar 18 2005 - 07:11:22 CST)
AMBER: layer Gustavo Pierdominici Sottile (Fri Mar 18 2005 - 08:42:53 CST)
Re: AMBER: layer Guanglei Cui (Fri Mar 18 2005 - 09:13:32 CST)
AMBER: lmanal input file problem Phineus Markwick (Fri Mar 18 2005 - 10:00:18 CST)
Re: AMBER: layer Carlos Simmerling (Fri Mar 18 2005 - 10:01:45 CST)
Re: AMBER: Making topology files of big moleucles in antechamber Hwankyu Lee (Fri Mar 18 2005 - 10:48:02 CST)
AMBER: parameter meaning Wei Wang (Fri Mar 18 2005 - 12:33:15 CST)
Re: AMBER: lmanal input file problem David A. Case (Fri Mar 18 2005 - 14:10:00 CST)
Re:AMBER: "personality" of Amber force field Asim Okur (Fri Mar 18 2005 - 15:01:19 CST)
AMBER: Problems with Iodine David.Maxwell_at_di.mdacc.tmc.edu (Fri Mar 18 2005 - 15:03:38 CST)
Re: AMBER: Problems with Iodine Carlos Simmerling (Fri Mar 18 2005 - 15:22:47 CST)
Re:AMBER: "personality" of Amber force field Hui-Hsu Tsai (Fri Mar 18 2005 - 15:22:11 CST)
Re: AMBER: "personality" of Amber force field Adrian E. Roitberg (Fri Mar 18 2005 - 15:24:50 CST)
AMBER: question about periodicity of torsion parameter jz7_at_duke.edu (Fri Mar 18 2005 - 16:08:50 CST)
Re: AMBER: question about periodicity of torsion parameter Carlos Simmerling (Fri Mar 18 2005 - 16:51:40 CST)
Re: AMBER: "personality" of Amber force field Hui-Hsu Tsai (Fri Mar 18 2005 - 17:05:07 CST)
AMBER: PMEMD with big systems Florian Barth (Fri Mar 18 2005 - 17:25:41 CST)
AMBER: substrate exit from protein in Amber 8.0 TI vdw simulation Eric Hu (Fri Mar 18 2005 - 17:35:39 CST)
Re: AMBER: "personality" of Amber force field Ray Luo (Thu Mar 17 2005 - 16:17:03 CST)
Re: AMBER: PMEMD with big systems Robert Duke (Fri Mar 18 2005 - 18:12:24 CST)
AMBER: igb=10 some vdW terms disappear? Wells, David H (Mon Mar 21 2005 - 01:54:23 CST)
AMBER: Making prepin file for individual residues of huge molecule. Hwankyu Lee (Mon Mar 21 2005 - 09:00:11 CST)
Re: AMBER: Making prepin file for individual residues of huge molecule. David A. Case (Mon Mar 21 2005 - 10:27:23 CST)
Re: AMBER: igb=10 some vdW terms disappear? Ray Luo (Mon Mar 21 2005 - 11:15:24 CST)
Re: AMBER: substrate exit from protein in Amber 8.0 TI vdw simulation David A. Case (Mon Mar 21 2005 - 12:27:40 CST)
AMBER: mm-pbsa with multiple-processors Eric Hu (Mon Mar 21 2005 - 16:21:16 CST)
Re: AMBER: mm-pbsa with multiple-processors FyD (Mon Mar 21 2005 - 16:39:54 CST)
AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Shekter, Lee (Mon Mar 21 2005 - 18:12:26 CST)
Re: AMBER: mm-pbsa with multiple-processors Piotr Cieplak (Mon Mar 21 2005 - 18:17:30 CST)
RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Ross Walker (Mon Mar 21 2005 - 18:54:52 CST)
RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Shekter, Lee (Mon Mar 21 2005 - 21:39:42 CST)
AMBER: TMD force constant Phineus Markwick (Tue Mar 22 2005 - 07:14:53 CST)
Re: AMBER: TMD force constant Viktor Hornak (Tue Mar 22 2005 - 07:42:37 CST)
Re: AMBER: TMD force constant Carlos Simmerling (Tue Mar 22 2005 - 07:57:01 CST)
Re: AMBER: MD: Water network analysis + visualization sanjeev_at_mbu.iisc.ernet.in (Tue Mar 22 2005 - 07:58:24 CST)
AMBER: nonbonded interaction Svetlana Kirillova (Tue Mar 22 2005 - 10:37:54 CST)
AMBER: ANAL module/AMBER8 Vineet Pande (Tue Mar 22 2005 - 11:32:06 CST)
RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Ross Walker (Tue Mar 22 2005 - 12:05:15 CST)
RE: AMBER: ANAL module/AMBER8 Vineet Pande (Tue Mar 22 2005 - 12:11:22 CST)
AMBER: Amber8 Parallel installation troubles Joe Nolan (Tue Mar 22 2005 - 13:03:05 CST)
RE: AMBER: Amber8 Parallel installation troubles Ross Walker (Tue Mar 22 2005 - 13:20:22 CST)
AMBER: wierd behavior of addions jz7_at_duke.edu (Tue Mar 22 2005 - 13:22:54 CST)
RE: AMBER: wierd behavior of addions Ross Walker (Tue Mar 22 2005 - 13:45:32 CST)
RE: AMBER: wierd behavior of addions Bill Ross (Tue Mar 22 2005 - 15:23:52 CST)
AMBER: Methionine with both C-ter and N-ter jz7_at_duke.edu (Tue Mar 22 2005 - 16:17:18 CST)
Re: AMBER: igb=10 some vdW terms disappear? Ray Luo (Tue Mar 22 2005 - 15:54:57 CST)
Re: AMBER: Amber8 Parallel installation troubles Wei Zhang (Tue Mar 22 2005 - 17:39:06 CST)
AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang_at_gmail.com (Tue Mar 22 2005 - 17:34:05 CST)
Re: AMBER: igb=10 some vdW terms disappear? Ray Luo (Tue Mar 22 2005 - 16:59:00 CST)
Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Tue Mar 22 2005 - 18:29:26 CST)
Re: AMBER: Methionine with both C-ter and N-ter FyD (Tue Mar 22 2005 - 18:26:35 CST)
Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang_at_gmail.com (Tue Mar 22 2005 - 18:46:26 CST)
Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Tue Mar 22 2005 - 19:34:26 CST)
AMBER: "ERROR TERMINATION DUE TO SHAKE OR TORCON" in Gibbs tanc_at_uci.edu (Tue Mar 22 2005 - 23:11:41 CST)
Re: AMBER: nonbonded interaction David A. Case (Tue Mar 22 2005 - 23:38:08 CST)
Re: AMBER: Amber8 Parallel installation troubles Atro Tossavainen (Wed Mar 23 2005 - 01:43:18 CST)
Re: AMBER: nonbonded interactions Svetlana Kirillova (Wed Mar 23 2005 - 03:23:47 CST)
AMBER: warning in PBSA Fabien Cailliez (Wed Mar 23 2005 - 07:39:00 CST)
AMBER: Could not open file (trajin) with mode (r) Maciej (Wed Mar 23 2005 - 07:52:20 CST)
RE: AMBER: Could not open file (trajin) with mode (r) Vineet Pande (Wed Mar 23 2005 - 10:26:06 CST)
RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Shekter, Lee (Wed Mar 23 2005 - 10:29:57 CST)
Re: AMBER: warning in PBSA Ray Luo (Wed Mar 23 2005 - 11:42:34 CST)
RE: AMBER: Could not open file (trajin) with mode (r) Ross Walker (Wed Mar 23 2005 - 12:13:56 CST)
Re: AMBER: igb=10 some vdW terms disappear? Wells, David H (Wed Mar 23 2005 - 12:40:53 CST)
AMBER: antechamber availability dmitri.mikhailov_at_novartis.com (Wed Mar 23 2005 - 14:40:47 CST)
Re: AMBER: PMEMD with big systems Florian Barth (Wed Mar 23 2005 - 14:48:10 CST)
Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang_at_gmail.com (Wed Mar 23 2005 - 16:18:45 CST)
Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang_at_gmail.com (Wed Mar 23 2005 - 17:01:49 CST)
Re: AMBER: antechamber availability Guanglei Cui (Wed Mar 23 2005 - 17:21:23 CST)
Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Wed Mar 23 2005 - 18:49:14 CST)
AMBER: A few question about RDF input preparation Maciej (Thu Mar 24 2005 - 05:13:10 CST)
Re: AMBER: A few question about RDF input preparation Wei Zhang (Thu Mar 24 2005 - 05:58:47 CST)
Re: AMBER: antechamber availability David A. Case (Thu Mar 24 2005 - 12:42:49 CST)
AMBER: Make test error Amber (Thu Mar 24 2005 - 15:10:53 CST)
AMBER: question about placing a substrate in a protein pocket Kara Di Giorgio (Thu Mar 24 2005 - 22:33:26 CST)
RE: AMBER: question about placing a substrate in a protein pocket Vineet Pande (Fri Mar 25 2005 - 03:41:18 CST)
AMBER: Re: ask for your help: parallel on mm_pbsa FyD (Sat Mar 26 2005 - 11:09:23 CST)
AMBER: PTRAJ:"hbond" doubts Vineet Pande (Sun Mar 27 2005 - 07:55:24 CST)
AMBER: missing residue xueping (Mon Mar 28 2005 - 01:34:17 CST)
Re: Re: AMBER: Sander: idecomp Xiao He (Mon Mar 28 2005 - 07:44:53 CST)
RE: AMBER: missing residue Ross Walker (Mon Mar 28 2005 - 10:23:47 CST)
AMBER: ptraj analysis Tatyana B Mamonova (Mon Mar 28 2005 - 11:24:55 CST)
AMBER: Parameter files for general lipids Nitin Bhardwaj (Mon Mar 28 2005 - 18:57:46 CST)
AMBER: REM mdinfo file Sergio E. Wong (Mon Mar 28 2005 - 19:51:45 CST)
AMBER: vlimit exceeded in thermalization Holly Freedman (Mon Mar 28 2005 - 22:16:12 CST)
RE: AMBER: Parameter files for general lipids Vineet Pande (Tue Mar 29 2005 - 01:28:48 CST)
AMBER: Are the constant pH simulations with explicit water possible? Kateryna Miroshnychenko (Tue Mar 29 2005 - 07:54:14 CST)
Re: AMBER: vlimit exceeded in thermalization David A. Case (Tue Mar 29 2005 - 11:22:20 CST)
Re: AMBER: Are the constant pH simulations with explicit water possible? David A. Case (Tue Mar 29 2005 - 11:37:27 CST)
Re: AMBER: REM mdinfo file Guanglei Cui (Tue Mar 29 2005 - 12:00:10 CST)
AMBER: protonated aspartic acid Adrian E. Roitberg (Tue Mar 29 2005 - 14:14:35 CST)
AMBER: align snapshots to a reference Wen Li (Tue Mar 29 2005 - 15:38:36 CST)
Re: AMBER: align snapshots to a reference Carlos Simmerling (Tue Mar 29 2005 - 16:15:29 CST)
AMBER: "The system has extended beyond" error Ilyas Yildirim (Tue Mar 29 2005 - 16:28:35 CST)
AMBER: tleap,xleap bond order for triple bonds Stern, Julie (Tue Mar 29 2005 - 16:49:38 CST)
RE: AMBER: tleap,xleap bond order for triple bonds Ross Walker (Tue Mar 29 2005 - 17:58:51 CST)
Re: AMBER: tleap,xleap bond order for triple bonds David A. Case (Tue Mar 29 2005 - 22:43:39 CST)
AMBER: Minimization failure S.Sundar Raman (Tue Mar 29 2005 - 22:47:22 CST)
AMBER: how to cap regions S.Sundar Raman (Tue Mar 29 2005 - 23:00:12 CST)
Re: AMBER: "The system has extended beyond" error David A. Case (Wed Mar 30 2005 - 09:08:07 CST)
AMBER: Amber Performance in Parallel on Itanium Robert J. Woods (Wed Mar 30 2005 - 09:32:10 CST)
Re: AMBER: align snapshots to a reference Wen Li (Wed Mar 30 2005 - 09:43:21 CST)
Re: AMBER: align snapshots to a reference Carlos Simmerling (Wed Mar 30 2005 - 10:08:01 CST)
Re: AMBER: align snapshots to a reference Wen Li (Wed Mar 30 2005 - 10:14:44 CST)
RE: AMBER: Amber Performance in Parallel on Itanium Ross Walker (Wed Mar 30 2005 - 10:20:14 CST)
Re: AMBER: align snapshots to a reference Thomas E. Cheatham, III (Wed Mar 30 2005 - 10:23:21 CST)
Re: AMBER: align snapshots to a reference Carlos Simmerling (Wed Mar 30 2005 - 10:28:13 CST)
Re: AMBER: Amber Performance in Parallel on Itanium Robert J. Woods (Wed Mar 30 2005 - 10:47:25 CST)
AMBER: PTRAJ:"hbond" analysis Vineet Pande (Wed Mar 30 2005 - 11:15:30 CST)
Re: AMBER: PTRAJ:"hbond" analysis Thomas E. Cheatham, III (Wed Mar 30 2005 - 11:40:16 CST)
AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 11:55:19 CST)
Re: AMBER: OH- dynamics Carlos Simmerling (Wed Mar 30 2005 - 13:14:07 CST)
Re: AMBER: align snapshots to a reference Wen Li (Wed Mar 30 2005 - 13:52:34 CST)
Re: AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 16:03:53 CST)
Re: AMBER: OH- dynamics Carlos Simmerling (Wed Mar 30 2005 - 16:32:09 CST)
Re: AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 16:50:03 CST)
Re: AMBER: OH- dynamics Carlos Simmerling (Wed Mar 30 2005 - 17:37:26 CST)
Re: AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 18:23:32 CST)
AMBER: igb10 vlimit exceeded Wells, David H (Thu Mar 31 2005 - 03:08:55 CST)
Re: AMBER: PTRAJ:"hbond" analysis Vineet Pande (Thu Mar 31 2005 - 03:17:57 CST)
AMBER: All the tests passed except prmtop and prepin... mmv_at_whu.edu.cn (Thu Mar 31 2005 - 03:59:26 CST)
Re: AMBER: "The system has extended beyond" error Ilyas Yildirim (Thu Mar 31 2005 - 06:26:21 CST)
AMBER: AMBER under MOSIX? Atro Tossavainen (Thu Mar 31 2005 - 05:47:47 CST)
Re: AMBER: All the tests passed except prmtop and prepin... David A. Case (Thu Mar 31 2005 - 09:40:18 CST)
AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS Marc Petitmermet (Thu Mar 31 2005 - 09:32:31 CST)
Re: AMBER: how to cap regions David A. Case (Thu Mar 31 2005 - 09:45:26 CST)
Re: AMBER: igb10 vlimit exceeded Ray Luo (Thu Mar 31 2005 - 10:52:50 CST)
AMBER: What does this mean .. ? Pavan Ghatty (Thu Mar 31 2005 - 13:14:53 CST)
Re: AMBER: What does this mean .. ? Carlos Simmerling (Thu Mar 31 2005 - 13:33:25 CST)
AMBER: leap bond error Stern, Julie (Thu Mar 31 2005 - 19:11:29 CST)
AMBER: Target MD and nmode test hang Mingfeng Yang (Thu Mar 31 2005 - 20:08:13 CST)
AMBER: GB dynamics mathew k varghese (Thu Mar 31 2005 - 22:01:30 CST)
AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!! chaiann ng (Thu Mar 31 2005 - 22:30:40 CST)
AMBER: How to fix the torsion angles during energy minimization Ananda Rama Krishnan Selvaraj (Fri Apr 01 2005 - 00:42:27 CST)
Re: AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!! Jiri Matousek (Fri Apr 01 2005 - 01:37:39 CST)
Re: AMBER: How to fix the torsion angles during energy minimization Ananda Rama Krishnan Selvaraj (Fri Apr 01 2005 - 06:54:18 CST)
AMBER: scaleCharges with polarisable force fields Phineus Markwick (Fri Apr 01 2005 - 06:57:43 CST)
AMBER: Problems with protonate on Linux Atro Tossavainen (Fri Apr 01 2005 - 07:09:32 CST)
Re: AMBER: GB dynamics David A. Case (Fri Apr 01 2005 - 10:16:46 CST)
Re: AMBER: scaleCharges with polarisable force fields David A. Case (Fri Apr 01 2005 - 10:31:22 CST)
Re: AMBER: How to fix the torsion angles during energy minimization David A. Case (Fri Apr 01 2005 - 11:24:37 CST)
Re: AMBER: Problems with protonate on Linux David A. Case (Fri Apr 01 2005 - 11:34:17 CST)
AMBER: trajectory alignment using ptraj Wen Li (Fri Apr 01 2005 - 11:38:02 CST)
Re: AMBER: trajectory alignment using ptraj Thomas E. Cheatham, III (Fri Apr 01 2005 - 11:47:30 CST)
Re: AMBER: trajectory alignment using ptraj Wen Li (Fri Apr 01 2005 - 12:42:36 CST)
Re: AMBER: trajectory alignment using ptraj Wen Li (Fri Apr 01 2005 - 14:12:34 CST)
Re: AMBER: trajectory alignment using ptraj Thomas E. Cheatham, III (Fri Apr 01 2005 - 14:39:07 CST)
Re: AMBER: trajectory alignment using ptraj Wen Li (Fri Apr 01 2005 - 15:23:14 CST)
Re: AMBER: trajectory alignment using ptraj Wen Li (Fri Apr 01 2005 - 15:37:57 CST)
Re: AMBER: trajectory alignment using ptraj Thomas E. Cheatham, III (Fri Apr 01 2005 - 15:38:50 CST)
AMBER: reference of Targeted MD xhu1_at_memphis.edu (Fri Apr 01 2005 - 15:52:59 CST)
Re: AMBER: GB dynamics Bill Ross (Fri Apr 01 2005 - 15:55:07 CST)
AMBER: oxo-heme Peter Gannett (Fri Apr 01 2005 - 16:32:47 CST)
Re: AMBER: trajectory alignment using ptraj Wen Li (Fri Apr 01 2005 - 20:42:43 CST)
Re: AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS Robert Duke (Sat Apr 02 2005 - 18:42:47 CST)
AMBER: problem with input files when using ff02EP + pol3 Phineus Markwick (Sun Apr 03 2005 - 07:35:28 CDT)
Re: AMBER: All the tests passed except prmtop and prepin... shuli (Sun Apr 03 2005 - 10:24:47 CDT)
Re: AMBER: problem with input files when using ff02EP + pol3 David A. Case (Mon Apr 04 2005 - 00:18:29 CDT)
AMBER: helical parameters obtaining Kateryna Miroshnychenko (Sat Apr 02 2005 - 05:08:17 CST)
AMBER: surface area John (Mon Apr 04 2005 - 05:35:58 CDT)
AMBER: Sander minimization & dynamic question chaiann ng (Mon Apr 04 2005 - 05:45:48 CDT)
Re: AMBER: Sander minimization & dynamic question Carlos Simmerling (Mon Apr 04 2005 - 06:48:26 CDT)
Re: AMBER: Sander minimization & dynamic question Andreas Svrcek-Seiler (Mon Apr 04 2005 - 07:01:32 CDT)
AMBER: ff02EP + pol3 (2) Phineus Markwick (Mon Apr 04 2005 - 07:06:36 CDT)
AMBER: emilia wu (Mon Apr 04 2005 - 09:11:48 CDT)
AMBER: single-stranded poly(rC) simulation Kateryna Miroshnychenko (Mon Apr 04 2005 - 08:49:39 CDT)
Re: AMBER: All the tests passed except prmtop and prepin... shuli (Mon Apr 04 2005 - 09:56:23 CDT)
AMBER: force constant Unit used in TMD xhu1_at_memphis.edu (Mon Apr 04 2005 - 10:05:30 CDT)
Re: AMBER: surface area Tim Meyer (Mon Apr 04 2005 - 10:38:12 CDT)
Re: AMBER: force constant Unit used in TMD Carlos Simmerling (Mon Apr 04 2005 - 11:06:45 CDT)
Re: AMBER: force constant Unit used in TMD xhu1_at_memphis.edu (Mon Apr 04 2005 - 11:33:01 CDT)
Re: AMBER: force constant Unit used in TMD Viktor Hornak (Mon Apr 04 2005 - 11:53:23 CDT)
Re: AMBER: force constant Unit used in TMD xhu1_at_memphis.edu (Mon Apr 04 2005 - 12:28:36 CDT)
Re: AMBER: force constant Unit used in TMD Asim Okur (Mon Apr 04 2005 - 12:36:08 CDT)
Re: AMBER: force constant Unit used in TMD xhu1_at_memphis.edu (Mon Apr 04 2005 - 12:59:02 CDT)
AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters Wu Yingliang (Tue Apr 05 2005 - 01:18:11 CDT)
Re: AMBER: David A. Case (Tue Apr 05 2005 - 01:06:34 CDT)
Re: AMBER: ff02EP + pol3 (2) David A. Case (Tue Apr 05 2005 - 01:28:22 CDT)
Re: AMBER: single-stranded poly(rC) simulation David A. Case (Tue Apr 05 2005 - 01:31:35 CDT)
Re: Re: AMBER: emilia wu (Tue Apr 05 2005 - 01:43:49 CDT)
RE: Re: AMBER: Wells, David H (Tue Apr 05 2005 - 02:13:56 CDT)
AMBER: AMBER 8.0 problems with impose (tleap) on linux Guillermo Mulliert Carlín (Tue Apr 05 2005 - 01:35:17 CDT)
Re: AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters Wei Zhang (Tue Apr 05 2005 - 02:49:38 CDT)
AMBER: how to make a nonsymmetric box around the solute Lina Nilsson (Tue Apr 05 2005 - 02:56:44 CDT)
AMBER: doble C and N terminal Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Tue Apr 05 2005 - 04:45:58 CDT)
Re: RE: Re: AMBER: emilia wu (Tue Apr 05 2005 - 07:25:42 CDT)
Re: AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters David A. Case (Tue Apr 05 2005 - 10:31:15 CDT)
AMBER: GB with Langevin dynamics problem Peter Varnai (Tue Apr 05 2005 - 11:04:15 CDT)
Re: AMBER: GB with Langevin dynamics problem Carlos Simmerling (Tue Apr 05 2005 - 11:17:24 CDT)
Re: AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters Bill Ross (Tue Apr 05 2005 - 11:26:34 CDT)
Re: AMBER: GB with Langevin dynamics problem Andreas Svrcek-Seiler (Tue Apr 05 2005 - 12:04:08 CDT)
AMBER: Re:Re:single-stranded poly(rC) simulation Kateryna Miroshnychenko (Tue Apr 05 2005 - 12:37:54 CDT)
Re: AMBER: Re:Re:single-stranded poly(rC) simulation Thomas E. Cheatham, III (Tue Apr 05 2005 - 13:32:15 CDT)
Re: AMBER: doble C and N terminal David A. Case (Tue Apr 05 2005 - 16:25:10 CDT)
AMBER: Protein with structural ions Kara Wald (Tue Apr 05 2005 - 16:29:46 CDT)
Re: AMBER: Protein with structural ions Oliver Hucke (Tue Apr 05 2005 - 16:42:29 CDT)
Re: Re: AMBER: Protein with structural ions Yong Xu (Tue Apr 05 2005 - 23:34:55 CDT)
Re: AMBER: AMBER 8.0 problems with impose (tleap) on linux David A. Case (Tue Apr 05 2005 - 23:48:14 CDT)
Re: AMBER: Problems with protonate on Linux Atro Tossavainen (Wed Apr 06 2005 - 01:46:34 CDT)
AMBER: FW: Amber installation Eric Mullins (Wed Apr 06 2005 - 10:36:20 CDT)
Re: AMBER: Problems with protonate on Linux David A. Case (Wed Apr 06 2005 - 11:19:11 CDT)
AMBER: a bimolecular reaction Eric Hu (Wed Apr 06 2005 - 12:14:23 CDT)
Re: AMBER: FW: Amber installation David A. Case (Wed Apr 06 2005 - 16:39:42 CDT)
AMBER: About Gaussian Key Words Katagiri Daisuke (Wed Apr 06 2005 - 22:10:12 CDT)
AMBER: value of SALTCON mathew k varghese (Wed Apr 06 2005 - 23:29:01 CDT)
AMBER: combine mdcrd using ptraj xueping (Wed Apr 06 2005 - 23:41:48 CDT)
Re: AMBER: combine mdcrd using ptraj Asim Okur (Thu Apr 07 2005 - 00:17:57 CDT)
Re: AMBER: combine mdcrd using ptraj xueping (Thu Apr 07 2005 - 01:59:54 CDT)
Re: AMBER: combine mdcrd using ptraj Lihua Wang (Thu Apr 07 2005 - 02:45:18 CDT)
RE: AMBER: About Gaussian Key Words Vineet Pande (Thu Apr 07 2005 - 03:36:04 CDT)
Re: AMBER: combine mdcrd using ptraj xueping (Thu Apr 07 2005 - 04:13:59 CDT)
AMBER: RADIOPT=1 Fabien Cailliez (Thu Apr 07 2005 - 08:19:09 CDT)
Re: AMBER: Protein with structural ions Tim Meyer (Thu Apr 07 2005 - 09:05:15 CDT)
AMBER: RE: system comparison for amber Ross Walker (Thu Apr 07 2005 - 11:41:06 CDT)
Re: AMBER: RE: system comparison for amber Carlos Simmerling (Thu Apr 07 2005 - 12:00:18 CDT)
AMBER: leap single precision Guanglei Cui (Thu Apr 07 2005 - 13:04:20 CDT)
Re: AMBER: value of SALTCON David A. Case (Thu Apr 07 2005 - 13:25:50 CDT)
Re: AMBER: About Gaussian Key Words (fwd) duan_list_at_albert.genomecenter.ucdavis.edu (Thu Apr 07 2005 - 18:09:25 CDT)
AMBER: makeDIST_RST ERROR Y. Xu (Thu Apr 07 2005 - 21:14:19 CDT)
AMBER: problems with "protonate" Kenley Barrett (Thu Apr 07 2005 - 21:27:07 CDT)
AMBER: how to get the parameters for modified amino acid residue? ying xiong (Thu Apr 07 2005 - 22:31:14 CDT)
Re: AMBER: Protein with structural ions Kara Di Giorgio (Fri Apr 08 2005 - 00:29:26 CDT)
Re: Re: AMBER: Protein with structural ions Y. Xu (Fri Apr 08 2005 - 01:39:45 CDT)
Re: AMBER: leap single precision Scott Brozell (Fri Apr 08 2005 - 02:07:31 CDT)
AMBER: linit in mm-pbsa Fabien Cailliez (Fri Apr 08 2005 - 04:08:52 CDT)
Re: AMBER: linit in mm-pbsa Arantxa Sanz (Fri Apr 08 2005 - 04:43:22 CDT)
AMBER: Disulfide bond michael chen (Fri Apr 08 2005 - 09:36:41 CDT)
Re: AMBER: Disulfide bond Carlos Simmerling (Fri Apr 08 2005 - 09:54:46 CDT)
Re: AMBER: makeDIST_RST ERROR David A. Case (Fri Apr 08 2005 - 10:36:30 CDT)
Re: AMBER: Protein with structural ions David A. Case (Fri Apr 08 2005 - 10:41:22 CDT)
Re: AMBER: problems with "protonate" David A. Case (Fri Apr 08 2005 - 10:49:29 CDT)
Re: AMBER: how to get the parameters for modified amino acid residue? FyD (Fri Apr 08 2005 - 11:03:34 CDT)
Re: AMBER: Disulfide bond FyD (Fri Apr 08 2005 - 11:09:03 CDT)
Re: AMBER: leap single precision Guanglei Cui (Fri Apr 08 2005 - 11:19:38 CDT)
Re: AMBER: Protein with structural ions Kara Di Giorgio (Fri Apr 08 2005 - 11:30:26 CDT)
AMBER: GB with Langevin dynamics problem 2 Peter Varnai (Fri Apr 08 2005 - 11:29:08 CDT)
Re: AMBER: linit in mm-pbsa Ray Luo (Thu Apr 07 2005 - 23:30:06 CDT)
AMBER: Announcment: Nucleic Acid Builder (NAB) version 5 is released David A. Case (Fri Apr 08 2005 - 11:52:54 CDT)
Re: AMBER: Protein with structural ions David A. Case (Fri Apr 08 2005 - 12:29:44 CDT)
Re: AMBER: GB with Langevin dynamics problem 2 David A. Case (Fri Apr 08 2005 - 12:48:27 CDT)
Re: AMBER: GB with Langevin dynamics problem 2 Andreas Svrcek-Seiler (Fri Apr 08 2005 - 12:55:48 CDT)
Re: AMBER: Protein with structural ions Kara Di Giorgio (Fri Apr 08 2005 - 13:55:41 CDT)
Re: AMBER: GB with Langevin dynamics problem 2 Carlos Simmerling (Fri Apr 08 2005 - 14:03:14 CDT)
AMBER: question about TGMD: vlimit exceeded for step xhu1_at_memphis.edu (Fri Apr 08 2005 - 15:31:10 CDT)
Re: AMBER: question about TGMD: vlimit exceeded for step Viktor Hornak (Fri Apr 08 2005 - 15:47:40 CDT)
Re: AMBER: question about TGMD: vlimit exceeded for step xhu1_at_memphis.edu (Fri Apr 08 2005 - 16:55:05 CDT)
Re: AMBER: question about TGMD: vlimit exceeded for step Viktor Hornak (Fri Apr 08 2005 - 17:24:13 CDT)
Re: AMBER: question about TGMD: vlimit exceeded for step xhu1_at_memphis.edu (Fri Apr 08 2005 - 18:04:17 CDT)
AMBER: average structure-ptraj xueping (Sat Apr 09 2005 - 03:23:23 CDT)
Re: AMBER: average structure-ptraj Carlos Simmerling (Sat Apr 09 2005 - 10:02:02 CDT)
Re: AMBER: how to get the parameters for modified amino acid residue? David A. Case (Sun Apr 10 2005 - 00:29:09 CDT)
Re: AMBER: GB with Langevin dynamics problem 2 David A. Case (Sun Apr 10 2005 - 00:34:48 CDT)
Re: AMBER: leap single precision David A. Case (Sun Apr 10 2005 - 00:27:52 CDT)
Re: AMBER: average structure-ptraj xueping (Sun Apr 10 2005 - 03:50:19 CDT)
Re: AMBER: average structure-ptraj xueping (Sun Apr 10 2005 - 04:10:55 CDT)
AMBER: A question on connecting residues in xleap Hwankyu Lee (Sun Apr 10 2005 - 11:54:55 CDT)
RE: AMBER: A question on connecting residues in xleap Ross Walker (Sun Apr 10 2005 - 13:25:16 CDT)
Re: AMBER: A question on connecting residues in xleap Hwankyu Lee (Sun Apr 10 2005 - 16:22:16 CDT)
Re: AMBER: Protein with structural ions Kara Di Giorgio (Sun Apr 10 2005 - 22:05:08 CDT)
Re: AMBER: Protein with structural ions David A. Case (Sun Apr 10 2005 - 23:04:52 CDT)
AMBER: Warnings as a file Pavan Ghatty (Sun Apr 10 2005 - 23:37:21 CDT)
Re: AMBER: Protein with structural ions Kara Di Giorgio (Sun Apr 10 2005 - 23:47:29 CDT)
RE: AMBER: A question on connecting residues in xleap Ross Walker (Mon Apr 11 2005 - 00:00:34 CDT)
Re: AMBER: Warnings as a file scopio (Mon Apr 11 2005 - 00:03:39 CDT)
AMBER: Two question about dielectric constant ìÇ Îä (Mon Apr 11 2005 - 03:02:10 CDT)
AMBER: rst file problems mathew k varghese (Mon Apr 11 2005 - 05:03:41 CDT)
AMBER:FAD can't be minimized. zhli_2000_at_126.com (Mon Apr 11 2005 - 07:48:15 CDT)
Re: AMBER: Two question about dielectric constant Carlos Simmerling (Mon Apr 11 2005 - 08:18:07 CDT)
Re: AMBER: rst file problems Carlos Simmerling (Mon Apr 11 2005 - 08:22:41 CDT)
Re: AMBER: A question on connecting residues in xleap Hwankyu Lee (Mon Apr 11 2005 - 09:49:47 CDT)
Re: AMBER: Protein with structural ions David A. Case (Mon Apr 11 2005 - 09:50:28 CDT)
Re: AMBER:FAD can't be minimized. David A. Case (Mon Apr 11 2005 - 09:58:45 CDT)
Re: AMBER: Protein with structural ions Kara Di Giorgio (Mon Apr 11 2005 - 10:40:45 CDT)
Re: AMBER: Two question about dielectric constant Lihua Wang (Mon Apr 11 2005 - 12:04:24 CDT)
RE: AMBER: A question on connecting residues in xleap Ross Walker (Mon Apr 11 2005 - 12:13:15 CDT)
AMBER: GB with Langevin dynamics - solution Peter Varnai (Mon Apr 11 2005 - 12:18:13 CDT)
AMBER: MM_PBSA error Xin Hu (Mon Apr 11 2005 - 13:46:30 CDT)
Re: AMBER: MM_PBSA error Holger Gohlke (Mon Apr 11 2005 - 15:49:37 CDT)
AMBER: breaking symmetry in minimization Stern, Julie (Mon Apr 11 2005 - 15:58:53 CDT)
Re: AMBER: problems with "protonate" Kenley Barrett (Mon Apr 11 2005 - 16:20:47 CDT)
Re: AMBER: breaking symmetry in minimization Bill Ross (Mon Apr 11 2005 - 17:25:25 CDT)
Re: AMBER: MM_PBSA error Xin Hu (Mon Apr 11 2005 - 17:33:51 CDT)
Re: AMBER: problems with "protonate" Bill Ross (Mon Apr 11 2005 - 17:33:17 CDT)
Re: AMBER: About Gaussian Key Words (fwd) Daisuke Katagiri (Mon Apr 11 2005 - 19:03:36 CDT)
AMBER: Fail to load the trajectory file. Jinzhi Lei (Mon Apr 11 2005 - 19:36:34 CDT)
Re: AMBER: Fail to load the trajectory file. Bill Ross (Mon Apr 11 2005 - 19:41:52 CDT)
Re: Re: AMBER: Fail to load the trajectory file. Jinzhi Lei (Mon Apr 11 2005 - 20:00:14 CDT)
Re: Re: AMBER: Fail to load the trajectory file. Bill Ross (Mon Apr 11 2005 - 20:11:19 CDT)
Re: AMBER: problems with "protonate" David A. Case (Mon Apr 11 2005 - 20:45:47 CDT)
Re: AMBER: Fail to load the trajectory file. Thomas E. Cheatham, III (Mon Apr 11 2005 - 21:08:11 CDT)
Re: AMBER: rst file problems mathew k varghese (Mon Apr 11 2005 - 22:13:21 CDT)
Re: Re: Re: AMBER: Fail to load the trajectory file. Jinzhi Lei (Mon Apr 11 2005 - 20:53:50 CDT)
Re: AMBER: MM_PBSA error Holger Gohlke (Tue Apr 12 2005 - 01:30:24 CDT)
Re: AMBER: rst file problems Carlos Simmerling (Tue Apr 12 2005 - 08:39:02 CDT)
AMBER: peptide side chain modification with LEAP Hannes Barsch (Tue Apr 12 2005 - 09:19:53 CDT)
AMBER: rdparm Tim Meyer (Tue Apr 12 2005 - 09:23:55 CDT)
AMBER: implementing AMBER in NAMD Lina Nilsson (Thu Apr 28 2005 - 09:23:16 CDT)
AMBER: nscm Ilyas Yildirim (Tue Apr 12 2005 - 09:55:50 CDT)
AMBER: Does anybody know the experimental solvation free energies of Efavirenz and some other DPC drugs Ye MEI (Tue Apr 12 2005 - 10:19:37 CDT)
RE: AMBER: peptide side chain modification with LEAP Ross Walker (Tue Apr 12 2005 - 10:45:23 CDT)
RE: AMBER: Protein with structural ions Kara Di Giorgio (Tue Apr 12 2005 - 10:51:32 CDT)
Re: AMBER: nscm David A. Case (Tue Apr 12 2005 - 10:55:58 CDT)
Re: AMBER: Protein with structural ions Carlos Simmerling (Tue Apr 12 2005 - 11:09:48 CDT)
AMBER: MM_PBSA problem Xin Hu (Tue Apr 12 2005 - 11:09:36 CDT)
Re: AMBER: problems with "protonate" Bill Ross (Tue Apr 12 2005 - 11:14:27 CDT)
Re: AMBER: MM_PBSA problem Nelson Fonseca (Tue Apr 12 2005 - 11:20:53 CDT)
Re: AMBER: peptide side chain modification with LEAP Bill Ross (Tue Apr 12 2005 - 11:22:40 CDT)
AMBER: Silicon related parameters luckyang_at_gmail.com (Tue Apr 12 2005 - 11:38:35 CDT)
Re: AMBER: nscm duan_list_at_albert.genomecenter.ucdavis.edu (Tue Apr 12 2005 - 11:45:49 CDT)
Re: AMBER: Protein with structural ions Kara Di Giorgio (Tue Apr 12 2005 - 11:59:40 CDT)
AMBER: ibelly not working Stern, Julie (Tue Apr 12 2005 - 11:52:56 CDT)
Re: AMBER: GB with Langevin dynamics - solution David A. Case (Tue Apr 12 2005 - 11:56:34 CDT)
Re: AMBER: a bimolecular reaction David A. Case (Tue Apr 12 2005 - 11:59:07 CDT)
Re: AMBER: MM_PBSA problem Fabien Cailliez (Tue Apr 12 2005 - 11:50:14 CDT)
AMBER: vdw or center box dimensions, periodicity, and the jagged edge Stern, Julie (Tue Apr 12 2005 - 12:30:38 CDT)
Re: AMBER: GB with Langevin dynamics - solution Peter Varnai (Tue Apr 12 2005 - 12:39:54 CDT)
AMBER: Protein With Structural Ions Kara Di Giorgio (Tue Apr 12 2005 - 12:47:52 CDT)
AMBER: No. of Snapshots in MM/GB/SA Sagar D Khare (Tue Apr 12 2005 - 12:48:44 CDT)
Re: AMBER: a bimolecular reaction duan_list_at_albert.genomecenter.ucdavis.edu (Tue Apr 12 2005 - 13:00:14 CDT)
Re: AMBER: ibelly not working Bill Ross (Tue Apr 12 2005 - 13:11:28 CDT)
Re: AMBER: No. of Snapshots in MM/GB/SA Guangyu Sun (Tue Apr 12 2005 - 13:17:35 CDT)
Re: AMBER: MM_PBSA problem Xin Hu (Tue Apr 12 2005 - 14:31:45 CDT)
Re: AMBER: MM_PBSA problem Xin Hu (Tue Apr 12 2005 - 14:36:07 CDT)
Re: AMBER: rst file problems Furse, Kristina Elisabet (Tue Apr 12 2005 - 15:39:35 CDT)
Re: Re: AMBER: Fail to load the trajectory file. Jinzhi Lei (Tue Apr 12 2005 - 15:54:52 CDT)
Re: AMBER: MM_PBSA problem Nelson Fonseca (Tue Apr 12 2005 - 16:15:00 CDT)
Re: AMBER: a bimolecular reaction Eric Hu (Tue Apr 12 2005 - 18:50:58 CDT)
AMBER: ptraj, hbond problem Joseph W.Toporowski (Tue Apr 12 2005 - 19:07:35 CDT)
Re: AMBER: a bimolecular reaction Yong Duan (Tue Apr 12 2005 - 19:22:51 CDT)
AMBER: MM-PBSA in protein-Zn-ligand system Yong Xu (Tue Apr 12 2005 - 20:37:55 CDT)
Re: AMBER: MM-PBSA in protein-Zn-ligand system Kara Di Giorgio (Tue Apr 12 2005 - 21:50:20 CDT)
Re: Re: AMBER: MM-PBSA in protein-Zn-ligand system Yong Xu (Tue Apr 12 2005 - 22:17:00 CDT)
AMBER: freee energy calculation without minimised structure S.Sundar Raman (Wed Apr 13 2005 - 02:00:08 CDT)
RE: AMBER: freee energy calculation without minimised structure Yong Duan (Wed Apr 13 2005 - 02:40:26 CDT)
AMBER: Watson-Crick restraints YoungJin Cho (Wed Apr 13 2005 - 09:43:22 CDT)
Re: AMBER: MM_PBSA problem David A. Case (Wed Apr 13 2005 - 10:23:17 CDT)
Re: AMBER: MM_PBSA problem Xin Hu (Wed Apr 13 2005 - 10:28:17 CDT)
Re: AMBER: MM_PBSA problem Xin Hu (Wed Apr 13 2005 - 12:49:05 CDT)
Re: AMBER: a bimolecular reaction Eric Hu (Wed Apr 13 2005 - 13:08:03 CDT)
AMBER: what is wrong with my amber job or installation? Amber (Wed Apr 13 2005 - 13:57:56 CDT)
RE: AMBER: a bimolecular reaction Yong Duan (Wed Apr 13 2005 - 14:51:08 CDT)
RE: AMBER: what is wrong with my amber job or installation? Ross Walker (Wed Apr 13 2005 - 15:46:01 CDT)
AMBER: Formatting a restraint file Kara Wald (Wed Apr 13 2005 - 15:57:24 CDT)
Re: AMBER: Formatting a restraint file Carlos Simmerling (Wed Apr 13 2005 - 16:18:54 CDT)
AMBER: xleap, lib file question opitz_at_che.udel.edu (Wed Apr 13 2005 - 16:36:51 CDT)
RE: AMBER: xleap, lib file question Ross Walker (Wed Apr 13 2005 - 17:07:04 CDT)
AMBER: About NAB Ilyas Yildirim (Wed Apr 13 2005 - 19:19:32 CDT)
Re: AMBER: Formatting a restraint file Kara Di Giorgio (Wed Apr 13 2005 - 19:31:25 CDT)
Re: AMBER: Formatting a restraint file Furse, Kristina Elisabet (Thu Apr 14 2005 - 00:06:49 CDT)
Re: AMBER: About NAB David A. Case (Thu Apr 14 2005 - 00:10:51 CDT)
Re: AMBER: Watson-Crick restraints David A. Case (Thu Apr 14 2005 - 00:37:16 CDT)
AMBER: solvate water box bybaker_at_itsa.ucsf.edu (Thu Apr 14 2005 - 01:42:21 CDT)
AMBER: Antechamber -reorders atom sequence Austin B. Yongye (Thu Apr 14 2005 - 07:05:09 CDT)
AMBER: Warning: Error opening "New" file from subroutine OPNMRG in pmemd Fabien Cailliez (Thu Apr 14 2005 - 08:05:32 CDT)
Re: AMBER: Antechamber -reorders atom sequence David A. Case (Thu Apr 14 2005 - 09:53:17 CDT)
Re: AMBER: Formatting a restraint file Kara Di Giorgio (Thu Apr 14 2005 - 10:26:17 CDT)
Re: AMBER: Formatting a restraint file Carlos Simmerling (Thu Apr 14 2005 - 11:13:49 CDT)
Re: AMBER: Formatting a restraint file David A. Case (Thu Apr 14 2005 - 11:28:23 CDT)
Re: AMBER: Formatting a restraint file Kara Di Giorgio (Thu Apr 14 2005 - 11:25:18 CDT)
Re: AMBER: solvate water box David A. Case (Thu Apr 14 2005 - 11:30:11 CDT)
Re: AMBER: About NAB Andreas Svrcek-Seiler (Thu Apr 14 2005 - 12:03:49 CDT)
AMBER: periodic boundaries and repeating structure Stern, Julie (Thu Apr 14 2005 - 12:55:09 CDT)
AMBER: antechamber for cyano group nlxc (Thu Apr 14 2005 - 13:03:35 CDT)
Re: AMBER: periodic boundaries and repeating structure Bill Ross (Thu Apr 14 2005 - 13:13:48 CDT)
AMBER: Sander/Mpich2 error with mpd_singinit Joe Nolan (Thu Apr 14 2005 - 15:00:09 CDT)
Re: AMBER: Formatting a restraint file Furse, Kristina Elisabet (Thu Apr 14 2005 - 15:02:20 CDT)
Re: AMBER: Sander/Mpich2 error with mpd_singinit David LeBard (Thu Apr 14 2005 - 15:17:54 CDT)
AMBER: small target pressure in constant pressure dynamics Eric Hu (Thu Apr 14 2005 - 16:37:49 CDT)
Re: AMBER: small target pressure in constant pressure dynamics Thomas E. Cheatham, III (Thu Apr 14 2005 - 17:09:18 CDT)
Re: AMBER: small target pressure in constant pressure dynamics Eric Hu (Thu Apr 14 2005 - 17:26:23 CDT)
AMBER: big fluctuation in MM-PBSA/GA Eric Hu (Thu Apr 14 2005 - 17:54:05 CDT)
Re: AMBER: big fluctuation in MM-PBSA/GA David A. Case (Thu Apr 14 2005 - 18:33:00 CDT)
RE: AMBER: small target pressure in constant pressure dynamics Yong Duan (Thu Apr 14 2005 - 18:30:09 CDT)
Re: AMBER: big fluctuation in MM-PBSA/GA Thomas E. Cheatham, III (Thu Apr 14 2005 - 18:53:48 CDT)
Re: AMBER: About NAB Ilyas Yildirim (Thu Apr 14 2005 - 19:19:14 CDT)
Re: AMBER: big fluctuation in MM-PBSA/GA Eric Hu (Thu Apr 14 2005 - 19:21:40 CDT)
Re: AMBER: About NAB David A. Case (Thu Apr 14 2005 - 20:33:26 CDT)
AMBER: parameters in gaff.dat Lihua Wang (Fri Apr 15 2005 - 00:21:29 CDT)
Re: AMBER: parameters in gaff.dat David A. Case (Fri Apr 15 2005 - 01:02:48 CDT)
AMBER: how to make the prepin file for dimer and clusters of organic molecule in Amber7 Ananda Rama Krishnan Selvaraj (Fri Apr 15 2005 - 03:11:27 CDT)
Re: AMBER: how to make the prepin file for dimer and clusters of organic molecule in Amber7 David A. Case (Fri Apr 15 2005 - 10:25:56 CDT)
AMBER: carnal problem Ed Pate (Fri Apr 15 2005 - 11:15:54 CDT)
Re: AMBER: Antechamber -reorders atom sequence FyD (Fri Apr 15 2005 - 11:10:27 CDT)
AMBER: SollvateBox with ethanol Huaer XC (Fri Apr 15 2005 - 11:21:01 CDT)
AMBER: gaff atom types Claudio Morgado (Fri Apr 15 2005 - 12:11:18 CDT)
Re: AMBER: carnal problem Bill Ross (Fri Apr 15 2005 - 12:32:02 CDT)
Re: AMBER: SollvateBox with ethanol Guanglei Cui (Fri Apr 15 2005 - 12:50:20 CDT)
Re: AMBER: carnal problem Ed Pate (Fri Apr 15 2005 - 13:10:37 CDT)
Re: AMBER: big fluctuation in MM-PBSA/GA Xin Hu (Fri Apr 15 2005 - 13:17:28 CDT)
Re: AMBER: carnal problem Bill Ross (Fri Apr 15 2005 - 13:42:16 CDT)
Re: AMBER: parameters in gaff.dat Lihua Wang (Fri Apr 15 2005 - 13:50:04 CDT)
Re: AMBER: carnal problem Ed Pate (Fri Apr 15 2005 - 13:53:37 CDT)
Re: AMBER: big fluctuation in MM-PBSA/GA Eric Hu (Fri Apr 15 2005 - 13:59:09 CDT)
Re: AMBER: carnal problem Bill Ross (Fri Apr 15 2005 - 14:20:03 CDT)
Re: AMBER: carnal problem Ed Pate (Fri Apr 15 2005 - 14:30:26 CDT)
Re: AMBER: Antechamber -reorders atom sequence Austin B. Yongye (Fri Apr 15 2005 - 15:12:40 CDT)
Re: AMBER: parameters in gaff.dat David A. Case (Fri Apr 15 2005 - 15:31:56 CDT)
Re: AMBER: big fluctuation in MM-PBSA/GA Xin Hu (Fri Apr 15 2005 - 15:53:02 CDT)
AMBER: RESP charges with Gaussian03 and Amber Delon Wilson (Fri Apr 15 2005 - 15:57:19 CDT)
AMBER: the restart of replica exchange method (REM) simulations in AMBER8 Scott E. Boesch (Fri Apr 15 2005 - 16:24:24 CDT)
Re: AMBER: big fluctuation in MM-PBSA/GA Eric Hu (Fri Apr 15 2005 - 16:42:45 CDT)
Re: AMBER: RESP charges with Gaussian03 and Amber FyD (Fri Apr 15 2005 - 17:16:05 CDT)
Re: AMBER: the restart of replica exchange method (REM) simulations in AMBER8 Carlos Simmerling (Sat Apr 16 2005 - 07:42:37 CDT)
AMBER: amber8/antechamber installation problem Xin Hu (Sat Apr 16 2005 - 20:39:07 CDT)
Re: AMBER: amber8/antechamber installation problem David A. Case (Sun Apr 17 2005 - 16:38:51 CDT)
AMBER: about equilibration dynamics S.Sundar Raman (Mon Apr 18 2005 - 02:18:10 CDT)
AMBER: ATTN REVISION ÂÀº£æÃ (Mon Apr 18 2005 - 03:19:46 CDT)
AMBER: dielectric constant Nina Fischer (Mon Apr 18 2005 - 03:22:34 CDT)
AMBER:Bond lengths aren't reasonable after minimisation. zhli_2000_at_126.com (Mon Apr 18 2005 - 05:39:22 CDT)
AMBER: Rep Exch. suggestion Brent Krueger (Mon Apr 18 2005 - 06:56:33 CDT)
AMBER: RESP charges with Gaussian03 and Amber Delon Wilson (Mon Apr 18 2005 - 08:19:16 CDT)
Re: AMBER: Rep Exch. suggestion Guanglei Cui (Mon Apr 18 2005 - 08:37:37 CDT)
Re: AMBER: dielectric constant David A. Case (Mon Apr 18 2005 - 10:00:41 CDT)
Re: AMBER: ATTN REVISION David A. Case (Mon Apr 18 2005 - 09:57:58 CDT)
AMBER: langevin, GB and simulated annealing? pascal.baillod_at_epfl.ch (Mon Apr 18 2005 - 10:14:08 CDT)
Re: AMBER: langevin, GB and simulated annealing? Adrian E. Roitberg (Mon Apr 18 2005 - 10:21:04 CDT)
Re: AMBER: langevin, GB and simulated annealing? Carlos Simmerling (Mon Apr 18 2005 - 10:36:19 CDT)
RE: AMBER:Bond lengths aren't reasonable after minimisation. Ross Walker (Mon Apr 18 2005 - 11:55:54 CDT)
AMBER: Dual Xeon EM64T Intel Fortran Compiler Shekter, Lee (Mon Apr 18 2005 - 13:17:58 CDT)
AMBER: local dielectric constant Xavier Deupi (Mon Apr 18 2005 - 20:17:40 CDT)
AMBER: Re: Re: AMBER: ATTN REVISION ÂÀº£æÃ (Mon Apr 18 2005 - 20:38:02 CDT)
AMBER: RESP charges - multiple conformations Austin B. Yongye (Mon Apr 18 2005 - 21:54:20 CDT)
Re: AMBER: Re: Re: AMBER: ATTN REVISION David A. Case (Mon Apr 18 2005 - 23:37:13 CDT)
AMBER: New parametrs Maciej (Tue Apr 19 2005 - 00:38:51 CDT)
Re: AMBER: RESP charges - multiple conformations FyD (Tue Apr 19 2005 - 00:44:04 CDT)
AMBER: GAFF: H type on carbon bearing a cyano group Claudio Morgado (Tue Apr 19 2005 - 03:34:12 CDT)
AMBER: Amber8 installation on IBM (power4) with SUSE 9.1 Linux (IBM XLF compiler) Soo Joo (Tue Apr 19 2005 - 04:36:26 CDT)
AMBER: solvent accessible surface area John (Tue Apr 19 2005 - 05:45:40 CDT)
AMBER: Gibbs compilation problem Maciej (Tue Apr 19 2005 - 06:36:52 CDT)
RE: AMBER: solvent accessible surface area John (Tue Apr 19 2005 - 07:22:04 CDT)
Re: AMBER: RESP charges - multiple conformations Austin B. Yongye (Tue Apr 19 2005 - 07:43:45 CDT)
AMBER: The effect appling paches Yagi Toru (Tue Apr 19 2005 - 08:11:54 CDT)
Re: AMBER: amber8/antechamber installation problem Xin Hu (Tue Apr 19 2005 - 09:14:41 CDT)
AMBER: a problem with mm_pbsa Ye MEI (Tue Apr 19 2005 - 09:23:01 CDT)
Re: AMBER: RESP charges - multiple conformations FyD (Tue Apr 19 2005 - 09:26:48 CDT)
Re: AMBER: Amber8 installation on IBM (power4) with SUSE 9.1 Linux (IBM XLF compiler) David A. Case (Tue Apr 19 2005 - 09:40:30 CDT)
Re: AMBER: solvent accessible surface area David A. Case (Tue Apr 19 2005 - 09:43:24 CDT)
Re: AMBER: a problem with mm_pbsa Xin Hu (Tue Apr 19 2005 - 09:44:35 CDT)
Re: AMBER: Gibbs compilation problem David A. Case (Tue Apr 19 2005 - 09:50:12 CDT)
AMBER: Amber compilation problem David A. Case (Tue Apr 19 2005 - 09:59:27 CDT)
Re: AMBER: The effect appling paches David A. Case (Tue Apr 19 2005 - 10:01:58 CDT)
Re: AMBER: solvent accessible surface area Ray Luo (Mon Apr 18 2005 - 21:12:54 CDT)
RE: AMBER: Re: Re: AMBER: ATTN REVISION Junmei Wang (Tue Apr 19 2005 - 11:08:58 CDT)
AMBER: Non-Bonded Cutoff vs PME Vineet Pande (Tue Apr 19 2005 - 11:13:26 CDT)
RE: AMBER: gaff atom types Junmei Wang (Tue Apr 19 2005 - 11:18:44 CDT)
RE: AMBER: antechamber for cyano group Junmei Wang (Tue Apr 19 2005 - 11:28:59 CDT)
AMBER: langevin, GB and simulated annealing - 2 pascal.baillod_at_epfl.ch (Tue Apr 19 2005 - 16:07:23 CDT)
Re: AMBER: Non-Bonded Cutoff vs PME David A. Case (Tue Apr 19 2005 - 16:35:51 CDT)
Re: AMBER: Non-Bonded Cutoff vs PME Thomas E. Cheatham, III (Tue Apr 19 2005 - 18:47:10 CDT)
Re: AMBER: langevin, GB and simulated annealing - 2 David A. Case (Tue Apr 19 2005 - 19:04:56 CDT)
Re: AMBER: ATTN REVISION lv haiting (Tue Apr 19 2005 - 21:08:14 CDT)
AMBER: Yong Xu (Tue Apr 19 2005 - 21:57:44 CDT)
Re: AMBER: langevin, GB and simulated annealing - 2 Andreas Svrcek-Seiler (Wed Apr 20 2005 - 03:03:56 CDT)
AMBER: tleap and water thenmalar (Wed Apr 20 2005 - 03:13:58 CDT)
Re: AMBER: Non-Bonded Cutoff vs PME Vineet Pande (Wed Apr 20 2005 - 04:17:20 CDT)
AMBER: GB and mm_pbsa.pl Nelson Fonseca (Wed Apr 20 2005 - 06:48:48 CDT)
AMBER: interaction between residues Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Wed Apr 20 2005 - 09:27:31 CDT)
RE: AMBER: ATTN REVISION Junmei Wang (Wed Apr 20 2005 - 09:31:47 CDT)
Re: AMBER: tleap and water Thomas E. Cheatham, III (Wed Apr 20 2005 - 09:28:33 CDT)
AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. zhli_2000 (Wed Apr 20 2005 - 08:52:18 CDT)
Re: AMBER: Non-Bonded Cutoff vs PME Thomas E. Cheatham, III (Wed Apr 20 2005 - 09:53:38 CDT)
Re: AMBER: GB and mm_pbsa.pl David A. Case (Wed Apr 20 2005 - 10:12:56 CDT)
Large files to AMBER, RE: AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. Yong Duan (Wed Apr 20 2005 - 10:16:55 CDT)
Re: AMBER: GB and mm_pbsa.pl Nelson Fonseca (Wed Apr 20 2005 - 11:05:12 CDT)
AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. Ross Walker (Wed Apr 20 2005 - 12:04:03 CDT)
Re: AMBER: GB and mm_pbsa.pl David A. Case (Wed Apr 20 2005 - 12:18:35 CDT)
AMBER: ibelly not working Stern, Julie (Wed Apr 20 2005 - 14:40:28 CDT)
AMBER: intramolecular nonbonded interactions in AMBER force field John Silvio Vieceli (Wed Apr 20 2005 - 17:06:48 CDT)
Re: AMBER: intramolecular nonbonded interactions in AMBER force field Carlos Simmerling (Wed Apr 20 2005 - 17:28:08 CDT)
RE: AMBER: intramolecular nonbonded interactions in AMBER force field Ross Walker (Wed Apr 20 2005 - 17:33:41 CDT)
AMBER: about run time in GB and PB Yong Xu (Thu Apr 21 2005 - 03:06:27 CDT)
Re: AMBER: about run time in GB and PB Phineus Markwick (Thu Apr 21 2005 - 03:26:26 CDT)
Re: AMBER: intramolecular nonbonded interactions in AMBER force field Vineet Pande (Thu Apr 21 2005 - 03:33:19 CDT)
Re: Re: AMBER: about run time in GB and PB Yong Xu (Thu Apr 21 2005 - 03:55:41 CDT)
RE: AMBER: about run time in GB and PB Yong Duan (Thu Apr 21 2005 - 03:57:32 CDT)
Re: AMBER: about run time in GB and PB Phineus Markwick (Thu Apr 21 2005 - 05:15:57 CDT)
AMBER: On the role of neutralizing ions in GB-MD and GBSA Wu Yingliang (Thu Apr 21 2005 - 05:26:05 CDT)
AMBER: On the role of neutralizing ions in GB-MD and GBSA Wu Yingliang (Thu Apr 21 2005 - 05:16:29 CDT)
AMBER: Nose-Hoover thermostat Sam Moors (Thu Apr 21 2005 - 07:40:44 CDT)
Re: AMBER: intramolecular nonbonded interactions in AMBER force field Carlos Simmerling (Thu Apr 21 2005 - 07:50:46 CDT)
Re: RE: AMBER: about run time in GB and PB Yong Xu (Thu Apr 21 2005 - 08:17:19 CDT)
Re: AMBER: intramolecular nonbonded interactions in AMBER force field Vineet Pande (Thu Apr 21 2005 - 08:26:30 CDT)
Re: AMBER: about run time in GB and PB Phineus Markwick (Thu Apr 21 2005 - 09:10:20 CDT)
AMBER: re: about run time in GB and PB Phineus Markwick (Thu Apr 21 2005 - 09:29:33 CDT)
Re: AMBER: intramolecular nonbonded interactions in AMBER force field Thomas E. Cheatham, III (Thu Apr 21 2005 - 09:50:24 CDT)
AMBER: Moil-view and Quicktime movie Steve Seibold (Thu Apr 21 2005 - 09:55:01 CDT)
Re: AMBER: On the role of neutralizing ions in GB-MD and GBSA David A. Case (Thu Apr 21 2005 - 10:22:37 CDT)
Re: AMBER: ibelly not working David A. Case (Thu Apr 21 2005 - 10:36:40 CDT)
Re: AMBER: Nose-Hoover thermostat David A. Case (Thu Apr 21 2005 - 10:44:13 CDT)
Re: AMBER: intramolecular nonbonded interactions in AMBER force field David A. Case (Thu Apr 21 2005 - 10:42:10 CDT)
AMBER: Sander bomb - atom out of bounds Joe Nolan (Thu Apr 21 2005 - 12:46:01 CDT)
RE: AMBER: Sander bomb - atom out of bounds Ross Walker (Thu Apr 21 2005 - 13:02:18 CDT)
AMBER: problem with belly calculation restart Ed Pate (Thu Apr 21 2005 - 19:28:59 CDT)
Re: Re: AMBER: On the role of neutralizing ions in GB-MD and GBSA Wu Yingliang (Thu Apr 21 2005 - 21:50:09 CDT)
Re: AMBER: about run time in GB and PB Yong Xu (Fri Apr 22 2005 - 03:19:05 CDT)
AMBER: mean structure calculation mmv (Fri Apr 22 2005 - 04:17:20 CDT)
AMBER: PB Bomb in circle(): Stored surface points over limit Nelson Fonseca (Fri Apr 22 2005 - 07:56:57 CDT)
Re: AMBER: intramolecular nonbonded interactions in AMBER force field Guanglei Cui (Fri Apr 22 2005 - 08:52:53 CDT)
AMBER: writing MASKs Sagar D Khare (Fri Apr 22 2005 - 09:58:24 CDT)
RE: AMBER: writing MASKs Vineet Pande (Fri Apr 22 2005 - 10:45:43 CDT)
AMBER: strange VDWAALS and EEL energies calculated by pbsa Fabien Cailliez (Fri Apr 22 2005 - 10:56:41 CDT)
Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa Carlos Simmerling (Fri Apr 22 2005 - 11:05:42 CDT)
Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa David A. Case (Fri Apr 22 2005 - 11:12:15 CDT)
AMBER: Induced dipole in AMBER8 Cenk Andac (Fri Apr 22 2005 - 11:57:56 CDT)
Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa Ray Luo (Thu Apr 21 2005 - 07:18:17 CDT)
AMBER: Amber Installation pmullins (Fri Apr 22 2005 - 13:28:34 CDT)
Re: AMBER: Amber Installation David A. Case (Fri Apr 22 2005 - 14:14:01 CDT)
AMBER: Calculate vdw parameters for alkaline earth metal ions Kenley Barrett (Fri Apr 22 2005 - 17:19:23 CDT)
Re: AMBER: Calculate vdw parameters for alkaline earth metal ions Bill Ross (Fri Apr 22 2005 - 17:48:15 CDT)
Re: AMBER: Induced dipole in AMBER8 David A. Case (Fri Apr 22 2005 - 20:23:41 CDT)
AMBER: Problem when converting AMBER trajectories to CHARMM format Chen Hu (Sat Apr 23 2005 - 17:20:56 CDT)
Re: AMBER: Problem when converting AMBER trajectories to CHARMM format Thomas E. Cheatham, III (Sat Apr 23 2005 - 18:33:48 CDT)
AMBER: serial and parallel Aknb (Sun Apr 24 2005 - 06:35:37 CDT)
AMBER: coordinates translation Ye MEI (Sun Apr 24 2005 - 11:26:39 CDT)
RE: AMBER: serial and parallel Ross Walker (Sun Apr 24 2005 - 13:49:38 CDT)
Re: AMBER: coordinates translation Jack Lei (Sun Apr 24 2005 - 18:51:16 CDT)
AMBER: AMBER Test Error tpatko (Sun Apr 24 2005 - 19:31:42 CDT)
AMBER: Re: AMBER Test Error (Follow Up) tpatko (Sun Apr 24 2005 - 19:55:18 CDT)
AMBER: How to deal with the Non-standard residue lv haiting (Mon Apr 25 2005 - 03:18:08 CDT)
AMBER: the restarting error zhli_2000_at_126.com (Mon Apr 25 2005 - 09:08:02 CDT)
Re: AMBER: the restarting error Guanglei Cui (Mon Apr 25 2005 - 09:37:50 CDT)
AMBER: Free energy pertubation (thermodynamic intergration) mrbroad_at_ilstu.edu (Mon Apr 25 2005 - 11:20:35 CDT)
Re: AMBER: Free energy pertubation (thermodynamic intergration) Sichun Yang (Mon Apr 25 2005 - 11:55:16 CDT)
AMBER: radius parameter for F atom Ye MEI (Mon Apr 25 2005 - 12:05:06 CDT)
Re: AMBER: Induced dipole in AMBER8 Cenk Andac (Mon Apr 25 2005 - 14:00:17 CDT)
Re: AMBER: How to deal with the Non-standard residue FyD (Mon Apr 25 2005 - 15:07:33 CDT)
Re: AMBER: Free energy pertubation (thermodynamic intergration) Ilyas Yildirim (Mon Apr 25 2005 - 15:43:36 CDT)
AMBER: mm_pbsa problem Husni Fattayer (Mon Apr 25 2005 - 15:59:22 CDT)
Re: AMBER: radius parameter for F atom scopio (Mon Apr 25 2005 - 20:36:16 CDT)
AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim (Mon Apr 25 2005 - 20:47:19 CDT)
AMBER: Free energy Maciej (Tue Apr 26 2005 - 02:01:16 CDT)
AMBER: Re:Gibbs compilation problem Maciej (Tue Apr 26 2005 - 02:05:31 CDT)
Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Thomas Steinbrecher (Tue Apr 26 2005 - 03:37:01 CDT)
AMBER: langevin, GB and simulated annealing - 3 pascal.baillod_at_epfl.ch (Tue Apr 26 2005 - 05:37:16 CDT)
AMBER: AMBER Test Anthony Cruz (Tue Apr 26 2005 - 05:36:27 CDT)
Re: AMBER: the restarting error zhli_2000_at_126.com (Tue Apr 26 2005 - 05:54:44 CDT)
Re: Re: AMBER: radius parameter for F atom Ye MEI (Tue Apr 26 2005 - 08:30:07 CDT)
Re: AMBER: langevin, GB and simulated annealing - 3 David Case (Tue Apr 26 2005 - 09:06:08 CDT)
Re: AMBER: AMBER Test David Case (Tue Apr 26 2005 - 09:12:05 CDT)
AMBER: langevin, GB and simulated annealing - 4 pascal.baillod_at_epfl.ch (Tue Apr 26 2005 - 10:23:20 CDT)
Re: AMBER: langevin, GB and simulated annealing - 4 David Case (Tue Apr 26 2005 - 10:44:32 CDT)
AMBER: How to restart MM_PBSA or doing the statistics only Xin Hu (Tue Apr 26 2005 - 11:00:05 CDT)
AMBER: doesn't work in pmemd, and no output in parallel simulations Hwankyu Lee (Tue Apr 26 2005 - 15:35:26 CDT)
AMBER: error in pbsa calculation mingche Pan (Tue Apr 26 2005 - 16:15:13 CDT)
Re: AMBER: doesn't work in pmemd, and no output in parallel simulations Robert Duke (Tue Apr 26 2005 - 16:24:04 CDT)
Re: AMBER: error in pbsa calculation Ray Luo (Tue Apr 26 2005 - 16:39:50 CDT)
Re: AMBER: doesn't work in pmemd, and no output in parallel simulations Hwankyu Lee (Tue Apr 26 2005 - 21:46:09 CDT)
AMBER: Solvate with mixture of ethanol and water(Newbie question) Huaer XC (Wed Apr 27 2005 - 00:41:00 CDT)
AMBER: capping amit_at_mbu.iisc.ernet.in (Wed Apr 27 2005 - 02:30:37 CDT)
Re: AMBER: doesn't work in pmemd, and no output in parallel simulations Robert Duke (Wed Apr 27 2005 - 07:06:46 CDT)
Re: AMBER: mm_pbsa problem Husni Fattayer (Wed Apr 27 2005 - 10:09:40 CDT)
Re: AMBER: error in pbsa calculation mingche Pan (Wed Apr 27 2005 - 11:20:10 CDT)
Re: AMBER: capping FyD (Wed Apr 27 2005 - 11:40:36 CDT)
Re: AMBER: capping John Mongan (Wed Apr 27 2005 - 11:50:43 CDT)
Re: AMBER: error in pbsa calculation Ray Luo (Wed Apr 27 2005 - 12:03:33 CDT)
Re: AMBER: capping Bill Ross (Wed Apr 27 2005 - 16:00:50 CDT)
AMBER: emilia wu (Wed Apr 27 2005 - 21:35:59 CDT)
Re: AMBER: Pyranose pucker parameters Thomas E. Cheatham, III (Wed Apr 27 2005 - 22:57:26 CDT)
AMBER: mixture solvent model Huaer XC (Wed Apr 27 2005 - 23:13:11 CDT)
Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim (Wed Apr 27 2005 - 23:34:32 CDT)
Re: AMBER: capping amit_at_mbu.iisc.ernet.in (Thu Apr 28 2005 - 01:15:19 CDT)
Re: AMBER: capping Bill Ross (Thu Apr 28 2005 - 01:41:48 CDT)
AMBER: distance restraints mathew k varghese (Thu Apr 28 2005 - 02:00:16 CDT)
Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Petr Kulhanek (Thu Apr 28 2005 - 02:02:47 CDT)
AMBER: Problem with "Thermodynamic integration calculations" tutorial ,unsuspected error Maciej (Thu Apr 28 2005 - 02:41:21 CDT)
Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth David Case (Thu Apr 28 2005 - 08:03:00 CDT)
Re: AMBER: capping FyD (Thu Apr 28 2005 - 11:21:03 CDT)
AMBER: false bond created upon coordinate retrieval Stern, Julie (Thu Apr 28 2005 - 16:29:38 CDT)
Re: AMBER: false bond created upon coordinate retrieval Bill Ross (Thu Apr 28 2005 - 17:00:38 CDT)
AMBER: segmentation problem aanzellotti_at_mail2.vcu.edu (Thu Apr 28 2005 - 18:46:36 CDT)
Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim (Thu Apr 28 2005 - 18:34:48 CDT)
Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim (Thu Apr 28 2005 - 19:00:11 CDT)
AMBER: atommask error Sergio E. Wong (Fri Apr 29 2005 - 01:02:05 CDT)
Re: AMBER: atommask error hornak_at_csb.sunysb.edu (Fri Apr 29 2005 - 02:41:09 CDT)
Re: AMBER: atommask error Sergio E. Wong (Fri Apr 29 2005 - 12:19:25 CDT)
AMBER: Re: R.E.D. question FyD (Fri Apr 29 2005 - 15:21:34 CDT)
AMBER: Odd Antechamber Behavior Kara Di Giorgio (Fri Apr 29 2005 - 23:48:01 CDT)
AMBER: ipol=1 & use_pme= ?? Cenk Andac (Sat Apr 30 2005 - 08:26:57 CDT)
AMBER: Identifying water molecules with ptraj Joseph Fernandez (Sun May 01 2005 - 16:00:59 CDT)
AMBER: fast 1/r methods Brent Krueger (Mon May 02 2005 - 06:51:56 CDT)
Re: AMBER: fast 1/r methods Andreas Svrcek-Seiler (Mon May 02 2005 - 09:18:22 CDT)
Re: AMBER: fast 1/r methods fangyu liang (Mon May 02 2005 - 09:17:32 CDT)
Re: AMBER: ipol=1 & use_pme= ?? David A. Case (Mon May 02 2005 - 11:44:47 CDT)
AMBER: How to fix the atom in NPT case? george Chen (Mon May 02 2005 - 13:19:54 CDT)
Re: AMBER: How to fix the atom in NPT case? David A. Case (Mon May 02 2005 - 13:31:26 CDT)
Re: AMBER: Re: R.E.D. question Yanze Zhang (Mon May 02 2005 - 14:19:14 CDT)
Re: AMBER: How to fix the atom in NPT case? george Chen (Mon May 02 2005 - 14:35:42 CDT)
Re: AMBER: Re: R.E.D. question FyD (Mon May 02 2005 - 14:53:35 CDT)
AMBER: sander run YoungJin Cho (Mon May 02 2005 - 15:45:01 CDT)
AMBER: GB with dipoles ! Pradipta Bandyopadhyay (Tue May 03 2005 - 06:54:44 CDT)
Fwd: Re: AMBER: AMBER Test Anthony Cruz (Tue May 03 2005 - 07:25:46 CDT)
AMBER: Can I add iodide anione? Myunggi Yi (Tue May 03 2005 - 12:36:07 CDT)
AMBER: rborn(i) in egb.f Harianto Tjong (Tue May 03 2005 - 14:04:39 CDT)
Re: AMBER: rborn(i) in egb.f John Mongan (Tue May 03 2005 - 13:26:15 CDT)
AMBER: NOE constraints Hui-Hsu Tsai (Tue May 03 2005 - 14:18:27 CDT)
Re: AMBER: rborn(i) in egb.f Harianto Tjong (Tue May 03 2005 - 15:31:43 CDT)
Re: AMBER: rborn(i) in egb.f David A. Case (Tue May 03 2005 - 15:23:14 CDT)
Re: AMBER: NOE constraints David A. Case (Tue May 03 2005 - 15:25:44 CDT)
Re: AMBER: How to fix the atom in NPT case? george Chen (Tue May 03 2005 - 15:50:59 CDT)
Re: AMBER: rborn(i) in egb.f Harianto Tjong (Tue May 03 2005 - 17:13:16 CDT)
Re: AMBER: rborn(i) in egb.f David A. Case (Tue May 03 2005 - 17:59:23 CDT)
Re: AMBER: How to fix the atom in NPT case? David A. Case (Tue May 03 2005 - 19:16:33 CDT)
AMBER: Relative stability with MMPBSA Angelo Pugliese (Wed May 04 2005 - 11:09:27 CDT)
AMBER: Bromelain PDF xleap load error Thomas Patko (Wed May 04 2005 - 12:13:35 CDT)
AMBER: mm/pbsa error Eric Hu (Wed May 04 2005 - 13:06:34 CDT)
AMBER: Meaning of induced dipole moments for atom pairs? Cenk Andac (Wed May 04 2005 - 15:52:06 CDT)
Re: AMBER: Meaning of induced dipole moments for atom pairs? David A. Case (Wed May 04 2005 - 17:13:14 CDT)
AMBER: How can I read parm99.dat file? Myunggi Yi (Wed May 04 2005 - 18:08:49 CDT)
Re: AMBER: How can I read parm99.dat file? Bill Ross (Wed May 04 2005 - 19:12:08 CDT)
Re: AMBER: How can I read parm99.dat file? Vineet Pande (Thu May 05 2005 - 04:12:09 CDT)
Re: AMBER: How can I read parm99.dat file? David A. Case (Thu May 05 2005 - 10:10:59 CDT)
AMBER: ibelly in nmode Dawei Zhang (Thu May 05 2005 - 14:23:13 CDT)
Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) Thomas Patko (Thu May 05 2005 - 17:02:40 CDT)
Re: AMBER: Meaning of induced dipole moments for atom pairs? Cenk Andac (Thu May 05 2005 - 19:28:49 CDT)
Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) JunJun Liu (Thu May 05 2005 - 19:37:36 CDT)
AMBER: keeping two domains closed together during a simulation Sergio E. Wong (Thu May 05 2005 - 19:44:45 CDT)
AMBER: problem with gb md emilia wu (Thu May 05 2005 - 21:05:00 CDT)
RE: AMBER: problem with gb md Ross Walker (Thu May 05 2005 - 23:47:40 CDT)
Re: RE: AMBER: problem with gb md Andreas Svrcek-Seiler (Fri May 06 2005 - 04:19:00 CDT)
Re: AMBER: No vdW parameters for HO.. David A. Case (Fri May 06 2005 - 09:38:16 CDT)
Re: AMBER: How can I read parm99.dat file? Myunggi Yi (Fri May 06 2005 - 09:14:04 CDT)
Re: RE: AMBER: problem with gb md emilia wu (Fri May 06 2005 - 01:29:33 CDT)
Re: AMBER: How can I read parm99.dat file? Myunggi Yi (Fri May 06 2005 - 09:14:15 CDT)
Re: AMBER: How can I read parm99.dat file? Myunggi Yi (Fri May 06 2005 - 08:18:47 CDT)
Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) Andy Purkiss (Fri May 06 2005 - 06:05:36 CDT)
AMBER: No vdW parameters for HO.. Vineet Pande (Fri May 06 2005 - 05:20:02 CDT)
Re: AMBER: No vdW parameters for HO.. Vineet Pande (Fri May 06 2005 - 10:40:09 CDT)
AMBER: a nomenclature question Kenley Barrett (Fri May 06 2005 - 11:11:24 CDT)
Re: AMBER: No vdW parameters for HO.. Yong Duan (Fri May 06 2005 - 11:28:25 CDT)
AMBER: Dr. Cornell's calculation of Sulfur vdw epsilon value in parm94.dat? Chris Moth (Fri May 06 2005 - 14:32:23 CDT)
Re: AMBER: How can I read parm99.dat file? Bill Ross (Fri May 06 2005 - 15:08:59 CDT)
75% Off for All New Softs Now! haberman Rogelio Adams (Fri May 06 2005 - 22:19:57 CDT)
Re: AMBER: ibelly in nmode David A. Case (Sat May 07 2005 - 11:44:21 CDT)
AMBER: langevin, GB and simulated annealing - 5 pascal.baillod_at_epfl.ch (Mon May 09 2005 - 11:25:12 CDT)
AMBER: radial distribution function Myunggi Yi (Mon May 09 2005 - 13:36:43 CDT)
Re: AMBER: langevin, GB and simulated annealing - 5 Carlos Simmerling (Mon May 09 2005 - 14:58:57 CDT)
Re: AMBER: langevin, GB and simulated annealing - 5 David A. Case (Mon May 09 2005 - 18:18:04 CDT)
The new ganaration of repliccas is here capella Linda Hooks (Mon May 09 2005 - 20:53:45 CDT)
AMBER: parameter for sulfur in thio-octyl-glucopyranoside Vijay Manickam Achari (Mon May 09 2005 - 22:23:07 CDT)
Re: AMBER: langevin, GB and simulated annealing - 5 Carlos Simmerling (Tue May 10 2005 - 06:58:42 CDT)
Re: AMBER: radius parameter for F atom Scott Pendley (Tue May 10 2005 - 14:49:21 CDT)
Re: AMBER: mm/pbsa error Scott Pendley (Tue May 10 2005 - 14:56:52 CDT)
Re: AMBER: radius parameter for F atom Scott Pendley (Tue May 10 2005 - 14:49:21 CDT)
Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) Thomas Patko (Wed May 11 2005 - 02:10:53 CDT)
AMBER: AMBER8 Build on Linux x64 running Opterons Thomas Patko (Wed May 11 2005 - 02:10:14 CDT)
AMBER: Trouble with example tutorial Maciej (Wed May 11 2005 - 06:08:02 CDT)
You wont believe these pr1ces on name-brannd soft's! kerchief Ismael Childers (Wed May 11 2005 - 10:06:11 CDT)
AMBER: Parameter for alpha-lactose Sagarika Dev (Wed May 11 2005 - 09:48:21 CDT)
Re: AMBER: AMBER8 Build on Linux x64 running Opterons Mark Rance (Wed May 11 2005 - 10:02:05 CDT)
Re: AMBER: AMBER8 Build on Linux x64 running Opterons Robert Duke (Wed May 11 2005 - 10:14:50 CDT)
Re: AMBER: AMBER8 Build on Linux x64 running Opterons Robert Duke (Wed May 11 2005 - 10:18:12 CDT)
Re: AMBER: AMBER8 Build on Linux x64 running Opterons Thomas Patko (Wed May 11 2005 - 10:34:18 CDT)
AMBER: Asking how to creat alanine "dipeptide" in amber8 Li Su (Wed May 11 2005 - 10:37:07 CDT)
Re: AMBER: Asking how to creat alanine "dipeptide" in amber8 Thomas E. Cheatham, III (Wed May 11 2005 - 10:38:54 CDT)
Fwd: Re: AMBER: AMBER Test Anthony Cruz (Wed May 11 2005 - 10:49:38 CDT)
Re: AMBER: Asking how to creat alanine "dipeptide" in amber8 FyD (Wed May 11 2005 - 11:06:27 CDT)
AMBER: SANDER BOMB: volume of ucell too big Stern, Julie (Wed May 11 2005 - 11:07:38 CDT)
RE: AMBER: Asking how to creat alanine "dipeptide" in amber8 Ross Walker (Wed May 11 2005 - 12:13:30 CDT)
AMBER: Problem with xleap Ilyas Yildirim (Wed May 11 2005 - 20:45:50 CDT)
Re: AMBER: Problem with xleap FyD (Wed May 11 2005 - 21:21:12 CDT)
AMBER: maximum number of processors MURAT CETINKAYA (Wed May 11 2005 - 22:53:44 CDT)
We can send you disccounted errection mads party Freeman William (Thu May 12 2005 - 00:23:35 CDT)
Re: AMBER: Problem with xleap JunJun Liu (Thu May 12 2005 - 02:19:24 CDT)
Re: AMBER: Parameter for alpha-lactose David A. Case (Thu May 12 2005 - 10:29:08 CDT)
Re: Fwd: Re: AMBER: AMBER Test David A. Case (Thu May 12 2005 - 10:33:15 CDT)
Re: AMBER: maximum number of processors Asim Okur (Thu May 12 2005 - 10:41:25 CDT)
Re: AMBER: AMBER8 Build on Linux x64 running Opterons David A. Case (Thu May 12 2005 - 11:58:19 CDT)
Re: AMBER: maximum number of processors Michael Crowley (Thu May 12 2005 - 12:00:09 CDT)
Re: AMBER: Trouble with example tutorial David A. Case (Thu May 12 2005 - 12:04:51 CDT)
AMBER: RESP charge fitting for N-methylguanine cation Grzegorz Jezierski (Thu May 12 2005 - 11:50:17 CDT)
Re: AMBER: SANDER BOMB: volume of ucell too big Michael Crowley (Thu May 12 2005 - 12:10:20 CDT)
RE: AMBER: SANDER BOMB: volume of ucell too big Stern, Julie (Thu May 12 2005 - 14:34:55 CDT)
Re: AMBER: AMBER8 Build on Linux x64 running Opterons Bill Ross (Thu May 12 2005 - 15:08:34 CDT)
Re: AMBER: SANDER BOMB: volume of ucell too big David A. Case (Thu May 12 2005 - 15:27:50 CDT)
Re: AMBER: SANDER BOMB: volume of ucell too big Robert Duke (Thu May 12 2005 - 15:44:11 CDT)
AMBER: Tutorial #1 ptraj/sander problem Daniela Kohen (Thu May 12 2005 - 17:03:07 CDT)
RE: AMBER: parameter for sulfur in thio-octyl-glucopyranoside Spero Manolatos (Thu May 12 2005 - 17:08:49 CDT)
Re: AMBER: a nomenclature question David A. Case (Thu May 12 2005 - 17:18:20 CDT)
RE: AMBER: Tutorial #1 ptraj/sander problem Ross Walker (Thu May 12 2005 - 17:33:44 CDT)
Re: AMBER: Problem with xleap Ilyas Yildirim (Thu May 12 2005 - 18:14:38 CDT)
AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang (Thu May 12 2005 - 20:44:04 CDT)
Re: AMBER: RESP charge fitting for N-methylguanine cation Kara Di Giorgio (Thu May 12 2005 - 21:40:17 CDT)
AMBER: amber8 test error Cordova, Luis E. (Thu May 12 2005 - 22:26:00 CDT)
Re: AMBER: the restraint MD fail with amber8,but success with amber7 Carlos Simmerling (Fri May 13 2005 - 05:50:10 CDT)
AMBER: creating residues - charge assign problems Hayden Eastwood (Fri May 13 2005 - 06:06:06 CDT)
Re: AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang (Fri May 13 2005 - 06:19:20 CDT)
Re: AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang (Fri May 13 2005 - 06:21:28 CDT)
Re: AMBER: creating residues - charge assign problems FyD (Fri May 13 2005 - 10:25:48 CDT)
Re: AMBER: RESP charge fitting for N-methylguanine cation FyD (Fri May 13 2005 - 10:33:05 CDT)
Re: AMBER: creating residues - charge assign problems David A. Case (Fri May 13 2005 - 11:43:41 CDT)
Re: AMBER: amber8 test error David A. Case (Fri May 13 2005 - 12:11:27 CDT)
AMBER: platinum atom in Xleap Chen Chengwen (Fri May 13 2005 - 21:11:12 CDT)
Re: AMBER: maximum number of processors Abd Ghani Abd Aziz (Sat May 14 2005 - 01:42:49 CDT)
AMBER: How to create a parallel job for amber 8? Ò×ºç (Sat May 14 2005 - 06:20:15 CDT)
Re: AMBER: How to create a parallel job for amber 8? Shulin Zhuang (Sat May 14 2005 - 08:45:54 CDT)
A new rollax repliccas is in the mark. attitudinal Russel Granger (Sat May 14 2005 - 11:02:36 CDT)
Re: AMBER: maximum number of processors C J Kenneth Tan -- OptimaNumerics (Sat May 14 2005 - 09:57:22 CDT)
AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? caoch_at_cherry.bio.titech.ac.jp (Sat May 14 2005 - 12:17:17 CDT)
Re: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? Carlos Simmerling (Sat May 14 2005 - 12:52:56 CDT)
AMBER: Calculating of radius of gyration in Carnal Hwankyu Lee (Sat May 14 2005 - 13:36:37 CDT)
RE: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? ross_at_rosswalker.co.uk (Sat May 14 2005 - 14:43:46 CDT)
Re: AMBER: Calculating of radius of gyration in Carnal Bill Ross (Sat May 14 2005 - 17:26:43 CDT)
AMBER: how to reduce box size and delete excess solvent hj zou (Sun May 15 2005 - 06:51:32 CDT)
AMBER: How to set constraint Li Su (Sun May 15 2005 - 13:58:51 CDT)
Re: AMBER: how to reduce box size and delete excess solvent Bill Ross (Sun May 15 2005 - 14:50:01 CDT)
AMBER: generating over 16 bps of DNA in nucgen Hwankyu Lee (Mon May 16 2005 - 10:33:04 CDT)
AMBER: strange mm_pbsa.pl bug Nelson Fonseca (Mon May 16 2005 - 10:39:21 CDT)
Re: AMBER: How to set constraint David A. Case (Mon May 16 2005 - 10:42:27 CDT)
AMBER: How to set up dihedral constraints in amber Li Su (Mon May 16 2005 - 10:39:50 CDT)
AMBER: output of force field info Stern, Julie (Mon May 16 2005 - 14:24:37 CDT)
AMBER: nmode in mmpbsa Joseph Fernandez (Mon May 16 2005 - 18:36:28 CDT)
Re: AMBER: output of force field info David A. Case (Mon May 16 2005 - 19:16:55 CDT)
AMBER: *** Proper torsion parameters missing *** Ilyas Yildirim (Mon May 16 2005 - 19:19:04 CDT)
Re: AMBER: output of force field info Thomas E. Cheatham, III (Mon May 16 2005 - 20:21:51 CDT)
AMBER: ATOM TYPE Ilyas Yildirim (Mon May 16 2005 - 21:10:48 CDT)
Re: AMBER: nmode in mmpbsa Holger Gohlke (Tue May 17 2005 - 01:44:17 CDT)
AMBER: MMPBSA calculations on Highly charged systems Vitor Manuel Sousa F?x (Tue May 17 2005 - 06:01:21 CDT)
Re: AMBER: MMPBSA calculations on Highly charged systems Nelson Fonseca (Tue May 17 2005 - 07:36:16 CDT)
Re: AMBER: generating over 16 bps of DNA in nucgen Garhan Attebury (Tue May 17 2005 - 10:27:13 CDT)
AMBER: Message in .out file Atilio Anzellotti (Tue May 17 2005 - 07:31:36 CDT)
Re: AMBER: generating over 16 bps of DNA in nucgen aanzellotti_at_mail2.vcu.edu (Tue May 17 2005 - 10:57:45 CDT)
AMBER: GAFF angle parameters Monica Civera (Tue May 17 2005 - 11:11:46 CDT)
AMBER: molsurf error mingche Pan (Tue May 17 2005 - 11:52:57 CDT)
AMBER: compiling pmemd on dual xeon Tiziano Tuccinardi (Tue May 17 2005 - 12:28:31 CDT)
Re: AMBER: compiling pmemd on dual xeon Robert Duke (Tue May 17 2005 - 12:49:48 CDT)
Re: AMBER: compiling pmemd on dual xeon Tiziano Tuccinardi (Tue May 17 2005 - 13:05:49 CDT)
AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Rajeev Ranjan Singh (Tue May 17 2005 - 15:15:33 CDT)
AMBER: gaff: ca-ca-c -o torsion parameter Oliver Hucke (Tue May 17 2005 - 15:54:24 CDT)
AMBER: amber 8 REM possible test problem Sergio E. Wong (Tue May 17 2005 - 16:51:04 CDT)
RE: AMBER: GAFF angle parameters Junmei Wang (Tue May 17 2005 - 17:08:47 CDT)
FW: Office XP - 60 dolars! coagulate Myra Cole (Tue May 17 2005 - 19:04:52 CDT)
AMBER: RE: Tutorial#1 ptraj/sander problem Ross Walker (Tue May 17 2005 - 17:56:59 CDT)
AMBER: MD on surface Yanze Zhang (Tue May 17 2005 - 18:58:29 CDT)
AMBER: error with ptraj Xiaowei (David) Li (Tue May 17 2005 - 23:27:33 CDT)
AMBER: loading pdb cbala_at_igib.res.in (Wed May 18 2005 - 00:56:13 CDT)
Re: AMBER: loading pdb David A. Case (Wed May 18 2005 - 01:38:27 CDT)
Re: AMBER: error with ptraj David A. Case (Wed May 18 2005 - 01:38:22 CDT)
Re: AMBER: gaff: ca-ca-c -o torsion parameter David A. Case (Wed May 18 2005 - 01:38:33 CDT)
Re: AMBER: Message in .out file David A. Case (Wed May 18 2005 - 01:38:40 CDT)
AMBER: Using AMBER for Carbon nanotubes Zhang Yingyan (Wed May 18 2005 - 03:21:42 CDT)
Re: AMBER: loading pdb Rajeev Ranjan Singh (Wed May 18 2005 - 09:01:34 CDT)
RE: AMBER: Using AMBER for Carbon nanotubes Ross Walker (Wed May 18 2005 - 12:12:29 CDT)
AMBER: error during MD run cbala_at_igib.res.in (Wed May 18 2005 - 13:39:25 CDT)
Re: AMBER: error during MD run Thomas E. Cheatham, III (Wed May 18 2005 - 13:10:36 CDT)
Re: AMBER: error during MD run Rajeev Ranjan Singh (Wed May 18 2005 - 13:16:12 CDT)
AMBER: frcmod info for Nickel Kara Di Giorgio (Wed May 18 2005 - 14:04:44 CDT)
Re: AMBER: loading pdb Ilyas Yildirim (Wed May 18 2005 - 15:21:24 CDT)
AMBER: parameter for sulfur in thio-glucoside residue Vijay Manickam Achari (Wed May 18 2005 - 20:58:57 CDT)
Re: AMBER: parameter for sulfur in thio-glucoside residue Ilyas Yildirim (Wed May 18 2005 - 21:11:34 CDT)
AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim (Wed May 18 2005 - 21:16:35 CDT)
Re: AMBER: Can we load prmtop and inpcrd files into xleap? Kara Di Giorgio (Wed May 18 2005 - 21:45:43 CDT)
Re: AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim (Wed May 18 2005 - 23:00:07 CDT)
Re: AMBER: Can we load prmtop and inpcrd files into xleap? Kara Di Giorgio (Wed May 18 2005 - 23:10:36 CDT)
Re: AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim (Wed May 18 2005 - 23:47:49 CDT)
Re: AMBER: Can we load prmtop and inpcrd files into xleap? Bill Ross (Wed May 18 2005 - 23:49:04 CDT)
AMBER: Amber 8 and LAM compilation problem Glen Otero (Thu May 19 2005 - 00:52:00 CDT)
AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Vijay Manickam Achari (Thu May 19 2005 - 01:55:21 CDT)
RE: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Ross Walker (Thu May 19 2005 - 02:16:41 CDT)
Re: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Ilyas Yildirim (Thu May 19 2005 - 02:37:22 CDT)
AMBER: GB - igb=1 versus dielc=? milion_at_c-box.cz (Thu May 19 2005 - 03:36:34 CDT)
Re: AMBER: Amber 8 and LAM compilation problem Robert Duke (Thu May 19 2005 - 07:05:48 CDT)
AMBER: write format of restart crd in sander/pmemd Peter Varnai (Thu May 19 2005 - 07:12:22 CDT)
AMBER: Using amber4 generated prep files in amber8? Simon Whitehead (Thu May 19 2005 - 07:51:00 CDT)
Re: AMBER: Using amber4 generated prep files in amber8? David A. Case (Thu May 19 2005 - 10:31:54 CDT)
Re: AMBER: GB - igb=1 versus dielc=? David A. Case (Thu May 19 2005 - 11:09:47 CDT)
Re: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Cenk Andac (Thu May 19 2005 - 12:03:43 CDT)
AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 20:19:04 CDT)
Re: AMBER: read pdb back to xleap after solvation of chloroform David A. Case (Thu May 19 2005 - 20:38:49 CDT)
RE: AMBER: read pdb back to xleap after solvation of chloroform Ross Walker (Thu May 19 2005 - 20:41:31 CDT)
Re: AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 20:59:47 CDT)
RE: AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 21:05:27 CDT)
RE: AMBER: read pdb back to xleap after solvation of chloroform Bill Ross (Thu May 19 2005 - 21:16:22 CDT)
RE: AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 21:55:23 CDT)
RE: AMBER: read pdb back to xleap after solvation of chloroform Bill Ross (Thu May 19 2005 - 22:56:58 CDT)
AMBER: MM_PBSA for NMR restrained structures Cenk Andac (Fri May 20 2005 - 03:36:10 CDT)
AMBER: leap problem: savepdb Hannes Barsch (Fri May 20 2005 - 04:30:29 CDT)
AMBER: Re: antechamber not working .. for thio residue.. Vijay Manickam Achari (Fri May 20 2005 - 04:32:19 CDT)
AMBER: how to creat leaprc.gaff Vijay Manickam Achari (Fri May 20 2005 - 04:36:25 CDT)
Re: AMBER: how to creat leaprc.gaff Ilyas Yildirim (Fri May 20 2005 - 04:48:14 CDT)
Re: AMBER: Re: antechamber not working .. for thio residue.. Shulin Zhuang (Fri May 20 2005 - 05:22:39 CDT)
AMBER: Error in minimization Priti Hansia (Fri May 20 2005 - 05:58:36 CDT)
Re: AMBER: Error in minimization Carlos Simmerling (Fri May 20 2005 - 07:57:37 CDT)
Re: AMBER: Representation of cations in MD David A. Case (Fri May 20 2005 - 10:16:15 CDT)
Re: AMBER: leap problem: savepdb David A. Case (Fri May 20 2005 - 10:21:13 CDT)
AMBER: Steve Seibold (Fri May 20 2005 - 12:45:24 CDT)
Re: AMBER: luckyang_at_gmail.com (Fri May 20 2005 - 13:28:17 CDT)
AMBER: crashing xleap Kenley Barrett (Fri May 20 2005 - 13:48:13 CDT)
AMBER: 1-4 scaling factors Stern, Julie (Fri May 20 2005 - 14:13:22 CDT)
Re: AMBER: 1-4 scaling factors Thomas E. Cheatham, III (Fri May 20 2005 - 14:43:34 CDT)
Re: AMBER: crashing xleap Bill Ross (Fri May 20 2005 - 14:55:15 CDT)
Re: AMBER: crashing xleap Scott Brozell (Fri May 20 2005 - 15:03:40 CDT)
Re: AMBER: crashing xleap Kenley Barrett (Fri May 20 2005 - 15:57:00 CDT)
Re: AMBER: read pdb back to xleap after solvation of chloroform Furse, Kristina Elisabet (Fri May 20 2005 - 16:20:55 CDT)
AMBER: Citing the PBSA module of AMBER8 Cenk Andac (Fri May 20 2005 - 16:27:03 CDT)
Re: AMBER: crashing xleap Ilyas Yildirim (Fri May 20 2005 - 16:47:09 CDT)
Re: AMBER: crashing xleap Furse, Kristina Elisabet (Fri May 20 2005 - 17:28:05 CDT)
Re: AMBER: JunJun Liu (Fri May 20 2005 - 21:41:24 CDT)
AMBER: modeller Zhang Bing (Fri May 20 2005 - 23:53:13 CDT)
AMBER: rotating and repositioning molecules in xleap Hwankyu Lee (Sat May 21 2005 - 01:09:45 CDT)
AMBER: Copyright for PBSA Cenk Andac (Sat May 21 2005 - 03:32:00 CDT)
Re: AMBER: Copyright for PBSA David A. Case (Sat May 21 2005 - 22:37:45 CDT)
Re: AMBER: rotating and repositioning molecules in xleap Angelo Pugliese (Sun May 22 2005 - 04:37:44 CDT)
Re: AMBER: rotating and repositioning molecules in xleap Hwankyu Lee (Sun May 22 2005 - 08:03:40 CDT)
Re: AMBER: rotating and repositioning molecules in xleap Bill Ross (Sun May 22 2005 - 10:36:16 CDT)
AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Sun May 22 2005 - 14:44:55 CDT)
Re: AMBER: Unexpected stop of Sander run Bill Ross (Sun May 22 2005 - 15:18:16 CDT)
Re: AMBER: Unexpected stop of Sander run Carlos Simmerling (Sun May 22 2005 - 15:22:11 CDT)
AMBER: Error in sander: stack trace terminated abnormally. Hwankyu Lee (Sun May 22 2005 - 16:05:31 CDT)
RE: AMBER: Error in sander: stack trace terminated abnormally. Ross Walker (Sun May 22 2005 - 16:53:36 CDT)
AMBER: antechamber not working .. for thio residue.. Vijay Manickam Achari (Sun May 22 2005 - 21:15:20 CDT)
Re: AMBER: antechamber not working .. for thio residue.. Shulin Zhuang (Sun May 22 2005 - 21:31:27 CDT)
Re: AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Mon May 23 2005 - 02:14:54 CDT)
AMBER: Setting Amber force field parameters Chen Chengwen (Mon May 23 2005 - 02:55:38 CDT)
AMBER: using antechamber ... to get prepin file Vijay Manickam Achari (Mon May 23 2005 - 03:59:16 CDT)
Re: AMBER: Unexpected stop of Sander run Carlos Simmerling (Mon May 23 2005 - 06:15:34 CDT)
RE: AMBER: using antechamber ... to get prepin file Vineet Pande (Mon May 23 2005 - 07:02:26 CDT)
Re: AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Mon May 23 2005 - 08:43:51 CDT)
Re: AMBER: Unexpected stop of Sander run Carlos Simmerling (Mon May 23 2005 - 08:57:00 CDT)
Re: AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Mon May 23 2005 - 09:38:58 CDT)
Re: AMBER: Unexpected stop of Sander run David A. Case (Mon May 23 2005 - 10:00:46 CDT)
AMBER: Connecting two molecules Hwankyu Lee (Mon May 23 2005 - 10:13:00 CDT)
Re: AMBER: Connecting two molecules David A. Case (Mon May 23 2005 - 10:23:51 CDT)
Re: AMBER: Connecting two molecules Hwankyu Lee (Mon May 23 2005 - 11:51:20 CDT)
Re: AMBER: crashing xleap; bugfix.44 Scott Brozell (Mon May 23 2005 - 12:22:51 CDT)
AMBER: hbond detailed analysis over time? pascal.baillod_at_epfl.ch (Mon May 23 2005 - 13:04:10 CDT)
AMBER: how to generate frcmod file for using prepin file.. Vijay Manickam Achari (Mon May 23 2005 - 21:52:18 CDT)
RE: AMBER: how to generate frcmod file for using prepin file.. chaiann ng (Mon May 23 2005 - 22:03:55 CDT)
AMBER: my frcmod file created using parmchk Vijay Manickam Achari (Mon May 23 2005 - 22:44:21 CDT)
Re: AMBER: my frcmod file created using parmchk Ilyas Yildirim (Mon May 23 2005 - 23:03:42 CDT)
AMBER: my prepin file in lowe-case Vijay Manickam Achari (Tue May 24 2005 - 02:51:55 CDT)
AMBER: Which forcefield? Simon Whitehead (Tue May 24 2005 - 03:13:01 CDT)
AMBER: conformational sampling of a peptide Hannes Barsch (Tue May 24 2005 - 03:58:04 CDT)
AMBER: amber code Juan Fernandez Carmona (Tue May 24 2005 - 05:08:00 CDT)
Re: AMBER: conformational sampling of a peptide Carlos Simmerling (Tue May 24 2005 - 08:11:53 CDT)
Re: AMBER: amber code Andreas Svrcek-Seiler (Tue May 24 2005 - 09:18:11 CDT)
AMBER: Fw: Installing PMEMD on IBM machine (CPU power4) running SUSE_9.1 Robert Duke (Tue May 24 2005 - 09:42:15 CDT)
Re: AMBER: conformational sampling of a peptide Joseph Nachman (Tue May 24 2005 - 10:26:52 CDT)
AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_' René Ranzinger (Tue May 24 2005 - 10:04:42 CDT)
AMBER: Sander Restart Problem Garhan Attebury (Tue May 24 2005 - 10:07:49 CDT)
AMBER: How to fix certain bond angles Li Su (Tue May 24 2005 - 10:27:14 CDT)
Re: AMBER: How to fix certain bond angles Guanglei Cui (Tue May 24 2005 - 10:40:00 CDT)
RE: AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_' Ross Walker (Tue May 24 2005 - 10:43:37 CDT)
AMBER: Error: vlimit exceeded for step Hwankyu Lee (Tue May 24 2005 - 12:20:10 CDT)
Re: AMBER: Error: vlimit exceeded for step Carlos Simmerling (Tue May 24 2005 - 12:51:14 CDT)
Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee (Tue May 24 2005 - 13:07:41 CDT)
Re: AMBER: Error: vlimit exceeded for step Thomas E. Cheatham, III (Tue May 24 2005 - 13:12:58 CDT)
Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee (Tue May 24 2005 - 13:34:34 CDT)
Solute-solvent boundary in pbsa ..Re: AMBER: Copyright for PBSA Cenk Andac (Tue May 24 2005 - 13:48:26 CDT)
AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Li Su (Tue May 24 2005 - 14:14:09 CDT)
Re: AMBER: Error: vlimit exceeded for step David Mobley (Tue May 24 2005 - 14:27:23 CDT)
Re: AMBER: Solute-solvent boundary in pbsa Ray Luo (Tue May 24 2005 - 03:48:10 CDT)
AMBER: charges difference of atom in xleap and prmtop chaiann ng (Tue May 24 2005 - 23:02:33 CDT)
Re: AMBER: charges difference of atom in xleap and prmtop David A. Case (Wed May 25 2005 - 00:27:51 CDT)
Re: AMBER: Which forcefield? David A. Case (Wed May 25 2005 - 00:32:09 CDT)
AMBER: PARMSCAN program Philippe ARNAUD (Wed May 25 2005 - 02:28:31 CDT)
AMBER: average structure after MD kuljeets_at_igib.res.in (Wed May 25 2005 - 04:14:19 CDT)
AMBER: quadrupole in resp riccardo nifosi (Wed May 25 2005 - 05:44:20 CDT)
Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Petr Kulhanek (Wed May 25 2005 - 06:56:34 CDT)
Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Guanglei Cui (Wed May 25 2005 - 08:55:23 CDT)
AMBER: error in chirality.c? Kenley Barrett (Wed May 25 2005 - 09:27:07 CDT)
Re: AMBER: error in chirality.c? David A. Case (Wed May 25 2005 - 10:21:48 CDT)
Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac (Wed May 25 2005 - 11:21:52 CDT)
Re#2:Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac (Wed May 25 2005 - 15:03:47 CDT)
Re: Re#2:Re: AMBER: Solute-solvent boundary in pbsa Ray Luo (Wed May 25 2005 - 00:56:08 CDT)
Re: AMBER: Solute-solvent boundary in pbsa Ray Luo (Wed May 25 2005 - 00:54:50 CDT)
AMBER: antechamber, reference? Cenk Andac (Wed May 25 2005 - 16:14:48 CDT)
Re: AMBER: antechamber, reference? David A. Case (Wed May 25 2005 - 16:36:19 CDT)
AMBER: dissolving micelle structure in water.. amber7 Vijay Manickam Achari (Wed May 25 2005 - 22:59:22 CDT)
Re: AMBER: average structure after MD kuljeets_at_igib.res.in (Thu May 26 2005 - 00:42:32 CDT)
AMBER: distance restraints between two centers of mass JAVIER PEREZ (Thu May 26 2005 - 03:37:30 CDT)
Re: AMBER: distance restraints between two centers of mass Fabien Cailliez (Thu May 26 2005 - 04:01:08 CDT)
Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Petr Kulhanek (Thu May 26 2005 - 05:44:37 CDT)
AMBER: Is the MD simulation normal Shulin Zhuang (Thu May 26 2005 - 10:30:48 CDT)
AMBER: setting up Parallel processing mathew k varghese (Thu May 26 2005 - 10:39:00 CDT)
Re: AMBER: setting up Parallel processing Robert Duke (Thu May 26 2005 - 11:15:30 CDT)
AMBER: hbond analysis in ptaj/carnal Jana Precechtelova (Thu May 26 2005 - 11:25:20 CDT)
Re: AMBER: dissolving micelle structure in water.. amber7 David A. Case (Thu May 26 2005 - 11:30:17 CDT)
Re: AMBER: hbond analysis in ptaj/carnal Bill Ross (Thu May 26 2005 - 11:44:13 CDT)
Re: AMBER: dissolving micelle structure in water.. amber7 Bill Ross (Thu May 26 2005 - 11:50:23 CDT)
RE: AMBER: Is the MD simulation normal Yong Duan (Thu May 26 2005 - 12:05:14 CDT)
Re: AMBER: hbond analysis in ptaj/carnal Thomas E. Cheatham, III (Thu May 26 2005 - 12:05:00 CDT)
AMBER: why is snaupe.f is empty? Cordova, Luis E. (Thu May 26 2005 - 12:06:24 CDT)
Re: AMBER: Is the MD simulation normal Thomas E. Cheatham, III (Thu May 26 2005 - 12:41:03 CDT)
AMBER: ptraj - hbond detailed analysis over time? pascal.baillod_at_epfl.ch (Thu May 26 2005 - 12:38:38 CDT)
RE: AMBER: why is snaupe.f is empty? 'Ross Walker' (Thu May 26 2005 - 13:14:34 CDT)
RE: AMBER: setting up Parallel processing 'Ross Walker' (Thu May 26 2005 - 13:14:18 CDT)
Re:Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac (Thu May 26 2005 - 15:58:55 CDT)
Re: AMBER: Solute-solvent boundary in pbsa Ray Luo (Wed May 25 2005 - 20:40:39 CDT)
AMBER: Mol2 to prepin file conversion Andrew Box (Thu May 26 2005 - 19:08:22 CDT)
Re: AMBER: Mol2 to prepin file conversion David A. Case (Thu May 26 2005 - 19:44:36 CDT)
Re: AMBER: dissolving micelle structure in water.. amber7 Vijay Manickam Achari (Thu May 26 2005 - 20:19:57 CDT)
Re: AMBER: Is the MD simulation normal Shulin Zhuang (Thu May 26 2005 - 23:23:37 CDT)
RE: AMBER: Is the MD simulation normal Yong Duan (Fri May 27 2005 - 01:17:00 CDT)
Re: AMBER: Is the MD simulation normal Shulin Zhuang (Fri May 27 2005 - 02:38:05 CDT)
RE: AMBER: Is the MD simulation normal Yong Duan (Fri May 27 2005 - 11:31:27 CDT)
Re: AMBER: Is the MD simulation normal Bill Ross (Fri May 27 2005 - 13:14:30 CDT)
AMBER: question about loadiing pdb file of a molecule complex gtg549i_at_mail.gatech.edu (Fri May 27 2005 - 16:39:28 CDT)
AMBER: Workshop Tutorials Downtime this weekend. Ross Walker (Fri May 27 2005 - 16:49:05 CDT)
Re: AMBER: question about loadiing pdb file of a molecule complex Chutintorn Punwong (Fri May 27 2005 - 17:07:52 CDT)
Re: AMBER: Is the MD simulation normal Shulin Zhuang (Sat May 28 2005 - 08:02:05 CDT)
Re: AMBER: Is the MD simulation normal Bill Ross (Sat May 28 2005 - 12:00:42 CDT)
Re: AMBER: question about loadiing pdb file of a molecule complex David A. Case (Sun May 29 2005 - 00:29:53 CDT)
Re: AMBER: Is the MD simulation normal Shulin Zhuang (Sun May 29 2005 - 09:53:35 CDT)
Re: AMBER: Is the MD simulation normal Bill Ross (Sun May 29 2005 - 10:33:13 CDT)
RE: AMBER: Is the MD simulation normal Yong Duan (Sun May 29 2005 - 11:46:44 CDT)
RE: AMBER: Is the MD simulation normal Bill Ross (Sun May 29 2005 - 12:04:01 CDT)
AMBER: Antechamber RESP failed for large organic molecule junwang (Sun May 29 2005 - 14:57:59 CDT)
AMBER: question about initial conditions for amber Ed Pate (Sun May 29 2005 - 21:42:21 CDT)
AMBER: density profiles in ptraj or carnal Hwankyu Lee (Sun May 29 2005 - 22:27:37 CDT)
AMBER: pairwise energy decomposition using MM-PBSA Xin Hu (Sun May 29 2005 - 22:38:30 CDT)
AMBER: Reference (?) for normal-mode analysis in nmode Cenk Andac (Mon May 30 2005 - 04:18:59 CDT)
Re: AMBER: question about initial conditions for amber Stefano Federico Pieraccini (Mon May 30 2005 - 06:44:54 CDT)
Re: AMBER: question about initial conditions for amber Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon May 30 2005 - 06:40:59 CDT)
AMBER: Force field modification problem yuann (Mon May 30 2005 - 06:16:27 CDT)
Re: AMBER: Is the MD simulation normal Shulin Zhuang (Mon May 30 2005 - 09:39:50 CDT)
Re: AMBER: question about loadiing pdb file of a molecule complex gtg549i_at_mail.gatech.edu (Mon May 30 2005 - 10:56:09 CDT)
AMBER: Bond angle restraints setting files Li Su (Mon May 30 2005 - 11:05:15 CDT)
Re: AMBER: Antechamber RESP failed for large organic molecule David A. Case (Mon May 30 2005 - 11:09:27 CDT)
Re: AMBER: Force field modification problem David A. Case (Mon May 30 2005 - 11:21:00 CDT)
Re: AMBER: Is the MD simulation normal Bill Ross (Mon May 30 2005 - 11:49:32 CDT)
Re: AMBER: density profiles in ptraj or carnal Bill Ross (Mon May 30 2005 - 12:00:08 CDT)
Re: AMBER: density profiles in ptraj or carnal Hwankyu Lee (Mon May 30 2005 - 17:58:54 CDT)
Re[2]: AMBER: Force field modification problem sychen (Mon May 30 2005 - 19:05:45 CDT)
Re: AMBER: density profiles in ptraj or carnal Hwankyu Lee (Mon May 30 2005 - 23:13:26 CDT)
Re: AMBER: Force field modification problem David A. Case (Tue May 31 2005 - 00:17:06 CDT)
AMBER: density problem cristian obiol (Tue May 31 2005 - 04:17:46 CDT)
AMBER: stack terminated abnormally drugdesign (Tue May 31 2005 - 05:20:33 CDT)
RE: AMBER: Antechamber RESP failed for large organic molecule Junmei Wang (Tue May 31 2005 - 09:37:35 CDT)
AMBER: if setting ntf=4, will it cause someproblem? Li Su (Tue May 31 2005 - 09:55:03 CDT)
Re: AMBER: if setting ntf=4, will it cause someproblem? Carlos Simmerling (Tue May 31 2005 - 10:12:30 CDT)
AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Tue May 31 2005 - 10:23:51 CDT)
Re: AMBER: Reference (?) for normal-mode analysis in nmode David A. Case (Tue May 31 2005 - 10:30:10 CDT)
RE: AMBER: density problem Ross Walker (Tue May 31 2005 - 10:33:39 CDT)
RE: AMBER: stack terminated abnormally Ross Walker (Tue May 31 2005 - 10:35:15 CDT)
AMBER: DNA base-flipping: TI vs PMF Lauren O'Neil (Tue May 31 2005 - 10:40:45 CDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7) David A. Case (Tue May 31 2005 - 10:45:01 CDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7) Viktor Hornak (Tue May 31 2005 - 10:52:48 CDT)
Re: RE: AMBER: Antechamber RESP failed for large organic molecule junwang (Tue May 31 2005 - 11:58:33 CDT)
AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Grzegorz Jezierski (Tue May 31 2005 - 11:04:20 CDT)
Re: AMBER: density profiles in ptraj or carnal Bill Ross (Tue May 31 2005 - 11:13:28 CDT)
RE: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Ross Walker (Tue May 31 2005 - 11:09:20 CDT)
Re: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Marcin Krol (Tue May 31 2005 - 11:17:30 CDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Tue May 31 2005 - 11:21:55 CDT)
AMBER: MM-PBSA calculation masi_at_nmr.mpibpc.mpg.de (Tue May 31 2005 - 11:37:40 CDT)
AMBER: STOP 0 masi_at_nmr.mpibpc.mpg.de (Tue May 31 2005 - 11:40:25 CDT)
RE: AMBER: Error on restrained MD equilibration (AMBER 7) Ross Walker (Tue May 31 2005 - 11:45:19 CDT)
RE: AMBER: STOP 0 Ross Walker (Tue May 31 2005 - 11:47:20 CDT)
AMBER: runtime error in sander? Dave S Walker (Tue May 31 2005 - 12:07:13 CDT)
AMBER:Sander errors: Unit 6 Error on OPEN: mdout Douali, Latifa (Tue May 31 2005 - 12:34:41 CDT)
RE: AMBER: runtime error in sander? Ross Walker (Tue May 31 2005 - 12:34:51 CDT)
Re: AMBER: STOP 0 Bill Ross (Tue May 31 2005 - 12:43:32 CDT)
RE: AMBER:Sander errors: Unit 6 Error on OPEN: mdout Ross Walker (Tue May 31 2005 - 12:45:53 CDT)
AMBER: Loading pdb-residue (re)numbering in leap gtg549i_at_mail.gatech.edu (Tue May 31 2005 - 12:48:13 CDT)
Re: AMBER: question about loadiing pdb file of a molecule complex David A. Case (Tue May 31 2005 - 13:00:59 CDT)
RE: AMBER:Sander errors: Unit 6 Error on OPEN: mdout Bill Ross (Tue May 31 2005 - 13:42:50 CDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7) Guanglei Cui (Tue May 31 2005 - 14:02:46 CDT)
Re: AMBER: question about loadiing pdb file of a molecule complex gtg549i_at_mail.gatech.edu (Tue May 31 2005 - 14:12:39 CDT)
AMBER: meaningful tax for sander question Cordova, Luis E. (Tue May 31 2005 - 14:19:30 CDT)
Re: AMBER: meaningful tax for sander question David A. Case (Tue May 31 2005 - 14:59:20 CDT)
RE: AMBER: meaningful tax for sander question Ross Walker (Tue May 31 2005 - 14:55:14 CDT)
RE: AMBER: meaningful tax for sander question Cordova, Luis E. (Tue May 31 2005 - 15:03:59 CDT)
RE: AMBER: meaningful tax for sander question Ross Walker (Tue May 31 2005 - 15:12:10 CDT)
Re: AMBER: if setting ntf=4, will it cause someproblem? Li Su (Tue May 31 2005 - 16:07:25 CDT)
AMBER: double counting of potentials Stern, Julie (Tue May 31 2005 - 18:04:43 CDT)
RE: AMBER: double counting of potentials Ross Walker (Tue May 31 2005 - 18:21:43 CDT)
AMBER: Working with a nickel-organometallic compound Kara Di Giorgio (Tue May 31 2005 - 18:36:30 CDT)
AMBER: External Field in AMBER? junwang (Tue May 31 2005 - 21:19:38 CDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7) Shulin Zhuang (Tue May 31 2005 - 20:36:32 CDT)
Re: AMBER: density problem Shulin Zhuang (Tue May 31 2005 - 20:49:47 CDT)
Re: AMBER: Is the MD simulation normal JunJun Liu (Tue May 31 2005 - 21:01:07 CDT)
Re: AMBER: Is the MD simulation normal Bill Ross (Tue May 31 2005 - 22:41:42 CDT)
AMBER: problem in minimization Ananda Rama Krishnan Selvaraj (Wed Jun 01 2005 - 03:48:46 CDT)
AMBER: Saturated DNA bases L.C. Heady (Wed Jun 01 2005 - 03:55:54 CDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Wed Jun 01 2005 - 05:24:12 CDT)
RE: AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Wed Jun 01 2005 - 05:20:40 CDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7) Petr Kulhanek (Wed Jun 01 2005 - 06:03:21 CDT)
AMBER: eigenvalues in vector of ptraj Hwankyu Lee (Wed Jun 01 2005 - 07:53:51 CDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7) Guanglei Cui (Wed Jun 01 2005 - 09:18:37 CDT)
AMBER: stripwater Lukasz Bielecki (Wed Jun 01 2005 - 09:16:05 CDT)
Re: AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Wed Jun 01 2005 - 10:05:12 CDT)
RE: AMBER: density problem Ross Walker (Wed Jun 01 2005 - 11:21:33 CDT)
RE: RE: AMBER: Antechamber RESP failed for large organic molecule Junmei Wang (Wed Jun 01 2005 - 11:54:42 CDT)
RE: AMBER: problem in minimization Ross Walker (Wed Jun 01 2005 - 11:56:46 CDT)
Re: AMBER: mm/pbsa error Eric Hu (Wed Jun 01 2005 - 12:23:53 CDT)
Re: RE: RE: AMBER: Antechamber RESP failed for large organic molecule junwang (Wed Jun 01 2005 - 16:18:05 CDT)
AMBER: Build of AMBER for YDL ? Gert Kiss (Wed Jun 01 2005 - 18:15:57 CDT)
RE: AMBER: Build of AMBER for YDL ? Ross Walker (Wed Jun 01 2005 - 18:29:49 CDT)
Re: AMBER: MM-PBSA calculation Scott Pendley (Wed Jun 01 2005 - 18:44:05 CDT)
AMBER: gaff.dat typo Brent Krueger (Wed Jun 01 2005 - 20:35:58 CDT)
AMBER: amber question about leap du yongchun (Thu Jun 02 2005 - 00:12:12 CDT)
AMBER: amber8 installation problems Zhang Bing (Thu Jun 02 2005 - 01:44:47 CDT)
AMBER: amber8 installation problems Zhang Bing (Thu Jun 02 2005 - 01:55:48 CDT)
AMBER: question whem using leap du yongchun (Thu Jun 02 2005 - 02:25:16 CDT)
Re: RE: AMBER: problem in minimization Ananda Rama Krishnan Selvaraj (Thu Jun 02 2005 - 02:39:36 CDT)
RE:AMBER: density problem cristian obiol (Thu Jun 02 2005 - 03:14:21 CDT)
AMBER: Argon Box Biswaroop Mukherjee (Thu Jun 02 2005 - 03:44:46 CDT)
AMBER: center-of-mass distance restraints JAVIER PEREZ (Thu Jun 02 2005 - 06:14:15 CDT)
Re: AMBER: question whem using leap Carlos Simmerling (Thu Jun 02 2005 - 06:45:53 CDT)
AMBER: Simon Whitehead (Thu Jun 02 2005 - 07:44:03 CDT)
AMBER: Protein ions? Anthony Cruz (Thu Jun 02 2005 - 09:12:56 CDT)
Re: AMBER: Protein ions? Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu Jun 02 2005 - 09:57:02 CDT)
Re: AMBER: gaff.dat typo David A. Case (Thu Jun 02 2005 - 10:01:58 CDT)
Re: AMBER: amber question about leap David A. Case (Thu Jun 02 2005 - 10:05:12 CDT)
Re: AMBER: amber8 installation problems David A. Case (Thu Jun 02 2005 - 10:07:19 CDT)
Re: AMBER: Protein ions? David A. Case (Thu Jun 02 2005 - 10:25:07 CDT)
AMBER: How does Amber8 implemnet ntf=4? Li Su (Thu Jun 02 2005 - 10:32:30 CDT)
Re: AMBER: How does Amber8 implemnet ntf=4? Carlos Simmerling (Thu Jun 02 2005 - 10:53:36 CDT)
Re: AMBER: How does Amber8 implemnet ntf=4? David A. Case (Thu Jun 02 2005 - 10:52:10 CDT)
Re: AMBER: Protein ions? Anthony Cruz (Thu Jun 02 2005 - 11:45:34 CDT)
Re: AMBER: DNA base-flipping: TI vs PMF Peter Varnai (Thu Jun 02 2005 - 12:21:56 CDT)
AMBER: checkoverlap Gustavo Pierdominici Sottile (Thu Jun 02 2005 - 12:45:19 CDT)
AMBER: pressure output Germán Sciaini (Thu Jun 02 2005 - 17:27:13 CDT)
AMBER: advice needed for minimization and dynamic protocol chaiann ng (Thu Jun 02 2005 - 20:33:44 CDT)
AMBER: New problem of parallel sander Zhang Bing (Thu Jun 02 2005 - 21:46:13 CDT)
AMBER: TI in Amber8 ½¨Æ½ ºú (Fri Jun 03 2005 - 04:49:02 CDT)
Re: AMBER: New problem of parallel sander David A. Case (Fri Jun 03 2005 - 10:00:30 CDT)
Re: AMBER: TI in Amber8 David A. Case (Fri Jun 03 2005 - 10:04:45 CDT)
Re: AMBER: pressure output David A. Case (Fri Jun 03 2005 - 10:05:59 CDT)
RE: AMBER: Ross Walker (Fri Jun 03 2005 - 11:51:48 CDT)
RE: AMBER: New problem of parallel sander Ross Walker (Fri Jun 03 2005 - 11:53:55 CDT)
AMBER: Nmode with residues excluded Martin Sippel (Fri Jun 03 2005 - 11:56:42 CDT)
AMBER: Nmode calculations Martin Sippel (Fri Jun 03 2005 - 12:17:48 CDT)
AMBER: radius parameter for Mg2+ in mm_pbsa calculation Ye Mei (Sat Jun 04 2005 - 09:37:04 CDT)
Re: AMBER: radius parameter for Mg2+ in mm_pbsa calculation Guanglei Cui (Sat Jun 04 2005 - 10:17:11 CDT)
AMBER: SHAKE in md with partial solvation Ye Mei (Sun Jun 05 2005 - 02:30:00 CDT)
Re: AMBER: SHAKE in md with partial solvation Ye Mei (Sun Jun 05 2005 - 06:19:45 CDT)
AMBER: fail of minimization in sander wendy (Sun Jun 05 2005 - 22:01:25 CDT)
Re: AMBER: fail of minimization in sander Bill Ross (Sun Jun 05 2005 - 22:50:48 CDT)
Re: AMBER: fail of minimization in sander wendy (Sun Jun 05 2005 - 23:59:15 CDT)
Re: AMBER: radius parameter for Mg2+ in mm_pbsa calculation Thomas Steinbrecher (Mon Jun 06 2005 - 02:23:16 CDT)
AMBER: nmode with ibelly Martin Sippel (Mon Jun 06 2005 - 04:38:42 CDT)
Re: AMBER: fail of minimization in sander wendy (Mon Jun 06 2005 - 05:06:01 CDT)
Re: AMBER: SHAKE in md with partial solvation Germán Sciaini (Mon Jun 06 2005 - 05:34:09 CDT)
AMBER: Solvate question? Anthony Cruz (Mon Jun 06 2005 - 05:30:44 CDT)
AMBER: Re: Re: AMBER: SHAKE in md with partial solvation Ye Mei (Mon Jun 06 2005 - 05:49:44 CDT)
Re: AMBER: fail of minimization in sander Carlos Simmerling (Mon Jun 06 2005 - 06:24:25 CDT)
Re: AMBER: Solvate question? Carlos Simmerling (Mon Jun 06 2005 - 06:26:53 CDT)
AMBER: Compile question?? Anthony Cruz (Mon Jun 06 2005 - 06:59:13 CDT)
Re: AMBER: Compile question?? Robert Duke (Mon Jun 06 2005 - 07:38:02 CDT)
Re: AMBER: Compile question?? Anthony Cruz (Mon Jun 06 2005 - 08:24:40 CDT)
AMBER: Error: vlimit exceeded for step Hwankyu Lee (Mon Jun 06 2005 - 08:55:57 CDT)
Re: AMBER: Compile question?? Robert Duke (Mon Jun 06 2005 - 09:17:48 CDT)
Re: AMBER: Compile question?? Robert Duke (Mon Jun 06 2005 - 09:32:06 CDT)
Re: AMBER: fail of minimization in sander Bill Ross (Mon Jun 06 2005 - 09:34:39 CDT)
Re: AMBER: fail of minimization in sander wendy (Mon Jun 06 2005 - 10:57:08 CDT)
Re: AMBER: Solvate question? Anthony Cruz (Mon Jun 06 2005 - 10:59:06 CDT)
AMBER: Solvents Anthony Cruz (Mon Jun 06 2005 - 11:00:07 CDT)
Re: AMBER: fail of minimization in sander Carlos Simmerling (Mon Jun 06 2005 - 11:12:38 CDT)
Re: AMBER: Solvate question? Carlos Simmerling (Mon Jun 06 2005 - 11:13:37 CDT)
Re: AMBER: fail of minimization in sander wendy (Mon Jun 06 2005 - 11:13:10 CDT)
AMBER: GB/SA/LD parallel sander Lwin, ThuZar (Mon Jun 06 2005 - 11:48:27 CDT)
RE: AMBER: SHAKE in md with partial solvation Ross Walker (Mon Jun 06 2005 - 12:12:20 CDT)
RE: AMBER: Error: vlimit exceeded for step Ross Walker (Mon Jun 06 2005 - 12:19:04 CDT)
RE: AMBER: fail of minimization in sander Ross Walker (Mon Jun 06 2005 - 12:25:26 CDT)
Re: AMBER: fail of minimization in sander Bill Ross (Mon Jun 06 2005 - 12:58:54 CDT)
Re: AMBER: nmode with ibelly David A. Case (Mon Jun 06 2005 - 15:09:08 CDT)
AMBER: eelnb Stern, Julie (Mon Jun 06 2005 - 15:16:31 CDT)
AMBER: Protein dynamics. Laurence Lavelle (Mon Jun 06 2005 - 16:43:50 CDT)
AMBER: segmentation fault in sander Kenley Barrett (Mon Jun 06 2005 - 17:07:59 CDT)
Re: AMBER: segmentation fault in sander Bill Ross (Mon Jun 06 2005 - 17:18:45 CDT)
Re: AMBER: Protein dynamics. David A. Case (Mon Jun 06 2005 - 17:37:10 CDT)
Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee (Mon Jun 06 2005 - 17:47:29 CDT)
Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee (Mon Jun 06 2005 - 18:26:16 CDT)
RE: AMBER: Error: vlimit exceeded for step Ross Walker (Mon Jun 06 2005 - 18:24:21 CDT)
Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee (Mon Jun 06 2005 - 18:48:56 CDT)
Re: AMBER: Error: vlimit exceeded for step Bill Ross (Mon Jun 06 2005 - 19:03:38 CDT)
RE: AMBER: Error: vlimit exceeded for step Ross Walker (Mon Jun 06 2005 - 22:49:05 CDT)
Re: AMBER: nmode with ibelly Martin Sippel (Tue Jun 07 2005 - 05:11:44 CDT)
AMBER: Gibbs perturb DNA strands separate ivan_at_mmb.pcb.ub.es (Tue Jun 07 2005 - 06:16:41 CDT)
Re: AMBER: fail of minimization in sander Andy Purkiss (Tue Jun 07 2005 - 07:17:24 CDT)
Re: AMBER: Solvate question? Anthony Cruz (Tue Jun 07 2005 - 07:31:30 CDT)
AMBER: nucgen problem cbala_at_igib.res.in (Tue Jun 07 2005 - 08:41:27 CDT)
Re: RE: AMBER: SHAKE in md with partial solvation Ye Mei (Tue Jun 07 2005 - 08:46:49 CDT)
Re: AMBER: nucgen problem David A. Case (Tue Jun 07 2005 - 09:38:15 CDT)
Re: AMBER: nmode with ibelly David A. Case (Tue Jun 07 2005 - 09:41:41 CDT)
Re: AMBER: segmentation fault in sander Kenley Barrett (Tue Jun 07 2005 - 10:36:44 CDT)
AMBER: Question about tutorial-9 Varsha Goyal (Tue Jun 07 2005 - 11:27:57 CDT)
Re: AMBER: segmentation fault in sander Bill Ross (Tue Jun 07 2005 - 11:35:27 CDT)
Re: AMBER: nucgen problem Bill Ross (Tue Jun 07 2005 - 11:47:42 CDT)
AMBER: AMBER frcmod+off input vs. prep input K. Yarem (Tue Jun 07 2005 - 11:57:19 CDT)
Re: AMBER: quadrupole in resp David A. Case (Tue Jun 07 2005 - 12:30:12 CDT)
Re: AMBER: AMBER frcmod+off input vs. prep input Bill Ross (Tue Jun 07 2005 - 12:58:06 CDT)
Re: AMBER: nucgen problem cbala_at_igib.res.in (Tue Jun 07 2005 - 14:48:13 CDT)
Re: AMBER: nucgen problem Bill Ross (Tue Jun 07 2005 - 14:27:14 CDT)
Re: AMBER: nucgen problem Carlos Simmerling (Tue Jun 07 2005 - 14:34:17 CDT)
Re: AMBER: nucgen problem David A. Case (Tue Jun 07 2005 - 15:17:12 CDT)
AMBER: TI calculation using sander Latifa Douali (Tue Jun 07 2005 - 19:10:54 CDT)
Re: AMBER: TI calculation using sander David A. Case (Tue Jun 07 2005 - 20:32:34 CDT)
AMBER: How to run amber more efficiently? alice (Tue Jun 07 2005 - 21:59:26 CDT)
AMBER: Protein dynamics. Laurence Lavelle (Wed Jun 08 2005 - 00:52:00 CDT)
RE:AMBER: density problem cristian obiol (Wed Jun 08 2005 - 03:56:23 CDT)
AMBER: Sander is changing directories Andreas Kerzmann (Wed Jun 08 2005 - 04:37:58 CDT)
AMBER: Sander is changing directories Andreas Kerzmann (Wed Jun 08 2005 - 04:39:23 CDT)
AMBER: total energy leaps cristian obiol (Wed Jun 08 2005 - 05:44:18 CDT)
Re: AMBER: total energy leaps Carlos Simmerling (Wed Jun 08 2005 - 06:22:06 CDT)
AMBER: TI tutorial in Amber 8 huhu (Wed Jun 08 2005 - 04:52:24 CDT)
Re: AMBER: Protein dynamics. Yong Duan (Wed Jun 08 2005 - 12:24:02 CDT)
AMBER: (no subject) Mohammed Mayeed (Wed Jun 08 2005 - 12:26:15 CDT)
Re: AMBER: nmode with ibelly Martin Sippel (Wed Jun 08 2005 - 12:48:04 CDT)
AMBER: Protein-surface interaction Mohammed Mayeed (Wed Jun 08 2005 - 13:37:30 CDT)
AMBER: GB/SA/LD parallel sander Lwin, ThuZar (Wed Jun 08 2005 - 14:36:41 CDT)
Re: AMBER: GB/SA/LD parallel sander Carlos Simmerling (Wed Jun 08 2005 - 15:09:59 CDT)
AMBER: Compile Problems of Parallel Amber8 on Mac G5 Suxin Zheng (Wed Jun 08 2005 - 18:02:23 CDT)
Re: AMBER: nmode with ibelly David A. Case (Wed Jun 08 2005 - 23:30:01 CDT)
Re: AMBER: TI tutorial in Amber 8 David A. Case (Wed Jun 08 2005 - 23:27:42 CDT)
AMBER: precision switch from 64 to 32 bit (double from single precision) Cordova, Luis E. (Thu Jun 09 2005 - 00:39:59 CDT)
Re: AMBER: precision switch from 64 to 32 bit (double from single precision) Robert Duke (Thu Jun 09 2005 - 07:20:52 CDT)
AMBER: normal mode mm/pbsa interupted Eric Hu (Thu Jun 09 2005 - 13:46:04 CDT)
AMBER: setting up restraint with ntr option Lwin, ThuZar (Thu Jun 09 2005 - 16:49:04 CDT)
AMBER: transfer data from Linux to windows gtg549i_at_mail.gatech.edu (Thu Jun 09 2005 - 17:24:05 CDT)
Re: AMBER: transfer data from Linux to windows Lihua Wang (Thu Jun 09 2005 - 17:32:14 CDT)
Re: AMBER: transfer data from Linux to windows Carlos Simmerling (Thu Jun 09 2005 - 17:41:26 CDT)
Re: AMBER: transfer data from Linux to windows Thomas Patko (Thu Jun 09 2005 - 17:49:02 CDT)
Re: AMBER: transfer data from Linux to windows Fajar Rakhman Wibowo (Thu Jun 09 2005 - 18:11:33 CDT)
Re: AMBER: setting up restraint with ntr option Viktor Hornak (Thu Jun 09 2005 - 18:53:05 CDT)
AMBER: atom type for -CH=CH- Qizhi Cui (Thu Jun 09 2005 - 20:46:13 CDT)
AMBER: substitute missing residues? Wai Keat Yam (Fri Jun 10 2005 - 03:20:29 CDT)
AMBER: Vibrational spectrum? milion_at_c-box.cz (Fri Jun 10 2005 - 03:31:27 CDT)
AMBER: SOURCE3 in gaff.dat Stern, Julie (Fri Jun 10 2005 - 04:40:20 CDT)
Re: AMBER: Vibrational spectrum? [SOLUTION] Mark Williamson (Fri Jun 10 2005 - 05:33:51 CDT)
Re: AMBER: atom type for -CH=CH- Guanglei Cui (Fri Jun 10 2005 - 08:56:52 CDT)
AMBER: Make Distance restraints for non-standard residues gtg549i_at_mail.gatech.edu (Fri Jun 10 2005 - 10:47:41 CDT)
AMBER: vdw for terminal phosphate Rhoad, Jonathan S. (Fri Jun 10 2005 - 11:16:47 CDT)
Re: AMBER: vdw for terminal phosphate Bill Ross (Fri Jun 10 2005 - 13:10:32 CDT)
Re: AMBER: Make Distance restraints for non-standard residues David A. Case (Fri Jun 10 2005 - 14:59:13 CDT)
Re: AMBER: Make Distance restraints for non-standard residues gtg549i_at_mail.gatech.edu (Fri Jun 10 2005 - 15:45:00 CDT)
AMBER: Can constant pH be used for minimization? Kenley Barrett (Fri Jun 10 2005 - 16:34:41 CDT)
AMBER: inpcrd file Douali, Latifa (Fri Jun 10 2005 - 18:04:24 CDT)
Re: AMBER: Can constant pH be used for minimization? David A. Case (Sat Jun 11 2005 - 07:42:51 CDT)
AMBER: Installation problem Sukjoon Yoon (Sun Jun 12 2005 - 04:21:50 CDT)
Re: AMBER: Installation problem Chris Harrison (Sun Jun 12 2005 - 18:04:22 CDT)
AMBER: no corrected reaction field energy in *.out files after running mm_pbsa haixiao jin (Sun Jun 12 2005 - 21:04:40 CDT)
RE: AMBER: Installation problem Sukjoon Yoon (Sun Jun 12 2005 - 21:35:37 CDT)
AMBER: Installation problem Sukjoon Yoon (Sun Jun 12 2005 - 23:07:26 CDT)
AMBER: how to pull out frames Vijay Manickam Achari (Mon Jun 13 2005 - 00:23:51 CDT)
AMBER: leap issues on a powerbook justin litchfield (Sun Jun 12 2005 - 18:21:02 CDT)
Re: AMBER: how to pull out frames Husni Fattayer (Mon Jun 13 2005 - 06:22:40 CDT)
AMBER: Need help in charge fitting through RESP S.Sundar Raman (Mon Jun 13 2005 - 08:55:29 CDT)
Re: AMBER: Need help in charge fitting through RESP Shulin Zhuang (Mon Jun 13 2005 - 09:29:02 CDT)
Re: AMBER: Need help in charge fitting through RESP FyD (Mon Jun 13 2005 - 11:15:42 CDT)
Re: AMBER: Need help in charge fitting through RESP Nadine Homeyer (Mon Jun 13 2005 - 11:20:49 CDT)
RE: AMBER: vdw for terminal phosphate Rhoad, Jonathan S. (Mon Jun 13 2005 - 11:21:49 CDT)
Re: AMBER: Need help in charge fitting through RESP junwang (Mon Jun 13 2005 - 12:51:41 CDT)
Re: AMBER: Installation problem. . Don.Bashford_at_stjude.org (Mon Jun 13 2005 - 12:56:46 CDT)
AMBER: Announcing the LMOD website Istvan Kolossvary (Mon Jun 13 2005 - 13:18:52 CDT)
AMBER: GBSA and thermodynamic ensemble Osmar Norberto de Souza (Mon Jun 13 2005 - 13:29:18 CDT)
AMBER: atom type question opitz_at_che.udel.edu (Mon Jun 13 2005 - 14:41:30 CDT)
Re: AMBER: GBSA and thermodynamic ensemble Julien Michel (Mon Jun 13 2005 - 14:51:23 CDT)
Re: AMBER: atom type question David A. Case (Mon Jun 13 2005 - 15:05:44 CDT)
Re: AMBER: GBSA and thermodynamic ensemble David A. Case (Mon Jun 13 2005 - 15:13:14 CDT)
RE: AMBER: vdw for terminal phosphate Bill Ross (Mon Jun 13 2005 - 15:22:47 CDT)
Re: AMBER: atom type question opitz_at_che.udel.edu (Mon Jun 13 2005 - 15:46:18 CDT)
AMBER: why the dipeptide always moving out the virtual box Li Su (Mon Jun 13 2005 - 16:40:47 CDT)
Re: AMBER: why the dipeptide always moving out the virtual box David A. Case (Mon Jun 13 2005 - 17:55:19 CDT)
AMBER: Restrained-MD Ananda Rama Krishnan Selvaraj (Mon Jun 13 2005 - 18:04:14 CDT)
Re: AMBER: Restrained-MD David A. Case (Mon Jun 13 2005 - 18:10:00 CDT)
Re: AMBER: Installation problem Chris Harrison (Mon Jun 13 2005 - 19:33:13 CDT)
Re: AMBER: how to pull out frames Vijay Manickam Achari (Mon Jun 13 2005 - 23:04:42 CDT)
AMBER: nmropt =1 AND ntr=1 in pmemd Christoph Brockmann (Tue Jun 14 2005 - 04:33:39 CDT)
AMBER: compiler Zhang Bing (Tue Jun 14 2005 - 03:14:08 CDT)
AMBER: creating pdb file.... Vijay Manickam Achari (Tue Jun 14 2005 - 05:49:09 CDT)
AMBER: compiler Zhang Bing (Tue Jun 14 2005 - 06:13:19 CDT)
Re: AMBER: creating pdb file.... Angelo Pugliese (Tue Jun 14 2005 - 06:11:41 CDT)
Re: AMBER: nmropt =1 AND ntr=1 in pmemd Robert Duke (Tue Jun 14 2005 - 07:18:20 CDT)
AMBER: time and lifetime in hbond analysis (ptraj) Giulio Rastelli (Tue Jun 14 2005 - 09:23:50 CDT)
Re: AMBER: time and lifetime in hbond analysis (ptraj) Angelo Pugliese (Tue Jun 14 2005 - 09:57:56 CDT)
AMBER: Request for g98 (IOP...) Paramasivam Manikandan (Tue Jun 14 2005 - 10:04:30 CDT)
Re: AMBER: Request for g98 (IOP...) FyD (Tue Jun 14 2005 - 10:55:27 CDT)
Re: AMBER: Request for g98 (IOP...) Oliver Hucke (Tue Jun 14 2005 - 11:20:51 CDT)
AMBER: sp2 carbon atom parametrization Gustavo Pierdominici Sottile (Tue Jun 14 2005 - 11:30:16 CDT)
AMBER: Extended bonds-MD Ananda Rama Krishnan Selvaraj (Tue Jun 14 2005 - 11:29:29 CDT)
RE: AMBER: Extended bonds-MD Ross Walker (Tue Jun 14 2005 - 12:28:43 CDT)
RE: AMBER: compiler Ross Walker (Tue Jun 14 2005 - 12:43:58 CDT)
Re: AMBER: compiler David LeBard (Tue Jun 14 2005 - 12:45:27 CDT)
RE: AMBER: creating pdb file.... Ross Walker (Tue Jun 14 2005 - 12:51:21 CDT)
AMBER: Free Energy Calculation torsion missing mrbroad_at_ilstu.edu (Tue Jun 14 2005 - 13:21:54 CDT)
Re: AMBER: compiler David A. Case (Tue Jun 14 2005 - 13:40:16 CDT)
Re: AMBER: why the dipeptide always moving out the virtual box Li Su (Tue Jun 14 2005 - 16:11:41 CDT)
Re: AMBER: why the dipeptide always moving out the virtual box David A. Case (Tue Jun 14 2005 - 17:50:03 CDT)
Re: AMBER: Can constant pH be used for minimization? John Mongan (Tue Jun 14 2005 - 19:03:38 CDT)
AMBER: puzzling gaff parameter Oliver Hucke (Tue Jun 14 2005 - 20:16:35 CDT)
AMBER: Thanks Zhang Bing (Tue Jun 14 2005 - 21:26:23 CDT)
AMBER: solutions of amber installation problems Zhang Bing (Tue Jun 14 2005 - 21:42:13 CDT)
RE: AMBER: solutions of amber installation problems Ross Walker (Tue Jun 14 2005 - 23:55:20 CDT)
AMBER: Installation problem. . Sukjoon Yoon (Wed Jun 15 2005 - 01:08:51 CDT)
AMBER: Extended bonds-MD Ananda Rama Krishnan Selvaraj (Wed Jun 15 2005 - 02:02:25 CDT)
Re: AMBER: fail of minimization in sander wendy (Wed Jun 15 2005 - 02:54:59 CDT)
AMBER: bad atom type: H alice (Wed Jun 15 2005 - 05:53:50 CDT)
Re: AMBER: fail of minimization in sander Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Wed Jun 15 2005 - 06:05:25 CDT)
Re: AMBER: Extended bonds-MD Carlos Simmerling (Wed Jun 15 2005 - 06:22:29 CDT)
Re: AMBER: fail of minimization in sander Carlos Simmerling (Wed Jun 15 2005 - 06:24:04 CDT)
Re: AMBER: Installation problem. . Andreas Svrcek-Seiler (Wed Jun 15 2005 - 07:31:46 CDT)
Re: AMBER: Extended bonds-MD Ananda Rama Krishnan Selvaraj (Wed Jun 15 2005 - 07:55:41 CDT)
Re: AMBER: bad atom type: H David A. Case (Wed Jun 15 2005 - 10:09:17 CDT)
Re: AMBER: atom type question David A. Case (Wed Jun 15 2005 - 10:18:18 CDT)
AMBER: Question about "quasih" Yen-Ting Lai (Wed Jun 15 2005 - 11:46:22 CDT)
RE: AMBER: Installation problem. . Ross Walker (Wed Jun 15 2005 - 11:46:25 CDT)
Re: AMBER: Question about "quasih" David A. Case (Wed Jun 15 2005 - 12:43:47 CDT)
Re: AMBER: Question about "quasih" Yen-Ting Lai (Wed Jun 15 2005 - 14:25:57 CDT)
Re: AMBER: Question about "quasih" David A. Case (Wed Jun 15 2005 - 16:01:33 CDT)
AMBER: position of protonation info from constant pH run Kenley Barrett (Wed Jun 15 2005 - 20:27:44 CDT)
Re: Re: AMBER: bad atom type: H alice (Wed Jun 15 2005 - 20:35:00 CDT)
AMBER: Cut pdb files Yogesh Sabnis (Thu Jun 16 2005 - 02:57:18 CDT)
Re: AMBER: fail of minimization in sander wendy (Thu Jun 16 2005 - 03:19:15 CDT)
AMBER: adenine test for LMOD in amber8 Giulio Rastelli (Thu Jun 16 2005 - 04:57:16 CDT)
Re: AMBER: fail of minimization in sander Carlos Simmerling (Thu Jun 16 2005 - 06:06:42 CDT)
Re: AMBER: adenine test for LMOD in amber8 Istvan Kolossvary (Thu Jun 16 2005 - 08:16:22 CDT)
AMBER: How to modify force constants and equalibrium values for standard residues Li Su (Thu Jun 16 2005 - 08:30:41 CDT)
Re: AMBER: How to modify force constants and equalibrium values for standard residues David A. Case (Thu Jun 16 2005 - 09:41:18 CDT)
Re: AMBER: fail of minimization in sander David A. Case (Thu Jun 16 2005 - 09:44:21 CDT)
AMBER: Installation problem. . Sukjoon Yoon (Thu Jun 16 2005 - 09:49:19 CDT)
Re: AMBER: Installation problem. . Mark Williamson (Thu Jun 16 2005 - 10:06:57 CDT)
Re: AMBER: Installation problem. . Mark Williamson (Thu Jun 16 2005 - 10:15:58 CDT)
AMBER: Question about GAFF atom types Herbert Georg (Thu Jun 16 2005 - 14:18:50 CDT)
RE: AMBER: How to modify force constants and equalibrium values for standard residues Ross Walker (Thu Jun 16 2005 - 16:05:33 CDT)
AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians Li Su (Thu Jun 16 2005 - 16:19:36 CDT)
RE: AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians Ross Walker (Thu Jun 16 2005 - 17:00:41 CDT)
Re: AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians Li Su (Thu Jun 16 2005 - 18:17:46 CDT)
Re: AMBER: fail of minimization in sander wendy (Thu Jun 16 2005 - 21:43:11 CDT)
Re: AMBER: Installation problem. . Andreas Svrcek-Seiler (Thu Jun 16 2005 - 23:54:42 CDT)
AMBER: antechamber problems hj zou (Fri Jun 17 2005 - 08:32:27 CDT)
Re: AMBER: How to modify force constants and equalibrium values for standard residues gsciaini (Fri Jun 17 2005 - 08:41:44 CDT)
RE: AMBER: Installation problem. . Ross Walker (Fri Jun 17 2005 - 11:33:42 CDT)
RE: AMBER: Installation problem. . Andreas Svrcek-Seiler (Fri Jun 17 2005 - 12:12:10 CDT)
RE: AMBER: Installation problem - wrong address Andreas Svrcek-Seiler (Fri Jun 17 2005 - 12:28:43 CDT)
RE: AMBER: Installation problem. . Ross Walker (Fri Jun 17 2005 - 12:39:15 CDT)
AMBER: RE: AMBER :LINMIN problem Ross Walker (Fri Jun 17 2005 - 13:27:25 CDT)
Re: AMBER: nmropt =1 AND ntr=1 in pmemd Furse, Kristina Elisabet (Fri Jun 17 2005 - 14:16:13 CDT)
Re: AMBER: Question about GAFF atom types Herbert Georg (Fri Jun 17 2005 - 14:49:53 CDT)
Re: AMBER: Question about GAFF atom types Ilyas Yildirim (Fri Jun 17 2005 - 15:42:18 CDT)
Re: AMBER: nmropt =1 AND ntr=1 in pmemd Robert Duke (Fri Jun 17 2005 - 16:58:44 CDT)
Re: AMBER: Question about GAFF atom types Herbert Georg (Fri Jun 17 2005 - 17:31:52 CDT)
Re: AMBER: Question about GAFF atom types Ilyas Yildirim (Fri Jun 17 2005 - 20:29:24 CDT)
AMBER: nonbond_list question . caoch_at_cherry.bio.titech.ac.jp (Fri Jun 17 2005 - 20:38:27 CDT)
AMBER: Analysing my simulation data.. Vijay Manickam Achari (Sat Jun 18 2005 - 03:32:13 CDT)
Re: AMBER: Analysing my simulation data.. Varsha Goyal (Sat Jun 18 2005 - 11:21:28 CDT)
Re: AMBER: Analysing my simulation data.. Ilyas Yildirim (Sat Jun 18 2005 - 11:47:06 CDT)
Re: AMBER: nonbond_list question . Michael Crowley (Sat Jun 18 2005 - 14:51:01 CDT)
Re: AMBER: nonbond_list question . Robert Duke (Sat Jun 18 2005 - 22:03:07 CDT)
Re: AMBER: nonbond_list question . Petr Kulhanek (Sun Jun 19 2005 - 05:06:31 CDT)
AMBER: antechamber problems hj zou (Sun Jun 19 2005 - 08:50:08 CDT)
Re: AMBER: nonbond_list question . Robert Duke (Sun Jun 19 2005 - 09:25:37 CDT)
AMBER: average structure emilia wu (Sun Jun 19 2005 - 19:15:53 CDT)
RE: AMBER: average structure Ross Walker (Sun Jun 19 2005 - 19:41:07 CDT)
AMBER: How to set the virtual box size for a calculation run in vacuum Li Su (Mon Jun 20 2005 - 08:27:33 CDT)
RE: AMBER: antechamber problems Junmei Wang (Mon Jun 20 2005 - 11:35:12 CDT)
Re: AMBER: Question about GAFF atom types Herbert Georg (Mon Jun 20 2005 - 11:47:38 CDT)
RE: AMBER: runtime error in sander? Dave S Walker (Mon Jun 20 2005 - 13:02:16 CDT)
AMBER: How to turn off pme when using periodic box Li Su (Mon Jun 20 2005 - 13:31:09 CDT)
Re: AMBER: Question about GAFF atom types Ilyas Yildirim (Mon Jun 20 2005 - 14:51:59 CDT)
RE: AMBER: How to turn off pme when using periodic box Ross Walker (Mon Jun 20 2005 - 15:31:04 CDT)
Re: AMBER: antechamber problems Shulin Zhuang (Mon Jun 20 2005 - 20:07:56 CDT)
AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Mon Jun 20 2005 - 20:51:11 CDT)
AMBER: large std error in entropy estimation Ye Mei (Tue Jun 21 2005 - 21:51:43 CDT)
AMBER: PBSA error: PB bomb in pd_aaradi Xin Hu (Wed Jun 22 2005 - 09:34:13 CDT)
Re: AMBER: PBSA error: PB bomb in pd_aaradi JunJun Liu (Wed Jun 22 2005 - 10:17:43 CDT)
AMBER: a question about varying positions of dihedral restraints with step number Li Su (Wed Jun 22 2005 - 14:42:02 CDT)
AMBER: question about Carnal opitz_at_che.udel.edu (Wed Jun 22 2005 - 15:03:45 CDT)
Re: AMBER: question about Carnal Bill Ross (Wed Jun 22 2005 - 15:51:34 CDT)
AMBER: RE: tutorial 8 Ross Walker (Wed Jun 22 2005 - 16:15:33 CDT)
AMBER: software for real polymer MD simulation xhu1_at_memphis.edu (Wed Jun 22 2005 - 16:31:51 CDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends FyD (Wed Jun 22 2005 - 16:56:30 CDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Wed Jun 22 2005 - 17:13:19 CDT)
AMBER: how the phosphated threonine to be recognized in leap haixiao jin (Thu Jun 23 2005 - 04:03:26 CDT)
AMBER: Parameters for phosphorylated amino acids Nadine Homeyer (Thu Jun 23 2005 - 08:54:22 CDT)
AMBER: Parameters for phosphorylated amino acids Nadine Homeyer (Thu Jun 23 2005 - 09:24:08 CDT)
AMBER: Searching for NAD parameter files / Problems with parameter file creation Daniel Wetzler (Thu Jun 23 2005 - 09:43:29 CDT)
RE: AMBER: Searching for NAD parameter files / Problems with parameter file creation Rhoad, Jonathan S. (Thu Jun 23 2005 - 10:08:01 CDT)
RE: AMBER: Searching for NAD parameter files / Problems with parameter file creation Ross Walker (Thu Jun 23 2005 - 11:26:56 CDT)
AMBER: GCC for AMBER on 64 bit machine mfyang (Thu Jun 23 2005 - 12:55:01 CDT)
Re: AMBER: large std error in entropy estimation David A. Case (Thu Jun 23 2005 - 13:25:03 CDT)
Re: AMBER: GCC for AMBER on 64 bit machine Andreas Svrcek-Seiler (Thu Jun 23 2005 - 13:44:44 CDT)
Re: AMBER: Parameters for phosphorylated amino acids Suxin Zheng (Thu Jun 23 2005 - 17:41:30 CDT)
AMBER: using xmgrace.... Vijay Manickam Achari (Thu Jun 23 2005 - 21:51:37 CDT)
Re: AMBER: a question about varying positions of dihedral restraints with step number David A. Case (Fri Jun 24 2005 - 10:09:21 CDT)
AMBER: Have the parameters for dUMP been calculated by somebody? Suxin Zheng (Fri Jun 24 2005 - 20:30:12 CDT)
AMBER: TI-FEP for ALA --> GLY Jiten (Sat Jun 25 2005 - 00:07:03 CDT)
Re: AMBER: TI-FEP for ALA --> GLY Ilyas Yildirim (Sat Jun 25 2005 - 01:48:36 CDT)
Re: AMBER: TI-FEP for VAL --> ALA Jiten (Sat Jun 25 2005 - 11:13:44 CDT)
AMBER: RED question Kara Di Giorgio (Sat Jun 25 2005 - 17:44:23 CDT)
Re: AMBER: TI-FEP for VAL --> ALA Ilyas Yildirim (Sat Jun 25 2005 - 18:39:11 CDT)
AMBER: MM_PBSA ! Pradipta Bandyopadhyay (Sun Jun 26 2005 - 07:43:18 CDT)
Re: AMBER: MM_PBSA ! Jiten (Sun Jun 26 2005 - 19:43:13 CDT)
AMBER: Hbond analysis xueping (Sun Jun 26 2005 - 20:27:48 CDT)
Re: AMBER: TI-FEP for VAL --> ALA Jiten (Sun Jun 26 2005 - 21:11:03 CDT)
Re: AMBER: RED question FyD (Sun Jun 26 2005 - 22:37:59 CDT)
Re: AMBER: RED question Kara Di Giorgio (Mon Jun 27 2005 - 00:13:13 CDT)
AMBER: mm_pbsa script ! Pradipta Bandyopadhyay (Mon Jun 27 2005 - 01:43:53 CDT)
AMBER: Request for calculating free energy using AMBER6 S.Sundar Raman (Mon Jun 27 2005 - 06:59:00 CDT)
AMBER: parallel error Zhang Bing (Mon Jun 27 2005 - 07:36:14 CDT)
Re: AMBER: Hbond analysis Fabian Boes (Mon Jun 27 2005 - 08:12:34 CDT)
AMBER: INTRA molecular hbonds Giulio Rastelli (Mon Jun 27 2005 - 09:09:23 CDT)
Re: AMBER: INTRA molecular hbonds Fabian Boes (Mon Jun 27 2005 - 09:45:13 CDT)
AMBER: pb_pgb test fail acb15885_at_uprm.edu (Mon Jun 27 2005 - 13:17:48 CDT)
Re: AMBER: pb_pgb test fail David A. Case (Mon Jun 27 2005 - 13:48:32 CDT)
Re: AMBER: TI-FEP for VAL --> ALA Ilyas Yildirim (Mon Jun 27 2005 - 18:43:16 CDT)
Re: AMBER: TI-FEP for ALA --> GLY Jiten (Mon Jun 27 2005 - 21:24:56 CDT)
AMBER: script for calculating hydrogen bond Vijay Manickam Achari (Mon Jun 27 2005 - 21:57:30 CDT)
RE: AMBER: script for calculating hydrogen bond Ross Walker (Mon Jun 27 2005 - 22:04:43 CDT)
AMBER: questions about RNA xinhuang_at_indiana.edu (Mon Jun 27 2005 - 22:19:58 CDT)
Re: AMBER: TI-FEP for ALA --> GLY Ilyas Yildirim (Tue Jun 28 2005 - 00:46:17 CDT)
AMBER: calculating torsion angles Vijay Manickam Achari (Tue Jun 28 2005 - 03:59:02 CDT)
AMBER: dielectric constant Germán Sciaini (Wed Jun 29 2005 - 06:02:24 CDT)
AMBER: compiler error, SGI Octane Peter Gannett (Tue Jun 28 2005 - 07:54:35 CDT)
AMBER: amber 8 leap topology file dihedral term problem Angela Liu (Tue Jun 28 2005 - 08:59:57 CDT)
AMBER: Re: TI tutorial Jiten (Tue Jun 28 2005 - 09:17:39 CDT)
AMBER: Fw: TI tutorial --> ALA --> GLY TI calculation Jiten (Tue Jun 28 2005 - 10:02:42 CDT)
Re: AMBER: Re: TI tutorial David A. Case (Tue Jun 28 2005 - 10:49:53 CDT)
Re: AMBER: Re: TI tutorial Jiten (Tue Jun 28 2005 - 11:36:59 CDT)
Re: AMBER: dielectric constant David LeBard (Tue Jun 28 2005 - 15:01:30 CDT)
Re: AMBER: Re: TI tutorial David A. Case (Tue Jun 28 2005 - 20:09:44 CDT)
AMBER: calculating hydrogen bonds Vijay Manickam Achari (Tue Jun 28 2005 - 21:50:36 CDT)
Re: AMBER: Re: TI tutorial Jiten (Tue Jun 28 2005 - 22:46:17 CDT)
AMBER: How to read unformatted restart file in PTRAJ ? JunJun Liu (Wed Jun 29 2005 - 01:20:57 CDT)
Re: AMBER: Is the MD simulation normal Shulin Zhuang (Wed Jun 29 2005 - 05:11:53 CDT)
Re: AMBER: Re: TI tutorial David A. Case (Wed Jun 29 2005 - 09:30:31 CDT)
Re: [pgannett@hsc.wvu.edu: AMBER: compiler error, SGI Octane] Roberto Gomperts (Wed Jun 29 2005 - 10:01:00 CDT)
Re: AMBER: Is the MD simulation normal Shulin Zhuang (Wed Jun 29 2005 - 10:03:20 CDT)
RE: AMBER: Is the MD simulation normal Ross Walker (Wed Jun 29 2005 - 11:09:13 CDT)
Re: AMBER: Re: TI tutorial Jiten (Wed Jun 29 2005 - 11:22:04 CDT)
Re: AMBER: RED question FyD (Wed Jun 29 2005 - 11:34:16 CDT)
Re: AMBER: Re: TI tutorial David A. Case (Wed Jun 29 2005 - 12:01:23 CDT)
Re: AMBER: Re: TI tutorial Jiten (Wed Jun 29 2005 - 12:24:19 CDT)
AMBER: error - compiling antechamber Peter Gannett (Wed Jun 29 2005 - 14:30:20 CDT)
Re: AMBER: error - compiling antechamber Roberto Gomperts (Wed Jun 29 2005 - 16:11:41 CDT)
AMBER: Free energy calculation for protein-protein complex using MM_PBSA Zhiguo Liu (Wed Jun 29 2005 - 20:59:01 CDT)
AMBER: acceptor and donor in hbond calculation Vijay Manickam Achari (Thu Jun 30 2005 - 00:01:58 CDT)
AMBER: example script for hbond calculation Vijay Manickam Achari (Thu Jun 30 2005 - 01:27:15 CDT)
Re: AMBER: Free energy calculation for protein-protein complex using MM_PBSA Thomas Steinbrecher (Thu Jun 30 2005 - 02:14:01 CDT)
Re: Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA Zhiguo Liu (Thu Jun 30 2005 - 04:56:42 CDT)
Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA Martin Sippel (Thu Jun 30 2005 - 05:32:11 CDT)
Re: AMBER: Is the MD simulation normal Shulin Zhuang (Thu Jun 30 2005 - 10:00:11 CDT)
Re: AMBER: Is the MD simulation normal Shulin Zhuang (Thu Jun 30 2005 - 09:52:03 CDT)
AMBER: 10-12 potential and create atom type Fabien CAILLIEZ (Thu Jun 30 2005 - 12:19:41 CDT)
AMBER: antechamber error Peter Gannett (Thu Jun 30 2005 - 14:05:25 CDT)
Re: AMBER: antechamber error David A. Case (Thu Jun 30 2005 - 16:38:11 CDT)
AMBER: Create new Unit Douali, Latifa (Thu Jun 30 2005 - 18:45:37 CDT)
Re: AMBER: Create new Unit FyD (Thu Jun 30 2005 - 19:25:02 CDT)
Re: AMBER: Create new Unit David A. Case (Thu Jun 30 2005 - 20:38:42 CDT)
AMBER: least square fit of snapshots in md trajectory to a reference frame Ye Mei (Thu Jun 30 2005 - 21:56:08 CDT)
AMBER: question about spline in sander -- array size of eed_cub Cordova, Luis E. (Thu Jun 30 2005 - 23:33:25 CDT)
AMBER: question about leaprc.gaff and xxx.top Vijay Manickam Achari (Fri Jul 01 2005 - 00:52:15 CDT)
AMBER: how to make cluster files? Ananda Rama Krishnan Selvaraj (Fri Jul 01 2005 - 02:10:05 CDT)
AMBER: Stacking energy Angelo Pugliese (Fri Jul 01 2005 - 03:32:34 CDT)
Re: AMBER: Stacking energy ivan_at_mmb.pcb.ub.es (Fri Jul 01 2005 - 03:44:57 CDT)
AMBER: molecular dynamics simulation of protein containing Mg2+ cation Ye Mei (Fri Jul 01 2005 - 04:33:31 CDT)
Re: AMBER: Stacking energy Jiri Sponer (Fri Jul 01 2005 - 04:52:45 CDT)
AMBER: cavity volume Anthony Cruz (Fri Jul 01 2005 - 07:46:24 CDT)
Re: AMBER: Stacking energy Angelo Pugliese (Fri Jul 01 2005 - 05:42:28 CDT)
AMBER: Replica exchange Anthony Cruz (Fri Jul 01 2005 - 09:33:46 CDT)
AMBER: Temperature varible in MMPBSA script JunJun Liu (Fri Jul 01 2005 - 08:59:05 CDT)
Re: AMBER: Stacking energy Jiri Sponer (Fri Jul 01 2005 - 09:01:24 CDT)
Re: AMBER: Stacking energy Angelo Pugliese (Fri Jul 01 2005 - 09:38:37 CDT)
Re: AMBER: Stacking energy Jiri Sponer (Fri Jul 01 2005 - 10:00:03 CDT)
AMBER: please help us on partial charge calculation of PT complex using RESP peng79_at_email.unc.edu (Fri Jul 01 2005 - 10:10:31 CDT)
AMBER: questions about topology file Fabien CAILLIEZ (Fri Jul 01 2005 - 10:49:20 CDT)
Re: AMBER: least square fit of snapshots in md trajectory to a reference frame David A. Case (Fri Jul 01 2005 - 10:51:21 CDT)
Re: AMBER: parallel error Peter Varnai (Fri Jul 01 2005 - 10:51:18 CDT)
Re: AMBER: example script for hbond calculation Thomas E. Cheatham, III (Fri Jul 01 2005 - 11:10:07 CDT)
Re: AMBER: please help us on partial charge calculation of PT complex using RESP FyD (Fri Jul 01 2005 - 11:07:40 CDT)
Re: AMBER: questions about topology file David A. Case (Fri Jul 01 2005 - 15:24:02 CDT)
AMBER: (no subject) Varsha Goyal (Fri Jul 01 2005 - 16:46:55 CDT)
Re: AMBER: (no subject) S.Sundar Raman (Sat Jul 02 2005 - 07:58:59 CDT)
AMBER: loading DNA-RNA hybrid in xleap cbala_at_igib.res.in (Sat Jul 02 2005 - 10:36:59 CDT)
Re: AMBER: (no subject) Varsha Goyal (Sat Jul 02 2005 - 11:10:49 CDT)
Re: AMBER: loading DNA-RNA hybrid in xleap David A. Case (Sat Jul 02 2005 - 12:30:58 CDT)
AMBER: Question about Lennard-Jones Parameters in Topology file Linda Prengaman (Sat Jul 02 2005 - 13:15:51 CDT)
Re: AMBER: loading DNA-RNA hybrid in xleap cbala_at_igib.res.in (Sat Jul 02 2005 - 14:57:33 CDT)
Re: AMBER: loading DNA-RNA hybrid in xleap Ilyas Yildirim (Sun Jul 03 2005 - 06:23:56 CDT)
AMBER: MM-PBSA-big energies John (Sun Jul 03 2005 - 16:31:56 CDT)
Re: AMBER: MM-PBSA-big energies Carlos Simmerling (Sun Jul 03 2005 - 17:13:48 CDT)
Re: AMBER: molecular dynamics simulation of protein containing Mg2+ cation David A. Case (Sun Jul 03 2005 - 18:34:14 CDT)
AMBER: estimation of interface size Ye Mei (Sun Jul 03 2005 - 21:19:55 CDT)
AMBER: Problems with parameter lib and prep püarameter files Daniel Wetzler (Mon Jul 04 2005 - 04:14:56 CDT)
Re: AMBER: cavity volume Germán Sciaini (Mon Jul 04 2005 - 05:29:59 CDT)
Re: AMBER: Question about Lennard-Jones Parameters in Topology file Germán Sciaini (Mon Jul 04 2005 - 05:46:00 CDT)
Re: AMBER: estimation of interface size Carlos Simmerling (Mon Jul 04 2005 - 06:39:11 CDT)
AMBER: Loading a macmodel file complex Yogesh Sabnis (Mon Jul 04 2005 - 10:02:49 CDT)
AMBER: pmemd - bug report Petr Kulhanek (Mon Jul 04 2005 - 11:33:05 CDT)
Re: AMBER: pmemd - bug report Robert Duke (Mon Jul 04 2005 - 15:30:54 CDT)
Re: AMBER: pmemd - bug report Robert Duke (Mon Jul 04 2005 - 16:40:18 CDT)
Re: AMBER: pmemd - bug report Robert Duke (Mon Jul 04 2005 - 22:58:14 CDT)
Re: AMBER: pmemd - bug report Petr Kulhanek (Tue Jul 05 2005 - 05:31:14 CDT)
AMBER: nucgen and nukit dthomas_at_chem.uwa.edu.au (Tue Jul 05 2005 - 09:55:44 CDT)
RE: AMBER: Problems with parameter lib and prep püarameter files Ross Walker (Tue Jul 05 2005 - 10:47:22 CDT)
RE: AMBER: Loading a macmodel file complex Ross Walker (Tue Jul 05 2005 - 10:54:57 CDT)
Re: AMBER: pmemd - bug report Petr Kulhanek (Tue Jul 05 2005 - 11:29:54 CDT)
Re: AMBER: nucgen and nukit Bill Ross (Tue Jul 05 2005 - 11:33:04 CDT)
Re: AMBER: pmemd - bug report Robert Duke (Tue Jul 05 2005 - 11:47:19 CDT)
Re: AMBER: Question about Lennard-Jones Parameters in Topology file Linda Prengaman (Tue Jul 05 2005 - 12:40:44 CDT)
Re: AMBER: pmemd - bug report David A. Case (Tue Jul 05 2005 - 12:43:18 CDT)
Re: AMBER: pmemd - bug report David A. Case (Tue Jul 05 2005 - 12:38:09 CDT)
AMBER: restart file Harianto Tjong (Tue Jul 05 2005 - 13:49:20 CDT)
RE: AMBER: restart file Ross Walker (Tue Jul 05 2005 - 14:29:27 CDT)
Re: AMBER: restart file Carlos Simmerling (Tue Jul 05 2005 - 14:36:43 CDT)
Re: AMBER: restart file Harianto Tjong (Tue Jul 05 2005 - 15:49:16 CDT)
RE: AMBER: restart file Ross Walker (Tue Jul 05 2005 - 16:15:49 CDT)
Re: AMBER: restart file Carlos Simmerling (Tue Jul 05 2005 - 16:22:16 CDT)
Re: AMBER: 10-12 potential and create atom type David A. Case (Tue Jul 05 2005 - 17:03:09 CDT)
AMBER: Re: AMBER: Problems with parameter lib and prep püarameter files Daniel Wetzler (Wed Jul 06 2005 - 05:40:53 CDT)
AMBER: DNA strands separate ivan_at_mmb.pcb.ub.es (Wed Jul 06 2005 - 05:39:24 CDT)
Re: AMBER: DNA strands separate Angelo Pugliese (Wed Jul 06 2005 - 07:46:05 CDT)
Re: AMBER: DNA strands separate ivan_at_mmb.pcb.ub.es (Wed Jul 06 2005 - 08:40:18 CDT)
AMBER: how to average the structure along md trajectory Ye Mei (Wed Jul 06 2005 - 08:51:56 CDT)
Re: AMBER: DNA strands separate Angelo Pugliese (Wed Jul 06 2005 - 09:04:36 CDT)
Re: AMBER: DNA strands separate ivan_at_mmb.pcb.ub.es (Wed Jul 06 2005 - 09:39:04 CDT)
AMBER: AMBER on Mac OS X Varsha Goyal (Wed Jul 06 2005 - 09:55:12 CDT)
Re: AMBER: how to average the structure along md trajectory Angelo Pugliese (Wed Jul 06 2005 - 10:02:48 CDT)
Re: AMBER: DNA strands separate Angelo Pugliese (Wed Jul 06 2005 - 10:00:00 CDT)
Re: AMBER: AMBER on Mac OS X David A. Case (Wed Jul 06 2005 - 10:36:08 CDT)
AMBER: box size in explicit water Lwin, ThuZar (Wed Jul 06 2005 - 11:39:47 CDT)
Re: AMBER: AMBER on Mac OS X Kara Di Giorgio (Wed Jul 06 2005 - 11:46:11 CDT)
Re: AMBER: box size in explicit water Melinda Layten (Wed Jul 06 2005 - 11:52:55 CDT)
Re: AMBER: box size in explicit water David A. Case (Wed Jul 06 2005 - 12:30:59 CDT)
AMBER: sander problem Anthony Cruz (Wed Jul 06 2005 - 18:05:44 CDT)
RE: AMBER: sander problem Ross Walker (Wed Jul 06 2005 - 16:19:34 CDT)
AMBER: problem with addIons Lwin, ThuZar (Wed Jul 06 2005 - 16:41:25 CDT)
Re: AMBER: problem with addIons David LeBard (Wed Jul 06 2005 - 17:08:35 CDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Wed Jul 06 2005 - 17:24:45 CDT)
Re: AMBER: sander problem David A. Case (Wed Jul 06 2005 - 17:30:59 CDT)
Re: AMBER: problem with addIons David A. Case (Wed Jul 06 2005 - 17:41:21 CDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Wed Jul 06 2005 - 22:18:46 CDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Qing Zhang (Thu Jul 07 2005 - 03:30:14 CDT)
AMBER: question about sander minimization error drugdesign (Thu Jul 07 2005 - 03:37:51 CDT)
Re: AMBER: question about sander minimization error Ilyas Yildirim (Thu Jul 07 2005 - 03:59:13 CDT)
Re: AMBER: sander problem Anthony Cruz (Thu Jul 07 2005 - 10:25:29 CDT)
Re: AMBER: Replica Exchange Carlos Simmerling (Thu Jul 07 2005 - 08:43:17 CDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends FyD (Thu Jul 07 2005 - 10:54:00 CDT)
AMBER: tyrosyl charges Ozlem Demir (Thu Jul 07 2005 - 12:07:24 CDT)
AMBER: Release of R.E.D-II FyD (Thu Jul 07 2005 - 12:58:54 CDT)
AMBER: problems with bonds in sander Fabien CAILLIEZ (Thu Jul 07 2005 - 13:18:19 CDT)
AMBER: how is truncated octahedron box calculated Lwin, ThuZar (Thu Jul 07 2005 - 15:38:05 CDT)
Re: AMBER: how is truncated octahedron box calculated Chris Moth (Thu Jul 07 2005 - 16:50:24 CDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Thu Jul 07 2005 - 16:56:14 CDT)
Re: AMBER: tyrosyl charges Ilyas Yildirim (Thu Jul 07 2005 - 17:30:20 CDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Qing Zhang (Thu Jul 07 2005 - 19:48:40 CDT)
AMBER: building nucleic acids mathew k varghese (Thu Jul 07 2005 - 23:07:03 CDT)
AMBER: Problem with building AMBER7 on SUSE Linux 9.2 Daniel Wetzler (Fri Jul 08 2005 - 06:18:09 CDT)
Re: AMBER: building nucleic acids Bill Ross (Fri Jul 08 2005 - 14:05:15 CDT)
AMBER: LCPO SASA parameters for other elements when using gbsa=1 option David.Maxwell_at_di.mdacc.tmc.edu (Fri Jul 08 2005 - 15:10:00 CDT)
AMBER: infinite DNA Stern, Julie (Fri Jul 08 2005 - 16:44:25 CDT)
Re: AMBER: infinite DNA Carlos Simmerling (Fri Jul 08 2005 - 18:33:59 CDT)
AMBER: Water simulation David LeBard (Fri Jul 08 2005 - 18:44:12 CDT)
Re: AMBER: Water simulation David A. Case (Fri Jul 08 2005 - 19:13:37 CDT)
Re: AMBER: infinite DNA David A. Case (Fri Jul 08 2005 - 19:26:04 CDT)
Re: AMBER: building nucleic acids mathew k varghese (Sat Jul 09 2005 - 00:55:00 CDT)
AMBER: glc0358_at_vip.sina.com (Sat Jul 09 2005 - 01:22:45 CDT)
AMBER: simulation with Mg2+ ions and counter ions Ye Mei (Sat Jul 09 2005 - 01:54:16 CDT)
AMBER: glc0358_at_vip.sina.com (Sat Jul 09 2005 - 02:03:23 CDT)
Re: AMBER: simulation with Mg2+ ions and counter ions Lihua Wang (Sat Jul 09 2005 - 03:11:42 CDT)
Re: AMBER: Zhiguo Liu (Sat Jul 09 2005 - 03:39:43 CDT)
Re: AMBER: simulation with Mg2+ ions and counter ions Jiri Sponer (Sat Jul 09 2005 - 03:50:10 CDT)
RE: Re: AMBER: glc0358_at_vip.sina.com (Sat Jul 09 2005 - 05:37:54 CDT)
AMBER: Position Restraints! Karthikeyan Pasupathy (Sat Jul 09 2005 - 12:24:51 CDT)
AMBER: how to see the box lines Ananda Rama Krishnan Selvaraj (Sat Jul 09 2005 - 13:10:50 CDT)
RE: Re: AMBER: Shan Jufang (Sat Jul 09 2005 - 14:37:54 CDT)
Re: AMBER: Position Restraints! justin litchfield (Sat Jul 09 2005 - 19:08:15 CDT)
Re: AMBER: Water simulation David LeBard (Sat Jul 09 2005 - 19:30:55 CDT)
AMBER: molecular dynamics Vijay Manickam Achari (Sat Jul 09 2005 - 21:55:55 CDT)
RE: AMBER: molecular dynamics Ross Walker (Sat Jul 09 2005 - 22:42:06 CDT)
Re: AMBER: molecular dynamics course Ilan Samish (Sun Jul 10 2005 - 01:23:05 CDT)
Re: RE: Re: AMBER: Zhiguo Liu (Sun Jul 10 2005 - 02:37:36 CDT)
AMBER: Leap compilation issues justin litchfield (Sun Jul 10 2005 - 20:41:50 CDT)
Re: AMBER: Leap compilation issues Bill Ross (Sun Jul 10 2005 - 21:11:43 CDT)
Re: AMBER: building nucleic acids David A. Case (Sun Jul 10 2005 - 23:51:46 CDT)
Re: AMBER: Leap compilation issues David A. Case (Mon Jul 11 2005 - 00:13:04 CDT)
Re: AMBER: Leap compilation issues justin litchfield (Mon Jul 11 2005 - 01:49:33 CDT)
Re: AMBER: Leap compilation issues Andreas Svrcek-Seiler (Mon Jul 11 2005 - 05:43:39 CDT)
AMBER: Critical PMEMD 8 Bugfix Robert Duke (Mon Jul 11 2005 - 07:38:59 CDT)
AMBER: Question about "nmanal" Yen-Ting Lai (Mon Jul 11 2005 - 09:11:25 CDT)
AMBER: MM_PBSA help, please opitz_at_che.udel.edu (Mon Jul 11 2005 - 10:55:47 CDT)
Re: AMBER: Question about "nmanal" David A. Case (Mon Jul 11 2005 - 11:15:32 CDT)
RE: AMBER: Leap compilation issues Ross Walker (Mon Jul 11 2005 - 12:05:25 CDT)
Re: AMBER: MM_PBSA help, please Scott Pendley (Mon Jul 11 2005 - 13:30:34 CDT)
Re: AMBER: MM_PBSA help, please opitz_at_che.udel.edu (Mon Jul 11 2005 - 16:15:19 CDT)
Re: AMBER: MM_PBSA help, please Scott Pendley (Mon Jul 11 2005 - 16:37:50 CDT)
AMBER: Ptraj and order of operations Furse, Kristina Elisabet (Mon Jul 11 2005 - 19:26:09 CDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Mon Jul 11 2005 - 20:25:00 CDT)
Re: AMBER: Leap compilation issues justin litchfield (Mon Jul 11 2005 - 20:25:10 CDT)
Re: AMBER: Leap compilation issues Bill Ross (Mon Jul 11 2005 - 20:34:35 CDT)
Re: AMBER: Leap compilation issues justin litchfield (Mon Jul 11 2005 - 20:55:54 CDT)
AMBER: MD simulation on a protein solvated by a combination of some water models ? B $BIp;V (Mon Jul 11 2005 - 23:10:12 CDT)
AMBER: doubt on the value of Pressure on MD run Ananda Rama Krishnan Selvaraj (Tue Jul 12 2005 - 03:21:07 CDT)
AMBER: Anal - problems with energy analysis Yogesh Sabnis (Tue Jul 12 2005 - 03:33:30 CDT)
Re: AMBER: Problem with building AMBER7 on SUSE Linux 9.2 Daniel Wetzler (Tue Jul 12 2005 - 02:53:40 CDT)
Re: AMBER: Question about "nmanal" Yen-Ting Lai (Tue Jul 12 2005 - 05:09:24 CDT)
Re: AMBER: doubt on the value of Pressure on MD run Carlos Simmerling (Tue Jul 12 2005 - 06:07:08 CDT)
Re: AMBER: Question about "nmanal" Yen-Ting Lai (Tue Jul 12 2005 - 08:36:25 CDT)
AMBER: molsurf error in MM/PBSA calculation JunJun Liu (Tue Jul 12 2005 - 08:43:55 CDT)
Re: AMBER: MM_PBSA help, please opitz_at_che.udel.edu (Tue Jul 12 2005 - 09:19:05 CDT)
Re: AMBER: Question about "nmanal" David A. Case (Tue Jul 12 2005 - 11:29:46 CDT)
Re: AMBER: MM_PBSA help, please David A. Case (Tue Jul 12 2005 - 11:34:56 CDT)
RE: AMBER: Leap compilation issues Ross Walker (Tue Jul 12 2005 - 11:47:05 CDT)
RE: AMBER: MD simulation on a protein solvated by a combination of some water models ? Ross Walker (Tue Jul 12 2005 - 11:41:44 CDT)
Re: AMBER: MM_PBSA help, please opitz_at_che.udel.edu (Tue Jul 12 2005 - 12:29:19 CDT)
AMBER: TI - frcmod file Oliver Hucke (Tue Jul 12 2005 - 14:21:44 CDT)
Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Qing Zhang (Tue Jul 12 2005 - 14:59:01 CDT)
AMBER: question replica exchange acceptance ratio Zhuang (Tue Jul 12 2005 - 16:01:19 CDT)
Re: AMBER: question replica exchange acceptance ratio Carlos Simmerling (Tue Jul 12 2005 - 16:42:55 CDT)
Re: AMBER: MM_PBSA help, please Scott Pendley (Tue Jul 12 2005 - 16:57:08 CDT)
Re: AMBER: Anal - problems with energy analysis David A. Case (Tue Jul 12 2005 - 17:00:45 CDT)
Re: AMBER: molsurf error in MM/PBSA calculation David A. Case (Tue Jul 12 2005 - 17:03:23 CDT)
Re: AMBER: TI - frcmod file Ilyas Yildirim (Tue Jul 12 2005 - 17:06:53 CDT)
Re: AMBER: MM_PBSA help, please opitz_at_che.udel.edu (Tue Jul 12 2005 - 17:18:50 CDT)
AMBER: Comparison of AMBER against DL-POLY Devashish Kumar (Tue Jul 12 2005 - 17:32:03 CDT)
Re: AMBER: question replica exchange acceptance ratio Zhuang (Tue Jul 12 2005 - 17:39:47 CDT)
Re: AMBER: Ptraj and order of operations Scott Pendley (Tue Jul 12 2005 - 18:22:29 CDT)
Re: AMBER: question replica exchange acceptance ratio Carlos Simmerling (Tue Jul 12 2005 - 18:43:01 CDT)
Re: AMBER: TI - frcmod file Oliver Hucke (Tue Jul 12 2005 - 18:54:11 CDT)
Re: AMBER: Ptraj and order of operations Furse, Kristina Elisabet (Tue Jul 12 2005 - 20:07:04 CDT)
Re: AMBER: molsurf error in MM/PBSA calculation David A. Case (Tue Jul 12 2005 - 20:23:50 CDT)
Re: AMBER: Ptraj and order of operations Petr Kulhanek (Wed Jul 13 2005 - 02:21:48 CDT)
FW: AMBER: TI - frcmod file Douali, Latifa (Wed Jul 13 2005 - 10:38:25 CDT)
AMBER: Amber 8: create topology for solvent - PBC box size problem Angela Liu (Wed Jul 13 2005 - 13:41:04 CDT)
AMBER: Amber 8: heterogeneous multiple copy LES method Angela Liu (Wed Jul 13 2005 - 13:47:08 CDT)
Re: AMBER: Ptraj and order of operations Furse, Kristina Elisabet (Wed Jul 13 2005 - 13:55:02 CDT)
Re: AMBER: TI - frcmod file Ilyas Yildirim (Wed Jul 13 2005 - 15:42:49 CDT)
Re: FW: AMBER: TI - frcmod file Ilyas Yildirim (Wed Jul 13 2005 - 15:51:00 CDT)
RE: AMBER: TI - frcmod file Rhoad, Jonathan S. (Wed Jul 13 2005 - 16:03:17 CDT)
AMBER: pdb files from traj file YoungJin Cho (Wed Jul 13 2005 - 16:06:30 CDT)
Re: AMBER: TI - frcmod file David A. Case (Wed Jul 13 2005 - 16:10:56 CDT)
Re: AMBER: pdb files from traj file Carlos Simmerling (Wed Jul 13 2005 - 16:16:52 CDT)
Re: AMBER: TI - frcmod file Oliver Hucke (Wed Jul 13 2005 - 16:18:08 CDT)
RE: AMBER: pdb files from traj file Rhoad, Jonathan S. (Wed Jul 13 2005 - 16:22:56 CDT)
Re: AMBER: pdb files from traj file David LeBard (Wed Jul 13 2005 - 16:30:07 CDT)
Re: AMBER: TI - frcmod file Ilyas Yildirim (Wed Jul 13 2005 - 16:32:41 CDT)
RE: AMBER: pdb files from traj file Ross Walker (Wed Jul 13 2005 - 16:37:05 CDT)
AMBER: lib file for nonstandard residue Eric Hu (Wed Jul 13 2005 - 18:52:19 CDT)
AMBER: units of mwcovar matrix befor conversion Kateryna Miroshnychenko (Thu Jul 14 2005 - 03:18:28 CDT)
Re:AMBER: MD simulation on a protein solvated by a combination of some water mod B $BIp;V (Thu Jul 14 2005 - 04:56:39 CDT)
AMBER: Modeling of a radical L Jin (Thu Jul 14 2005 - 05:46:20 CDT)
AMBER: Apologies - LMOD website down Istvan Kolossvary (Thu Jul 14 2005 - 09:39:54 CDT)
AMBER: Leap question Kara Di Giorgio (Thu Jul 14 2005 - 10:10:12 CDT)
Re: AMBER: MD simulation on a protein solvated by a combination of some water mod David A. Case (Thu Jul 14 2005 - 10:29:20 CDT)
Re: AMBER: Leap question David A. Case (Thu Jul 14 2005 - 10:39:59 CDT)
Re: AMBER: Modeling of a radical David A. Case (Thu Jul 14 2005 - 10:48:54 CDT)
Re: AMBER: lib file for nonstandard residue Bill Ross (Thu Jul 14 2005 - 14:08:03 CDT)
Re: AMBER: lib file for nonstandard residue Bill Ross (Thu Jul 14 2005 - 14:37:01 CDT)
Re: AMBER: Amber 8: heterogeneous multiple copy LES method Carlos Simmerling (Thu Jul 14 2005 - 16:17:07 CDT)
Re: AMBER: lib file for nonstandard residue Eric Hu (Thu Jul 14 2005 - 17:02:35 CDT)
Re: AMBER: lib file for nonstandard residue Bill Ross (Thu Jul 14 2005 - 17:20:25 CDT)
Re: AMBER: lib file for nonstandard residue David A. Case (Thu Jul 14 2005 - 17:35:47 CDT)
RE: AMBER: molsurf error in MM/PBSA calculation Paul Beroza (Thu Jul 14 2005 - 18:01:08 CDT)
AMBER: Leap problem Kara Di Giorgio (Thu Jul 14 2005 - 19:06:50 CDT)
Re: AMBER: Leap problem Furse, Kristina Elisabet (Thu Jul 14 2005 - 19:31:40 CDT)
Re: AMBER: Leap problem Kara Di Giorgio (Thu Jul 14 2005 - 20:19:00 CDT)
Re: AMBER: Leap problem Oliver Hucke (Thu Jul 14 2005 - 20:48:52 CDT)
AMBER: Can GB and MS work correctly together in mmpbsa? zhli_2000_at_126.com (Thu Jul 14 2005 - 21:38:08 CDT)
Re: AMBER: Can GB and MS work correctly together in mmpbsa? Holger Gohlke (Fri Jul 15 2005 - 00:39:21 CDT)
Re: AMBER: Can GB and MS work correctly together in mmpbsa? zhli_2000_at_126.com (Fri Jul 15 2005 - 02:10:41 CDT)
AMBER: Energy decomposition parameters Angelo Pugliese (Fri Jul 15 2005 - 03:57:21 CDT)
Re: AMBER: Leap problem Kara Di Giorgio (Fri Jul 15 2005 - 08:59:47 CDT)
Re: AMBER: Amber 8: heterogeneous multiple copy LES method Angela Liu (Fri Jul 15 2005 - 09:16:23 CDT)
AMBER: P4 EM64T Intel Fortran Compile Problem Dawei Zhang (Fri Jul 15 2005 - 12:04:49 CDT)
RE: AMBER: P4 EM64T Intel Fortran Compile Problem Ross Walker (Fri Jul 15 2005 - 12:26:36 CDT)
Re: AMBER: Can GB and MS work correctly together in mmpbsa? Scott Pendley (Fri Jul 15 2005 - 12:46:46 CDT)
Re: AMBER: P4 EM64T Intel Fortran Compile Problem Andreas Svrcek-Seiler (Fri Jul 15 2005 - 12:49:47 CDT)
AMBER: Re: Problems with ptraj/rdparm Thomas E. Cheatham, III (Fri Jul 15 2005 - 14:22:28 CDT)
Re: AMBER: Can GB and MS work correctly together in mmpbsa? Scott Pendley (Fri Jul 15 2005 - 15:08:43 CDT)
Re: AMBER: P4 EM64T Intel Fortran Compile Problem Dawei Zhang (Fri Jul 15 2005 - 15:54:39 CDT)
AMBER: problem with protein ligand complex Claire Zerafa (Sat Jul 16 2005 - 11:31:56 CDT)
Re: AMBER: problem with protein ligand complex David A. Case (Sat Jul 16 2005 - 14:05:02 CDT)
AMBER: random-coil polymer Varsha Goyal (Sat Jul 16 2005 - 17:35:19 CDT)
Re: AMBER: Can GB and MS work correctly together in mmpbsa? zhli_2000_at_126.com (Sat Jul 16 2005 - 22:30:47 CDT)
AMBER: AMBER-process_mdout.perl Praveena Gopal (Mon Jul 18 2005 - 02:26:19 CDT)
Re: AMBER: AMBER-process_mdout.perl julien (Mon Jul 18 2005 - 02:48:01 CDT)
AMBER: PMF calculations with TI using the sander Vitor Manuel Sousa F?x (Mon Jul 18 2005 - 02:30:59 CDT)
Re: AMBER: AMBER-process_mdout.perl mathew k varghese (Mon Jul 18 2005 - 06:22:56 CDT)
AMBER: cap simulations questions Fabien CAILLIEZ (Mon Jul 18 2005 - 09:50:32 CDT)
RE: AMBER: AMBER-process_mdout.perl Ross Walker (Mon Jul 18 2005 - 10:24:18 CDT)
Re: AMBER: cap simulations questions David A. Case (Mon Jul 18 2005 - 11:01:34 CDT)
Re: AMBER: PMF calculations with TI using the sander David A. Case (Mon Jul 18 2005 - 11:03:47 CDT)
AMBER: segmentation fault in radial ptraj Kateryna Miroshnychenko (Mon Jul 18 2005 - 11:55:08 CDT)
Re: AMBER: Can GB and MS work correctly together in mmpbsa? Scott Pendley (Mon Jul 18 2005 - 12:31:29 CDT)
AMBER: Using Antechamber with Gamess and other molecular manipulations Charles Karney (Mon Jul 18 2005 - 12:28:20 CDT)
Re: AMBER: Can GB and MS work correctly together in mmpbsa? Alfonso Garcia-Sosa (Mon Jul 18 2005 - 14:16:21 CDT)
AMBER: Re: (ÈðÐÇÌáÊ¾-´ËÓÊ¼þ¿ÉÄÜÊÇÀ¬»øÓÊ¼þ)Re: AMBER: Can GB and MS work correctly together in mmpbsa? zhli_2000_at_126.com (Mon Jul 18 2005 - 20:23:39 CDT)
AMBER: comparing md trajectories ayongye_at_chem.uga.edu (Mon Jul 18 2005 - 20:12:15 CDT)
AMBER: Re: (ÈðÐÇÌáÊ¾-´ËÓÊ¼þ¿ÉÄÜÊÇÀ¬»øÓÊ¼þ)Re: AMBER: Can GB and MS work correctly together in mmpbsa? zhli_2000_at_126.com (Mon Jul 18 2005 - 20:09:23 CDT)
AMBER: pdb file and xleap Wai Keat Yam (Tue Jul 19 2005 - 05:06:50 CDT)
AMBER: mm_pbsa question Matthew Davies (Tue Jul 19 2005 - 05:07:51 CDT)
AMBER: Amber 7 Compiler Error Stephen P. Molnar, Ph.D. (Tue Jul 19 2005 - 07:26:14 CDT)
Re: AMBER: comparing md trajectories Carlos Simmerling (Tue Jul 19 2005 - 07:58:44 CDT)
RE: AMBER: Amber 7 Compiler Error Ross Walker (Tue Jul 19 2005 - 10:36:03 CDT)
RE: AMBER: pdb file and xleap Ross Walker (Tue Jul 19 2005 - 10:33:44 CDT)
AMBER: Compiling Amber7 wint Intel Fortran v8 Compiler Stephen P. Molnar, Ph.D. (Tue Jul 19 2005 - 15:14:30 CDT)
AMBER: Trouble with Amber8 Dustin (Tue Jul 19 2005 - 15:16:10 CDT)
RE: AMBER: Trouble with Amber8 Ross Walker (Tue Jul 19 2005 - 15:41:27 CDT)
AMBER: cap and ptraj Fabien CAILLIEZ (Tue Jul 19 2005 - 17:14:50 CDT)
AMBER: FW: Andrew Box (Tue Jul 19 2005 - 21:07:44 CDT)
Re: AMBER: FW: David A. Case (Tue Jul 19 2005 - 21:46:48 CDT)
Re: AMBER: Amber 7 Compiler Error Daniel Wetzler (Wed Jul 20 2005 - 04:38:25 CDT)
AMBER: P4 EM64T Intel Fortran Compile Problem Zhang Bing (Wed Jul 20 2005 - 21:24:20 CDT)
RE: AMBER: pdb file and xleap Wai Keat Yam (Thu Jul 21 2005 - 01:01:07 CDT)
AMBER: Atom type :Si Ananda Rama Krishnan Selvaraj (Thu Jul 21 2005 - 14:02:23 CDT)
AMBER: [OT] A nab programming question M. L. Dodson (Thu Jul 21 2005 - 15:07:09 CDT)
AMBER: Question about Prep file opitz_at_che.udel.edu (Thu Jul 21 2005 - 15:52:41 CDT)
AMBER: Carbonane Kara Di Giorgio (Thu Jul 21 2005 - 19:55:26 CDT)
AMBER: Error in MD mathew k varghese (Thu Jul 21 2005 - 22:53:08 CDT)
Re: AMBER: Error in MD Guanglei Cui (Thu Jul 21 2005 - 23:08:56 CDT)
Re: AMBER: Question about Prep file Marc Baaden (Fri Jul 22 2005 - 01:38:42 CDT)
AMBER: Lipid bilayer parameters nag raj (Fri Jul 22 2005 - 02:18:24 CDT)
AMBER: An atom name with 4 characters is not compatible with Leap ? Arnoult, Eric [PRDFR] (Fri Jul 22 2005 - 02:53:24 CDT)
Re: AMBER: An atom name with 4 characters is not compatible with Leap ? ivan_at_mmb.pcb.ub.es (Fri Jul 22 2005 - 03:16:52 CDT)
Re: AMBER: Atom type :Si Stefano.Pieraccini_at_unimi.it (Fri Jul 22 2005 - 03:37:50 CDT)
AMBER: problem with xleap Alessio Coi (Fri Jul 22 2005 - 08:47:23 CDT)
AMBER: SHAKE error Agata Jurkiewicz (Fri Jul 22 2005 - 09:09:34 CDT)
Re: AMBER: SHAKE error Carlos Simmerling (Fri Jul 22 2005 - 09:56:53 CDT)
Re: AMBER: An atom name with 4 characters is not compatible with Leap ? Tim Meyer (Fri Jul 22 2005 - 10:06:52 CDT)
Re: AMBER: problem with xleap David A. Case (Fri Jul 22 2005 - 10:59:24 CDT)
Re: AMBER: SHAKE error David A. Case (Fri Jul 22 2005 - 11:04:15 CDT)
Re: AMBER: SHAKE error Agata Jurkiewicz (Fri Jul 22 2005 - 12:01:16 CDT)
Re: AMBER: An atom name with 4 characters is not compatible with Leap ? David A. Case (Fri Jul 22 2005 - 12:27:31 CDT)
Re: AMBER: SHAKE error Carlos Simmerling (Fri Jul 22 2005 - 12:24:46 CDT)
Re: AMBER: An atom name with 4 characters is not compatible with Leap ? David A. Case (Fri Jul 22 2005 - 12:24:58 CDT)
Re: AMBER: a bimolecular reaction Yong Duan (Fri Jul 22 2005 - 12:44:23 CDT)
Re: AMBER: Question about Prep file David A. Case (Fri Jul 22 2005 - 13:34:57 CDT)
Re: AMBER: SHAKE error Agata Jurkiewicz (Fri Jul 22 2005 - 14:12:10 CDT)
Re: AMBER: Question about Prep file opitz_at_che.udel.edu (Fri Jul 22 2005 - 14:21:20 CDT)
Re: AMBER: SHAKE error Ilyas Yildirim (Fri Jul 22 2005 - 14:23:06 CDT)
RE: AMBER: a bimolecular reaction Yong Duan (Fri Jul 22 2005 - 14:25:09 CDT)
Re: AMBER: SHAKE error Carlos Simmerling (Fri Jul 22 2005 - 14:26:36 CDT)
Re: AMBER: Atom type :Si Ananda Rama Krishnan Selvaraj (Fri Jul 22 2005 - 14:45:30 CDT)
Re: AMBER: SHAKE error David A. Case (Fri Jul 22 2005 - 15:46:42 CDT)
Re: AMBER: SHAKE error Agata Jurkiewicz (Fri Jul 22 2005 - 17:06:49 CDT)
AMBER: nucgen bdna types Stern, Julie (Fri Jul 22 2005 - 20:01:20 CDT)
AMBER: mmpbsa test problem Suxin Zheng (Fri Jul 22 2005 - 20:41:11 CDT)
AMBER: Lipid bilayer parameters and charmm force field parameters nag raj (Fri Jul 22 2005 - 22:15:35 CDT)
Re: AMBER: Modeling of a radical Peter Gannett (Sat Jul 23 2005 - 09:21:25 CDT)
Re: AMBER: nucgen bdna types David A. Case (Sun Jul 24 2005 - 18:42:44 CDT)
AMBER: Adding residues to a DNA sequence Kara Di Giorgio (Sun Jul 24 2005 - 20:50:45 CDT)
AMBER: fit Yong Xu (Mon Jul 25 2005 - 04:04:57 CDT)
Re: AMBER: fit Kateryna Miroshnychenko (Mon Jul 25 2005 - 05:11:11 CDT)
AMBER: NTWPRY problem wenfei Li (Mon Jul 25 2005 - 10:44:31 CDT)
AMBER: ptraj-acceptor mask format Peter Gannett (Mon Jul 25 2005 - 14:10:47 CDT)
AMBER: antechamber Dustin (Mon Jul 25 2005 - 15:30:40 CDT)
Re: AMBER: [OT] A nab programming question David A. Case (Mon Jul 25 2005 - 16:35:49 CDT)
Re: AMBER: Adding residues to a DNA sequence David A. Case (Mon Jul 25 2005 - 16:39:23 CDT)
Re: AMBER: antechamber David A. Case (Mon Jul 25 2005 - 18:42:32 CDT)
Re: AMBER: NTWPRY problem David A. Case (Mon Jul 25 2005 - 18:54:25 CDT)
Re: AMBER: SHAKE error David A. Case (Mon Jul 25 2005 - 18:57:02 CDT)
Re: AMBER: NTWPRY problem wenfei Li (Mon Jul 25 2005 - 20:39:21 CDT)
Re: AMBER: NTWPRY problem wenfei Li (Mon Jul 25 2005 - 20:42:16 CDT)
Re: AMBER: NTWPRY problem wenfei Li (Mon Jul 25 2005 - 20:51:09 CDT)
AMBER: nucgen H5T H3T Stern, Julie (Mon Jul 25 2005 - 20:55:52 CDT)
Re: AMBER: Adding residues to a DNA sequence Kara Di Giorgio (Mon Jul 25 2005 - 21:20:53 CDT)
AMBER: potential of mean force calculation along reaction coordinates Ye Mei (Tue Jul 26 2005 - 02:04:00 CDT)
AMBER: Lipid parameters nag raj (Tue Jul 26 2005 - 05:55:22 CDT)
AMBER: Periodic box imaging using ptraj Grzegorz Jezierski (Tue Jul 26 2005 - 08:25:53 CDT)
Re: AMBER: [OT] A nab programming question M. L. Dodson (Tue Jul 26 2005 - 09:32:47 CDT)
Re: AMBER: nucgen H5T H3T David A. Case (Tue Jul 26 2005 - 09:54:32 CDT)
AMBER: why not minimize snapshots before MM/PBSA calculations JunJun Liu (Tue Jul 26 2005 - 10:02:00 CDT)
RE: AMBER: Tutoial 8 (Case Study) Ross Walker (Tue Jul 26 2005 - 12:03:37 CDT)
AMBER: Thermodynamic Integration for conformational changes? Grzegorz Jezierski (Tue Jul 26 2005 - 12:33:00 CDT)
Re: AMBER: Thermodynamic Integration for conformational changes? Carlos Simmerling (Tue Jul 26 2005 - 13:02:57 CDT)
Re: AMBER: Thermodynamic Integration for conformational changes? David A. Case (Tue Jul 26 2005 - 13:42:54 CDT)
Re: AMBER: ptraj-acceptor mask format Thomas E. Cheatham, III (Tue Jul 26 2005 - 15:06:08 CDT)
Re: AMBER: Periodic box imaging using ptraj Thomas E. Cheatham, III (Tue Jul 26 2005 - 15:11:39 CDT)
AMBER: new residue Douali, Latifa (Tue Jul 26 2005 - 19:50:51 CDT)
Re: AMBER: new residue Furse, Kristina Elisabet (Tue Jul 26 2005 - 20:40:51 CDT)
RE: AMBER: why not minimize snapshots before MM/PBSA calculations Arnoult, Eric [PRDFR] (Wed Jul 27 2005 - 02:21:30 CDT)
RE: AMBER: An atom name with 4 characters is not compatible with Leap ? Arnoult, Eric [PRDFR] (Wed Jul 27 2005 - 02:20:27 CDT)
AMBER: cutoff in ANAL Madjid Taghdir (Wed Jul 27 2005 - 03:06:54 CDT)
AMBER: prepi format and question about it Ilyas Yildirim (Wed Jul 27 2005 - 04:20:00 CDT)
Re: AMBER: Periodic box imaging using ptraj Grzegorz Jezierski (Wed Jul 27 2005 - 04:27:24 CDT)
Re: AMBER: Periodic box imaging using ptraj Grzegorz Jezierski (Wed Jul 27 2005 - 06:28:29 CDT)
AMBER: Protein residue numbering Sukjoon Yoon (Wed Jul 27 2005 - 06:52:42 CDT)
Re: Re: AMBER: how to reduce box size and delete excess solvent hj zou (Wed Jul 27 2005 - 08:36:40 CDT)
Re: AMBER: prepi format and question about it David A. Case (Wed Jul 27 2005 - 09:57:30 CDT)
Re: AMBER: An atom name with 4 characters is not compatible with Leap ? David A. Case (Wed Jul 27 2005 - 10:08:11 CDT)
AMBER: [FWD] water minimalization problems blakrose_at_gazeta.pl (Wed Jul 27 2005 - 10:46:47 CDT)
RE: AMBER: An atom name with 4 characters is not compatible with Leap ? Arnoult, Eric [PRDFR] (Wed Jul 27 2005 - 10:59:43 CDT)
RE: AMBER: new residue Douali, Latifa (Wed Jul 27 2005 - 11:09:01 CDT)
RE: AMBER: Periodic box imaging using ptraj Ross Walker (Wed Jul 27 2005 - 11:28:05 CDT)
RE: AMBER: new residue Ross Walker (Wed Jul 27 2005 - 11:54:14 CDT)
AMBER: How to insert a protein in lipid bilayer nag raj (Wed Jul 27 2005 - 11:56:07 CDT)
Re: AMBER: new residue David A. Case (Wed Jul 27 2005 - 12:20:42 CDT)
Re: AMBER: An atom name with 4 characters is not compatible with Leap ? David A. Case (Wed Jul 27 2005 - 12:39:08 CDT)
AMBER: pbsa problem Suxin Zheng (Wed Jul 27 2005 - 14:47:29 CDT)
RE: AMBER: new residue Douali, Latifa (Wed Jul 27 2005 - 15:45:17 CDT)
Re: AMBER: ptraj-acceptor mask format Peter Gannett (Wed Jul 27 2005 - 15:54:50 CDT)
AMBER: convert_trajectory Wei Chen (Wed Jul 27 2005 - 15:58:36 CDT)
Re: AMBER: new residue David A. Case (Wed Jul 27 2005 - 16:13:32 CDT)
Re: AMBER: Adding residues to a DNA sequence David A. Case (Wed Jul 27 2005 - 16:31:16 CDT)
Re: AMBER: convert_trajectory Thomas E. Cheatham, III (Wed Jul 27 2005 - 16:27:57 CDT)
RE: AMBER: new residue Douali, Latifa (Wed Jul 27 2005 - 16:36:27 CDT)
Re: AMBER: convert_trajectory Wei Chen (Wed Jul 27 2005 - 18:07:55 CDT)
Re: AMBER: convert_trajectory Thomas E. Cheatham, III (Wed Jul 27 2005 - 18:45:34 CDT)
Re: AMBER: How to insert a protein in lipid bilayer Yong Xu (Wed Jul 27 2005 - 20:47:22 CDT)
Re: AMBER: convert_trajectory Wei Chen (Wed Jul 27 2005 - 21:06:28 CDT)
AMBER: Minimized structure Yam (Wed Jul 27 2005 - 22:02:03 CDT)
AMBER: nucgen error (U not generated) mathew k varghese (Wed Jul 27 2005 - 22:28:51 CDT)
Re: AMBER: Minimized structure Thomas E. Cheatham, III (Wed Jul 27 2005 - 22:47:28 CDT)
Re: AMBER: nucgen error (U not generated) Thomas E. Cheatham, III (Wed Jul 27 2005 - 22:49:33 CDT)
Re: AMBER: prepi format and question about it Ilyas Yildirim (Thu Jul 28 2005 - 00:10:36 CDT)
RE: Re: AMBER: Minimized structure Linchen Gong (Thu Jul 28 2005 - 01:55:05 CDT)
Re: AMBER: Minimized structure Carlos Simmerling (Thu Jul 28 2005 - 05:53:45 CDT)
Re: AMBER: Minimized structure Vitor Manuel Sousa F?x (Thu Jul 28 2005 - 06:07:09 CDT)
AMBER: dihedral term in prmtop file Ye Mei (Thu Jul 28 2005 - 09:38:55 CDT)
AMBER: Division by zero in sander Caleb S Howe (cshowe_at_Princeton.EDU) (Thu Jul 28 2005 - 09:57:00 CDT)
Re: AMBER: dihedral term in prmtop file Carlos Simmerling (Thu Jul 28 2005 - 09:59:36 CDT)
AMBER: Fatal Error on loading a pdb in xLeap Kara Di Giorgio (Thu Jul 28 2005 - 10:10:45 CDT)
Re: AMBER: cutoff in ANAL David A. Case (Thu Jul 28 2005 - 11:26:40 CDT)
Re: AMBER: Fatal Error on loading a pdb in xLeap David A. Case (Thu Jul 28 2005 - 17:17:14 CDT)
Re: AMBER: Minimized structure Yam (Thu Jul 28 2005 - 21:25:29 CDT)
Re: AMBER: Minimized structure Thomas E. Cheatham, III (Thu Jul 28 2005 - 22:09:55 CDT)
Re: AMBER: Fatal Error on loading a pdb in xLeap Ilyas Yildirim (Thu Jul 28 2005 - 22:56:32 CDT)
Re: AMBER: Minimized structure Yam (Thu Jul 28 2005 - 23:03:40 CDT)
AMBER: ambpdb core dump Peter Gannett (Fri Jul 29 2005 - 06:27:46 CDT)
Re: AMBER: ambpdb core dump David A. Case (Fri Jul 29 2005 - 09:40:03 CDT)
Re: AMBER: ambpdb core dump David A. Case (Fri Jul 29 2005 - 09:56:42 CDT)
AMBER: ptraj output missing opitz_at_che.udel.edu (Fri Jul 29 2005 - 10:05:19 CDT)
Re: AMBER: Adding residues to a DNA sequence Kara Di Giorgio (Fri Jul 29 2005 - 11:39:43 CDT)
AMBER: temperature keep increasing in high temp. Hwankyu Lee (Fri Jul 29 2005 - 16:27:04 CDT)
AMBER: mm_pbsa Wei Chen (Fri Jul 29 2005 - 19:10:46 CDT)
Re: AMBER: temperature keep increasing in high temp. Carlos Simmerling (Fri Jul 29 2005 - 19:28:42 CDT)
Re: AMBER: mm_pbsa Suxin Zheng (Fri Jul 29 2005 - 19:39:15 CDT)
Re: AMBER: mm_pbsa Wei Chen (Fri Jul 29 2005 - 19:55:07 CDT)
Re: AMBER: mm_pbsa JunJun Liu (Fri Jul 29 2005 - 19:58:53 CDT)
Re: AMBER: mm_pbsa Wei Chen (Fri Jul 29 2005 - 20:09:13 CDT)
Re: AMBER: mm_pbsa JunJun Liu (Fri Jul 29 2005 - 21:22:20 CDT)
AMBER: Failed sander runs for large systems Pratul K. Agarwal (Fri Jul 29 2005 - 21:41:44 CDT)
RE: AMBER: temperature keep increasing in high temp. Yong Duan (Fri Jul 29 2005 - 22:43:52 CDT)
Re: AMBER: mm_pbsa Wei Chen (Fri Jul 29 2005 - 22:53:36 CDT)
Re: AMBER: Failed sander runs for large systems Guanglei Cui (Fri Jul 29 2005 - 23:33:27 CDT)
AMBER: RESTARTED DUE TO LINMIN FAILURE Sukjoon Yoon (Sat Jul 30 2005 - 01:00:24 CDT)
Re: AMBER: RESTARTED DUE TO LINMIN FAILURE David A. Case (Sat Jul 30 2005 - 11:59:19 CDT)
AMBER: Amber parameters for ADP zgleo (Sat Jul 30 2005 - 00:22:19 CDT)
Re: AMBER: Failed sander runs for large systems David A. Case (Sat Jul 30 2005 - 11:57:14 CDT)
Re: AMBER: Amber parameters for ADP David A. Case (Sat Jul 30 2005 - 12:08:08 CDT)
Re: Re: AMBER: mm_pbsa zgleo (Sun Jul 31 2005 - 10:26:02 CDT)
AMBER: questions about MG ions JIANING WANG (Sun Jul 31 2005 - 18:12:36 CDT)
AMBER: AMBER8 crashes machine(nodes) under IBM compiler, Suse Linux, amd IBM loadleveler Soo (Sun Jul 31 2005 - 21:45:01 CDT)
Re: AMBER: questions about MG ions Kara Di Giorgio (Sun Jul 31 2005 - 23:55:46 CDT)
AMBER: coordinated water molecules deleted when addions Ye Mei (Mon Aug 01 2005 - 04:20:11 CDT)
Re: AMBER: coordinated water molecules deleted when addions David A. Case (Mon Aug 01 2005 - 08:39:39 CDT)
Re: AMBER: Modeling of a radical L Jin (Mon Aug 01 2005 - 08:50:55 CDT)
Re: AMBER: questions about MG ions JIANING WANG (Mon Aug 01 2005 - 09:27:45 CDT)
AMBER: ptraj help, how to enable disabled ptraj routine? opitz_at_che.udel.edu (Mon Aug 01 2005 - 10:19:20 CDT)
RE: AMBER: coordinated water molecules deleted when addions Ross Walker (Mon Aug 01 2005 - 12:09:17 CDT)
Re: AMBER: ptraj help, how to enable disabled ptraj routine? Thomas E. Cheatham, III (Mon Aug 01 2005 - 15:51:27 CDT)
AMBER: antechamber problem using RESP luckyang_at_gmail.com (Mon Aug 01 2005 - 20:29:26 CDT)
AMBER: AMBER8 limitation of memory in QM/MM calculation nadtanet nunthaboot (Mon Aug 01 2005 - 21:21:59 CDT)
RE: AMBER: AMBER8 limitation of memory in QM/MM calculation Ross Walker (Mon Aug 01 2005 - 21:52:29 CDT)
RE: AMBER: AMBER8 limitation of memory in QM/MM calculation Ross Walker (Mon Aug 01 2005 - 21:52:32 CDT)
AMBER: memory_mm_pbsa Wei Chen (Mon Aug 01 2005 - 22:00:34 CDT)
RE: AMBER: memory_mm_pbsa Ross Walker (Mon Aug 01 2005 - 22:14:47 CDT)
RE: AMBER: memory_mm_pbsa Wei Chen (Mon Aug 01 2005 - 23:03:34 CDT)
AMBER: strange minimalization output blakrose_at_gazeta.pl (Tue Aug 02 2005 - 09:56:38 CDT)
RE: AMBER: strange minimalization output Ross Walker (Tue Aug 02 2005 - 10:47:59 CDT)
AMBER: Leap set head/tail question Kara Di Giorgio (Tue Aug 02 2005 - 13:01:08 CDT)
RE: AMBER: Leap set head/tail question Rhoad, Jonathan S. (Tue Aug 02 2005 - 13:10:42 CDT)
RE: AMBER: Leap set head/tail question Ross Walker (Tue Aug 02 2005 - 13:28:03 CDT)
AMBER: Boron and Amber Kara Di Giorgio (Tue Aug 02 2005 - 15:18:46 CDT)
AMBER: bond breaking/ energetic ion vannajan_at_chiangmai.ac.th (Tue Aug 02 2005 - 21:11:16 CDT)
RE: AMBER: bond breaking/ energetic ion Ross Walker (Tue Aug 02 2005 - 21:26:02 CDT)
AMBER: power supply crash==>boot problems Kristof Stevens (Wed Aug 03 2005 - 03:20:08 CDT)
AMBER: bond parameters Gustavo Pierdominici Sottile (Wed Aug 03 2005 - 09:39:34 CDT)
Re: AMBER: bond parameters ivan_at_mmb.pcb.ub.es (Wed Aug 03 2005 - 09:54:29 CDT)
AMBER: installing amber7 on 64bit cluster MURAT CETINKAYA (Wed Aug 03 2005 - 10:46:20 CDT)
RE: AMBER: bond parameters Ross Walker (Wed Aug 03 2005 - 11:11:00 CDT)
Re: AMBER: power supply crash==>boot problems David LeBard (Wed Aug 03 2005 - 12:20:30 CDT)
Re: AMBER: bond breaking/ energetic ion Bill Ross (Wed Aug 03 2005 - 12:41:36 CDT)
AMBER: Strange difference in speed between Altix (Itanium2) and Tezro (MIPS) SGI for small GB/SA run David.Maxwell_at_di.mdacc.tmc.edu (Wed Aug 03 2005 - 12:39:43 CDT)
AMBER: Error with antechamber Joseph Fernandez (Wed Aug 03 2005 - 14:45:29 CDT)
RE: AMBER: Leap set head/tail question Ilyas Yildirim (Wed Aug 03 2005 - 16:40:23 CDT)
RE: AMBER: installing amber7 on 64bit cluster Zhang Bing (Wed Aug 03 2005 - 20:33:55 CDT)
RE: AMBER: installing amber7 on 64bit cluster Ross Walker (Thu Aug 04 2005 - 01:39:22 CDT)
AMBER: a trivial question Linchen Gong (Thu Aug 04 2005 - 04:14:04 CDT)
Re: AMBER: a trivial question Carlos Simmerling (Thu Aug 04 2005 - 06:28:36 CDT)
Re: AMBER: Strange difference in speed between Altix (Itanium2) and Tezro (MIPS) SGI for small GB/SA run Roberto Gomperts (Thu Aug 04 2005 - 06:57:12 CDT)
RE: AMBER: installing amber7 on 64bit cluster MURAT CETINKAYA (Thu Aug 04 2005 - 10:04:47 CDT)
AMBER: nmode Wei Chen (Thu Aug 04 2005 - 13:04:17 CDT)
AMBER: Incorrect imaging when using Periodic Boundary Conditions in NAMD with AMBER parameters Grzegorz Jezierski (Thu Aug 04 2005 - 13:24:42 CDT)
RE: AMBER: nmode Yong Duan (Thu Aug 04 2005 - 19:03:26 CDT)
RE: AMBER: nmode Wei Chen (Thu Aug 04 2005 - 22:07:43 CDT)
AMBER: about salt bridges xueping (Fri Aug 05 2005 - 01:34:18 CDT)
AMBER: Conformational energy (QM) for parameterization yuann (Fri Aug 05 2005 - 05:09:14 CDT)
Re: AMBER: about salt bridges Carlos Simmerling (Fri Aug 05 2005 - 06:53:06 CDT)
Re: AMBER: Error with antechamber David A. Case (Fri Aug 05 2005 - 07:26:36 CDT)
RE: Re: AMBER: a trivial question Linchen Gong (Fri Aug 05 2005 - 10:26:25 CDT)
RE: Re: AMBER: a trivial question David LeBard (Fri Aug 05 2005 - 11:32:47 CDT)
AMBER: leap question Kara Di Giorgio (Fri Aug 05 2005 - 11:38:47 CDT)
AMBER: NMR refinement Lei Jia (Fri Aug 05 2005 - 14:50:29 CDT)
Re: AMBER: leap question David A. Case (Fri Aug 05 2005 - 17:34:39 CDT)
Re: AMBER: leap question Kara Di Giorgio (Fri Aug 05 2005 - 20:56:40 CDT)
RE: RE: Re: AMBER: a trivial question Linchen Gong (Fri Aug 05 2005 - 21:52:39 CDT)
RE: RE: Re: AMBER: a trivial question Linchen Gong (Fri Aug 05 2005 - 21:52:39 CDT)
AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6) Hwankyu Lee (Fri Aug 05 2005 - 22:44:07 CDT)
Re: AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6) David A. Case (Sat Aug 06 2005 - 06:26:14 CDT)
Re: AMBER: leap question David A. Case (Sat Aug 06 2005 - 06:33:44 CDT)
RE: AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6) Ross Walker (Sat Aug 06 2005 - 13:47:26 CDT)
Re: AMBER: leap question Kara Di Giorgio (Sat Aug 06 2005 - 22:02:45 CDT)
AMBER: is calculated B-factors always smaller than experimental ones? haixiao jin (Sun Aug 07 2005 - 09:57:54 CDT)
Re: AMBER: is calculated B-factors always smaller than experimental ones? Carlos Simmerling (Sun Aug 07 2005 - 10:23:42 CDT)
AMBER: How to calculate hydrogen bond involved with water molecules quickly? haixiao jin (Mon Aug 08 2005 - 00:07:48 CDT)
Re: AMBER: is calculated B-factors always smaller than experimental ones? haixiao jin (Mon Aug 08 2005 - 00:33:48 CDT)
AMBER: Zymeworks job posting John Vieceli (Mon Aug 08 2005 - 12:11:42 CDT)
AMBER: RE: is calculated B-factors always smaller than experimental ones? Yong Duan (Mon Aug 08 2005 - 13:24:26 CDT)
Re: AMBER: RE: is calculated B-factors always smaller than experimental ones? haixiao jin (Tue Aug 09 2005 - 00:47:19 CDT)
AMBER: Tutorial question and some more... blakrose_at_gazeta.pl (Tue Aug 09 2005 - 01:49:45 CDT)
Re: AMBER: Tutorial question and some more... Bill Ross (Tue Aug 09 2005 - 13:30:46 CDT)
RE: AMBER: Tutorial question and some more... Ross Walker (Tue Aug 09 2005 - 14:03:01 CDT)
Re: AMBER: Tutorial question and some more... blakrose_at_gazeta.pl (Tue Aug 09 2005 - 16:00:20 CDT)
Re: AMBER: Tutorial question and some more... Yam (Wed Aug 10 2005 - 02:50:54 CDT)
AMBER: The “crystallographic” waters should be retained or deleted? haixiao jin (Wed Aug 10 2005 - 07:35:34 CDT)
AMBER: Creating protonated cytidine residue Peter Cornish (Wed Aug 10 2005 - 09:57:17 CDT)
AMBER: replica exchange Anthony Cruz (Wed Aug 10 2005 - 13:13:41 CDT)
Re: AMBER: comparing md trajectories Austin B. Yongye (Wed Aug 10 2005 - 16:16:08 CDT)
AMBER: ptraj command inputs opitz_at_che.udel.edu (Wed Aug 10 2005 - 17:29:34 CDT)
Re: AMBER: ptraj command inputs Thomas E. Cheatham, III (Wed Aug 10 2005 - 17:43:31 CDT)
AMBER: group-based cutoff John Vieceli (Wed Aug 10 2005 - 19:44:56 CDT)
RE: AMBER: group-based cutoff Ross Walker (Wed Aug 10 2005 - 20:57:35 CDT)
Re: AMBER: group-based cutoff Thomas E. Cheatham, III (Wed Aug 10 2005 - 21:53:38 CDT)
AMBER: solvent problem blakrose_at_gazeta.pl (Thu Aug 11 2005 - 02:14:17 CDT)
AMBER: Atom type problem nag raj (Thu Aug 11 2005 - 09:18:31 CDT)
Re: AMBER: Atom type problem Ilyas Yildirim (Thu Aug 11 2005 - 10:15:28 CDT)
Re: AMBER: Atom type problem Ilyas Yildirim (Thu Aug 11 2005 - 11:40:12 CDT)
AMBER: molsurf: problem with calculate surface area Magne Olufsen (Fri Aug 12 2005 - 03:06:45 CDT)
AMBER: How is the origin of the grid defined?(PBSA question) JunJun Liu (Sun Aug 14 2005 - 11:35:46 CDT)
Purchased a New Home Anderson Bond (Mon Aug 15 2005 - 00:52:56 CDT)
AMBER: wtmol and resp Guanglei Cui (Mon Aug 15 2005 - 09:59:42 CDT)
Re: AMBER: How is the origin of the grid defined?(PBSA question) Ray Luo (Sat Aug 13 2005 - 14:40:54 CDT)
AMBER: difference of energy in sander and nmode in amber 7 sebnem (Mon Aug 15 2005 - 16:55:24 CDT)
AMBER: AMBER on g5 10.4 w/g95 or gfortran Rachel Burdge (Tue Aug 16 2005 - 10:12:40 CDT)
Re: AMBER: AMBER on g5 10.4 w/g95 or gfortran justin litchfield (Tue Aug 16 2005 - 11:27:26 CDT)
AMBER: Format of atom specifiication after FIND Joseph Nachman (Tue Aug 16 2005 - 14:02:55 CDT)
Re: AMBER: How is the origin of the grid defined?(PBSA question) Suxin Zheng (Tue Aug 16 2005 - 15:54:27 CDT)
Re: AMBER: How is the origin of the grid defined?(PBSA question) Ray Luo (Tue Aug 16 2005 - 08:46:01 CDT)
AMBER: min problem Gustavo Pierdominici Sottile (Tue Aug 16 2005 - 18:05:56 CDT)
AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8 Ilyas Yildirim (Tue Aug 16 2005 - 20:40:11 CDT)
AMBER: QM/MM jojartb_at_pharm.u-szeged.hu (Wed Aug 17 2005 - 06:42:06 CDT)
Re: AMBER: difference of energy in sander and nmode in amber 7 sebnem (Wed Aug 17 2005 - 10:39:02 CDT)
Re: AMBER: difference of energy in sander and nmode in amber 7 David A. Case (Wed Aug 17 2005 - 11:36:11 CDT)
Re: AMBER: difference of energy in sander and nmode in amber 7 sebnem (Wed Aug 17 2005 - 12:51:15 CDT)
AMBER: glycan Wei Chen (Wed Aug 17 2005 - 13:25:27 CDT)
Re: AMBER: glycan kkirschn_at_hamilton.edu (Wed Aug 17 2005 - 14:55:35 CDT)
AMBER: residence time of electrons/holes in DNA ioana_at_pegasus.arc.nasa.gov (Wed Aug 17 2005 - 16:48:43 CDT)
AMBER: Energy Comparisons Kara Di Giorgio (Wed Aug 17 2005 - 17:00:44 CDT)
Re: AMBER: Energy Comparisons Wei Chen (Wed Aug 17 2005 - 17:24:08 CDT)
Re: AMBER: glycan Wei Chen (Wed Aug 17 2005 - 17:29:52 CDT)
AMBER: Amber 8: all_nucleic94.lib nucleotide geometry Angela Liu (Wed Aug 17 2005 - 17:42:03 CDT)
Re: AMBER: Amber 8: all_nucleic94.lib nucleotide geometry Bill Ross (Wed Aug 17 2005 - 18:04:49 CDT)
Re: AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8 S. Teletchéa (Wed Aug 17 2005 - 18:22:43 CDT)
Re: AMBER: residence time of electrons/holes in DNA David LeBard (Wed Aug 17 2005 - 18:43:47 CDT)
Re: AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8 Ilyas Yildirim (Wed Aug 17 2005 - 19:04:37 CDT)
AMBER: ew_bspline.h error khn _ (Wed Aug 17 2005 - 22:33:08 CDT)
Re: AMBER: difference of energy in sander and nmode in amber 7 David A. Case (Thu Aug 18 2005 - 09:39:55 CDT)
AMBER: mm_pbsa amit_at_mbu.iisc.ernet.in (Thu Aug 18 2005 - 16:04:40 CDT)
Re: AMBER: mm_pbsa Ray Luo (Thu Aug 18 2005 - 16:43:51 CDT)
AMBER: parm99.dat non-bonded parameters Angela Liu (Thu Aug 18 2005 - 17:00:45 CDT)
AMBER: parallel amber8 with mpi through qsnet Ye Mei (Thu Aug 18 2005 - 21:11:55 CDT)
AMBER: How to construct a lipid bilayer nag raj (Fri Aug 19 2005 - 00:01:06 CDT)
AMBER: ptraj correlation facility Simon Whitehead (Fri Aug 19 2005 - 04:15:41 CDT)
AMBER: amber8installation cbala_at_igib.res.in (Fri Aug 19 2005 - 07:53:03 CDT)
Re: AMBER: amber8installation Carlos Simmerling (Fri Aug 19 2005 - 07:13:24 CDT)
Re: AMBER: amber8installation cbala_at_igib.res.in (Fri Aug 19 2005 - 10:33:44 CDT)
Re: AMBER: ew_bspline.h error Michael Crowley (Fri Aug 19 2005 - 10:54:39 CDT)
AMBER: shake Gustavo Pierdominici Sottile (Fri Aug 19 2005 - 11:37:46 CDT)
Re: AMBER: parm99.dat non-bonded parameters Anthony Fejes (Fri Aug 19 2005 - 11:35:36 CDT)
Re: AMBER: shake Carlos Simmerling (Fri Aug 19 2005 - 11:45:16 CDT)
Re: AMBER: parm99.dat non-bonded parameters Angela Liu (Fri Aug 19 2005 - 12:44:03 CDT)
Re: AMBER: parm99.dat non-bonded parameters Anthony Fejes (Fri Aug 19 2005 - 13:18:36 CDT)
RE: AMBER: QM/MM Ross Walker (Fri Aug 19 2005 - 13:27:44 CDT)
RE: AMBER: ew_bspline.h error Ross Walker (Fri Aug 19 2005 - 13:33:57 CDT)
RE: AMBER: parallel amber8 with mpi through qsnet Ross Walker (Fri Aug 19 2005 - 13:42:40 CDT)
RE: AMBER: min problem Ross Walker (Fri Aug 19 2005 - 13:52:36 CDT)
AMBER: structures extracted from mmpbsa Lwin, ThuZar (Fri Aug 19 2005 - 18:25:44 CDT)
Re: AMBER: mm_pbsa amit_at_mbu.iisc.ernet.in (Sat Aug 20 2005 - 02:46:24 CDT)
AMBER: minimization stuck problem blakrose_at_gazeta.pl (Sat Aug 20 2005 - 06:46:07 CDT)
Re: AMBER: minimization stuck problem Carlos Simmerling (Sat Aug 20 2005 - 07:10:45 CDT)
AMBER: minimization stuck problem blakrose_at_gazeta.pl (Sat Aug 20 2005 - 07:32:31 CDT)
RE: AMBER: minimization stuck problem Yong Duan (Sat Aug 20 2005 - 08:05:03 CDT)
RE: AMBER: minimization stuck problem Ross Walker (Sat Aug 20 2005 - 13:00:11 CDT)
Re: AMBER: minimization stuck problem blakrose_at_gazeta.pl (Sat Aug 20 2005 - 16:11:54 CDT)
Re: AMBER: mm_pbsa Ray Luo (Sun Aug 21 2005 - 13:29:41 CDT)
RE: AMBER: minimization stuck problem Ross Walker (Sun Aug 21 2005 - 15:02:09 CDT)
Re: AMBER: minimization stuck problem Adrian Roitberg (Sun Aug 21 2005 - 16:29:53 CDT)
AMBER: AMBER topology file format santanu chatterjee (Mon Aug 22 2005 - 04:18:18 CDT)
AMBER: Restraints kanon gemini (Mon Aug 22 2005 - 05:58:25 CDT)
Re: AMBER: Restraints Carlos Simmerling (Mon Aug 22 2005 - 07:12:26 CDT)
AMBER: minimization stuck problem blakrose_at_gazeta.pl (Mon Aug 22 2005 - 10:17:29 CDT)
Re: AMBER: How is the origin of the grid defined?(PBSA question) JunJun Liu (Tue Aug 23 2005 - 03:46:03 CDT)
RE: AMBER: minimization stuck problem Ross Walker (Tue Aug 23 2005 - 10:22:53 CDT)
Re: AMBER: How is the origin of the grid defined?(PBSA question) Ray Luo (Mon Aug 22 2005 - 20:15:48 CDT)
AMBER: How to deal with the problem that a molecule go out the virtual box in vaccum Li Su (Tue Aug 23 2005 - 12:37:38 CDT)
RE: AMBER: How to deal with the problem that a molecule go out the virtual box in vaccum Ross Walker (Tue Aug 23 2005 - 23:42:52 CDT)
Bank of the West Alert online-banking-rep4958_at_bankofthewest.com (Wed Aug 24 2005 - 03:27:44 CDT)
AMBER: mm_pbsa energy decomposition error amit_at_mbu.iisc.ernet.in (Wed Aug 24 2005 - 07:06:34 CDT)
Re: AMBER: mm_pbsa energy decomposition error David A. Case (Wed Aug 24 2005 - 08:26:49 CDT)
AMBER: essential dynamics Anthony Cruz (Wed Aug 24 2005 - 12:50:03 CDT)
AMBER: Replica exchange Anthony Cruz (Wed Aug 24 2005 - 12:57:42 CDT)
Re: AMBER: essential dynamics John Mongan (Wed Aug 24 2005 - 11:27:46 CDT)
AMBER: a problem encountered when trying to equalibrate alanine dipeptide in explicit water Li Su (Wed Aug 24 2005 - 12:36:06 CDT)
RE: AMBER: a problem encountered when trying to equalibrate alanine dipeptide in explicit water Ross Walker (Wed Aug 24 2005 - 12:45:59 CDT)
AMBER: ptraj efficiency justin litchfield (Wed Aug 24 2005 - 13:13:03 CDT)
RE: AMBER: ptraj efficiency Ross Walker (Wed Aug 24 2005 - 13:29:36 CDT)
AMBER: RED II and Gaussian Raviprasad Aduri (Wed Aug 24 2005 - 21:01:46 CDT)
Re: AMBER: mm_pbsa energy decomposition error amit_at_mbu.iisc.ernet.in (Thu Aug 25 2005 - 06:57:18 CDT)
AMBER: Antechamber error "Cannot successfully assign bond type for this molecule" Whitney Allen (Thu Aug 25 2005 - 11:13:11 CDT)
AMBER: PLease remove my post rpaduri_at_chem.wayne.edu (Thu Aug 25 2005 - 11:08:38 CDT)
AMBER: Add constraints over time Andrew Box (Fri Aug 26 2005 - 00:51:49 CDT)
AMBER: minimization blakrose_at_gazeta.pl (Fri Aug 26 2005 - 07:20:25 CDT)
AMBER: replica exchange Anthony Cruz (Fri Aug 26 2005 - 11:53:48 CDT)
RE: AMBER: ew_bspline.h error Ross Walker (Fri Aug 26 2005 - 10:03:29 CDT)
RE: AMBER: minimization Ross Walker (Fri Aug 26 2005 - 10:07:59 CDT)
Re: AMBER: replica exchange Carlos Simmerling (Fri Aug 26 2005 - 10:16:51 CDT)
AMBER: compilation problem (Mac OS X.4) Mark H. Schofield (Fri Aug 26 2005 - 11:07:05 CDT)
Re: AMBER: replica exchange Anthony Cruz (Fri Aug 26 2005 - 13:14:47 CDT)
RE: AMBER: Add constraints over time Ross Walker (Fri Aug 26 2005 - 11:41:04 CDT)
Re: AMBER: RED II and Gaussian FyD (Sat Aug 27 2005 - 10:02:09 CDT)
AMBER: NRESPA Sergio E. Wong (Sat Aug 27 2005 - 14:12:29 CDT)
Re: AMBER: RED II and Gaussian rpaduri_at_chem.wayne.edu (Sat Aug 27 2005 - 17:40:53 CDT)
Re: AMBER: Replica exchange Carlos Simmerling (Sun Aug 28 2005 - 08:16:46 CDT)
AMBER: can I setup a simulation with restrain the COM of a group to a reference structure? bzlu_at_ucsd.edu (Sun Aug 28 2005 - 15:32:33 CDT)
Re: AMBER: Replica exchange Anthony Cruz (Mon Aug 29 2005 - 07:46:52 CDT)
AMBER: Temperature equilibration Anthony Cruz (Mon Aug 29 2005 - 07:44:04 CDT)
RE: AMBER: Temperature equilibration Ross Walker (Mon Aug 29 2005 - 10:44:08 CDT)
Re: AMBER: Temperature equilibration Anthony Cruz (Mon Aug 29 2005 - 14:47:36 CDT)
AMBER: params for cofactors Michael Dolan (Mon Aug 29 2005 - 14:54:41 CDT)
RE: AMBER: params for cofactors Ross Walker (Mon Aug 29 2005 - 15:10:55 CDT)
Re: AMBER: params for cofactors Michael Dolan (Mon Aug 29 2005 - 15:23:10 CDT)
AMBER: floating point exception anwar_at_cdfd.org.in (Mon Aug 29 2005 - 23:00:31 CDT)
AMBER: anwar_at_cdfd.org.in (Mon Aug 29 2005 - 22:59:49 CDT)
AMBER: in vacuo? Yam (Tue Aug 30 2005 - 04:53:07 CDT)
AMBER: nmode minimization and normal mode calculation Bing Xiong (Tue Aug 30 2005 - 08:53:11 CDT)
Re: AMBER: nmode minimization and normal mode calculation David A. Case (Tue Aug 30 2005 - 09:38:14 CDT)
AMBER: Temperature regulation Monica Civera (Tue Aug 30 2005 - 09:43:26 CDT)
AMBER: Lennard-Jones coeff... Pavan G (Tue Aug 30 2005 - 15:26:49 CDT)
Re: AMBER: Temperature regulation David A. Case (Tue Aug 30 2005 - 17:45:13 CDT)
AMBER: Re:Antechamber Raviprasad Aduri (Tue Aug 30 2005 - 18:34:33 CDT)
AMBER: floating point exception anwar_at_cdfd.org.in (Tue Aug 30 2005 - 21:27:47 CDT)
Re: AMBER: in vacuo? blakrose_at_gazeta.pl (Wed Aug 31 2005 - 04:44:00 CDT)
AMBER: MM-PBSA and 1-4 nonbonded interactions Nelson Fonseca (Wed Aug 31 2005 - 09:55:31 CDT)
AMBER: disulfide bonds by "bond" or "edit -> draw" ? Benjamin Juhl (Wed Aug 31 2005 - 11:23:45 CDT)
RE: AMBER: floating point exception Ross Walker (Wed Aug 31 2005 - 11:51:27 CDT)
RE: AMBER: disulfide bonds by "bond" or "edit -> draw" ? Ross Walker (Wed Aug 31 2005 - 11:48:39 CDT)
Re: AMBER: disulfide bonds by "bond" or "edit -> draw" ? Bill Ross (Wed Aug 31 2005 - 11:57:23 CDT)
AMBER: Interpreting Amber8 Benchmark Results Nikhil Kelshikar $nkelshik$ (Wed Aug 31 2005 - 12:07:24 CDT)
AMBER: Why are some of the Lennard-Jones coeffs 0 ? Pavan G (Wed Aug 31 2005 - 12:18:28 CDT)
Re: AMBER: Why are some of the Lennard-Jones coeffs 0 ? Thomas E. Cheatham, III (Wed Aug 31 2005 - 12:53:38 CDT)
RE: AMBER: Interpreting Amber8 Benchmark Results Ross Walker (Wed Aug 31 2005 - 15:09:20 CDT)
Re: AMBER: Interpreting Amber8 Benchmark Results Robert Duke (Wed Aug 31 2005 - 15:34:42 CDT)
RE: AMBER: Interpreting Amber8 Benchmark Results Bill Ross (Wed Aug 31 2005 - 15:44:55 CDT)
RE: AMBER: Interpreting Amber8 Benchmark Results Ross Walker (Wed Aug 31 2005 - 16:00:55 CDT)
RE: AMBER: Interpreting Amber8 Benchmark Results Bill Ross (Wed Aug 31 2005 - 16:29:58 CDT)
Re: AMBER: Interpreting Amber8 Benchmark Results Robert Duke (Wed Aug 31 2005 - 16:37:53 CDT)
AMBER: addles question Kevin Murphy (Wed Aug 31 2005 - 16:46:00 CDT)
AMBER: broblem of replica exchange MD with polarizable force field wenfei Li (Wed Aug 31 2005 - 19:51:32 CDT)
AMBER: Opinion needed-Solvents chaiann ng (Wed Aug 31 2005 - 20:59:00 CDT)
AMBER: ptraj problem Zhang Bing (Thu Sep 01 2005 - 02:01:20 CDT)
AMBER: H-bond energy Sebastian Fernandez Alberti (Thu Sep 01 2005 - 08:16:14 CDT)
Re: AMBER: broblem of replica exchange MD with polarizable force field Guanglei Cui (Thu Sep 01 2005 - 10:01:46 CDT)
AMBER: unstable MD velocities hayden (Thu Sep 01 2005 - 12:38:11 CDT)
RE: AMBER: unstable MD velocities Ross Walker (Thu Sep 01 2005 - 13:06:08 CDT)
Re: AMBER: ptraj problem Thomas E. Cheatham, III (Thu Sep 01 2005 - 15:54:24 CDT)
AMBER: Tyrosine CZ Parameterization Bug continues in Amber 8 Chris Moth (Thu Sep 01 2005 - 17:04:21 CDT)
AMBER: Error in MD run! Ananda Rama Krishnan Selvaraj (Fri Sep 02 2005 - 05:42:54 CDT)
Re: AMBER: Error in MD run! David A. Case (Fri Sep 02 2005 - 11:27:33 CDT)
Re: AMBER: addles question Carlos Simmerling (Fri Sep 02 2005 - 14:07:30 CDT)
RE: AMBER: Antechamber error "Cannot successfully assign bond type for this molecule" Junmei Wang (Fri Sep 02 2005 - 15:30:29 CDT)
AMBER: RED-II failure to recognize GAMESS output Cenk Andac (Fri Sep 02 2005 - 15:47:07 CDT)
AMBER: Equilibration MD mathew k varghese (Sat Sep 03 2005 - 00:55:22 CDT)
Re: AMBER: RED-II failure to recognize GAMESS output FyD (Sat Sep 03 2005 - 02:33:38 CDT)
AMBER: fixing protein for minimisation of solvent Simon Whitehead (Sat Sep 03 2005 - 05:56:55 CDT)
Re: AMBER: fixing protein for minimisation of solvent Bill Ross (Sat Sep 03 2005 - 11:49:18 CDT)
Re: AMBER: Equilibration MD Bill Ross (Sat Sep 03 2005 - 11:53:17 CDT)
AMBER: STARTING WHERE I LEFT OFF Claire Zerafa (Sat Sep 03 2005 - 12:13:59 CDT)
Re: AMBER: STARTING WHERE I LEFT OFF Bill Ross (Sat Sep 03 2005 - 12:36:23 CDT)
Re: AMBER: STARTING WHERE I LEFT OFF Claire Zerafa (Sat Sep 03 2005 - 12:49:31 CDT)
Re: AMBER: STARTING WHERE I LEFT OFF Carlos Simmerling (Sat Sep 03 2005 - 12:58:29 CDT)
Re: AMBER: STARTING WHERE I LEFT OFF Bill Ross (Sat Sep 03 2005 - 13:12:40 CDT)
Re: AMBER: STARTING WHERE I LEFT OFF Carlos Simmerling (Sat Sep 03 2005 - 13:28:27 CDT)
Re: AMBER: STARTING WHERE I LEFT OFF Bill Ross (Sat Sep 03 2005 - 17:55:19 CDT)
Important Information About Your Sky Bank Account support_at_skyfi.com (Mon Sep 05 2005 - 11:32:11 CDT)
AMBER: MM-PBSA error MURAT CETINKAYA (Mon Sep 05 2005 - 11:00:13 CDT)
AMBER: RED and Multi-Orientation Raviprasad Aduri (Mon Sep 05 2005 - 21:34:56 CDT)
Re: AMBER: RED and Multi-Orientation FyD (Tue Sep 06 2005 - 02:35:58 CDT)
Re: AMBER: RED-II failure to recognize GAMESS output Cenk Andac (Tue Sep 06 2005 - 03:30:19 CDT)
Re: AMBER: RED-II failure to recognize GAMESS output FyD (Tue Sep 06 2005 - 03:48:41 CDT)
AMBER: How to get PDB structures optimized for RED-II Cenk Andac (Tue Sep 06 2005 - 03:49:13 CDT)
Re: AMBER: How to get PDB structures optimized for RED-II FyD (Tue Sep 06 2005 - 04:36:51 CDT)
AMBER: masks in ptraj - Hbond analysis Fabien Cailliez (Tue Sep 06 2005 - 06:38:11 CDT)
AMBER: generation of conformations for multi-conf. RESP fitting Kateryna Miroshnychenko (Tue Sep 06 2005 - 09:29:40 CDT)
Re: AMBER: generation of conformations for multi-conf. RESP fitting FyD (Tue Sep 06 2005 - 11:20:52 CDT)
RE: AMBER: masks in ptraj - Hbond analysis Ross Walker (Tue Sep 06 2005 - 15:13:50 CDT)
Re: AMBER: RED and Multi-Orientation Raviprasad Aduri (Tue Sep 06 2005 - 20:24:29 CDT)
AMBER: AMBER antechamber; dimenion size Toshifumi Yui (Tue Sep 06 2005 - 22:22:17 CDT)
AMBER: solvation energy Madjid Taghdir (Wed Sep 07 2005 - 05:08:31 CDT)
Re: AMBER: RED and Multi-Orientation FyD (Wed Sep 07 2005 - 06:29:54 CDT)
Re: AMBER: How to get PDB structures optimized for RED-II FyD (Wed Sep 07 2005 - 07:40:25 CDT)
Re: AMBER: solvation energy Peter Gannett (Wed Sep 07 2005 - 08:10:45 CDT)
RE: AMBER: AMBER antechamber; dimenion size Junmei Wang (Wed Sep 07 2005 - 11:02:24 CDT)
Re: AMBER: solvation energy Wei Chen (Wed Sep 07 2005 - 11:19:47 CDT)
AMBER: carnal problem Priti Hansia (Thu Sep 08 2005 - 04:25:53 CDT)
AMBER: Quick question about xLeap Kara Di Giorgio (Thu Sep 08 2005 - 09:31:59 CDT)
Re: AMBER: Quick question about xLeap FyD (Thu Sep 08 2005 - 09:54:12 CDT)
Re: AMBER: Quick question about xLeap S.Sundar Raman (Thu Sep 08 2005 - 10:33:36 CDT)
Re: AMBER: carnal problem Bill Ross (Thu Sep 08 2005 - 10:51:34 CDT)
AMBER: Amber 8 and PATH buffer overflow Amber Correspondece (Thu Sep 08 2005 - 12:01:45 CDT)
Ptraj question -- Re: AMBER: carnal problem Joseph Fernandez (Thu Sep 08 2005 - 12:04:14 CDT)
RE: AMBER: Amber 8 and PATH buffer overflow Ross Walker (Thu Sep 08 2005 - 12:22:23 CDT)
RE: AMBER: Amber 8 and PATH buffer overflow Ross Walker (Thu Sep 08 2005 - 12:26:52 CDT)
RE: AMBER: Amber 8 and PATH buffer overflow Bill Ross (Thu Sep 08 2005 - 12:57:42 CDT)
AMBER: Amber8 compilation error Joe Nolan (Thu Sep 08 2005 - 14:47:08 CDT)
AMBER: Equillibration run mathew k varghese (Fri Sep 09 2005 - 01:40:08 CDT)
Re: AMBER: Amber8 compilation error Scott Brozell (Fri Sep 09 2005 - 01:55:23 CDT)
AMBER: mm_pbsa example number 3 Thomas Whitington (Fri Sep 09 2005 - 03:14:19 CDT)
Re: AMBER: Equillibration run Carlos Simmerling (Fri Sep 09 2005 - 06:16:55 CDT)
Re: AMBER: mm_pbsa example number 3 Carlos Simmerling (Fri Sep 09 2005 - 06:19:59 CDT)
Re: AMBER: Equillibration run mathew k varghese (Fri Sep 09 2005 - 08:16:24 CDT)
AMBER: leap segmentation fault-bugfix1 didn't work Kateryna Miroshnychenko (Fri Sep 09 2005 - 08:28:43 CDT)
Re: AMBER: Equillibration run Bill Ross (Fri Sep 09 2005 - 09:30:40 CDT)
AMBER: amber compilation on SGI ALTIX 350 (TEST FAILD) Anthony Cruz (Fri Sep 09 2005 - 14:19:12 CDT)
RE: AMBER: amber compilation on SGI ALTIX 350 (TEST FAILD) Ross Walker (Fri Sep 09 2005 - 12:37:30 CDT)
AMBER: parralel test Anthony Cruz (Fri Sep 09 2005 - 15:41:44 CDT)
Re: AMBER: parralel test David A. Case (Fri Sep 09 2005 - 14:07:16 CDT)
AMBER: AMBBER: ptraj question Douali, Latifa (Fri Sep 09 2005 - 15:49:24 CDT)
Re: AMBER: mm_pbsa example number 3 Thomas Whitington (Sat Sep 10 2005 - 21:32:58 CDT)
Re: AMBER: mm_pbsa example number 3 Carlos Simmerling (Sun Sep 11 2005 - 08:12:17 CDT)
AMBER: Amber 8: questions about free energy perturbation Angela Liu (Sun Sep 11 2005 - 19:43:41 CDT)
RE: AMBER: Amber 8: questions about free energy perturbation case (Mon Sep 12 2005 - 02:29:15 CDT)
AMBER: umbrella sampling output question caoch_at_cherry.bio.titech.ac.jp (Mon Sep 12 2005 - 02:50:32 CDT)
Re: AMBER: Amber 8: questions about free energy perturbation Angela Liu (Mon Sep 12 2005 - 05:40:34 CDT)
RE: AMBER: Amber 8: questions about free energy perturbation Angela Liu (Mon Sep 12 2005 - 05:37:30 CDT)
AMBER: Fail to run parallel Anthony Cruz (Mon Sep 12 2005 - 07:52:29 CDT)
Re: AMBER: Fail to run parallel Anthony Cruz (Mon Sep 12 2005 - 08:27:50 CDT)
Re: AMBER: Amber 8: questions about free energy perturbation Angela Liu (Mon Sep 12 2005 - 07:28:49 CDT)
Re: AMBER: umbrella sampling output question Guanglei Cui (Mon Sep 12 2005 - 08:06:31 CDT)
AMBER: ibelly and free energy calculations David Mobley (Mon Sep 12 2005 - 16:36:25 CDT)
AMBER: REM error Anthony Cruz (Mon Sep 12 2005 - 19:06:05 CDT)
AMBER: Can I get each corresponding sanpshots' delta delta energy term from mm_pbsa Suxin Zheng (Mon Sep 12 2005 - 17:43:13 CDT)
Re: AMBER: REM error Guanglei Cui (Mon Sep 12 2005 - 20:04:33 CDT)
Re: AMBER: leap segmentation fault-bugfix1 didn't work Kateryna Miroshnychenko (Tue Sep 13 2005 - 03:06:45 CDT)
Re: AMBER: REM error Anthony Cruz (Tue Sep 13 2005 - 07:37:13 CDT)
Re: AMBER: REM error Carlos Simmerling (Tue Sep 13 2005 - 06:25:11 CDT)
Re: AMBER: Amber 8: questions about free energy perturbation Angela Liu (Tue Sep 13 2005 - 08:34:25 CDT)
AMBER: How to split LES trajectory using TRAJ Xin Hu (Tue Sep 13 2005 - 10:03:20 CDT)
Re: AMBER: Amber 8: questions about free energy perturbation darden (Tue Sep 13 2005 - 10:13:14 CDT)
Re: AMBER: Amber 8: questions about free energy perturbation Angela Liu (Tue Sep 13 2005 - 11:06:18 CDT)
Re: AMBER: REM error Anthony Cruz (Tue Sep 13 2005 - 13:37:19 CDT)
AMBER: improper torsion parameters Simon Whitehead (Tue Sep 13 2005 - 12:23:13 CDT)
Re: AMBER: REM error Carlos Simmerling (Tue Sep 13 2005 - 12:40:20 CDT)
Re: AMBER: REM error Anthony Cruz (Tue Sep 13 2005 - 16:36:21 CDT)
AMBER: about the %occupied of hydrogen bond haixiao jin (Wed Sep 14 2005 - 00:39:05 CDT)
AMBER: New information about AmberFFC FyD (Wed Sep 14 2005 - 05:18:36 CDT)
AMBER: How does leap choose params ? ivan_at_mmb.pcb.ub.es (Wed Sep 14 2005 - 09:47:14 CDT)
AMBER: Glycam-parameters and antechamber Michele Porro (Wed Sep 14 2005 - 11:06:42 CDT)
AMBER: Error in "restrt" output file Alexander Rubinstein (Wed Sep 14 2005 - 16:30:49 CDT)
Re: AMBER: Error in "restrt" output file Thomas E. Cheatham, III (Wed Sep 14 2005 - 16:41:41 CDT)
RE: AMBER: Error in "restrt" output file Ross Walker (Wed Sep 14 2005 - 16:46:40 CDT)
AMBER: strange case quch 2004 (Wed Sep 14 2005 - 16:57:28 CDT)
AMBER: about radius of Br in MMPBSA calculation Yong Xu (Wed Sep 14 2005 - 21:36:35 CDT)
AMBER: mm_pbsa: problems with dielec constant when using Magne Olufsen (Thu Sep 15 2005 - 06:02:35 CDT)
AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers Daniel Wetzler (Thu Sep 15 2005 - 06:46:14 CDT)
RE: AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers Ross Walker (Thu Sep 15 2005 - 12:05:36 CDT)
AMBER: antechamber + mopac failure Nitin Bhardwaj (Thu Sep 15 2005 - 14:59:27 CDT)
AMBER: creating a respgen file without Gaussian. Nitin Bhardwaj (Thu Sep 15 2005 - 15:08:36 CDT)
RE: AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers Ross Walker (Thu Sep 15 2005 - 15:48:38 CDT)
RE: AMBER: about radius of Br in MMPBSA calculation Shan Jufang (Thu Sep 15 2005 - 17:00:56 CDT)
RE: AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers Ross Walker (Thu Sep 15 2005 - 19:36:49 CDT)
AMBER: roar question Lishan Yao (Thu Sep 15 2005 - 20:08:37 CDT)
AMBER: sander prob cbala_at_igib.res.in (Fri Sep 16 2005 - 03:18:42 CDT)
AMBER: charges jojartb_at_pharm.u-szeged.hu (Fri Sep 16 2005 - 02:33:00 CDT)
Re: RE: AMBER: about radius of Br in MMPBSA calculation Yong Xu (Fri Sep 16 2005 - 03:41:30 CDT)
Re: AMBER: Amber 8: questions about free energy perturbation David A. Case (Fri Sep 16 2005 - 04:00:13 CDT)
Re: AMBER: sander prob Carlos Simmerling (Fri Sep 16 2005 - 06:03:03 CDT)
AMBER: GB refinement of CYANA structures Eugene DeRose (Fri Sep 16 2005 - 08:25:52 CDT)
Re: AMBER: about the %occupied of hydrogen bond Thomas E. Cheatham, III (Fri Sep 16 2005 - 09:30:58 CDT)
Re: AMBER: about the %occupied of hydrogen bond Carlos Simmerling (Fri Sep 16 2005 - 09:49:04 CDT)
Re: AMBER: Amber 8: questions about free energy perturbation Angela Liu (Fri Sep 16 2005 - 10:15:26 CDT)
Re: AMBER: GB refinement of CYANA structures David A. Case (Fri Sep 16 2005 - 16:40:37 CDT)
Re: AMBER: sander prob cbala_at_igib.res.in (Sat Sep 17 2005 - 05:28:51 CDT)
RE: AMBER: sander prob Ross Walker (Sat Sep 17 2005 - 11:23:27 CDT)
AMBER: using SALTCON for human cell cytoplasm Kenley Barrett (Sun Sep 18 2005 - 11:45:42 CDT)
Re: AMBER: using SALTCON for human cell cytoplasm Carlos Simmerling (Sun Sep 18 2005 - 12:11:29 CDT)
Re: AMBER: about the %occupied of hydrogen bond haixiao jin (Sun Sep 18 2005 - 23:44:07 CDT)
Re: AMBER: about the %occupied of hydrogen bond Carlos Simmerling (Mon Sep 19 2005 - 08:04:14 CDT)
Re: AMBER: about the %occupied of hydrogen bond haixiao jin (Mon Sep 19 2005 - 09:12:42 CDT)
Re: AMBER: about the %occupied of hydrogen bond Carlos Simmerling (Mon Sep 19 2005 - 09:28:19 CDT)
RE: AMBER: sander prob cbala_at_igib.res.in (Mon Sep 19 2005 - 10:57:58 CDT)
Re: AMBER: about the %occupied of hydrogen bond haixiao jin (Mon Sep 19 2005 - 10:17:31 CDT)
AMBER: creating a resp input file without Gaussian. Nitin Bhardwaj (Mon Sep 19 2005 - 11:37:29 CDT)
AMBER: antechamber + mopac failure Nitin Bhardwaj (Mon Sep 19 2005 - 11:36:30 CDT)
AMBER: Could not open file (Melb.mdcrd) with mode (r) Varsha Goyal (Mon Sep 19 2005 - 11:50:42 CDT)
Re: AMBER: Could not open file (Melb.mdcrd) with mode (r) Melinda Layten (Mon Sep 19 2005 - 12:00:51 CDT)
RE: AMBER: Could not open file (Melb.mdcrd) with mode (r) Ross Walker (Mon Sep 19 2005 - 12:17:29 CDT)
Re: AMBER: How to split LES trajectory using TRAJ Carlos Simmerling (Mon Sep 19 2005 - 12:40:47 CDT)
Re: AMBER: creating a resp input file without Gaussian. Kenley Barrett (Mon Sep 19 2005 - 14:08:25 CDT)
AMBER: Xleap menu bar problems Steve Seibold (Mon Sep 19 2005 - 14:29:09 CDT)
RE: AMBER: Xleap menu bar problems Ross Walker (Mon Sep 19 2005 - 14:44:11 CDT)
RE: AMBER: Xleap menu bar problems Steve Seibold (Mon Sep 19 2005 - 15:44:52 CDT)
Re: AMBER: How to split LES trajectory using TRAJ Xin Hu (Mon Sep 19 2005 - 15:49:47 CDT)
Re: AMBER: Can I get each corresponding sanpshots' delta delta energy term from mm_pbsa JunJun Liu (Mon Sep 19 2005 - 21:51:32 CDT)
Re: AMBER: creating a resp input file without Gaussian. FyD (Tue Sep 20 2005 - 01:47:20 CDT)
AMBER: building monosaccharides with glycam force field Lina Nilsson (Tue Sep 20 2005 - 11:09:41 CDT)
AMBER: D-enantiomers M. Scott Shell (Tue Sep 20 2005 - 13:43:03 CDT)
AMBER: How to build a crystal structure from a unit cell pdb? Chunhu Tan (Tue Sep 20 2005 - 13:55:06 CDT)
Re: AMBER: building monosaccharides with glycam force field kkirschn_at_hamilton.edu (Tue Sep 20 2005 - 14:12:33 CDT)
Re: AMBER: Glycam-parameters and antechamber kkirschn_at_hamilton.edu (Tue Sep 20 2005 - 15:37:16 CDT)
RE: AMBER: Could not open file (Melb.mdcrd) with mode (r) Varsha Goyal (Tue Sep 20 2005 - 16:25:45 CDT)
RE: AMBER: Could not open file (Melb.mdcrd) with mode (r) Ross Walker (Tue Sep 20 2005 - 16:39:20 CDT)
AMBER: antechamber problem bybaker_at_itsa.ucsf.edu (Tue Sep 20 2005 - 17:20:59 CDT)
RE: AMBER: antechamber problem Junmei Wang (Tue Sep 20 2005 - 18:05:36 CDT)
Re: AMBER: D-enantiomers David A. Case (Tue Sep 20 2005 - 18:07:53 CDT)
Re: AMBER: Could not open file (Melb.mdcrd) with mode (r) Brent Krueger (Tue Sep 20 2005 - 19:13:32 CDT)
AMBER: Linear Interaction Energy Daniel Oehme (Tue Sep 20 2005 - 20:39:53 CDT)
Re: AMBER: D-enantiomers Thomas E. Cheatham, III (Tue Sep 20 2005 - 21:36:34 CDT)
Re: AMBER: D-enantiomers FyD (Wed Sep 21 2005 - 01:53:49 CDT)
AMBER: Build an acetone Box gtg549i_at_mail.gatech.edu (Wed Sep 21 2005 - 02:18:49 CDT)
Re: AMBER: D-enantiomers justin litchfield (Wed Sep 21 2005 - 02:50:36 CDT)
Re: AMBER: D-enantiomers Piotr Cieplak (Wed Sep 21 2005 - 03:13:26 CDT)
Re: RE: AMBER: about radius of Br in MMPBSA calculation Shan Jufang (Wed Sep 21 2005 - 10:05:54 CDT)
Re: AMBER: How to split LES trajectory using TRAJ Melinda Layten (Wed Sep 21 2005 - 15:09:29 CDT)
AMBER: Leap compilation with pgf77 under 64bit platform Mingfeng Yang (Wed Sep 21 2005 - 16:09:39 CDT)
Re: AMBER: antechamber problem bybaker_at_itsa.ucsf.edu (Wed Sep 21 2005 - 19:55:45 CDT)
Re: AMBER: D-enantiomers FyD (Thu Sep 22 2005 - 02:03:55 CDT)
AMBER: highly fluctuating reaction field energies in MM/PBSA Ulf Ryde (Thu Sep 22 2005 - 05:32:05 CDT)
AMBER: AMBER7 xleap problem Kristof Stevens (Thu Sep 22 2005 - 06:00:54 CDT)
Re: AMBER: D-enantiomers Carlos Simmerling (Thu Sep 22 2005 - 06:35:06 CDT)
Re: AMBER: AMBER7 xleap problem Andreas Svrcek-Seiler (Thu Sep 22 2005 - 07:28:31 CDT)
Re: AMBER: D-enantiomers FyD (Thu Sep 22 2005 - 07:15:49 CDT)
AMBER: Problem finding transition state using NMODE Peter Anderson (Thu Sep 22 2005 - 07:36:00 CDT)
AMBER: clustering julien (Thu Sep 22 2005 - 07:10:00 CDT)
AMBER: Query: Problem during Production jpragati_at_ibab.ac.in (Thu Sep 22 2005 - 08:52:05 CDT)
Re: AMBER: Problem finding transition state using NMODE David A. Case (Thu Sep 22 2005 - 09:56:59 CDT)
AMBER: How to split LES trajectory using TRAJ Xin Hu (Thu Sep 22 2005 - 10:12:51 CDT)
AMBER: no statistics part Zhang Bing (Thu Sep 22 2005 - 10:23:30 CDT)
RE: AMBER: Problem finding transition state using NMODE Zhang Bing (Thu Sep 22 2005 - 10:27:45 CDT)
AMBER: no statistics part Zhang Bing (Thu Sep 22 2005 - 10:29:52 CDT)
Re: AMBER: amber8 parallel sander Kathleen Erickson (Thu Sep 22 2005 - 11:44:39 CDT)
EBAY Update Information James Link (Thu Sep 22 2005 - 12:55:50 CDT)
Re: AMBER: amber8 parallel sander Robert Duke (Thu Sep 22 2005 - 11:57:53 CDT)
Re: AMBER: D-enantiomers Piotr Cieplak (Thu Sep 22 2005 - 12:41:24 CDT)
Re: AMBER: amber8 parallel sander Peter Gannett (Thu Sep 22 2005 - 16:15:12 CDT)
Re: AMBER: amber8 parallel sander Peter Gannett (Thu Sep 22 2005 - 16:18:22 CDT)
Re: AMBER: amber8 parallel sander Robert Duke (Thu Sep 22 2005 - 16:47:10 CDT)
Re: AMBER: amber8 parallel sander Carlos Simmerling (Thu Sep 22 2005 - 17:25:07 CDT)
Re: AMBER: D-enantiomers FyD (Fri Sep 23 2005 - 02:12:36 CDT)
Re: AMBER: amber8 parallel sander Carlos P. Sosa (Fri Sep 23 2005 - 07:02:26 CDT)
AMBER: atommask question Istvan Kolossvary (Fri Sep 23 2005 - 10:57:44 CDT)
Re: AMBER: atommask question Viktor Hornak (Fri Sep 23 2005 - 11:46:39 CDT)
Re: AMBER: Amber 8: questions about free energy perturbation David Mobley (Fri Sep 23 2005 - 14:40:03 CDT)
AMBER: Problem during Production jpragati_at_ibab.ac.in (Sat Sep 24 2005 - 09:04:10 CDT)
RE: AMBER: Problem during Production Ross Walker (Sat Sep 24 2005 - 10:54:38 CDT)
AMBER: Unformatted restart file cannot be read by sander when PME in use (AMBER8) John D. Chodera (Sun Sep 25 2005 - 20:08:37 CDT)
AMBER: Modified RNA Bases Raviprasad Aduri (Mon Sep 26 2005 - 21:41:12 CDT)
AMBER: Mg2+ radius in my_parse_delphi.siz JunJun Liu (Mon Sep 26 2005 - 22:30:14 CDT)
AMBER: (no subject) Andrew Box (Mon Sep 26 2005 - 23:40:51 CDT)
Re: AMBER: Modified RNA Bases FyD (Tue Sep 27 2005 - 00:45:17 CDT)
Re: AMBER: Mg2+ radius in my_parse_delphi.siz Thomas Steinbrecher (Tue Sep 27 2005 - 01:49:05 CDT)
Re: AMBER: Mg2+ radius in my_parse_delphi.siz JunJun Liu (Tue Sep 27 2005 - 02:11:45 CDT)
AMBER: Trajectory Problem Anthony Cruz (Thu Sep 22 2005 - 15:24:10 CDT)
Re: AMBER: (no subject) Carlos Simmerling (Tue Sep 27 2005 - 06:06:16 CDT)
Re: AMBER: Trajectory Problem Wei Zhang (Tue Sep 27 2005 - 11:40:45 CDT)
Re: AMBER: Trajectory Problem Thomas E. Cheatham, III (Tue Sep 27 2005 - 11:59:50 CDT)
Re: AMBER: Modified RNA Bases Raviprasad Aduri (Tue Sep 27 2005 - 12:22:45 CDT)
RE: AMBER: number of processors Douali, Latifa (Wed Sep 28 2005 - 12:41:21 CDT)
Re: AMBER: number of processors Carlos Simmerling (Wed Sep 28 2005 - 13:01:04 CDT)
AMBER: Invalid Digit "*" Gert Kiss (Wed Sep 28 2005 - 13:18:04 CDT)
Re: AMBER: Invalid Digit "*" Melinda Layten (Wed Sep 28 2005 - 14:17:29 CDT)
RE: AMBER: Invalid Digit "*" Yong Duan (Wed Sep 28 2005 - 15:50:21 CDT)
AMBER: antechamber -- missing improper torsions David Mobley (Wed Sep 28 2005 - 17:35:25 CDT)
AMBER: Making prep file of sugar derivative Toshifumi Yui (Thu Sep 29 2005 - 07:02:12 CDT)
FW: AMBER: number of processors Douali, Latifa (Thu Sep 29 2005 - 15:49:29 CDT)
Re: FW: AMBER: number of processors Carlos Simmerling (Thu Sep 29 2005 - 16:44:26 CDT)
AMBER: Minimization in sander and nmode Mingfeng Yang (Thu Sep 29 2005 - 18:01:24 CDT)
AMBER: MM_PB/GBSA Zhang Bing (Thu Sep 29 2005 - 22:13:05 CDT)
Re: AMBER: MM_PB/GBSA Thomas E. Cheatham, III (Thu Sep 29 2005 - 23:04:46 CDT)
AMBER: Amber compilation on opteron with PGI compiler Mingfeng Yang (Fri Sep 30 2005 - 08:15:43 CDT)
Re: AMBER: Amber compilation on opteron with PGI compiler Robert Duke (Fri Sep 30 2005 - 08:53:58 CDT)
AMBER: Error check COM velocity!! jpragati_at_ibab.ac.in (Mon Oct 03 2005 - 06:58:01 CDT)
AMBER: cut-offs in non-periodic simulations Fabien Cailliez (Mon Oct 03 2005 - 11:31:26 CDT)
Re: AMBER: cut-offs in non-periodic simulations Andreas Svrcek-Seiler (Mon Oct 03 2005 - 14:15:19 CDT)
Re: AMBER: amber8 parallel sander Kathleen Erickson (Mon Oct 03 2005 - 15:37:47 CDT)
AMBER: question temperature coupling tautp value for RNA Zhuang (Mon Oct 03 2005 - 17:40:23 CDT)
AMBER: question temperature coupling tautp value for RNA Zhuang (Mon Oct 03 2005 - 17:40:09 CDT)
RE: AMBER: question temperature coupling tautp value for RNA Ross Walker (Mon Oct 03 2005 - 17:50:47 CDT)
Re: AMBER: amber8 parallel sander MURAT CETINKAYA (Mon Oct 03 2005 - 21:04:04 CDT)
Re: AMBER: amber8 parallel sander Robert Duke (Tue Oct 04 2005 - 00:26:28 CDT)
AMBER: Problem during production!! jpragati_at_ibab.ac.in (Tue Oct 04 2005 - 03:33:48 CDT)
AMBER: Can I trust ANAL result? Madjid Taghdir (Tue Oct 04 2005 - 05:55:51 CDT)
AMBER: Manganese ion parameter nadtanet (Tue Oct 04 2005 - 06:55:59 CDT)
AMBER: Energy output problem! Pradipta Bandyopadhyay (Tue Oct 04 2005 - 07:08:04 CDT)
Re: AMBER: question temperature coupling tautp value for RNA Carlos Simmerling (Tue Oct 04 2005 - 07:42:07 CDT)
AMBER: The default of HIS in leaprc : HID or HIE ? Jiten (Tue Oct 04 2005 - 11:21:52 CDT)
AMBER: Fw: The default of HIS in leaprc : HID or HIE ? Jiten (Tue Oct 04 2005 - 11:34:54 CDT)
AMBER: Installation error - icc: command not found Sukjoon Yoon (Tue Oct 04 2005 - 20:13:11 CDT)
AMBER: AMBER compilation - RH Enterprise 4, Xeon EM64T Sukjoon Yoon (Wed Oct 05 2005 - 00:55:07 CDT)
AMBER: Is AMBER package suitable for simulating multiple molecule in solvent? wulei (Wed Oct 05 2005 - 04:26:00 CDT)
Re: AMBER: Installation error - icc: command not found Andreas Svrcek-Seiler (Wed Oct 05 2005 - 04:47:31 CDT)
Re: AMBER: Installation error - icc: command not found Mingfeng Yang (Wed Oct 05 2005 - 09:14:16 CDT)
AMBER: antechamber dimesion size, again Toshifumi Yui (Thu Oct 06 2005 - 04:44:29 CDT)
Re: AMBER: Minimization in sander and nmode David A. Case (Thu Oct 06 2005 - 05:06:33 CDT)
AMBER: question about grid in ptraj Linchen Gong (Thu Oct 06 2005 - 08:03:00 CDT)
AMBER: R factors in NMR intensity refinement Yuqin Cai (Thu Oct 06 2005 - 11:29:31 CDT)
Re: AMBER: R factors in NMR intensity refinement YoungJin Cho (Thu Oct 06 2005 - 11:56:02 CDT)
RE: AMBER: antechamber dimesion size, again Junmei Wang (Thu Oct 06 2005 - 14:29:04 CDT)
Re: AMBER: antechamber dimesion size, again Toshifumi Yui (Thu Oct 06 2005 - 21:14:47 CDT)
AMBER: AMBER compilation error Sukjoon Yoon (Thu Oct 06 2005 - 21:32:36 CDT)
AMBER: QMMM question xiaoqin huang (Thu Oct 06 2005 - 23:09:53 CDT)
Re: AMBER: question about grid in ptraj Angelo Pugliese (Fri Oct 07 2005 - 04:23:17 CDT)
Re: AMBER: AMBER compilation error Andreas Svrcek-Seiler (Fri Oct 07 2005 - 04:46:24 CDT)
AMBER: parameters for pyridoxal phosphate Anna Feldman-Salit (Fri Oct 07 2005 - 08:46:29 CDT)
AMBER: problem with temperature weights Manish Datt (Fri Oct 07 2005 - 10:43:52 CDT)
Re: AMBER: problem with temperature weights Carlos Simmerling (Fri Oct 07 2005 - 11:55:12 CDT)
Re: AMBER: problem with temperature weights Manish Datt (Fri Oct 07 2005 - 23:50:07 CDT)
Re: AMBER: problem with temperature weights Carlos Simmerling (Sat Oct 08 2005 - 06:03:41 CDT)
Re: AMBER: How to get PDB structures optimized for RED-II Cenk Andac (Sat Oct 08 2005 - 08:34:42 CDT)
AMBER: sander error Yam (Sun Oct 09 2005 - 21:04:20 CDT)
Re: AMBER: sander error Guanglei Cui (Mon Oct 10 2005 - 08:52:29 CDT)
Re: AMBER: QMMM question Guanglei Cui (Mon Oct 10 2005 - 09:14:20 CDT)
RE: AMBER: sander error Ross Walker (Mon Oct 10 2005 - 09:13:35 CDT)
RE: AMBER: QMMM question Ross Walker (Mon Oct 10 2005 - 09:38:50 CDT)
AMBER: Parameters and topology for Diacylglycerol (DAG) Nitin Bhardwaj (Mon Oct 10 2005 - 13:02:14 CDT)
Re: AMBER: QMMM question xiaoqin huang (Mon Oct 10 2005 - 13:59:55 CDT)
RE: AMBER: sander error Yam (Tue Oct 11 2005 - 04:21:08 CDT)
AMBER: how to constitute T-phosphotyrosine group? luaj_at_sohu.com (Tue Oct 11 2005 - 07:28:38 CDT)
AMBER: PCA Claire Zerafa (Tue Oct 11 2005 - 08:33:49 CDT)
AMBER: how can I constitute T-phosphotyrosine group ? luaj_at_sohu.com (Tue Oct 11 2005 - 09:25:02 CDT)
Re: AMBER: sander error David A. Case (Tue Oct 11 2005 - 09:27:20 CDT)
Re: AMBER: PCA David A. Case (Tue Oct 11 2005 - 09:32:36 CDT)
AMBER: maxgrp error Javier Pérez Mirón (Tue Oct 11 2005 - 14:55:46 CDT)
AMBER: warning in leap Marcela Madrid (Tue Oct 11 2005 - 16:26:42 CDT)
Re: AMBER: warning in leap David A. Case (Tue Oct 11 2005 - 17:17:20 CDT)
AMBER: How to simulate a crystal structure? Chunhu Tan (Tue Oct 11 2005 - 18:22:39 CDT)
AMBER: F,Cl,Br,I in MMPBSA Yong Xu (Wed Oct 12 2005 - 03:58:53 CDT)
Re: AMBER: How to simulate a crystal structure? David A. Case (Wed Oct 12 2005 - 10:17:35 CDT)
Re: AMBER: How to simulate a crystal structure? Joseph Nachman (Wed Oct 12 2005 - 11:57:56 CDT)
AMBER: troubleshooting replica exchange Zhuang (Wed Oct 12 2005 - 18:46:08 CDT)
Re: AMBER: troubleshooting replica exchange Sergio E. Wong (Wed Oct 12 2005 - 19:48:45 CDT)
AMBER: how can I constitute T-phosphotyrosine group ? luaj_at_sohu.com (Wed Oct 12 2005 - 23:50:16 CDT)
Re: AMBER: troubleshooting replica exchange Peter Varnai (Thu Oct 13 2005 - 02:44:59 CDT)
AMBER: AMBER goes in a Loop Imran Khan (Thu Oct 13 2005 - 12:05:40 CDT)
AMBER: Scaling factor of NMR restraint FyD (Fri Oct 14 2005 - 09:28:24 CDT)
RE: AMBER: Scaling factor of NMR restraint Ross Walker (Fri Oct 14 2005 - 09:55:44 CDT)
Re: AMBER: Scaling factor of NMR restraint David A. Case (Fri Oct 14 2005 - 10:00:01 CDT)
Re: AMBER: AMBER goes in a Loop David A. Case (Fri Oct 14 2005 - 10:05:41 CDT)
AMBER: oxidised methionine residue Megan G (Fri Oct 14 2005 - 10:45:21 CDT)
Re: AMBER: AMBER goes in a Loop Imran Khan (Fri Oct 14 2005 - 11:37:44 CDT)
Re: AMBER: How to get PDB structures optimized for RED-II Cenk Andac (Fri Oct 14 2005 - 12:14:02 CDT)
Re: AMBER: AMBER goes in a Loop Robert Duke (Fri Oct 14 2005 - 12:58:50 CDT)
AMBER: again: F, Cl, Br, I in MMPBSA Yong Xu (Fri Oct 14 2005 - 22:07:59 CDT)
RE: AMBER: Scaling factor of NMR restraint FyD (Sat Oct 15 2005 - 01:34:58 CDT)
AMBER: GNU Autotool integration for Amber8! mk mk (Sun Oct 16 2005 - 02:06:11 CDT)
AMBER: Free energy for L and D amino acids S.Sundar Raman (Sun Oct 16 2005 - 10:40:24 CDT)
Re: AMBER: Free energy for L and D amino acids Carlos Simmerling (Sun Oct 16 2005 - 11:05:03 CDT)
AMBER: Cyclohexane solvent Box chaiann ng (Sun Oct 16 2005 - 23:43:21 CDT)
RE: AMBER: Cyclohexane solvent Box Ross Walker (Mon Oct 17 2005 - 09:03:54 CDT)
Re: AMBER: Cyclohexane solvent Box chai ann ng (Mon Oct 17 2005 - 09:27:13 CDT)
Re: AMBER: F,Cl,Br,I in MMPBSA David A. Case (Mon Oct 17 2005 - 10:10:17 CDT)
Re: AMBER: Cyclohexane solvent Box Brent Krueger (Mon Oct 17 2005 - 09:59:44 CDT)
AMBER: antechamber -- missing improper torsions David Mobley (Mon Oct 17 2005 - 13:33:43 CDT)
RE: AMBER: antechamber -- missing improper torsions Ross Walker (Mon Oct 17 2005 - 17:04:23 CDT)
AMBER: pca with ptraj Claire Zerafa (Mon Oct 17 2005 - 18:11:21 CDT)
AMBER: sander error Yam (Mon Oct 17 2005 - 21:10:50 CDT)
AMBER: Question about NVE simulation. tanc_at_uci.edu (Tue Oct 18 2005 - 00:45:51 CDT)
AMBER: program to visualize crystal symmetries Hannes Loeffler (Tue Oct 18 2005 - 03:36:31 CDT)
Re: AMBER: program to visualize crystal symmetries Karsten Suhre (Tue Oct 18 2005 - 04:13:23 CDT)
Re: AMBER: Question about NVE simulation. Carlos Simmerling (Tue Oct 18 2005 - 07:02:39 CDT)
AMBER: problem with xleap Vlad Cojocaru (Tue Oct 18 2005 - 08:56:38 CDT)
Re: AMBER: problem with xleap Mark Williamson (Tue Oct 18 2005 - 09:04:43 CDT)
Re: AMBER: problem with xleap Heike.Meiselbach_at_chemie.uni-erlangen.de (Tue Oct 18 2005 - 09:07:02 CDT)
RE: AMBER: sander error Ross Walker (Tue Oct 18 2005 - 09:23:18 CDT)
Re: AMBER: sander error Robert Duke (Tue Oct 18 2005 - 09:49:05 CDT)
Re: AMBER: sander error David A. Case (Tue Oct 18 2005 - 09:59:39 CDT)
Re: AMBER: sander error Robert Duke (Tue Oct 18 2005 - 10:18:05 CDT)
Re: AMBER: program to visualize crystal symmetries Joseph Nachman (Tue Oct 18 2005 - 11:21:22 CDT)
AMBER: Simple 3D Molecule Visualization Alec M. Resnick (Tue Oct 18 2005 - 11:29:43 CDT)
Re: AMBER: Simple 3D Molecule Visualization Joachim Reichelt (Tue Oct 18 2005 - 11:45:42 CDT)
Re: AMBER: Simple 3D Molecule Visualization Karsten Suhre (Tue Oct 18 2005 - 11:45:36 CDT)
Re: AMBER: Simple 3D Molecule Visualization Mark Williamson (Tue Oct 18 2005 - 11:50:07 CDT)
Re: AMBER: GNU Autotool integration for Amber8! David A. Case (Tue Oct 18 2005 - 11:54:37 CDT)
Re: AMBER: Simple 3D Molecule Visualization FyD (Tue Oct 18 2005 - 14:16:19 CDT)
Re: AMBER: antechamber -- missing improper torsions David Mobley (Tue Oct 18 2005 - 14:21:39 CDT)
Re: AMBER: Question about NVE simulation. Chunhu Tan (Tue Oct 18 2005 - 14:39:43 CDT)
Re: AMBER: Question about NVE simulation. Carlos Simmerling (Tue Oct 18 2005 - 15:23:02 CDT)
Re: AMBER: Simple 3D Molecule Visualization Furse, Kristina Elisabet (Tue Oct 18 2005 - 17:10:54 CDT)
RE: AMBER: antechamber -- missing improper torsions Ross Walker (Tue Oct 18 2005 - 22:33:13 CDT)
AMBER: Neutral C-terminal residue Sébastien Fiorucci (Wed Oct 19 2005 - 05:12:44 CDT)
Re: AMBER: Neutral C-terminal residue Carlos Simmerling (Wed Oct 19 2005 - 06:40:10 CDT)
AMBER: Fw: pca with ptraj Claire Zerafa (Wed Oct 19 2005 - 07:02:08 CDT)
Re: AMBER: Neutral C-terminal residue FyD (Wed Oct 19 2005 - 07:17:12 CDT)
AMBER: ptraj hbond analysis S.Sundar Raman (Wed Oct 19 2005 - 08:28:09 CDT)
Re: AMBER: GNU Autotool integration for Amber8! Xuebin Qiao (Wed Oct 19 2005 - 10:17:54 CDT)
Re: AMBER: Simple 3D Molecule Visualization Mingfeng Yang (Wed Oct 19 2005 - 13:19:18 CDT)
Re: AMBER: Simple 3D Molecule Visualization Mingfeng Yang (Wed Oct 19 2005 - 13:19:01 CDT)
AMBER: amber file formats. Shishir (Wed Oct 19 2005 - 15:16:04 CDT)
Re: AMBER: GNU Autotool integration for Amber8! David A. Case (Wed Oct 19 2005 - 18:41:32 CDT)
AMBER: (no subject) mathew k varghese (Thu Oct 20 2005 - 00:19:06 CDT)
Re: AMBER: (no subject) Yam (Thu Oct 20 2005 - 02:31:37 CDT)
Re: AMBER: (no subject) mathew k varghese (Thu Oct 20 2005 - 03:31:21 CDT)
AMBER: porblem in ptraj julien (Thu Oct 20 2005 - 04:19:47 CDT)
AMBER: Simulating transition metals in amber Thomas Steinbrecher (Thu Oct 20 2005 - 04:32:58 CDT)
AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue haixiao jin (Thu Oct 20 2005 - 05:49:29 CDT)
Re: AMBER: ptraj hbond analysis haixiao jin (Thu Oct 20 2005 - 06:07:30 CDT)
AMBER: REMD error!!! Anthony Cruz (Thu Oct 20 2005 - 08:53:18 CDT)
Re: AMBER: REMD error!!! Carlos Simmerling (Thu Oct 20 2005 - 07:05:41 CDT)
Re: AMBER: REMD error!!! Anthony Cruz (Thu Oct 20 2005 - 09:45:32 CDT)
Re: AMBER: REMD error!!! Carlos Simmerling (Thu Oct 20 2005 - 08:35:13 CDT)
Re: AMBER: GNU Autotool integration for Amber8! Xuebin Qiao (Thu Oct 20 2005 - 08:55:10 CDT)
AMBER: delphi and surface in MMPBSA Yong Xu (Thu Oct 20 2005 - 09:07:17 CDT)
Re: AMBER: REMD error!!! Anthony Cruz (Thu Oct 20 2005 - 11:48:12 CDT)
Re: AMBER: REMD error!!! Carlos Simmerling (Thu Oct 20 2005 - 10:00:22 CDT)
Re: AMBER: REMD error!!! Guanglei Cui (Thu Oct 20 2005 - 10:51:21 CDT)
Re: AMBER: delphi and surface in MMPBSA David A. Case (Thu Oct 20 2005 - 11:06:15 CDT)
Re: AMBER: REMD error!!! Wei Zhang (Thu Oct 20 2005 - 11:15:51 CDT)
Re: AMBER: REMD error!!! Carlos Simmerling (Thu Oct 20 2005 - 11:14:25 CDT)
Re: AMBER: amber file formats. David A. Case (Thu Oct 20 2005 - 11:20:36 CDT)
Re: AMBER: REMD error!!! Carlos Simmerling (Thu Oct 20 2005 - 11:28:15 CDT)
Re: AMBER: REMD error!!! Anthony Cruz (Thu Oct 20 2005 - 14:13:20 CDT)
Re: AMBER: REMD error!!! Carlos Simmerling (Thu Oct 20 2005 - 12:30:13 CDT)
AMBER: Targeted MD Whitney Allen (Thu Oct 20 2005 - 13:04:31 CDT)
AMBER: xleap with modified residue Whitney Allen (Thu Oct 20 2005 - 13:12:42 CDT)
Re: AMBER: xleap with modified residue Kenley Barrett (Thu Oct 20 2005 - 13:25:41 CDT)
Re: AMBER: Targeted MD Carlos Simmerling (Thu Oct 20 2005 - 13:31:21 CDT)
RE: AMBER: xleap with modified residue Ross Walker (Thu Oct 20 2005 - 13:58:53 CDT)
Re: AMBER: amber file formats. Shishir (Thu Oct 20 2005 - 15:37:16 CDT)
Re: AMBER: amber file formats. David A. Case (Thu Oct 20 2005 - 16:32:29 CDT)
Re: Re: AMBER: delphi and surface in MMPBSA Yong Xu (Thu Oct 20 2005 - 20:09:07 CDT)
Re: Re: AMBER: F,Cl,Br,I in MMPBSA Yong Xu (Thu Oct 20 2005 - 20:12:15 CDT)
Re: (2) Re: AMBER: F,Cl,Br,I in MMPBSA Yong Xu (Thu Oct 20 2005 - 20:21:33 CDT)
Re: AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue Thomas Cheatham (Thu Oct 20 2005 - 20:50:43 CDT)
Re: AMBER: ptraj hbond analysis Thomas Cheatham (Thu Oct 20 2005 - 21:03:36 CDT)
Re: AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue haixiao jin (Thu Oct 20 2005 - 21:03:43 CDT)
AMBER: Dipolar coupling refinement s0344557_at_sms.ed.ac.uk (Fri Oct 21 2005 - 08:04:39 CDT)
Re: (2) Re: AMBER: F,Cl,Br,I in MMPBSA David A. Case (Fri Oct 21 2005 - 10:31:06 CDT)
Re: AMBER: antechamber -- missing improper torsions David Mobley (Fri Oct 21 2005 - 12:21:01 CDT)
Re: AMBER: antechamber -- missing improper torsions David A. Case (Fri Oct 21 2005 - 12:57:31 CDT)
AMBER: using position restraints in target MD? Ben-Zhuo Lu (Fri Oct 21 2005 - 13:58:05 CDT)
Re: AMBER: using position restraints in target MD? Viktor Hornak (Fri Oct 21 2005 - 15:14:42 CDT)
Re: AMBER: Dipolar coupling refinement David A. Case (Fri Oct 21 2005 - 20:03:43 CDT)
Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA JunJun Liu (Sat Oct 22 2005 - 02:45:25 CDT)
Re: Re: AMBER: delphi and surface in MMPBSA David A. Case (Sat Oct 22 2005 - 11:44:37 CDT)
Problem solved! Re: AMBER: How to get PDB structures optimized for RED-II Cenk Andac (Sat Oct 22 2005 - 12:38:58 CDT)
Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED Cenk Andac (Sat Oct 22 2005 - 13:02:00 CDT)
AMBER: Hi..I am new to AMBER.(compilation with MPICH-G2 libraries)... konnipati murali (Sun Oct 23 2005 - 01:38:28 CDT)
AMBER: Problem with the QMMM example in AMBER 2004 tutorial Cenk Andac (Sun Oct 23 2005 - 11:31:45 CDT)
RE: AMBER: Problem with the QMMM example in AMBER 2004 tutorial Ross Walker (Sun Oct 23 2005 - 12:02:55 CDT)
Re: Problem solved! Re: AMBER: How to get PDB structures optimized for RED-II FyD (Mon Oct 24 2005 - 03:27:07 CDT)
Re: AMBER: Simulating transition metals in amber FyD (Mon Oct 24 2005 - 03:21:52 CDT)
Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED FyD (Mon Oct 24 2005 - 03:44:31 CDT)
AMBER: rdparm: a parameter array overflowed ying xiong (Mon Oct 24 2005 - 04:17:33 CDT)
AMBER: compiling amber with pgi 5.2.4 Hannes Barsch (Mon Oct 24 2005 - 07:21:11 CDT)
Re: AMBER: compiling amber with pgi 5.2.4 Robert Duke (Mon Oct 24 2005 - 07:44:42 CDT)
AMBER: error in safe Claire Zerafa (Mon Oct 24 2005 - 08:18:50 CDT)
RE: AMBER: error in safe Ross Walker (Mon Oct 24 2005 - 09:25:38 CDT)
Re: AMBER: compiling amber with pgi 5.2.4 Xuebin Qiao (Mon Oct 24 2005 - 10:20:08 CDT)
Re: AMBER: error in safe Xuebin Qiao (Mon Oct 24 2005 - 10:26:41 CDT)
Re: AMBER: rdparm: a parameter array overflowed David A. Case (Mon Oct 24 2005 - 11:00:50 CDT)
Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED Cenk Andac (Mon Oct 24 2005 - 11:12:30 CDT)
RE: AMBER: xleap with modified residue Whitney Allen (Mon Oct 24 2005 - 11:24:25 CDT)
Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED Cenk Andac (Mon Oct 24 2005 - 11:43:36 CDT)
AMBER: Is MM-PBSA doable for transition metals ? Cenk Andac (Mon Oct 24 2005 - 11:55:27 CDT)
Re: AMBER: Is MM-PBSA doable for transition metals ? Bill Ross (Mon Oct 24 2005 - 12:10:44 CDT)
AMBER: QMMM for copper complexes! Cenk Andac (Mon Oct 24 2005 - 12:12:22 CDT)
Re: AMBER: xleap with modified residue David A. Case (Mon Oct 24 2005 - 12:36:40 CDT)
AMBER: atmtypenumbers Yong Xu (Mon Oct 24 2005 - 22:25:00 CDT)
Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED FyD (Tue Oct 25 2005 - 00:58:56 CDT)
Re: Re: AMBER: rdparm: a parameter array overflowed ying xiong (Tue Oct 25 2005 - 01:03:27 CDT)
AMBER: How to calculate binding free energy of ligand bound to complex with two active-site water molecules? haixiao jin (Tue Oct 25 2005 - 02:55:46 CDT)
AMBER: Using RED to calculate partial charges of new amino acid Donald Thomas (Tue Oct 25 2005 - 09:50:40 CDT)
AW: AMBER: compiling amber with pgi 5.2.4 Hannes Barsch (Tue Oct 25 2005 - 10:42:53 CDT)
AMBER: I am looking forward to hearing from you. Mehdi Davari (Tue Oct 25 2005 - 13:38:28 CDT)
AMBER: parmchk error : Cannot open CONNECT.TPL, exit Nitin Bhardwaj (Tue Oct 25 2005 - 16:08:02 CDT)
Re: AMBER: parmchk error : Cannot open CONNECT.TPL, exit David A. Case (Tue Oct 25 2005 - 16:16:35 CDT)
Re: AMBER: parmchk error : Cannot open CONNECT.TPL, exit Nitin Bhardwaj (Tue Oct 25 2005 - 16:52:32 CDT)
AMBER: Antechamber error Nitin Bhardwaj (Tue Oct 25 2005 - 18:27:39 CDT)
Re: AMBER: Antechamber error Nitin Bhardwaj (Tue Oct 25 2005 - 19:16:20 CDT)
AMBER: AMBER tests (x86-64, PGI / Intel) Hannes Barsch (Wed Oct 26 2005 - 02:54:36 CDT)
AMBER: Increase the runtime of Amber benchmarks Imran Khan (Wed Oct 26 2005 - 04:23:10 CDT)
Re: AMBER: I am looking forward to hearing from you. Majid moghaddam (Wed Oct 26 2005 - 05:18:58 CDT)
Re: AMBER: Using RED to calculate partial charges of new amino acid FyD (Wed Oct 26 2005 - 05:36:21 CDT)
Re: AMBER: Increase the runtime of Amber benchmarks Carlos Simmerling (Wed Oct 26 2005 - 06:30:37 CDT)
AMBER: seg fault error in resp Kateryna Miroshnychenko (Wed Oct 26 2005 - 08:24:37 CDT)
AMBER: xleap, opteron, pgi and segmentation fault. Lars Packschies (Wed Oct 26 2005 - 08:57:40 CDT)
Re: AMBER: seg fault error in resp FyD (Wed Oct 26 2005 - 09:06:40 CDT)
Re: AMBER: seg fault error in resp Kateryna Miroshnychenko (Wed Oct 26 2005 - 10:26:37 CDT)
Re: AMBER: seg fault error in resp FyD (Wed Oct 26 2005 - 11:13:05 CDT)
Re: AMBER: seg fault error in resp Bill Ross (Wed Oct 26 2005 - 11:35:38 CDT)
AMBER: using constraints with QM/MM Jakub Kostal (Wed Oct 26 2005 - 13:58:40 CDT)
AMBER: Re: restraints xiaoqin huang (Wed Oct 26 2005 - 16:25:03 CDT)
AMBER: some questions when using ATP du yongchun (Wed Oct 26 2005 - 21:28:44 CDT)
Re: AMBER: seg fault error in resp Kateryna Miroshnychenko (Thu Oct 27 2005 - 09:14:24 CDT)
Re: AMBER: seg fault error in resp FyD (Thu Oct 27 2005 - 09:39:44 CDT)
AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 08:37:29 CDT)
AMBER: problems installing amber 7 on a RH Linux 8 machine Marios Constantinou (Thu Oct 27 2005 - 10:28:00 CDT)
Re: AMBER: restart file and crd file Mingfeng Yang (Thu Oct 27 2005 - 11:11:16 CDT)
Re: AMBER: restart file and crd file Carlos Simmerling (Thu Oct 27 2005 - 11:18:18 CDT)
Re: AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 10:33:20 CDT)
AMBER: Unknown atomtypes in amber Nitin Bhardwaj (Thu Oct 27 2005 - 12:26:49 CDT)
Re: AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 10:50:15 CDT)
Re: AMBER: restart file and crd file Melinda Layten (Thu Oct 27 2005 - 13:35:54 CDT)
Re: AMBER: seg fault error in resp Bill Ross (Thu Oct 27 2005 - 13:40:47 CDT)
Re: AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 12:03:58 CDT)
Re: AMBER: restart file and crd file Carlos Simmerling (Thu Oct 27 2005 - 14:03:13 CDT)
Re: AMBER: problems installing amber 7 on a RH Linux 8 machine David A. Case (Thu Oct 27 2005 - 14:33:33 CDT)
Re: AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 12:54:26 CDT)
Re: AMBER: restart file and crd file Mingfeng Yang (Thu Oct 27 2005 - 14:40:51 CDT)
Re: AMBER: restart file and crd file Carlos Simmerling (Thu Oct 27 2005 - 15:03:20 CDT)
Re: AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 13:59:29 CDT)
Re: AMBER: AMBER tests (x86-64, PGI / Intel) Scott Brozell (Thu Oct 27 2005 - 19:42:37 CDT)
Re: AMBER: problems installing amber 7 on a RH Linux 8 machine Andreas Svrcek-Seiler (Fri Oct 28 2005 - 02:44:20 CDT)
Fwd: Re: AMBER: REMD error!!! Anthony Cruz (Fri Oct 28 2005 - 08:06:39 CDT)
AMBER: Cluster analysis by MMTSB or ptraj Shuting Wei (Fri Oct 28 2005 - 10:30:49 CDT)
Re: Re: AMBER: REMD error!!! Melinda Layten (Fri Oct 28 2005 - 10:26:46 CDT)
Re: AMBER: REMD trajectory error!!! Carlos Simmerling (Fri Oct 28 2005 - 12:06:44 CDT)
AMBER: Metals with Amber Anton B. Guliaev (Fri Oct 28 2005 - 12:09:07 CDT)
AMBER: REMD trajectory error!!! Anthony Cruz (Fri Oct 28 2005 - 13:10:18 CDT)
Re: Fwd: Re: AMBER: REMD error!!! Carlos Simmerling (Fri Oct 28 2005 - 09:38:48 CDT)
AMBER: vdw of h atoms Gustavo Pierdominici Sottile (Fri Oct 28 2005 - 14:16:10 CDT)
Re: AMBER: Metals with Amber Bill Ross (Fri Oct 28 2005 - 15:56:50 CDT)
Re: AMBER: vdw of h atoms Jiri Sponer (Fri Oct 28 2005 - 15:00:19 CDT)
Re: AMBER: vdw of h atoms Bill Ross (Fri Oct 28 2005 - 17:13:59 CDT)
RE: AMBER: vdw of h atoms Rhoad, Jonathan S. (Fri Oct 28 2005 - 18:56:24 CDT)
RE: AMBER: vdw of h atoms Bill Ross (Fri Oct 28 2005 - 19:21:56 CDT)
AMBER: Improper Torsional Parameters Ilyas Yildirim (Fri Oct 28 2005 - 19:59:35 CDT)
AMBER: rounding in xleap when using saveoff command... Ilyas Yildirim (Fri Oct 28 2005 - 20:26:22 CDT)
AMBER: amber7.0: F,Br,radius in MMPBSA Yong Xu (Sat Oct 29 2005 - 09:46:00 CDT)
AMBER: amber7.0: F,Br,radius in MMPBSA Yong Xu (Sat Oct 29 2005 - 09:47:21 CDT)
Re: AMBER: Unknown atomtypes in amber David A. Case (Sat Oct 29 2005 - 12:06:20 CDT)
Re: AMBER: Unknown atomtypes in amber Nitin Bhardwaj (Sat Oct 29 2005 - 14:24:04 CDT)
AMBER: with two water molecules in active site, how to calculate the free energy of ligand bound to complex? haixiao jin (Mon Oct 31 2005 - 00:27:08 CST)
AMBER: GBSA simulation problem Guillaume Bollot (Mon Oct 31 2005 - 02:23:26 CST)
Re: AMBER: GBSA simulation problem Carlos Simmerling (Mon Oct 31 2005 - 06:25:22 CST)
AMBER: tkbc2 Mingfeng Yang (Mon Oct 31 2005 - 16:59:17 CST)
AMBER: mm_pbsa problem emilia wu (Mon Oct 31 2005 - 20:53:51 CST)
Re: AMBER: mm_pbsa problem Cenk Andac (Tue Nov 01 2005 - 02:15:23 CST)
Re: AMBER: mm_pbsa problem Scott Pendley (Tue Nov 01 2005 - 16:36:48 CST)
AMBER: About WHAM program Atsutoshi Okabe (Tue Nov 01 2005 - 21:29:14 CST)
Re: AMBER: About WHAM program Guanglei Cui (Wed Nov 02 2005 - 07:47:01 CST)
AMBER: fedora installation problem Simon Whitehead (Wed Nov 02 2005 - 10:11:26 CST)
Re: AMBER: Improper Torsional Parameters David A. Case (Wed Nov 02 2005 - 10:47:34 CST)
RE: AMBER: fedora installation problem Ross Walker (Wed Nov 02 2005 - 10:50:03 CST)
Re: AMBER: rounding in xleap when using saveoff command... David A. Case (Wed Nov 02 2005 - 10:50:41 CST)
AMBER: ptraj distance mask Peter Gannett (Wed Nov 02 2005 - 11:04:48 CST)
Re: AMBER: ptraj distance mask Thomas E. Cheatham, III (Wed Nov 02 2005 - 11:32:09 CST)
Re: AMBER: Improper Torsional Parameters Ilyas Yildirim (Wed Nov 02 2005 - 12:00:50 CST)
AMBER: Leap error: Could not find atom type: CE Vlad Cojocaru (Wed Nov 02 2005 - 12:08:33 CST)
Re: AMBER: Leap error: Could not find atom type: CE Ilyas Yildirim (Wed Nov 02 2005 - 12:31:23 CST)
Re: AMBER: Leap error: Could not find atom type: CE David A. Case (Wed Nov 02 2005 - 12:57:59 CST)
Re: AMBER: rounding in xleap when using saveoff command... Wei Zhang (Wed Nov 02 2005 - 13:34:10 CST)
Re: AMBER: rounding in xleap when using saveoff command... Ilyas Yildirim (Wed Nov 02 2005 - 19:15:36 CST)
RE: AMBER: fedora installation problem Scott Brozell (Wed Nov 02 2005 - 21:35:16 CST)
AMBER: Density of Cyclohexane box chaiann ng (Wed Nov 02 2005 - 21:57:49 CST)
RE: AMBER: Improper Torsional Parameters Ross Walker (Wed Nov 02 2005 - 22:06:28 CST)
AMBER: EEL and EAMBER values Andrew Box (Wed Nov 02 2005 - 22:19:14 CST)
RE: AMBER: Density of Cyclohexane box Ross Walker (Wed Nov 02 2005 - 22:52:32 CST)
RE: AMBER: EEL and EAMBER values Ross Walker (Wed Nov 02 2005 - 23:02:44 CST)
Re: AMBER: Density of Cyclohexane box FyD (Thu Nov 03 2005 - 01:47:41 CST)
Re: AMBER: Metals with Amber Marc Baaden (Thu Nov 03 2005 - 06:33:34 CST)
Re: AMBER: fedora installation problem caoch_at_cherry.bio.titech.ac.jp (Thu Nov 03 2005 - 07:17:32 CST)
AMBER: REM difficulties Peter Varnai (Thu Nov 03 2005 - 12:15:01 CST)
Re: AMBER: REM difficulties Carlos Simmerling (Thu Nov 03 2005 - 12:38:23 CST)
Re: AMBER: REM difficulties David A. Case (Thu Nov 03 2005 - 12:41:40 CST)
Re: AMBER: fedora installation problem David A. Case (Thu Nov 03 2005 - 12:50:42 CST)
Re: AMBER: REM difficulties Peter Varnai (Thu Nov 03 2005 - 13:26:11 CST)
AMBER: Ask for helpf to get examples for MM-PBSA with AMBER8 Peng Tao (Thu Nov 03 2005 - 13:45:39 CST)
Re: AMBER: REM difficulties Carlos Simmerling (Thu Nov 03 2005 - 13:41:05 CST)
Re: AMBER: Ask for helpf to get examples for MM-PBSA with AMBER8 Wei Chen (Thu Nov 03 2005 - 14:07:25 CST)
Re: AMBER: Antechamber error David A. Case (Thu Nov 03 2005 - 17:06:35 CST)
Re: AMBER: Improper Torsional Parameters David A. Case (Thu Nov 03 2005 - 18:41:53 CST)
AMBER: How to generate a RMSd-residue number graph using AMBER8 ptraj? Jiapu.Zhang_at_csiro.au (Thu Nov 03 2005 - 19:16:17 CST)
Re: AMBER: How to generate a RMSd-residue number graph using AMBER8 ptraj? Carlos Simmerling (Thu Nov 03 2005 - 19:31:39 CST)
RE: AMBER: Density of Cyclohexane box chaiann ng (Thu Nov 03 2005 - 21:10:50 CST)
AMBER: MM_PBSA problem haixiao jin (Fri Nov 04 2005 - 00:43:49 CST)
Re: AMBER: MM_PBSA problem Magne Olufsen (Fri Nov 04 2005 - 01:50:30 CST)
Re: AMBER: MM_PBSA problem haixiao jin (Fri Nov 04 2005 - 02:58:14 CST)
AMBER: Leap task Vlad Cojocaru (Fri Nov 04 2005 - 05:44:39 CST)
AMBER: just one more try:) xleap, opteron, pgi and segmentation fault. (fwd) Lars Packschies (Fri Nov 04 2005 - 06:09:40 CST)
Re: AMBER: restart file and crd file Heiko Meyer (Fri Nov 04 2005 - 06:56:41 CST)
Re: AMBER: restart file and crd file Heiko Meyer (Fri Nov 04 2005 - 09:49:18 CST)
RE: AMBER: restart file and crd file Ross Walker (Fri Nov 04 2005 - 10:22:41 CST)
Re: AMBER: MM_PBSA problem Scott Pendley (Fri Nov 04 2005 - 12:18:17 CST)
AMBER: PMEMD limitation on NFFT Chng Choon-Peng (Fri Nov 04 2005 - 18:38:38 CST)
Re: AMBER: PMEMD limitation on NFFT Robert Duke (Fri Nov 04 2005 - 21:29:17 CST)
Re: AMBER: PMEMD limitation on NFFT Chng Choon-Peng (Fri Nov 04 2005 - 21:44:58 CST)
AMBER: About WHAM program Atsutoshi Okabe (Sat Nov 05 2005 - 22:16:43 CST)
AMBER: bug report Ye Mei (Sun Nov 06 2005 - 00:21:50 CST)
AMBER: bugfix 49 Lihua Wang (Sun Nov 06 2005 - 17:05:20 CST)
AMBER: rluo_at_uci.edu (Sun Nov 06 2005 - 18:42:30 CST)
AMBER: DNA simulations Andrew Box (Sun Nov 06 2005 - 23:15:15 CST)
Re: AMBER: MM_PBSA problem haixiao jin (Mon Nov 07 2005 - 02:59:27 CST)
AMBER: AMBER 8 compilation with lahey F95 ! Pradipta Bandyopadhyay (Mon Nov 07 2005 - 04:13:57 CST)
AMBER: addition to the last mail (lahey F95) ! Pradipta Bandyopadhyay (Mon Nov 07 2005 - 04:20:06 CST)
AMBER: XRED II error while initializing tomjas_at_poczta.onet.pl (Mon Nov 07 2005 - 06:17:12 CST)
Re: AMBER: XRED II error while initializing FyD (Mon Nov 07 2005 - 07:03:05 CST)
AMBER: tRNA's modified bases in the Amber parameters database Whitney Allen (Mon Nov 07 2005 - 08:52:45 CST)
AMBER: Making movie from AMBER trajectory Varsha Goyal (Mon Nov 07 2005 - 10:03:01 CST)
Re: AMBER: tRNA's modified bases in the Amber parameters database David A. Case (Mon Nov 07 2005 - 10:26:41 CST)
Re: AMBER: Making movie from AMBER trajectory Carlos Simmerling (Mon Nov 07 2005 - 10:28:26 CST)
Re: AMBER: bug report David A. Case (Mon Nov 07 2005 - 10:36:29 CST)
AMBER: calculating time correlation functions with ptraj John S Zintsmaster (Mon Nov 07 2005 - 10:39:38 CST)
RE: AMBER: Making movie from AMBER trajectory Ross Walker (Mon Nov 07 2005 - 10:55:48 CST)
RE: AMBER: Making movie from AMBER trajectory Varsha Goyal (Mon Nov 07 2005 - 11:25:41 CST)
Re: AMBER: Making movie from AMBER trajectory Varsha Goyal (Mon Nov 07 2005 - 11:23:50 CST)
Re: AMBER: Making movie from AMBER trajectory Carlos Simmerling (Mon Nov 07 2005 - 11:45:27 CST)
Re: AMBER: Making movie from AMBER trajectory Varsha Goyal (Mon Nov 07 2005 - 12:13:09 CST)
Re: AMBER: Making movie from AMBER trajectory Carlos Simmerling (Mon Nov 07 2005 - 12:28:20 CST)
Re: AMBER: Making movie from AMBER trajectory Knut Langsetmo (Mon Nov 07 2005 - 12:42:08 CST)
Re: AMBER: Making movie from AMBER trajectory David Bevan (Mon Nov 07 2005 - 12:50:19 CST)
Re: AMBER: AMBER 8 compilation with lahey F95 ! Amber admin (Mon Nov 07 2005 - 13:08:03 CST)
Re: AMBER: Making movie from AMBER trajectory caoch_at_cherry.bio.titech.ac.jp (Mon Nov 07 2005 - 20:09:16 CST)
Re: AMBER: Making movie from AMBER trajectory Carlos Simmerling (Tue Nov 08 2005 - 06:44:38 CST)
Re: AMBER: Making movie from AMBER trajectory YoungJin Cho (Tue Nov 08 2005 - 09:00:07 CST)
Re: AMBER: Making movie from AMBER trajectory Mingfeng Yang (Tue Nov 08 2005 - 10:01:52 CST)
AMBER: Time Correlation Functions with Amber John S Zintsmaster (Tue Nov 08 2005 - 10:15:45 CST)
Re: AMBER: Time Correlation Functions with Amber David A. Case (Tue Nov 08 2005 - 10:25:50 CST)
Re: AMBER: tkbc2 David A. Case (Tue Nov 08 2005 - 10:50:51 CST)
Re: AMBER: Time Correlation Functions with Amber John S Zintsmaster (Tue Nov 08 2005 - 11:57:26 CST)
Re: AMBER: Time Correlation Functions with Amber David A. Case (Tue Nov 08 2005 - 12:43:55 CST)
Re: AMBER: Making movie from AMBER trajectory David E. Konerding (Tue Nov 08 2005 - 12:56:55 CST)
Re: AMBER: Time Correlation Functions with Amber John S. Zintsmaster (Tue Nov 08 2005 - 13:56:54 CST)
Re: AMBER: Making movie from AMBER trajectory David E. Konerding (Tue Nov 08 2005 - 17:01:13 CST)
Re: Re: AMBER: bug report Ye Mei (Tue Nov 08 2005 - 19:30:35 CST)
Re: AMBER: XRED II error while initializing tomjas (Wed Nov 09 2005 - 00:38:40 CST)
Re: AMBER: XRED II error while initializing FyD (Wed Nov 09 2005 - 02:06:58 CST)
Re: AMBER: Making movie from AMBER trajectory using UCSF Chimera David E. Konerding (Wed Nov 09 2005 - 10:21:29 CST)
AMBER: mm_pbsa Wei Chen (Wed Nov 09 2005 - 13:51:01 CST)
Re: AMBER: mm_pbsa Ray Luo (Tue Nov 08 2005 - 23:26:52 CST)
AMBER: Resp install problem Jianzhong Liu (Wed Nov 09 2005 - 17:21:09 CST)
Re: AMBER: Resp install problem David A. Case (Wed Nov 09 2005 - 17:51:10 CST)
AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj (Wed Nov 09 2005 - 18:55:41 CST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Bill Ross (Wed Nov 09 2005 - 19:40:41 CST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Ilyas Yildirim (Wed Nov 09 2005 - 21:56:24 CST)
AMBER: ESP exceeds the MAXESP(20000), nag raj (Thu Nov 10 2005 - 04:36:37 CST)
AMBER: restart coordinate file s0344557_at_sms.ed.ac.uk (Thu Nov 10 2005 - 07:55:43 CST)
Re: AMBER: mm_pbsa Cenk Andac (Thu Nov 10 2005 - 08:08:24 CST)
Re: AMBER: restart coordinate file Carlos Simmerling (Thu Nov 10 2005 - 09:31:18 CST)
RE: AMBER: ESP exceeds the MAXESP(20000), Junmei Wang (Thu Nov 10 2005 - 09:37:05 CST)
Re: AMBER: restart coordinate file Bill Ross (Thu Nov 10 2005 - 09:42:53 CST)
AMBER: Resp install problem, again Jianzhong Liu (Thu Nov 10 2005 - 10:03:24 CST)
Re: AMBER: restart coordinate file s0344557_at_sms.ed.ac.uk (Thu Nov 10 2005 - 10:11:49 CST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj (Thu Nov 10 2005 - 10:40:21 CST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list David A. Case (Thu Nov 10 2005 - 11:00:12 CST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj (Thu Nov 10 2005 - 11:13:33 CST)
Re: AMBER: Resp install problem, again David A. Case (Thu Nov 10 2005 - 11:39:49 CST)
Re: AMBER: Resp install problem, again FyD (Thu Nov 10 2005 - 15:49:21 CST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Ilyas Yildirim (Thu Nov 10 2005 - 20:58:23 CST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj (Fri Nov 11 2005 - 10:25:52 CST)
Re: AMBER: mm_pbsa Wei Chen (Fri Nov 11 2005 - 11:05:40 CST)
Re: AMBER: mm_pbsa Wei Chen (Fri Nov 11 2005 - 11:21:32 CST)
Re: AMBER: mm_pbsa Ray Luo (Fri Nov 11 2005 - 17:57:04 CST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list David A. Case (Fri Nov 11 2005 - 20:58:21 CST)
CORRENDUM: Re: AMBER: mm_pbsa Cenk Andac (Sat Nov 12 2005 - 02:31:27 CST)
Re: AMBER: mm_pbsa Wei Chen (Sat Nov 12 2005 - 22:45:14 CST)
Re: AMBER: mm_pbsa Ray Luo (Sat Nov 12 2005 - 02:09:13 CST)
AMBER: Error message Sukjoon Yoon (Mon Nov 14 2005 - 02:14:07 CST)
AMBER: RESP problem RESP laura zan (Mon Nov 14 2005 - 07:54:28 CST)
Re: AMBER: RESP problem RESP FyD (Mon Nov 14 2005 - 08:59:12 CST)
RE: AMBER: Error message Ross Walker (Mon Nov 14 2005 - 09:04:04 CST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list David A. Case (Mon Nov 14 2005 - 11:01:25 CST)
AMBER: iwork array for nmr Peter Varnai (Mon Nov 14 2005 - 14:20:38 CST)
Re: AMBER: mm_pbsa Wei Chen (Mon Nov 14 2005 - 16:06:44 CST)
Re: AMBER: iwork array for nmr Guanglei Cui (Mon Nov 14 2005 - 17:17:31 CST)
AMBER: Antechamber/Leap, problem with Improper angles Christophe Guilbert (Mon Nov 14 2005 - 20:06:28 CST)
AMBER: ew_legal.h Yam (Mon Nov 14 2005 - 20:54:03 CST)
RE: AMBER: ew_legal.h Ross Walker (Mon Nov 14 2005 - 21:22:31 CST)
RE: AMBER: ew_legal.h Yam (Mon Nov 14 2005 - 22:40:37 CST)
Re: AMBER: ew_legal.h David A. Case (Mon Nov 14 2005 - 23:41:54 CST)
Re: AMBER: ew_legal.h Yam (Tue Nov 15 2005 - 01:10:18 CST)
AMBER: calculating end-end distance C Balasubramanian (Tue Nov 15 2005 - 04:24:21 CST)
Re: AMBER: ew_legal.h darden (Tue Nov 15 2005 - 07:44:26 CST)
Re: AMBER: calculating end-end distance David A. Case (Tue Nov 15 2005 - 10:24:01 CST)
Re: AMBER: Antechamber/Leap, problem with Improper angles David A. Case (Tue Nov 15 2005 - 15:03:11 CST)
AMBER: recent Chimera MD enhancements Eric Pettersen (Tue Nov 15 2005 - 14:59:16 CST)
Re: AMBER: recent Chimera MD enhancements Eric Pettersen (Tue Nov 15 2005 - 15:09:21 CST)
AMBER: pH=1 MD simulation Harianto Tjong (Tue Nov 15 2005 - 16:16:12 CST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj (Tue Nov 15 2005 - 18:11:31 CST)
AMBER: Quantifying DNA perterbation Kara Di Giorgio (Tue Nov 15 2005 - 19:44:03 CST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Ilyas Yildirim (Tue Nov 15 2005 - 22:43:09 CST)
Re: AMBER: Quantifying DNA perterbation Thomas Cheatham (Tue Nov 15 2005 - 23:55:55 CST)
Re: AMBER: Quantifying DNA perterbation Carlos Simmerling (Wed Nov 16 2005 - 05:08:41 CST)
AMBER: anal and periodic boundary conditions Rachel Burdge (Wed Nov 16 2005 - 10:18:34 CST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list David A. Case (Wed Nov 16 2005 - 10:56:44 CST)
Re: AMBER: anal and periodic boundary conditions Bill Ross (Wed Nov 16 2005 - 11:32:57 CST)
AMBER: using periodic boundary conditions to create infinite double helix Kenley Barrett (Wed Nov 16 2005 - 11:32:39 CST)
Re: AMBER: Resp install problem, again Jianzhong Liu (Wed Nov 16 2005 - 12:14:51 CST)
Re: AMBER: Resp install problem, again David A. Case (Wed Nov 16 2005 - 12:43:13 CST)
Re: AMBER: Resp install problem, again Jianzhong Liu (Wed Nov 16 2005 - 12:55:06 CST)
Re: AMBER: Resp install problem, again David A. Case (Wed Nov 16 2005 - 15:53:27 CST)
Re: AMBER: using periodic boundary conditions to create infinite double helix David A. Case (Wed Nov 16 2005 - 18:10:17 CST)
Re: AMBER: using periodic boundary conditions to create infinite double helix Bill Ross (Wed Nov 16 2005 - 18:34:53 CST)
AMBER: ptraj Hbond analysis mathew k varghese (Wed Nov 16 2005 - 22:28:52 CST)
Re: AMBER: ptraj Hbond analysis Thomas Cheatham (Wed Nov 16 2005 - 23:28:42 CST)
AMBER: FATAL error with ATP, MG2 residue Michael Mazanetz (Thu Nov 17 2005 - 03:41:12 CST)
AMBER: need clarification on EWALD BOMB error S.Sundar Raman (Thu Nov 17 2005 - 04:03:22 CST)
AMBER: FATAL error with ATP and MG2 - fixed Michael Mazanetz (Thu Nov 17 2005 - 06:45:27 CST)
RE: AMBER: need clarification on EWALD BOMB error Ross Walker (Thu Nov 17 2005 - 10:20:02 CST)
Re: AMBER: need clarification on EWALD BOMB error Thomas Cheatham (Thu Nov 17 2005 - 11:45:28 CST)
AMBER: Question about using MM_PBSA gtg549i_at_mail.gatech.edu (Thu Nov 17 2005 - 15:28:19 CST)
Re: AMBER: Question about using MM_PBSA Wei Chen (Thu Nov 17 2005 - 17:50:05 CST)
Re: AMBER: need clarification on EWALD BOMB error S.Sundar Raman (Thu Nov 17 2005 - 21:38:43 CST)
Re: AMBER: ptraj Hbond analysis mathew k varghese (Thu Nov 17 2005 - 22:09:14 CST)
Re: AMBER: ptraj Hbond analysis Thomas Cheatham (Thu Nov 17 2005 - 23:20:00 CST)
AMBER: RED and EP from GAMESS Vlad Cojocaru (Fri Nov 18 2005 - 04:12:49 CST)
AMBER: Polarization & energy analysis GUILBAUD Philippe 153683 (Fri Nov 18 2005 - 04:52:26 CST)
AMBER: RED and EP from GAMESS FyD (Fri Nov 18 2005 - 06:04:47 CST)
AMBER: RED&GAMESS: sorry ... my mistake Vlad Cojocaru (Fri Nov 18 2005 - 06:28:31 CST)
AMBER: MM/PBSA basic questions Peng Tao (Fri Nov 18 2005 - 09:41:26 CST)
Re: AMBER: Polarization & energy analysis David A. Case (Fri Nov 18 2005 - 11:05:43 CST)
Re: AMBER: MM/PBSA basic questions Wei Chen (Fri Nov 18 2005 - 11:06:04 CST)
Re: AMBER: MM/PBSA basic questions David A. Case (Fri Nov 18 2005 - 11:09:05 CST)
Re: AMBER: MM/PBSA basic questions Peng Tao (Fri Nov 18 2005 - 12:59:39 CST)
AMBER: Question about PDB format FyD (Sat Nov 19 2005 - 02:11:23 CST)
Re: AMBER: ptraj Hbond analysis mathew k varghese (Sat Nov 19 2005 - 05:36:12 CST)
RE: AMBER: Question about PDB format Ross Walker (Sat Nov 19 2005 - 10:55:11 CST)
Re: AMBER: Question about PDB format David A. Case (Sat Nov 19 2005 - 12:47:45 CST)
Re: AMBER: Question about PDB format Andy Purkiss (Sat Nov 19 2005 - 13:19:00 CST)
Re: AMBER: Question about PDB format FyD (Sun Nov 20 2005 - 08:21:22 CST)
AMBER: RED: extra variable definition Vlad Cojocaru (Sun Nov 20 2005 - 08:48:32 CST)
Re: AMBER: ptraj Hbond analysis Thomas Cheatham (Sun Nov 20 2005 - 17:13:44 CST)
AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file) Jiapu.Zhang_at_csiro.au (Sun Nov 20 2005 - 19:35:57 CST)
AMBER: Will Amber 9 available? Xioling Chuang (Sun Nov 20 2005 - 19:54:55 CST)
Re: AMBER: Will Amber 9 available? David A. Case (Sun Nov 20 2005 - 20:16:09 CST)
RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file) Ross Walker (Sun Nov 20 2005 - 23:59:18 CST)
AMBER: temprature and restraint in constant volumm MD tonglei (Mon Nov 21 2005 - 02:55:40 CST)
Re: AMBER: Will Amber 9 available? bmbbjm_at_bmb.leeds.ac.uk (Mon Nov 21 2005 - 03:54:45 CST)
Re: AMBER: Will Amber 9 available? Barbault Florent (Mon Nov 21 2005 - 04:25:04 CST)
Re: AMBER: temprature and restraint in constant volumm MD Carlos Simmerling (Mon Nov 21 2005 - 07:00:08 CST)
AMBER: average struct without solvent C Balasubramanian (Mon Nov 21 2005 - 07:51:26 CST)
Re: AMBER: temprature and restraint in constant volumm MD tonglei (Mon Nov 21 2005 - 07:56:12 CST)
Re: AMBER: average struct without solvent mcpreto_at_fc.up.pt (Mon Nov 21 2005 - 08:20:39 CST)
Re: AMBER: RED: extra variable definition FyD (Mon Nov 21 2005 - 08:58:17 CST)
RE: AMBER: average struct without solvent Ross Walker (Mon Nov 21 2005 - 10:28:23 CST)
Re: AMBER: Will Amber 9 available? David A. Case (Mon Nov 21 2005 - 10:28:34 CST)
RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file) Ross Walker (Mon Nov 21 2005 - 10:33:44 CST)
Re: AMBER: average struct without solvent Thomas Cheatham (Mon Nov 21 2005 - 10:34:23 CST)
AMBER: ANAL problem Sébastien Fiorucci (Mon Nov 21 2005 - 11:18:07 CST)
RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in ano Andrew Box (Mon Nov 21 2005 - 16:48:34 CST)
AMBER: how to extract the residues of first solvation shell from the simulated system after the production? gtg549i_at_mail.gatech.edu (Mon Nov 21 2005 - 17:46:04 CST)
Re: AMBER: ANAL problem David A. Case (Mon Nov 21 2005 - 18:17:14 CST)
AMBER: Question about PB bomb zgleo (Mon Nov 21 2005 - 20:11:08 CST)
Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? Thomas Cheatham (Mon Nov 21 2005 - 21:50:09 CST)
AMBER: Question of PB bomb zgleo (Mon Nov 21 2005 - 22:59:54 CST)
AMBER: sp0 console message after using addAtomTypes Lorna Stimson (Tue Nov 22 2005 - 02:44:19 CST)
Re: AMBER: RED: extra variable definition Vlad Cojocaru (Tue Nov 22 2005 - 03:08:32 CST)
Re: AMBER: RED: extra variable definition FyD (Tue Nov 22 2005 - 03:34:33 CST)
Re: AMBER: RED: extra variable definition FyD (Tue Nov 22 2005 - 03:40:09 CST)
AMBER: Leap handling crystallographic waters Vlad Cojocaru (Tue Nov 22 2005 - 07:44:57 CST)
Re: AMBER: Leap handling crystallographic waters Andy Purkiss (Tue Nov 22 2005 - 08:31:07 CST)
Re: AMBER: RED: extra variable definition Vlad Cojocaru (Tue Nov 22 2005 - 08:26:49 CST)
AMBER: GRID program used to add ions and solvate AMBER minimized structures Vlad Cojocaru (Tue Nov 22 2005 - 08:53:55 CST)
Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? gtg549i_at_mail.gatech.edu (Tue Nov 22 2005 - 09:13:49 CST)
AMBER: MM_PBSA problem Zhang Bing (Tue Nov 22 2005 - 09:37:32 CST)
AMBER: Using OPLS atom types Lorna Stimson (Tue Nov 22 2005 - 10:18:48 CST)
Re: AMBER: sp0 console message after using addAtomTypes David A. Case (Tue Nov 22 2005 - 10:44:30 CST)
Re: AMBER: MM_PBSA problem David A. Case (Tue Nov 22 2005 - 10:49:59 CST)
Re: AMBER: sp0 console message after using addAtomTypes Lorna Stimson (Tue Nov 22 2005 - 11:04:07 CST)
Re: AMBER: Using OPLS atom types Furse, Kristina Elisabet (Tue Nov 22 2005 - 11:10:06 CST)
Re: AMBER: Leap handling crystallographic waters Furse, Kristina Elisabet (Tue Nov 22 2005 - 11:13:57 CST)
RE: AMBER: Leap handling crystallographic waters Ross Walker (Tue Nov 22 2005 - 11:46:38 CST)
Re: AMBER: Using OPLS atom types Bill Ross (Tue Nov 22 2005 - 11:44:16 CST)
RE: AMBER: Leap handling crystallographic waters Furse, Kristina Elisabet (Tue Nov 22 2005 - 13:18:34 CST)
AMBER: RE: gaff sugar residue instability hayden (Tue Nov 22 2005 - 13:32:14 CST)
Re: AMBER: RE: gaff sugar residue instability David A. Case (Tue Nov 22 2005 - 13:40:18 CST)
Re: AMBER: Leap handling crystallographic waters David A. Case (Tue Nov 22 2005 - 14:08:39 CST)
RE: AMBER: Leap handling crystallographic waters Ross Walker (Tue Nov 22 2005 - 14:09:27 CST)
Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? gtg549i_at_mail.gatech.edu (Tue Nov 22 2005 - 15:28:36 CST)
AMBER: MM_PBSA problem---Illegal division by zero at ... Zhang Bing (Tue Nov 22 2005 - 18:15:40 CST)
Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? Thomas Cheatham (Tue Nov 22 2005 - 22:35:11 CST)
AMBER: cluster analysis mathew k varghese (Wed Nov 23 2005 - 01:03:27 CST)
RE: AMBER: cluster analysis Ross Walker (Wed Nov 23 2005 - 10:15:53 CST)
AMBER: MM_PBSA_parameter Wei Chen (Wed Nov 23 2005 - 13:48:12 CST)
Re: AMBER: MM_PBSA_parameter Ray Luo (Wed Nov 23 2005 - 15:48:17 CST)
Re: AMBER: MM_PBSA_parameter Wei Chen (Wed Nov 23 2005 - 16:51:16 CST)
Re: AMBER: MM_PBSA_parameter Ray Luo (Wed Nov 23 2005 - 17:23:33 CST)
AMBER: MM_PBSA question Tiziano Tuccinardi (Thu Nov 24 2005 - 03:01:53 CST)
AMBER: Parameters for S-substituted nucleic acids E.A.Moore (Thu Nov 24 2005 - 03:29:18 CST)
AMBER: gaff sugar residue instability hayden (Thu Nov 24 2005 - 08:43:03 CST)
AMBER: My model loses its motion in MD Lukasz Bielecki (Thu Nov 24 2005 - 09:06:14 CST)
Re: AMBER: My model loses its motion in MD Thomas Cheatham (Thu Nov 24 2005 - 10:03:07 CST)
Re: AMBER: My model loses its motion in MD Andreas Svrcek-Seiler (Thu Nov 24 2005 - 10:07:42 CST)
Re: AMBER: gaff sugar residue instability David A. Case (Thu Nov 24 2005 - 12:28:23 CST)
Re: AMBER: MM_PBSA question David A. Case (Thu Nov 24 2005 - 12:25:56 CST)
Re: AMBER: gaff sugar residue instability Bill Ross (Thu Nov 24 2005 - 12:45:16 CST)
Re: AMBER: gaff sugar residue instability Bill Ross (Thu Nov 24 2005 - 12:48:02 CST)
AMBER: aloks_at_mbu.iisc.ernet.in (Fri Nov 25 2005 - 06:11:01 CST)
AMBER: PARM-99 Angelo Pugliese (Fri Nov 25 2005 - 08:03:23 CST)
Re: AMBER: PARM-99 Carlos Simmerling (Fri Nov 25 2005 - 10:36:45 CST)
AMBER: reordering atoms after antechamber Vlad Cojocaru (Fri Nov 25 2005 - 11:02:38 CST)
Re: AMBER: reordering atoms after antechamber David A. Case (Fri Nov 25 2005 - 11:19:28 CST)
Re: AMBER: PARM-99 Piotr Cieplak (Fri Nov 25 2005 - 19:46:31 CST)
Re: AMBER: PARM-99 Claire Zerafa (Sat Nov 26 2005 - 03:24:25 CST)
AMBER: How to wrap a truncated octahedron water box into the primary box? Xioling Chuang (Sat Nov 26 2005 - 04:19:44 CST)
AMBER: input for mm_pbsa Xioling Chuang (Sun Nov 27 2005 - 00:31:09 CST)
AMBER: Comparing EELEC from amber and that calculated in the trivial fashion. Pavan G (Sun Nov 27 2005 - 21:14:48 CST)
AMBER: How to check for water mediated hydrogen bonds? Hannes Loeffler (Sun Nov 27 2005 - 22:52:44 CST)
Re: AMBER: Comparing EELEC from amber and that calculated in the trivial fashion. David A. Case (Mon Nov 28 2005 - 00:12:55 CST)
AMBER: Cluster - input files Ananda Rama Krishnan Selvaraj (Mon Nov 28 2005 - 04:37:22 CST)
Re: AMBER: Comparing EELEC from amber and that calculated in the trivial fashion. Carlos Simmerling (Mon Nov 28 2005 - 06:41:30 CST)
AMBER: CD spectrum Anthony Cruz (Mon Nov 28 2005 - 11:58:34 CST)
Re: AMBER: reordering atoms after antechamber FyD (Mon Nov 28 2005 - 09:10:17 CST)
Re: AMBER: CD spectrum Adrian Roitberg (Mon Nov 28 2005 - 09:10:15 CST)
AMBER: antechamber charge methods Sagar S. Rane (Mon Nov 28 2005 - 10:20:45 CST)
Re: AMBER: Cluster - input files David A. Case (Mon Nov 28 2005 - 12:47:12 CST)
Re: AMBER: Cluster - input files Ananda Rama Krishnan Selvaraj (Mon Nov 28 2005 - 14:39:44 CST)
Re: AMBER: Cluster - input files David A. Case (Mon Nov 28 2005 - 15:28:14 CST)
Re: AMBER: Cluster - input files Bill Ross (Mon Nov 28 2005 - 15:51:04 CST)
AMBER: MM_PBSA stopped at some snapshot Xioling Chuang (Mon Nov 28 2005 - 23:57:54 CST)
AMBER: AMBER compilation with -DREM Sergey Krishtal (Tue Nov 29 2005 - 06:45:46 CST)
AMBER: some problems with Antechamber David Mobley (Tue Nov 29 2005 - 10:39:26 CST)
Re: AMBER: some problems with Antechamber Wei Zhang (Tue Nov 29 2005 - 11:14:53 CST)
Re: AMBER: AMBER compilation with -DREM David A. Case (Tue Nov 29 2005 - 11:40:18 CST)
Re: AMBER: MM_PBSA stopped at some snapshot Ray Luo (Sun Nov 27 2005 - 20:37:12 CST)
AMBER: constant pressure vs. constant volume heating Vlad Cojocaru (Tue Nov 29 2005 - 12:50:39 CST)
Re: AMBER: some problems with Antechamber David Mobley (Tue Nov 29 2005 - 13:08:00 CST)
Re: AMBER: constant pressure vs. constant volume heating David Mobley (Tue Nov 29 2005 - 13:20:46 CST)
RE: AMBER: constant pressure vs. constant volume heating Ross Walker (Tue Nov 29 2005 - 13:20:38 CST)
Re: AMBER: constant pressure vs. constant volume heating Bill Ross (Tue Nov 29 2005 - 13:51:12 CST)
AMBER: Solvation in trifluoroethanol Ann Vilan Tran (Tue Nov 29 2005 - 13:57:17 CST)
AMBER: rdparm bug David Mobley (Tue Nov 29 2005 - 20:40:02 CST)
AMBER: question convert crd files to pdb files Zhuang (Tue Nov 29 2005 - 22:02:08 CST)
AMBER: parmchk segfaulting David A. Case (Tue Nov 29 2005 - 22:06:03 CST)
RE: AMBER: question convert crd files to pdb files Ross Walker (Tue Nov 29 2005 - 22:27:02 CST)
Re[2]: AMBER: AMBER compilation with -DREM Sergey Krishtal (Wed Nov 30 2005 - 05:38:17 CST)
AMBER: more data points on the parmchk problem David A. Case (Wed Nov 30 2005 - 09:30:12 CST)
AMBER: ifort compiling problem Simon Whitehead (Wed Nov 30 2005 - 09:27:48 CST)
Re: AMBER: ifort compiling problem Andy Purkiss (Wed Nov 30 2005 - 09:39:48 CST)
AMBER: Targeted MD Whitney Allen (Wed Nov 30 2005 - 10:20:10 CST)
RE: Re[2]: AMBER: AMBER compilation with -DREM Ross Walker (Wed Nov 30 2005 - 10:26:29 CST)
AMBER: Fluorine in MM-PBSA (AMBER8) yuann_at_bioinfo.ndhu.edu.tw (Wed Nov 30 2005 - 10:30:36 CST)
Re: AMBER: more data points on the parmchk problem David Mobley (Wed Nov 30 2005 - 11:04:01 CST)
AMBER: Residual Dipolar Refinement RadhaKumari Yadav (Wed Nov 30 2005 - 11:16:23 CST)
Re: AMBER: MM_PBSA stopped at some snapshot Ray Luo (Tue Nov 29 2005 - 20:55:41 CST)
Re: AMBER: Targeted MD Viktor Hornak (Wed Nov 30 2005 - 11:46:55 CST)
Re: AMBER: Targeted MD Carlos Simmerling (Wed Nov 30 2005 - 11:51:47 CST)
AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time Lihong Song (Wed Nov 30 2005 - 12:15:28 CST)
Re: AMBER: more data points on the parmchk problem John Mongan (Wed Nov 30 2005 - 15:01:35 CST)
Re: AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time Nelson Fonseca (Wed Nov 30 2005 - 15:33:09 CST)
AMBER: Any way to get different charge on same type atom Jianzhong Liu (Wed Nov 30 2005 - 17:07:28 CST)
Re: AMBER: Any way to get different charge on same type atom rpaduri_at_chem.wayne.edu (Wed Nov 30 2005 - 18:37:13 CST)
Re: AMBER: Fluorine in MM-PBSA (AMBER8) sychen (Wed Nov 30 2005 - 23:43:55 CST)
Re: AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time Holger Gohlke (Thu Dec 01 2005 - 01:06:49 CST)
AMBER: Creating an Ester with Antechamber/Gaff John O'Mahony (Thu Dec 01 2005 - 03:46:40 CST)
AMBER: regarding ambpdb S.Sundar Raman (Thu Dec 01 2005 - 04:40:58 CST)
Re: AMBER: regarding ambpdb Ilyas Yildirim (Thu Dec 01 2005 - 04:54:03 CST)
Re: AMBER: regarding ambpdb S.Sundar Raman (Thu Dec 01 2005 - 07:39:31 CST)
Re: AMBER: regarding ambpdb Carlos Simmerling (Thu Dec 01 2005 - 07:57:39 CST)
Re: AMBER: Residual Dipolar Refinement David A. Case (Thu Dec 01 2005 - 08:22:11 CST)
AMBER: MD without a thermostat Vlad Cojocaru (Thu Dec 01 2005 - 09:32:57 CST)
AMBER: no thermostat versus very weak thermostat Vlad Cojocaru (Thu Dec 01 2005 - 09:57:15 CST)
AMBER: Some explanations of MM_PBSA @DECOMP OUTPUT file? Peng Tao (Thu Dec 01 2005 - 10:35:09 CST)
AMBER: Mg2+ issues of using MM-PB/GBSA mingche Pan (Thu Dec 01 2005 - 13:01:24 CST)
Re: AMBER: Mg2+ issues of using MM-PB/GBSA Carlos Simmerling (Thu Dec 01 2005 - 13:26:11 CST)
Re: AMBER: MD without a thermostat David A. Case (Thu Dec 01 2005 - 13:42:51 CST)
AMBER: Radial Distribution functions by ptraj Priti Hansia (Thu Dec 01 2005 - 13:44:02 CST)
Re: AMBER: Mg2+ issues of using MM-PB/GBSA Ray Luo (Wed Nov 30 2005 - 10:46:56 CST)
Re: AMBER: Mg2+ issues of using MM-PB/GBSA David A. Case (Thu Dec 01 2005 - 13:47:20 CST)
AMBER: Position restraints and Models Steve Seibold (Thu Dec 01 2005 - 14:54:06 CST)
AMBER: Questions about MM-PBSA in Amber8 zgleo (Thu Dec 01 2005 - 23:04:26 CST)
Re: AMBER: Mg2+ issues of using MM-PB/GBSA Thomas Cheatham (Thu Dec 01 2005 - 23:27:21 CST)
Re: AMBER: Questions about MM-PBSA in Amber8 Ray Luo (Wed Nov 30 2005 - 18:39:50 CST)
AMBER: Problem in running AMBER 7 in solaris ! Pradipta Bandyopadhyay (Fri Dec 02 2005 - 03:17:19 CST)
Re: AMBER: Problem in running AMBER 7 in solaris ! Atro Tossavainen (Fri Dec 02 2005 - 06:14:42 CST)
AMBER: Problem with sander test suites in solaris ! Pradipta Bandyopadhyay (Fri Dec 02 2005 - 08:26:05 CST)
Re: AMBER: Mg2+ issues of using MM-PB/GBSA mingche Pan (Fri Dec 02 2005 - 10:32:15 CST)
AMBER: ptraj crash error Simon Whitehead (Fri Dec 02 2005 - 11:51:47 CST)
Re: AMBER: Mg2+ issues of using MM-PB/GBSA mingche Pan (Fri Dec 02 2005 - 12:09:28 CST)
Re: AMBER: ptraj crash error David E. Konerding (Fri Dec 02 2005 - 12:24:35 CST)
Re: AMBER: Mg2+ issues of using MM-PB/GBSA Ray Luo (Wed Nov 30 2005 - 20:04:55 CST)
AMBER: rotational motion in periodic simulation Douali, Latifa (Fri Dec 02 2005 - 12:50:28 CST)
Re: AMBER: Mg2+ issues of using MM-PB/GBSA mingche Pan (Fri Dec 02 2005 - 13:36:53 CST)
Re: AMBER: Mg2+ issues of using MM-PB/GBSA Ray Luo (Wed Nov 30 2005 - 22:31:29 CST)
AMBER: Replica-Exchange MD from AMBER8! Peng Tao (Fri Dec 02 2005 - 16:28:27 CST)
Re: AMBER: Replica-Exchange MD from AMBER8! Carlos Simmerling (Fri Dec 02 2005 - 16:49:25 CST)
AMBER: ERROR in readParm: ...failed to find BONDS_WITHOUT_HYDROGEN Rhoad, Jonathan S. (Fri Dec 02 2005 - 17:02:36 CST)
Re: AMBER: rotational motion in periodic simulation David A. Case (Fri Dec 02 2005 - 17:06:22 CST)
Re: AMBER: Creating an Ester with Antechamber/Gaff David A. Case (Fri Dec 02 2005 - 22:05:16 CST)
Re: AMBER: Using OPLS atom types David A. Case (Fri Dec 02 2005 - 22:01:17 CST)
AMBER: parmchk bug fix David A. Case (Fri Dec 02 2005 - 22:22:21 CST)
AMBER: parmchk bug fix, with attachment David A. Case (Fri Dec 02 2005 - 22:33:20 CST)
AMBER: Alignment tensor and Interia tensor RadhaKumari Yadav (Sat Dec 03 2005 - 10:58:01 CST)
Re: AMBER: Replica-Exchange MD from AMBER8! Peng Tao (Sat Dec 03 2005 - 11:13:15 CST)
Re: AMBER: Using OPLS atom types Bill Ross (Sat Dec 03 2005 - 12:15:53 CST)
Re: AMBER: Alignment tensor and Interia tensor David A. Case (Sat Dec 03 2005 - 13:05:30 CST)
Re: AMBER: Replica-Exchange MD from AMBER8! Peng Tao (Sat Dec 03 2005 - 14:19:12 CST)
Re: AMBER: Replica-Exchange MD from AMBER8! Carlos Simmerling (Sat Dec 03 2005 - 15:11:07 CST)
AMBER: The error during calculating PB with pbsa zhli_2000_at_126.com (Sun Dec 04 2005 - 22:39:19 CST)
Re: AMBER: The error during calculating PB with pbsa Ray Luo (Sun Dec 04 2005 - 20:16:09 CST)
AMBER: RMSD Calculations Kara Di Giorgio (Mon Dec 05 2005 - 09:22:03 CST)
Re: AMBER: RMSD Calculations Carlos Simmerling (Mon Dec 05 2005 - 10:00:23 CST)
Re: AMBER: RMSD Calculations Kara Wald (Mon Dec 05 2005 - 10:39:44 CST)
Re: AMBER: RMSD Calculations Carlos Simmerling (Mon Dec 05 2005 - 10:56:36 CST)
Re: AMBER: RMSD Calculations kkirschn_at_hamilton.edu (Mon Dec 05 2005 - 10:29:23 CST)
AMBER: RESP: Question Carlos Jaime (Mon Dec 05 2005 - 11:43:16 CST)
Re: AMBER: RESP: Question Piotr Cieplak (Mon Dec 05 2005 - 12:00:37 CST)
Re: AMBER: Mg2+ issues of using MM-PB/GBSA. . Don.Bashford_at_stjude.org (Mon Dec 05 2005 - 12:09:20 CST)
Re: AMBER: RESP: Question FyD (Mon Dec 05 2005 - 15:31:32 CST)
Re: AMBER: RMSD Calculations Thomas Cheatham (Mon Dec 05 2005 - 16:50:36 CST)
Re[2]: AMBER: What does a crash mean while running a md simulation? sychen (Tue Dec 06 2005 - 06:16:49 CST)
Re: AMBER: RESP: Question FyD (Tue Dec 06 2005 - 07:13:49 CST)
AMBER: 6-thioguanine E.A.Moore (Tue Dec 06 2005 - 08:31:59 CST)
AMBER: MM_PBSA parameters Nelson Fonseca (Tue Dec 06 2005 - 09:26:55 CST)
RE: Re[2]: AMBER: What does a crash mean while running a md simulation? Ross Walker (Tue Dec 06 2005 - 10:54:11 CST)
AMBER: hi Germán Sciaini (Wed Dec 07 2005 - 04:51:06 CST)
AMBER: about resp JAVIER PEREZ (Wed Dec 07 2005 - 06:12:48 CST)
Re:AMBER: about resp Kateryna Miroshnychenko (Wed Dec 07 2005 - 07:50:07 CST)
AMBER: Relax in tLEaP ? FyD (Wed Dec 07 2005 - 08:00:38 CST)
AMBER: AMBER vs QM: base pairing and stacking Jiri Sponer (Wed Dec 07 2005 - 12:22:02 CST)
AMBER: Clustering - MMTSB Toolkit kclust kkirschn_at_hamilton.edu (Wed Dec 07 2005 - 12:43:52 CST)
Re: AMBER: hi David A. Case (Wed Dec 07 2005 - 14:01:52 CST)
Re: AMBER: Relax in tLEaP ? David A. Case (Wed Dec 07 2005 - 13:58:43 CST)
Re: AMBER: Clustering - MMTSB Toolkit kclust Adrian Roitberg (Wed Dec 07 2005 - 14:46:50 CST)
AMBER: Adding/recognizing calcium atoms Nitin Bhardwaj (Wed Dec 07 2005 - 15:24:38 CST)
Re: AMBER: Adding/recognizing calcium atoms Bill Ross (Wed Dec 07 2005 - 15:32:05 CST)
AMBER: error about using ambmask zhli_2000_at_126.com (Thu Dec 08 2005 - 07:40:34 CST)
Re: AMBER: error about using ambmask Viktor Hornak (Thu Dec 08 2005 - 07:53:22 CST)
AMBER: Question on makeing up of missing atoms Benjamin Juhl (Fri Dec 09 2005 - 06:30:57 CST)
Re: AMBER: Question on makeing up of missing atoms Carlos Simmerling (Fri Dec 09 2005 - 06:57:06 CST)
AMBER: reading frcmod torsional parameters ivan_at_mmb.pcb.ub.es (Mon Dec 12 2005 - 07:44:36 CST)
Re: AMBER: reading frcmod torsional parameters David A. Case (Mon Dec 12 2005 - 10:56:02 CST)
AMBER: question about mmpbsa cui wei (Tue Dec 13 2005 - 01:33:08 CST)
Re: AMBER: question about mmpbsa Ray Luo (Mon Dec 12 2005 - 21:34:13 CST)
Re: AMBER: reading frcmod torsional parameters ivan_at_mmb.pcb.ub.es (Tue Dec 13 2005 - 09:42:37 CST)
Re: AMBER: question about mmpbsa cui wei (Tue Dec 13 2005 - 19:09:29 CST)
AMBER: How to add water to calculate MMPBSA Kitiyaporn Wittayanarakul (Wed Dec 14 2005 - 12:06:53 CST)
Re: AMBER: How to add water to calculate MMPBSA David A. Case (Wed Dec 14 2005 - 17:50:13 CST)
AMBER: E of amber calculations YoungJin Cho (Wed Dec 14 2005 - 11:34:47 CST)
AMBER: nmode error: GNORM is greater than the requested maximum zhli_2000_at_126.com (Wed Dec 14 2005 - 20:16:07 CST)
AMBER: error with compiling amber8 with lam on intel pc clusters Ye Mei (Wed Dec 14 2005 - 21:36:54 CST)
AMBER: about antechamber(amber8) linfu (Thu Dec 15 2005 - 01:51:16 CST)
Re: AMBER: error with compiling amber8 with lam on intel pc clusters Xuebin Qiao (Thu Dec 15 2005 - 01:57:24 CST)
AMBER: aniso and iso Yam (Thu Dec 15 2005 - 04:11:45 CST)
Re: AMBER: E of amber calculations Carlos Simmerling (Thu Dec 15 2005 - 06:30:08 CST)
AMBER: parameters for fluorine atom Morena Spreafico (Thu Dec 15 2005 - 06:33:52 CST)
Re: AMBER: about antechamber(amber8) Carlos Simmerling (Thu Dec 15 2005 - 06:45:59 CST)
Re: AMBER: parameters for fluorine atom Carlos Simmerling (Thu Dec 15 2005 - 06:47:20 CST)
AMBER: Build for single precision David Caliga (Thu Dec 15 2005 - 09:31:02 CST)
RE: AMBER: about antechamber(amber8) Junmei Wang (Thu Dec 15 2005 - 09:54:40 CST)
RE: AMBER: error with compiling amber8 with lam on intel pc clusters Ross Walker (Thu Dec 15 2005 - 10:11:05 CST)
Re: AMBER: Build for single precision Robert Duke (Thu Dec 15 2005 - 10:23:49 CST)
RE: AMBER: E of amber calculations Ross Walker (Thu Dec 15 2005 - 10:23:46 CST)
Re: AMBER: aniso and iso David A. Case (Thu Dec 15 2005 - 10:28:28 CST)
RE: AMBER: Build for single precision Ross Walker (Thu Dec 15 2005 - 10:29:35 CST)
Re: AMBER: How to add water to calculate MMPBSA. . Don.Bashford_at_stjude.org (Thu Dec 15 2005 - 11:13:30 CST)
Re: AMBER: question about mmpbsa Ray Luo (Thu Dec 15 2005 - 12:08:55 CST)
Re: AMBER: How to add water to calculate MMPBSA. . Thomas Cheatham (Thu Dec 15 2005 - 12:09:47 CST)
AMBER: parallel AMBER on cluster Kateryna Miroshnychenko (Thu Dec 15 2005 - 12:16:17 CST)
Re: AMBER: parallel AMBER on cluster Robert Duke (Thu Dec 15 2005 - 12:37:22 CST)
RE: AMBER: parallel AMBER on cluster Ross Walker (Thu Dec 15 2005 - 12:38:57 CST)
Re: AMBER: parallel AMBER on cluster Carlos Simmerling (Thu Dec 15 2005 - 12:55:55 CST)
AMBER: | ERROR: Could not read coords from rst file Jiapu.Zhang_at_csiro.au (Thu Dec 15 2005 - 20:26:46 CST)
Re: AMBER: | ERROR: Could not read coords from rst file Robert Duke (Thu Dec 15 2005 - 21:14:35 CST)
AMBER: installation on a dual core Barbault Florent (Fri Dec 16 2005 - 08:00:08 CST)
Re: AMBER: installation on a dual core Nelson Fonseca (Fri Dec 16 2005 - 08:14:22 CST)
Re: AMBER: nmode error: GNORM is greater than the requested maximum David A. Case (Fri Dec 16 2005 - 16:08:21 CST)
AMBER: About Salt concentration Varsha Goyal (Fri Dec 16 2005 - 18:03:05 CST)
Re: AMBER: About Salt concentration Jiri Sponer (Fri Dec 16 2005 - 19:05:13 CST)
Re: AMBER: About Salt concentration Varsha Goyal (Fri Dec 16 2005 - 19:37:45 CST)
AMBER: distance restraints Ed Pate (Sat Dec 17 2005 - 16:43:32 CST)
Re: AMBER: distance restraints Carlos Simmerling (Sat Dec 17 2005 - 17:08:28 CST)
AMBER: | ERROR: Could not read coords from *.rst Jiapu.Zhang_at_csiro.au (Sat Dec 17 2005 - 17:59:22 CST)
AMBER: No exchange among replicas in REMD! Peng Tao (Sun Dec 18 2005 - 16:01:28 CST)
AMBER: No exchange among replicas in REMD! Peng Tao (Sun Dec 18 2005 - 16:11:06 CST)
Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling (Sun Dec 18 2005 - 16:26:42 CST)
Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling (Sun Dec 18 2005 - 16:27:25 CST)
Re: AMBER: No exchange among replicas in REMD! Adrian E. Roitberg (Sun Dec 18 2005 - 17:16:22 CST)
Re: AMBER: No exchange among replicas in REMD! Peng Tao (Sun Dec 18 2005 - 19:45:03 CST)
Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling (Sun Dec 18 2005 - 20:22:48 CST)
Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling (Sun Dec 18 2005 - 20:23:14 CST)
Re: AMBER: aniso and iso Yam (Mon Dec 19 2005 - 02:17:43 CST)
AMBER: a quistion about compile cui wei (Mon Dec 19 2005 - 06:10:07 CST)
Re: AMBER: aniso and iso Carlos Simmerling (Mon Dec 19 2005 - 06:26:37 CST)
AMBER: MD problems (SHAKE) blakrose_at_gazeta.pl (Mon Dec 19 2005 - 06:49:41 CST)
AMBER: Atoms restrain Angelo Pugliese (Mon Dec 19 2005 - 07:09:35 CST)
Re: AMBER: No exchange among replicas in REMD! Peng Tao (Mon Dec 19 2005 - 08:57:30 CST)
AMBER: compiling leap with Xeon EM64 (suse linux 9.2) HL Eastwood (Mon Dec 19 2005 - 09:17:08 CST)
AMBER: re: leap compilation problems xeon EM64 processor HL Eastwood (Mon Dec 19 2005 - 09:30:57 CST)
Re: AMBER: a quistion about compile David A. Case (Mon Dec 19 2005 - 10:22:58 CST)
Re: AMBER: Atoms restrain David A. Case (Mon Dec 19 2005 - 10:20:25 CST)
Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling (Mon Dec 19 2005 - 10:35:30 CST)
Re: AMBER: a quistion about compile Wei Zhang (Mon Dec 19 2005 - 11:01:22 CST)
Re: AMBER: No exchange among replicas in REMD! Peng Tao (Mon Dec 19 2005 - 12:35:24 CST)
AMBER: MD problems/shake blakrose_at_gazeta.pl (Mon Dec 19 2005 - 14:34:52 CST)
Re: AMBER: MD problems/shake Thomas E. Cheatham, III (Mon Dec 19 2005 - 14:53:40 CST)
Re: AMBER: MD problems/shake Bill Ross (Mon Dec 19 2005 - 14:59:04 CST)
Re: AMBER: MD problems/shake blakrose_at_gazeta.pl (Mon Dec 19 2005 - 16:45:43 CST)
AMBER: rdc multiple tensors dmcelh_at_uchicago.edu (Mon Dec 19 2005 - 17:01:13 CST)
Re: AMBER: MD problems/shake Bill Ross (Mon Dec 19 2005 - 17:14:10 CST)
Re: AMBER: MD problems/shake blakrose_at_gazeta.pl (Mon Dec 19 2005 - 17:33:12 CST)
Re: AMBER: MD problems/shake Thomas E. Cheatham, III (Mon Dec 19 2005 - 17:40:40 CST)
Re: AMBER: MD problems/shake blakrose_at_gazeta.pl (Mon Dec 19 2005 - 17:44:59 CST)
Re: AMBER: MD problems/shake Bill Ross (Mon Dec 19 2005 - 17:50:33 CST)
Re: AMBER: MD problems/shake Bill Ross (Mon Dec 19 2005 - 17:54:01 CST)
Re: AMBER: MD problems/shake blakrose_at_gazeta.pl (Mon Dec 19 2005 - 18:03:08 CST)
Re: AMBER: MD problems/shake blakrose_at_gazeta.pl (Mon Dec 19 2005 - 18:07:44 CST)
AMBER: Ligand problem bybaker_at_itsa.ucsf.edu (Mon Dec 19 2005 - 18:40:22 CST)
Re: AMBER: a quistion about compile cui wei (Mon Dec 19 2005 - 19:00:20 CST)
Re: AMBER: Ligand problem blakrose_at_gazeta.pl (Mon Dec 19 2005 - 19:02:54 CST)
Re: AMBER: a quistion about compile cui wei (Mon Dec 19 2005 - 19:03:46 CST)
Re: AMBER: Ligand problem Suxin Zheng (Mon Dec 19 2005 - 19:05:13 CST)
Re: AMBER: a quistion about compile snowyowls (Tue Dec 20 2005 - 07:30:07 CST)
AMBER: Sander.LES questions Bing Liu (Tue Dec 20 2005 - 08:51:09 CST)
Re: AMBER: Sander.LES questions Carlos Simmerling (Tue Dec 20 2005 - 09:07:12 CST)
AMBER: rmsd Anthony Cruz (Tue Dec 20 2005 - 13:17:51 CST)
Re: AMBER: a quistion about compile Wei Zhang (Tue Dec 20 2005 - 10:35:34 CST)
Re: AMBER: a quistion about compile David A. Case (Tue Dec 20 2005 - 10:56:58 CST)
Fwd: AMBER: rdc multiple tensors dmcelh_at_uchicago.edu (Tue Dec 20 2005 - 11:55:51 CST)
AMBER: Re: Ligand problem bybaker_at_itsa.ucsf.edu (Tue Dec 20 2005 - 12:50:03 CST)
Re: AMBER: MD problems/shake Thomas E. Cheatham, III (Tue Dec 20 2005 - 13:20:26 CST)
Re: AMBER: MD problems/shake-many thanks blakrose_at_gazeta.pl (Tue Dec 20 2005 - 17:04:24 CST)
Re: AMBER: MD problems/shake blakrose_at_gazeta.pl (Tue Dec 20 2005 - 17:17:45 CST)
Re: AMBER: Re: Ligand problem Ilyas Yildirim (Tue Dec 20 2005 - 18:39:02 CST)
AMBER: some questions about nmode zhli_2000_at_126.com (Tue Dec 20 2005 - 20:30:22 CST)
Re: AMBER: a quistion about compile snowyowls (Wed Dec 21 2005 - 08:53:21 CST)
AMBER: No skew or curtosis when zero variance in moment Ye Mei (Wed Dec 21 2005 - 09:56:43 CST)
Re: AMBER: a quistion about compile David A. Case (Wed Dec 21 2005 - 15:01:52 CST)
RE: AMBER: About Salt concentration David Cowburn (Wed Dec 21 2005 - 15:33:15 CST)
AMBER: lib-4324 : UNRECOVERABLE library error lv haiting (Wed Dec 21 2005 - 20:31:46 CST)
Re: AMBER: lib-4324 : UNRECOVERABLE library error Thomas Cheatham (Wed Dec 21 2005 - 21:16:22 CST)
Re: AMBER: lib-4324 : UNRECOVERABLE library error lv haiting (Wed Dec 21 2005 - 22:21:50 CST)
Re: AMBER: antechamber problem bybaker_at_itsa.ucsf.edu (Wed Dec 21 2005 - 23:39:24 CST)
AMBER: Amber crashes at simulation in the NVT ensemble with the periodic box equiilbrated in the NPT ensemble. Sergey Krishtal (Thu Dec 22 2005 - 00:15:14 CST)
AMBER: Merry Xmas Angelo Pugliese (Thu Dec 22 2005 - 05:43:14 CST)
Re: AMBER: No skew or curtosis when zero variance in moment David A. Case (Thu Dec 22 2005 - 12:14:25 CST)
AMBER: increase the limit of restraintmask Sichun Yang (Thu Dec 22 2005 - 12:58:14 CST)
Re: AMBER: Amber crashes at simulation in the NVT ensemble with the periodic box equiilbrated in the NPT ensemble. David A. Case (Thu Dec 22 2005 - 13:56:36 CST)
AMBER: does the result of H bond is consistent with the âˆ†Eele of MM_PBSA? haixiao jin (Thu Dec 22 2005 - 22:12:46 CST)
AMBER: the averaged structure VS the specific snapshot haixiao jin (Thu Dec 22 2005 - 22:24:04 CST)
RE: AMBER: the averaged structure VS the specific snapshot Yong Duan (Fri Dec 23 2005 - 00:38:00 CST)
RE: AMBER: does the result of H bond is consistent with the ?Eele of MM_PBSA? Yong Duan (Fri Dec 23 2005 - 00:43:53 CST)
AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Priti Hansia (Fri Dec 23 2005 - 05:28:57 CST)
Re: AMBER: does the result of H bond is consistent with the ?Eele of MM_PBSA? cristian obiol (Fri Dec 23 2005 - 05:01:42 CST)
Re: AMBER: a quistion about compile snowyowls (Fri Dec 23 2005 - 06:32:52 CST)
AMBER: ambpdb TER problems Sam (Fri Dec 23 2005 - 10:23:26 CST)
AMBER: To post or mail to the list (subscribers only) ping jiang (Fri Dec 23 2005 - 14:07:45 CST)
AMBER: (no subject) ping jiang (Fri Dec 23 2005 - 14:46:58 CST)
Re: AMBER: (no subject) Thomas Cheatham (Fri Dec 23 2005 - 15:37:57 CST)
Re: AMBER: (no subject) David A. Case (Fri Dec 23 2005 - 19:43:28 CST)
Re: AMBER: ambpdb TER problems David A. Case (Fri Dec 23 2005 - 19:53:50 CST)
Re: AMBER: (no subject) ping jiang (Fri Dec 23 2005 - 20:25:19 CST)
AMBER: problem with improper torsions in parmchk Kateryna Miroshnychenko (Mon Dec 26 2005 - 10:55:54 CST)
Re: AMBER: ambpdb TER problems samuel.arey_at_epfl.ch (Mon Dec 26 2005 - 13:26:27 CST)
AMBER: building amino acid based surfactants? Eugene Billiot (Mon Dec 26 2005 - 15:25:33 CST)
Re: AMBER: ambpdb TER problems Bill Ross (Mon Dec 26 2005 - 15:27:07 CST)
Re: AMBER: building amino acid based surfactants? David A. Case (Mon Dec 26 2005 - 19:53:19 CST)
Re: AMBER: ambpdb TER problems David A. Case (Mon Dec 26 2005 - 20:08:26 CST)
Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN David A. Case (Tue Dec 27 2005 - 10:17:49 CST)
Re: AMBER: ambpdb TER problems Sam (Tue Dec 27 2005 - 10:23:39 CST)
Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Priti Hansia (Tue Dec 27 2005 - 11:35:41 CST)
AMBER: distance restraint simulation Ed Pate (Tue Dec 27 2005 - 12:36:44 CST)
Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN David A. Case (Tue Dec 27 2005 - 13:18:06 CST)
AMBER: problem with ssh and xleap A D (Tue Dec 27 2005 - 14:12:51 CST)
Re: AMBER: distance restraint simulation David A. Case (Tue Dec 27 2005 - 14:31:03 CST)
Re: AMBER: ambpdb TER problems David A. Case (Tue Dec 27 2005 - 14:30:48 CST)
AMBER: problem of calculate the charge ping jiang (Tue Dec 27 2005 - 18:47:16 CST)
AMBER: problem of calculate the charge2 ping jiang (Tue Dec 27 2005 - 20:17:05 CST)
Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Priti Hansia (Wed Dec 28 2005 - 07:05:56 CST)
Re: AMBER: ambpdb TER problems Sam (Wed Dec 28 2005 - 11:17:14 CST)
Re: AMBER: problem with ssh and xleap Scott Brozell (Wed Dec 28 2005 - 16:02:48 CST)
AMBER: Question about partial charge for ligand molecules Woojin Lee (Wed Dec 28 2005 - 20:37:47 CST)
AMBER: non bond over flow S.Sundar Raman (Wed Dec 28 2005 - 21:50:27 CST)
RE: AMBER: non bond over flow Ross Walker (Thu Dec 29 2005 - 10:15:35 CST)
AMBER:how to deal with metal ion? snowyowls (Fri Dec 30 2005 - 00:24:58 CST)
Re: AMBER:how to deal with metal ion? samuel.arey_at_epfl.ch (Fri Dec 30 2005 - 04:56:08 CST)
Re: AMBER:how to deal with metal ion? samuel.arey_at_epfl.ch (Fri Dec 30 2005 - 05:05:39 CST)
Re: AMBER:how to deal with metal ion? Tim Meyer (Fri Dec 30 2005 - 10:05:06 CST)
Re: AMBER:how to deal with metal ion? Tim Meyer (Fri Dec 30 2005 - 10:09:07 CST)
Re: AMBER: problem of calculate the charge David A. Case (Fri Dec 30 2005 - 11:58:47 CST)
Re: AMBER: ambpdb TER problems David A. Case (Fri Dec 30 2005 - 12:05:10 CST)
Re: AMBER: problem of calculate the charge ping jiang (Fri Dec 30 2005 - 12:48:41 CST)
Re: AMBER: antechamber problem Ilyas Yildirim (Fri Dec 30 2005 - 18:25:38 CST)
Re: AMBER: problem with ssh and xleap A D (Fri Dec 30 2005 - 21:06:15 CST)
AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU Cenk Andac (Sat Dec 31 2005 - 12:24:30 CST)

Last message date: Sat Dec 31 2005 - 12:51:27 CST
Archived on: Sat Dec 31 2005 - 12:51:44 CST

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