AMBER Archive (2007) - Aug 2007 By Date

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Starting: Wed Aug 01 2007 - 04:36:31 CDT
Ending: Fri Aug 31 2007 - 20:14:32 CDT

AMBER: how to calculate the ps/day of md simulation using using my cluster system in amber7 Syed Tarique Moin (Wed Aug 01 2007 - 04:36:31 CDT)
AMBER: problem compiling Amber9 on 64-machine fatima.chami_at_durham.ac.uk (Wed Aug 01 2007 - 06:03:48 CDT)
Fwd: RE: AMBER: Average potential energies and conformer ratios Francesco Pietra (Wed Aug 01 2007 - 08:58:02 CDT)
Re: AMBER: problem compiling Amber9 on 64-machine David A. Case (Wed Aug 01 2007 - 09:50:30 CDT)
Re: AMBER: problem compiling Amber9 on 64-machine S.Sundar Raman (Wed Aug 01 2007 - 10:46:10 CDT)
Re: AMBER: problem compiling Amber9 on 64-machine fatima.chami_at_durham.ac.uk (Wed Aug 01 2007 - 10:52:13 CDT)
Re: AMBER: problem compiling Amber9 on 64-machine fatima.chami_at_durham.ac.uk (Wed Aug 01 2007 - 10:55:26 CDT)
RE: AMBER: problem compiling Amber9 on 64-machine Ross Walker (Wed Aug 01 2007 - 11:10:17 CDT)
Re: AMBER: problem compiling Amber9 on 64-machine David A. Case (Wed Aug 01 2007 - 11:36:37 CDT)
Re: AMBER: problem compiling Amber9 on 64-machine David A. Case (Wed Aug 01 2007 - 11:43:21 CDT)
AMBER: Problem with Antechamber and point charges anna duraj (Wed Aug 01 2007 - 14:40:44 CDT)
Re: AMBER: Problem with Antechamber and point charges Carlos Simmerling (Wed Aug 01 2007 - 14:52:53 CDT)
AMBER: neutral terminals Jena M (Wed Aug 01 2007 - 19:15:46 CDT)
Re: AMBER: bugfix for impropers in parmchk Jiten (Wed Aug 01 2007 - 23:02:24 CDT)
Re: AMBER: bugfix for impropers in parmchk David A. Case (Thu Aug 02 2007 - 00:04:20 CDT)
Re: AMBER: problem compiling Amber9 on 64-machine S.Sundar Raman (Thu Aug 02 2007 - 00:03:32 CDT)
Re: AMBER: Problem while saving .top and .crd files. Anju Sharma (Thu Aug 02 2007 - 00:25:19 CDT)
Re: AMBER: bugfix for impropers in parmchk Jiten (Thu Aug 02 2007 - 01:23:20 CDT)
AMBER: Problem with antechamber Anju Sharma (Thu Aug 02 2007 - 01:34:39 CDT)
AMBER: (no subject) Syed Tarique Moin (Thu Aug 02 2007 - 01:50:59 CDT)
Re: AMBER: Problem with antechamber gurpreet singh (Thu Aug 02 2007 - 03:24:18 CDT)
Re: AMBER: (no subject) gurpreet singh (Thu Aug 02 2007 - 03:39:07 CDT)
Re: AMBER: Problem with antechamber Anju Sharma (Thu Aug 02 2007 - 04:03:36 CDT)
Re: AMBER: neutral terminals Carlos Simmerling (Thu Aug 02 2007 - 07:04:15 CDT)
Re: AMBER: (no subject) Syed Tarique Moin (Thu Aug 02 2007 - 07:36:21 CDT)
Re: AMBER: (no subject) Carlos Simmerling (Thu Aug 02 2007 - 07:48:36 CDT)
AMBER: planarity restraints for NA Seth Lilavivat (Thu Aug 02 2007 - 08:12:18 CDT)
Re: AMBER: planarity restraints for NA Carlos Simmerling (Thu Aug 02 2007 - 08:17:56 CDT)
Re: AMBER: planarity restraints for NA Seth Lilavivat (Thu Aug 02 2007 - 09:07:23 CDT)
AMBER: restrained md and mm pbsa Christopher Gaughan (Thu Aug 02 2007 - 09:15:17 CDT)
Re: AMBER: planarity restraints for NA Carlos Simmerling (Thu Aug 02 2007 - 09:17:32 CDT)
RE: AMBER: Problem while saving .top and .crd files. Ross Walker (Thu Aug 02 2007 - 09:54:21 CDT)
Re: AMBER: Problem with antechamber David A. Case (Thu Aug 02 2007 - 10:07:30 CDT)
RE: AMBER: Problem with antechamber Ross Walker (Thu Aug 02 2007 - 10:22:52 CDT)
AMBER: vector corrplane Servaas Michielssens (Thu Aug 02 2007 - 10:25:45 CDT)
AMBER: Force Field Parameters Beale, John (Thu Aug 02 2007 - 11:46:16 CDT)
AMBER: Calculating cumulative average Francesco Pietra (Thu Aug 02 2007 - 12:00:10 CDT)
Re: AMBER: planarity restraints for NA Seth Lilavivat (Thu Aug 02 2007 - 12:01:39 CDT)
Re: AMBER: Force Field Parameters Prashanth Athri (Thu Aug 02 2007 - 12:39:10 CDT)
AMBER: edit.out amber version 9 Greg Gannon (Thu Aug 02 2007 - 13:21:31 CDT)
Re: AMBER: edit.out amber version 9 David A. Case (Thu Aug 02 2007 - 14:00:22 CDT)
RE: AMBER: planarity restraints for NA Hu, Shaowen (JSC-SK)[USRA] (Thu Aug 02 2007 - 13:49:15 CDT)
AMBER: Problem generating .prepin file in Antechamber Lili Peng (Thu Aug 02 2007 - 14:07:11 CDT)
Re: AMBER: Problem generating .prepin file in Antechamber Lili Peng (Thu Aug 02 2007 - 14:15:41 CDT)
Re: AMBER: planarity restraints for NA Seth Lilavivat (Thu Aug 02 2007 - 14:29:42 CDT)
Re: AMBER: Force Field Parameters Raviprasad Aduri (Thu Aug 02 2007 - 14:49:37 CDT)
RE: AMBER: (no subject) Gustavo Seabra (Thu Aug 02 2007 - 15:19:05 CDT)
Re: AMBER: edit.out amber version 9 WANG,YING (Thu Aug 02 2007 - 15:33:49 CDT)
Re: AMBER: Problem generating .prepin file in Antechamber David A. Case (Thu Aug 02 2007 - 15:53:03 CDT)
Re: AMBER: Problem with antechamber Bill Ross (Thu Aug 02 2007 - 15:14:37 CDT)
AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Thu Aug 02 2007 - 19:33:40 CDT)
Re: AMBER: Antechamber formal charges with Gasteiger method Scott Brozell (Thu Aug 02 2007 - 20:44:28 CDT)
Re: AMBER: Any experience on Dell two quad core system? Ye Mei (Thu Aug 02 2007 - 22:57:00 CDT)
Re: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler (Thu Aug 02 2007 - 23:18:42 CDT)
Re: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Thu Aug 02 2007 - 23:23:17 CDT)
AMBER: Information about Amber 9 Lycourgos Chiniadis (Fri Aug 03 2007 - 00:11:17 CDT)
AMBER: force field for hydrogels Prem Prakash Pathak (Fri Aug 03 2007 - 01:03:48 CDT)
AMBER: unable to save prmtop/inpcrd for chcl3box Francesco Pietra (Fri Aug 03 2007 - 05:09:03 CDT)
AMBER: Successful compile on Mac OSX + Intel compilers Viv Kendon (Fri Aug 03 2007 - 07:28:56 CDT)
AMBER: Fwd: unable to save prmtop/inpcrd for chcl3box Francesco Pietra (Fri Aug 03 2007 - 07:24:24 CDT)
Re: AMBER: Information about Amber 9 David A. Case (Fri Aug 03 2007 - 09:53:22 CDT)
Re: AMBER: unable to save prmtop/inpcrd for chcl3box David A. Case (Fri Aug 03 2007 - 09:58:03 CDT)
Re: AMBER: bug in nonbond_list.f (nee ew_setup.f) David A. Case (Fri Aug 03 2007 - 10:14:27 CDT)
Re: AMBER: Successful compile on Mac OSX + Intel compilers Viv Kendon (Fri Aug 03 2007 - 11:00:57 CDT)
RE: AMBER: Any experience on Dell two quad core system? Ross Walker (Fri Aug 03 2007 - 11:28:57 CDT)
Re: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Fri Aug 03 2007 - 11:35:26 CDT)
Re: AMBER: Problem with Antechamber and point charges anna duraj (Fri Aug 03 2007 - 14:47:17 CDT)
Re: AMBER: Problem with Antechamber and point charges Carlos Simmerling (Fri Aug 03 2007 - 14:55:43 CDT)
Re: AMBER: Antechamber formal charges with Gasteiger method David A. Case (Fri Aug 03 2007 - 15:17:11 CDT)
AMBER: Binary file curiosities David LeBard (Fri Aug 03 2007 - 17:59:45 CDT)
Re: AMBER: Binary file curiosities David A. Case (Fri Aug 03 2007 - 18:21:25 CDT)
Re: AMBER: Binary file curiosities Thomas Cheatham III (Fri Aug 03 2007 - 18:32:55 CDT)
RE: AMBER: (no subject) Syed Tarique Moin (Sat Aug 04 2007 - 01:11:51 CDT)
AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 03:32:40 CDT)
Re: AMBER: (no subject) Carlos Simmerling (Sat Aug 04 2007 - 05:55:29 CDT)
AMBER: nucleic acid electrostatic energy Tiago Sobreira (Sat Aug 04 2007 - 08:45:46 CDT)
Re: AMBER: (no subject) Syed Tarique Moin (Sat Aug 04 2007 - 09:07:23 CDT)
Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson (Sat Aug 04 2007 - 09:32:17 CDT)
AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 09:33:35 CDT)
Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson (Sat Aug 04 2007 - 09:51:22 CDT)
Re: AMBER: nucleic acid electrostatic energy David A. Case (Sat Aug 04 2007 - 10:28:36 CDT)
RE: AMBER: (no subject) Ross Walker (Sat Aug 04 2007 - 10:30:36 CDT)
RE: AMBER: Fwd: QM region + cutoff larger that box Gustavo Seabra (Sat Aug 04 2007 - 10:33:12 CDT)
AMBER: GAFF atom typing for flavin Hans Martin Senn (Sat Aug 04 2007 - 11:15:30 CDT)
Re: AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 11:42:33 CDT)
AMBER: force field for irregulate DNA ends Hu, Shaowen (JSC-SK)[USRA] (Sat Aug 04 2007 - 13:20:42 CDT)
Re: AMBER: Antechamber formal charges with Gasteiger method Scott Brozell (Sat Aug 04 2007 - 14:42:43 CDT)
AMBER: setting dimensions of truncated octahedron Lillian chong (Sat Aug 04 2007 - 15:34:59 CDT)
Re: AMBER: Binary file curiosities David LeBard (Sat Aug 04 2007 - 16:34:23 CDT)
Re: AMBER: setting dimensions of truncated octahedron Thomas Cheatham (Sat Aug 04 2007 - 17:38:15 CDT)
Re: AMBER: setting dimensions of truncated octahedron Lillian chong (Sun Aug 05 2007 - 08:25:01 CDT)
AMBER: RE: tutorial file polyAT_vac.prmtop Ross Walker (Sun Aug 05 2007 - 22:09:46 CDT)
AMBER: Problem while carrying out minimisation of drug molecule using sander Anju Sharma (Sun Aug 05 2007 - 22:51:11 CDT)
RE: AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Mon Aug 06 2007 - 01:28:13 CDT)
Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson (Mon Aug 06 2007 - 07:58:56 CDT)
AMBER: Specific heat graph is a straight line priya priya (Mon Aug 06 2007 - 08:33:52 CDT)
Re: AMBER: Problem while carrying out minimisation of drug molecule using sander David A. Case (Mon Aug 06 2007 - 09:35:25 CDT)
Re: AMBER: Binary file curiosities David A. Case (Mon Aug 06 2007 - 10:03:07 CDT)
Re: AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Mon Aug 06 2007 - 10:07:09 CDT)
Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson (Mon Aug 06 2007 - 10:29:43 CDT)
RE: AMBER: Fwd: QM region + cutoff larger that box Gustavo Seabra (Mon Aug 06 2007 - 10:38:19 CDT)
AMBER: Integrating the alpha-helix bias correction into ff94 Andrew Borgert (Mon Aug 06 2007 - 14:18:58 CDT)
Re: AMBER: Integrating the alpha-helix bias correction into ff94 Carlos Simmerling (Mon Aug 06 2007 - 14:42:17 CDT)
AMBER: hybridization in Amber, pertaining to resonant structures, ions Karen Callahan (Mon Aug 06 2007 - 23:13:27 CDT)
Re: AMBER: Problem while carrying out minimisation of drug molecule using sander Anju Sharma (Tue Aug 07 2007 - 00:32:43 CDT)
AMBER: heical content in simulations priya priya (Tue Aug 07 2007 - 02:58:12 CDT)
Re: AMBER: heical content in simulations Chng Choon-Peng (Tue Aug 07 2007 - 03:19:26 CDT)
Re: AMBER: heical content in simulations priya priya (Tue Aug 07 2007 - 03:41:16 CDT)
Re: AMBER: Problem while carrying out minimisation of drug molecule using sander Carlos Simmerling (Tue Aug 07 2007 - 05:57:53 CDT)
AMBER: Problem with minimization Syed Tarique Moin (Tue Aug 07 2007 - 08:11:32 CDT)
AMBER: compile amber8 with mpich2 Kailee (Tue Aug 07 2007 - 08:18:14 CDT)
RE: AMBER: Problem with minimization Ross Walker (Tue Aug 07 2007 - 08:57:18 CDT)
AMBER: Positive EPtot in QM-MM Francesco Pietra (Tue Aug 07 2007 - 09:34:35 CDT)
AMBER: about shake linfu (Tue Aug 07 2007 - 20:36:59 CDT)
AMBER: msubhamoy_at_ibab.ac.in (Wed Aug 08 2007 - 08:01:00 CDT)
AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA msubhamoy_at_ibab.ac.in (Wed Aug 08 2007 - 08:08:04 CDT)
RE: AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA Ross Walker (Wed Aug 08 2007 - 09:49:11 CDT)
AMBER: RE: TUTORIAL B1 file polyAT_vac.prmtop Ross Walker (Wed Aug 08 2007 - 09:52:39 CDT)
Re: AMBER: about shake Steven Winfield (Wed Aug 08 2007 - 10:59:45 CDT)
AMBER: RE: Problem loading pdf into tleap Ross Walker (Wed Aug 08 2007 - 12:29:19 CDT)
Re: AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA linfu (Wed Aug 08 2007 - 08:33:58 CDT)
Re: AMBER: bug in nonbond_list.f (nee ew_setup.f) neville forlemu (Wed Aug 08 2007 - 13:35:51 CDT)
AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 16:33:22 CDT)
Re: AMBER: Cygwin error Bill Ross (Wed Aug 08 2007 - 16:43:49 CDT)
Re: AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 16:56:00 CDT)
Re: AMBER: Cygwin error Mark Williamson (Wed Aug 08 2007 - 17:02:15 CDT)
Re: AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 17:13:54 CDT)
Re: AMBER: Cygwin error Gustavo Seabra (Wed Aug 08 2007 - 17:21:01 CDT)
Re: AMBER: Cygwin error Bill Ross (Wed Aug 08 2007 - 17:29:24 CDT)
Re: AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 18:04:31 CDT)
Re: AMBER: Cygwin error Gustavo Seabra (Wed Aug 08 2007 - 18:36:29 CDT)
Re: Re: AMBER: about shake linfu (Wed Aug 08 2007 - 20:10:05 CDT)
Re: AMBER: program bug? M. Maeda (Wed Aug 08 2007 - 21:37:13 CDT)
Re: AMBER: compile amber8 with mpich2 Scott Brozell (Wed Aug 08 2007 - 21:46:22 CDT)
AMBER: how to combine two molecules Wenyong Tong (Thu Aug 09 2007 - 00:34:33 CDT)
Re: AMBER: Cygwin error Lili Peng (Thu Aug 09 2007 - 13:13:27 CDT)
RE: AMBER: Cygwin error Ross Walker (Thu Aug 09 2007 - 13:52:36 CDT)
Re: AMBER: Cygwin error Lili Peng (Thu Aug 09 2007 - 14:06:03 CDT)
Re: AMBER: Cygwin error Gustavo Seabra (Thu Aug 09 2007 - 14:08:27 CDT)
Re: AMBER: Cygwin error Lili Peng (Thu Aug 09 2007 - 14:16:20 CDT)
AMBER: NVE energy and temperature drift Nikola Trbovic (Thu Aug 09 2007 - 15:24:11 CDT)
Re: AMBER: Cygwin error Gustavo Seabra (Thu Aug 09 2007 - 15:30:19 CDT)
Re: AMBER: Cygwin error Bill Ross (Thu Aug 09 2007 - 15:42:48 CDT)
Re: AMBER: Cygwin error Gustavo Seabra (Thu Aug 09 2007 - 16:40:14 CDT)
Re: AMBER: NVE energy and temperature drift Robert Duke (Thu Aug 09 2007 - 17:15:58 CDT)
Re: AMBER: NVE energy and temperature drift Thomas Cheatham III (Thu Aug 09 2007 - 17:27:50 CDT)
Re: AMBER: NVE energy and temperature drift Nikola Trbovic (Thu Aug 09 2007 - 17:50:45 CDT)
Re: AMBER: NVE energy and temperature drift Robert Duke (Thu Aug 09 2007 - 18:43:42 CDT)
RE: AMBER: NVE energy and temperature drift Nikola Trbovic (Thu Aug 09 2007 - 19:11:07 CDT)
Re: AMBER: NVE energy and temperature drift Robert Duke (Thu Aug 09 2007 - 21:15:19 CDT)
Re: AMBER: NVE energy and temperature drift Vlad Cojocaru (Fri Aug 10 2007 - 04:03:15 CDT)
Re: AMBER: NVE energy and temperature drift Vlad Cojocaru (Fri Aug 10 2007 - 04:10:51 CDT)
Re: AMBER: how to combine two molecules Benjamin Juhl (Fri Aug 10 2007 - 04:11:07 CDT)
AMBER: Implicit solvent simulation is too slow. SeungPyo Hong (Fri Aug 10 2007 - 07:42:11 CDT)
Re: AMBER: Implicit solvent simulation is too slow. Carlos Simmerling (Fri Aug 10 2007 - 08:07:50 CDT)
Re: AMBER: Implicit solvent simulation is too slow. SeungPyo Hong (Fri Aug 10 2007 - 09:04:28 CDT)
AMBER: How to couple only one residue to the temperature bath? Michael Lerner (Fri Aug 10 2007 - 09:45:10 CDT)
RE: AMBER: Implicit solvent simulation is too slow. Ross Walker (Fri Aug 10 2007 - 10:56:32 CDT)
Re: AMBER: How to couple only one residue to the temperature bath? Carlos Simmerling (Fri Aug 10 2007 - 10:55:02 CDT)
AMBER: short 2'OH-OP contacts in RNA Jose Gallego (Fri Aug 10 2007 - 11:22:35 CDT)
AMBER: vlimit exceeded for the step Sudha Mani Karra (Fri Aug 10 2007 - 14:31:08 CDT)
RE: AMBER: vlimit exceeded for the step Ross Walker (Fri Aug 10 2007 - 15:04:10 CDT)
AMBER: Steve Seibold (Fri Aug 10 2007 - 15:17:47 CDT)
Re: AMBER: Thomas Pochapsky (Fri Aug 10 2007 - 15:34:32 CDT)
Re: AMBER: How to couple only one residue to the temperature bath? Michael Lerner (Fri Aug 10 2007 - 16:35:38 CDT)
Re: AMBER: How to couple only one residue to the temperature bath? Carlos Simmerling (Fri Aug 10 2007 - 17:43:29 CDT)
AMBER: Citation for Langevin thermostat? Marc Baaden (Sat Aug 11 2007 - 02:13:28 CDT)
AMBER: Using charmm force field in amber Seongeun Yang (Sat Aug 11 2007 - 03:44:44 CDT)
AMBER: Failure to SCF convergence Francesco Pietra (Sat Aug 11 2007 - 11:56:53 CDT)
Re: AMBER: Citation for Langevin thermostat? David A. Case (Sat Aug 11 2007 - 14:47:59 CDT)
AMBER: imin=5 and inptraj Nikola Trbovic (Sat Aug 11 2007 - 15:11:08 CDT)
Re: AMBER: NVE energy and temperature drift David A. Case (Sat Aug 11 2007 - 15:28:30 CDT)
Re: AMBER: hybridization in Amber, pertaining to resonant structures, ions David A. Case (Sat Aug 11 2007 - 15:35:15 CDT)
Re: AMBER: imin=5 and inptraj Carlos Simmerling (Sat Aug 11 2007 - 16:23:29 CDT)
Re: AMBER: imin=5 and inptraj Nikola Trbovic (Sat Aug 11 2007 - 16:31:40 CDT)
Re: AMBER: NVE energy and temperature drift Nikola Trbovic (Sat Aug 11 2007 - 16:33:09 CDT)
Re: AMBER: imin=5 and inptraj Chris Moth (Sat Aug 11 2007 - 16:37:11 CDT)
AMBER: Neutralize charges for simulated annealing? Francesco Pietra (Sat Aug 11 2007 - 17:35:30 CDT)
RE: AMBER: Failure to SCF convergence Ross Walker (Sat Aug 11 2007 - 18:14:54 CDT)
Re: AMBER: how to combine two molecules Wenyong Tong (Sat Aug 11 2007 - 20:48:48 CDT)
RE: AMBER: Failure to SCF convergence & parallelization and memory Francesco Pietra (Sun Aug 12 2007 - 02:37:33 CDT)
AMBER: MM_PBSA No radius found for Br!! Urszula Uciechowska (Mon Aug 13 2007 - 04:52:34 CDT)
Re: AMBER: MM_PBSA No radius found for Br!! Antonio Morreale (Mon Aug 13 2007 - 06:39:52 CDT)
RE: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler (Mon Aug 13 2007 - 10:12:15 CDT)
Re: AMBER: Any experience on Dell two quad core system? M. L. Dodson (Mon Aug 13 2007 - 10:59:11 CDT)
AMBER: setbox command error priya priya (Mon Aug 13 2007 - 11:18:16 CDT)
Re: AMBER: how to combine two molecules David A. Case (Mon Aug 13 2007 - 11:43:57 CDT)
RE: AMBER: Failure to SCF convergence & parallelization and memory Ross Walker (Mon Aug 13 2007 - 12:16:25 CDT)
Re: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler (Mon Aug 13 2007 - 12:21:39 CDT)
AMBER: unsubscribe Pan, Yongmei (Mon Aug 13 2007 - 12:35:12 CDT)
Re: AMBER: Any experience on Dell two quad core system? M. L. Dodson (Mon Aug 13 2007 - 12:37:47 CDT)
RE: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Mon Aug 13 2007 - 14:25:22 CDT)
Re: AMBER: setbox command error David A. Case (Mon Aug 13 2007 - 15:38:30 CDT)
RE: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler (Mon Aug 13 2007 - 15:46:58 CDT)
Re: AMBER: Any experience on Dell two quad core system? David Cerutti (Mon Aug 13 2007 - 15:59:58 CDT)
AMBER: Using TLEAP to set up MD in the crystal lattice space? David Cerutti (Mon Aug 13 2007 - 16:09:51 CDT)
Re: AMBER: how to combine two molecules Wenyong Tong (Mon Aug 13 2007 - 18:14:49 CDT)
Re: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Mon Aug 13 2007 - 19:39:01 CDT)
Re: AMBER: Using TLEAP to set up MD in the crystal lattice space? David A. Case (Mon Aug 13 2007 - 20:26:24 CDT)
Re: AMBER: Using TLEAP to set up MD in the crystal lattice space? Thomas Cheatham (Mon Aug 13 2007 - 21:45:19 CDT)
AMBER: Normal Mode Analysis Kresimir Sikic (Mon Aug 13 2007 - 10:12:59 CDT)
AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 01:03:07 CDT)
AMBER: regarding implicit simulation gurpreet singh (Tue Aug 14 2007 - 01:21:35 CDT)
Re: AMBER: setbox command error priya priya (Tue Aug 14 2007 - 01:42:45 CDT)
Re: AMBER: setbox command error Steven Winfield (Tue Aug 14 2007 - 02:45:08 CDT)
AMBER: MMPBSA NOT Getting results msubhamoy_at_ibab.ac.in (Tue Aug 14 2007 - 03:26:57 CDT)
Re: AMBER: Machine environment to install AMBER 8 Benjamin Juhl (Tue Aug 14 2007 - 03:28:09 CDT)
RE: AMBER: MMPBSA NOT Getting results Rafi Ahmad (Tue Aug 14 2007 - 03:34:35 CDT)
AMBER: How to carry out drug-dna complex simulations Anju Sharma (Tue Aug 14 2007 - 03:50:04 CDT)
Re: AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 03:54:03 CDT)
Re: AMBER: setbox command error priya priya (Tue Aug 14 2007 - 03:58:40 CDT)
Re: AMBER: setbox command error Steven Winfield (Tue Aug 14 2007 - 04:00:39 CDT)
Re: AMBER: Machine environment to install AMBER 8 Benjamin Juhl (Tue Aug 14 2007 - 04:10:16 CDT)
Re: AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 04:19:37 CDT)
Re: AMBER: Machine environment to install AMBER 8 Bertrand Russell (Tue Aug 14 2007 - 04:21:07 CDT)
Re: AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 04:45:53 CDT)
Re: AMBER: Machine environment to install AMBER 8 Bertrand Russell (Tue Aug 14 2007 - 04:50:07 CDT)
AMBER: Tutorial about SMD? Qiang Zhong (Tue Aug 14 2007 - 05:19:09 CDT)
Re: AMBER: Machine environment to install AMBER 8 Benjamin Juhl (Tue Aug 14 2007 - 05:49:13 CDT)
Re: AMBER: regarding implicit simulation Carlos Simmerling (Tue Aug 14 2007 - 06:22:24 CDT)
AMBER: Parallelizin antechamber? Francesco Pietra (Tue Aug 14 2007 - 08:29:11 CDT)
Re: AMBER: MM_PBSA No radius found for Br!! Urszula Uciechowska (Tue Aug 14 2007 - 08:49:06 CDT)
Re: AMBER: Parallelizin antechamber? M. L. Dodson (Tue Aug 14 2007 - 09:29:16 CDT)
Re: AMBER: Any experience on Dell two quad core system? David Cerutti (Tue Aug 14 2007 - 10:05:34 CDT)
Re: AMBER: How to carry out drug-dna complex simulations David A. Case (Tue Aug 14 2007 - 10:18:47 CDT)
Re: AMBER: David A. Case (Tue Aug 14 2007 - 10:27:48 CDT)
AMBER: MM_PBSA No radius found for Br!! Urszula Uciechowska (Tue Aug 14 2007 - 10:53:32 CDT)
Re: AMBER: Any experience on Dell two quad core system? Robert Duke (Tue Aug 14 2007 - 11:13:07 CDT)
AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 15:31:34 CDT)
Re: AMBER: torsional restraints in a solvated MD simulation. Carlos Simmerling (Tue Aug 14 2007 - 15:41:52 CDT)
Re: AMBER: torsional restraints in a solvated MD simulation. David A. Case (Tue Aug 14 2007 - 15:50:31 CDT)
Re: AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 18:11:27 CDT)
Re: AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 18:15:06 CDT)
Re: AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 20:04:24 CDT)
Re: AMBER: Machine environment to install AMBER 8 M. Maeda (Wed Aug 15 2007 - 00:17:03 CDT)
Re: AMBER: Machine environment to install AMBER 8 Bertrand Russell (Wed Aug 15 2007 - 01:34:02 CDT)
AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 03:43:45 CDT)
AMBER: Building parallel Amber 9.0 Beale, John (Wed Aug 15 2007 - 07:21:56 CDT)
Re: AMBER: antechamber, how does it work Junmei Wang (Wed Aug 15 2007 - 08:33:36 CDT)
Re: AMBER: Parallelizin antechamber? Junmei Wang (Wed Aug 15 2007 - 08:41:45 CDT)
Re: AMBER: Building parallel Amber 9.0 Gustavo Seabra (Wed Aug 15 2007 - 08:46:59 CDT)
Re: AMBER: antechamber, how does it work Gustavo Seabra (Wed Aug 15 2007 - 09:15:48 CDT)
Re: AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 09:25:12 CDT)
RE: AMBER: Building parallel Amber 9.0 Ross Walker (Wed Aug 15 2007 - 09:26:36 CDT)
AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra (Wed Aug 15 2007 - 09:38:06 CDT)
Re: AMBER: Distance restraints between center of mass of two molecules Carlos Simmerling (Wed Aug 15 2007 - 09:54:40 CDT)
Re: AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 10:05:31 CDT)
Re: AMBER: antechamber, how does it work Seth Hayik (Wed Aug 15 2007 - 10:10:22 CDT)
Re: AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra (Wed Aug 15 2007 - 10:40:37 CDT)
RE: AMBER: Building parallel Amber 9.0 Rajendra P. OJHA (Wed Aug 15 2007 - 10:41:25 CDT)
Re: AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra (Wed Aug 15 2007 - 10:40:37 CDT)
RE: AMBER: Building parallel Amber 9.0 Rajendra P. OJHA (Wed Aug 15 2007 - 10:44:10 CDT)
Re: AMBER: Distance restraints between center of mass of two molecules Carlos Simmerling (Wed Aug 15 2007 - 10:52:27 CDT)
Re: AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 11:08:37 CDT)
AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade (Wed Aug 15 2007 - 11:50:57 CDT)
Re: AMBER: antechamber, how does it work David A. Case (Wed Aug 15 2007 - 12:07:22 CDT)
AMBER: docking ability anna duraj (Wed Aug 15 2007 - 12:34:37 CDT)
Re: AMBER: EXTRA_PTS: frtype 2 Should not be here David A. Case (Wed Aug 15 2007 - 12:34:49 CDT)
RE: AMBER: Building parallel Amber 9.0 Ross Walker (Wed Aug 15 2007 - 12:43:28 CDT)
AMBER: Bug in ptraj mask processing? Steve Spronk (Wed Aug 15 2007 - 14:18:15 CDT)
Re: AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra (Wed Aug 15 2007 - 16:02:55 CDT)
Re: AMBER: Distance restraints between center of mass of two molecules Carlos Simmerling (Wed Aug 15 2007 - 16:17:33 CDT)
Re: AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 16:53:55 CDT)
Re: AMBER: Normal Mode Analysis David A. Case (Wed Aug 15 2007 - 17:56:46 CDT)
Re: AMBER: antechamber, how does it work Thomas Cheatham III (Wed Aug 15 2007 - 18:02:07 CDT)
RE: AMBER: Building parallel Amber 9.0 Balvinder Singh (Wed Aug 15 2007 - 22:53:44 CDT)
RE: AMBER: Building parallel Amber 9.0 Balvinder Singh (Wed Aug 15 2007 - 23:02:38 CDT)
Re: AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade (Wed Aug 15 2007 - 23:39:37 CDT)
Re: AMBER: antechamber, how does it work Francesco Pietra (Thu Aug 16 2007 - 00:53:34 CDT)
Re: AMBER: antechamber, how does it work David A. Case (Thu Aug 16 2007 - 10:40:16 CDT)
Re: AMBER: EXTRA_PTS: frtype 2 Should not be here David A. Case (Thu Aug 16 2007 - 11:33:52 CDT)
Re: AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade (Thu Aug 16 2007 - 11:52:56 CDT)
Re: AMBER: antechamber, how does it work Francesco Pietra (Thu Aug 16 2007 - 12:25:35 CDT)
AMBER: Missplaced TERs Steve Seibold (Thu Aug 16 2007 - 13:35:26 CDT)
Re: AMBER: Missplaced TERs David A. Case (Thu Aug 16 2007 - 13:53:10 CDT)
RE: AMBER: Missplaced TERs Steve Seibold (Thu Aug 16 2007 - 14:47:38 CDT)
AMBER: What is the best computer for running AMBER simulations? Lili Peng (Thu Aug 16 2007 - 16:37:03 CDT)
Re: AMBER: What is the best computer for running AMBER simulations? David LeBard (Thu Aug 16 2007 - 17:17:42 CDT)
Re: AMBER: What is the best computer for running AMBER simulations? Andreas Svrcek-Seiler (Thu Aug 16 2007 - 17:51:06 CDT)
Re: AMBER: MPI Quiescence problem in REMD In Hee Park (Thu Aug 16 2007 - 17:56:37 CDT)
Re: AMBER: What is the best computer for running AMBER simulations? David A. Case (Thu Aug 16 2007 - 18:42:54 CDT)
Re: AMBER: What is the best computer for running AMBER simulations? Yu Chen (Thu Aug 16 2007 - 22:44:49 CDT)
Re: AMBER: What is the best computer for running AMBER simulations? Lili Peng (Thu Aug 16 2007 - 23:50:42 CDT)
AMBER: NAN and vlimit exceeded errors in restrained MD.. using IBELLY Sandeep Kaushik (Fri Aug 17 2007 - 00:44:17 CDT)
Re: AMBER: about parallelization in QM-MM Francesco Pietra (Fri Aug 17 2007 - 01:41:02 CDT)
AMBER: Thermodynamic Integration for a CHARGED molecule ming hui (Fri Aug 17 2007 - 04:12:38 CDT)
AMBER: MPI Beale, John (Fri Aug 17 2007 - 07:00:33 CDT)
Re: AMBER: MPI Mark Williamson (Fri Aug 17 2007 - 07:58:00 CDT)
Re: AMBER: Thermodynamic Integration for a CHARGED molecule David Mobley (Fri Aug 17 2007 - 08:56:33 CDT)
Re: AMBER: Thermodynamic Integration for a CHARGED molecule David A. Case (Fri Aug 17 2007 - 10:46:38 CDT)
RE: AMBER: about parallelization in QM-MM Ross Walker (Fri Aug 17 2007 - 11:58:54 CDT)
AMBER: Molsurf error Pankaj R. Daga (Fri Aug 17 2007 - 12:46:54 CDT)
RE: AMBER: about parallelization in QM-MM Ross Walker (Fri Aug 17 2007 - 13:45:08 CDT)
AMBER: ptraj hydrogen bonding defaults Michael Lerner (Fri Aug 17 2007 - 17:26:09 CDT)
Re: AMBER: ptraj hydrogen bonding defaults Thomas Cheatham (Fri Aug 17 2007 - 21:33:55 CDT)
AMBER: DFTB email address Francesco Pietra (Sat Aug 18 2007 - 02:14:53 CDT)
Re: AMBER: What is the best computer for running AMBER simulations? Prem Prakash Pathak (Sat Aug 18 2007 - 04:36:00 CDT)
AMBER: question about a 20 kDa protein David A. Case (Sat Aug 18 2007 - 11:07:09 CDT)
AMBER: charges in PBSA calculation Neha Gandhi (Sat Aug 18 2007 - 21:20:16 CDT)
Re: AMBER: charges in PBSA calculation Ray Luo (Sun Aug 19 2007 - 08:32:19 CDT)
Re: AMBER: MM_PBSA No radius found for Br!! Scott Brozell (Sun Aug 19 2007 - 12:40:20 CDT)
Re: AMBER: How to carry out drug-dna complex simulations Scott Brozell (Sun Aug 19 2007 - 13:06:22 CDT)
Re: AMBER: docking ability Scott Brozell (Sun Aug 19 2007 - 13:19:08 CDT)
Re: AMBER: DFTB email address tomas.kubar_at_marge.uochb.cas.cz (Sun Aug 19 2007 - 15:27:48 CDT)
Re: AMBER: charges in PBSA calculation Neha Gandhi (Sun Aug 19 2007 - 18:01:47 CDT)
Re: AMBER: charges in PBSA calculation David A. Case (Sun Aug 19 2007 - 19:57:14 CDT)
AMBER: CRESP charges in antechamber prepin Francesco Pietra (Mon Aug 20 2007 - 02:23:24 CDT)
AMBER: mmpbsa calculation msubhamoy_at_ibab.ac.in (Mon Aug 20 2007 - 04:53:42 CDT)
AMBER: TEST_FAILURES Qiang Zhong (Mon Aug 20 2007 - 07:59:28 CDT)
Re: AMBER: TEST_FAILURES Martin Stennett (Mon Aug 20 2007 - 07:56:36 CDT)
AMBER: Entropy in MM_PBSA Sergey Samsonov (Mon Aug 20 2007 - 10:01:37 CDT)
AMBER: Beale, John (Mon Aug 20 2007 - 10:41:06 CDT)
Re: AMBER: David A. Case (Mon Aug 20 2007 - 19:31:21 CDT)
Re: AMBER: TEST_FAILURES Qiang Zhong (Mon Aug 20 2007 - 19:43:23 CDT)
AMBER: $tleap is not normal Qiang Zhong (Mon Aug 20 2007 - 20:34:00 CDT)
RE: AMBER: $tleap is not normal Ross Walker (Mon Aug 20 2007 - 21:51:16 CDT)
AMBER: Regarding free energy calculation and covalent bond nag raj (Mon Aug 20 2007 - 23:07:04 CDT)
AMBER: Error in MMPBSA Calculation msubhamoy_at_ibab.ac.in (Tue Aug 21 2007 - 00:53:17 CDT)
Re: AMBER: Error in MMPBSA Calculation jitrayut jitonnom (Tue Aug 21 2007 - 02:11:52 CDT)
AMBER: command tleap is not normal Qiang Zhong (Tue Aug 21 2007 - 03:12:44 CDT)
Re: AMBER: command tleap is not normal Ilyas Yildirim (Tue Aug 21 2007 - 03:50:35 CDT)
AMBER: how to include mpirun in this script Syed Tarique Moin (Tue Aug 21 2007 - 05:50:12 CDT)
AMBER: How to use AMBER Parameter Database ? Qiang Zhong (Tue Aug 21 2007 - 07:36:46 CDT)
AMBER: Thermodynamic Integration for conformational changes? Francesco Pietra (Tue Aug 21 2007 - 11:57:47 CDT)
RE: AMBER: how to include mpirun in this script Ross Walker (Tue Aug 21 2007 - 13:45:23 CDT)
AMBER: xLeap "Could not find type" error Lili Peng (Tue Aug 21 2007 - 14:28:46 CDT)
AMBER: Octahedral box orientation David Cerutti (Tue Aug 21 2007 - 08:08:38 CDT)
AMBER: Force field for RNA with U-turn motif Cenk Andac (Tue Aug 21 2007 - 08:52:48 CDT)
AMBER: Tutorial of document about QM/MM in reaction pathways? Qiang Zhong (Tue Aug 21 2007 - 09:06:53 CDT)
Re: AMBER: Octahedral box orientation David Cerutti (Tue Aug 21 2007 - 19:07:32 CDT)
Re: AMBER: xLeap "Could not find type" error David A. Case (Tue Aug 21 2007 - 19:40:09 CDT)
Re: AMBER: xLeap "Could not find type" error Lili Peng (Tue Aug 21 2007 - 20:17:44 CDT)
Re: AMBER: Thermodynamic Integration for conformational changes? Gustavo Seabra (Tue Aug 21 2007 - 22:33:36 CDT)
Re: AMBER: Thermodynamic Integration for conformational changes? Gustavo Seabra (Tue Aug 21 2007 - 22:41:23 CDT)
AMBER: a question about xleap WANG,YING (Tue Aug 21 2007 - 14:16:48 CDT)
Re: AMBER: Thermodynamic Integration for conformational changes? Francesco Pietra (Wed Aug 22 2007 - 01:53:15 CDT)
Re: AMBER: Force field for RNA with U-turn motif Vlad Cojocaru (Wed Aug 22 2007 - 03:07:24 CDT)
AMBER: How to use AMBER Parameter Database ? Qiang Zhong (Wed Aug 22 2007 - 03:53:04 CDT)
AMBER: How to delete particular frame from mdcrd file (not with ptraj). saurabh agrawal (Wed Aug 22 2007 - 04:48:52 CDT)
Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj). Steven Winfield (Wed Aug 22 2007 - 05:12:16 CDT)
Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj). saurabh agrawal (Wed Aug 22 2007 - 05:25:53 CDT)
AMBER: MM-PBSA calculations of entropy within the sphere Sergey Samsonov (Wed Aug 22 2007 - 08:49:25 CDT)
AMBER: xLeap "Could not find type" error WANG,YING (Wed Aug 22 2007 - 09:04:37 CDT)
Re: AMBER: xLeap "Could not find type" error David A. Case (Wed Aug 22 2007 - 10:15:25 CDT)
Re: AMBER: xLeap "Could not find type" error Wei Zhang (Wed Aug 22 2007 - 10:18:11 CDT)
Re: AMBER: xLeap "Could not find type" error David A. Case (Wed Aug 22 2007 - 10:45:02 CDT)
Re: AMBER: xLeap "Could not find type" error WANG,YING (Wed Aug 22 2007 - 10:46:58 CDT)
Re: AMBER: Force field for RNA with U-turn motif Cenk Andac (Wed Aug 22 2007 - 11:08:29 CDT)
Re: AMBER: Force field for RNA with U-turn motif Jiri Sponer (Wed Aug 22 2007 - 11:33:46 CDT)
Re: AMBER: Force field for RNA with U-turn motif Cenk Andac (Wed Aug 22 2007 - 13:31:04 CDT)
AMBER: Running Gaussian to get .out files Lili Peng (Wed Aug 22 2007 - 15:27:25 CDT)
AMBER: Performance of polarizable model simulations Jones de Andrade (Wed Aug 22 2007 - 23:17:52 CDT)
AMBER: Parse charges for small molecules Neha Gandhi (Wed Aug 22 2007 - 23:50:38 CDT)
AMBER: Ca(2+) parameter Qiang Zhong (Thu Aug 23 2007 - 06:01:24 CDT)
RE: AMBER: Running Gaussian to get .out files Steve Spronk (Thu Aug 23 2007 - 08:05:25 CDT)
RE: AMBER: How to delete particular frame from mdcrd file (not with ptraj). Steve Spronk (Thu Aug 23 2007 - 08:25:50 CDT)
[Fwd: Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj).] Steven Winfield (Thu Aug 23 2007 - 08:31:49 CDT)
Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj). Adrian Roitberg (Thu Aug 23 2007 - 08:32:28 CDT)
Re: AMBER: Ca(2+) parameter David A. Case (Thu Aug 23 2007 - 10:04:01 CDT)
AMBER: Unable to open MDCRD file using vmd priya priya (Thu Aug 23 2007 - 10:04:19 CDT)
AMBER: How to perform MD simulation in NVT ensemble? WANG,YING (Thu Aug 23 2007 - 11:13:51 CDT)
Re: AMBER: How to use AMBER Parameter Database ? David A. Case (Thu Aug 23 2007 - 11:53:55 CDT)
Re: AMBER: Regarding free energy calculation and covalent bond David A. Case (Thu Aug 23 2007 - 11:52:17 CDT)
Re: AMBER: How to perform MD simulation in NVT ensemble? Chris Moth (Thu Aug 23 2007 - 12:07:30 CDT)
RE: AMBER: Unable to open MDCRD file using vmd Ross Walker (Thu Aug 23 2007 - 15:40:27 CDT)
AMBER: Prepin error (?) in xleap Lili Peng (Thu Aug 23 2007 - 16:04:03 CDT)
Re: AMBER: How to perform MD simulation in NVT ensemble? WANG,YING (Thu Aug 23 2007 - 15:53:05 CDT)
Re: AMBER: Prepin error (?) in xleap David A. Case (Thu Aug 23 2007 - 19:28:29 CDT)
AMBER: protonation of His residue! Qiang Zhong (Thu Aug 23 2007 - 21:39:51 CDT)
Re: AMBER: protonation of His residue! jitrayut jitonnom (Thu Aug 23 2007 - 22:52:51 CDT)
AMBER: ow to split MDCRD file using ptraj priya priya (Fri Aug 24 2007 - 02:34:27 CDT)
AMBER: QM/MM in reaction pathways? Qiang Zhong (Fri Aug 24 2007 - 03:00:50 CDT)
AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 05:19:30 CDT)
AMBER: SMD simulation Qiang Zhong (Fri Aug 24 2007 - 05:33:41 CDT)
AMBER: NETCDF Geoff Wood (Fri Aug 24 2007 - 05:43:11 CDT)
Re: AMBER: SMD simulation Adrian Roitberg (Fri Aug 24 2007 - 07:43:35 CDT)
Re: AMBER: NETCDF Chris Moth (Fri Aug 24 2007 - 07:58:34 CDT)
AMBER: articles Beale, John (Fri Aug 24 2007 - 08:02:05 CDT)
AMBER: NETCDF Chris Moth (Fri Aug 24 2007 - 08:03:37 CDT)
Re: AMBER: solvateCap minin and mdin for qm-mm dftb M. L. Dodson (Fri Aug 24 2007 - 08:11:06 CDT)
RE: AMBER: solvateCap minin and mdin for qm-mm dftb Ross Walker (Fri Aug 24 2007 - 08:10:54 CDT)
RE: AMBER: SMD simulation Ross Walker (Fri Aug 24 2007 - 08:12:43 CDT)
AMBER: PM6? Thomas Patko (CSULB) (Fri Aug 24 2007 - 08:46:16 CDT)
AMBER: Running Gaussian to get .out files Steve Spronk (Fri Aug 24 2007 - 09:08:13 CDT)
Re: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 11:01:31 CDT)
Re: AMBER: solvateCap minin and mdin for qm-mm dftb M. L. Dodson (Fri Aug 24 2007 - 11:17:37 CDT)
Re: AMBER: Entropy in MM_PBSA David Mobley (Fri Aug 24 2007 - 11:31:28 CDT)
RE: AMBER: PM6? Ross Walker (Fri Aug 24 2007 - 11:36:26 CDT)
RE: AMBER: solvateCap minin and mdin for qm-mm dftb Ross Walker (Fri Aug 24 2007 - 11:57:55 CDT)
RE: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 12:28:32 CDT)
Re: AMBER: PM6? Thomas Patko (Fri Aug 24 2007 - 12:43:35 CDT)
Re: AMBER: articles Lili Peng (Fri Aug 24 2007 - 14:10:12 CDT)
Re: AMBER: Prepin error (?) in xleap Lili Peng (Fri Aug 24 2007 - 14:19:07 CDT)
Re: AMBER: Prepin error (?) in xleap Lili Peng (Fri Aug 24 2007 - 14:26:17 CDT)
RE: AMBER: PM6? Ross Walker (Fri Aug 24 2007 - 15:19:22 CDT)
Re: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 15:42:50 CDT)
Re: AMBER: solvateCap minin and mdin for qm-mm dftb M. L. Dodson (Fri Aug 24 2007 - 15:59:04 CDT)
RE: AMBER: solvateCap minin and mdin for qm-mm dftb Ross Walker (Fri Aug 24 2007 - 16:05:24 CDT)
RE: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 16:37:12 CDT)
Re: AMBER: ow to split MDCRD file using ptraj Gustavo Seabra (Fri Aug 24 2007 - 21:17:27 CDT)
Re: AMBER: How to perform MD simulation in NVT ensemble? Gustavo Seabra (Fri Aug 24 2007 - 21:21:59 CDT)
Re: AMBER: SMD simulation Qiang Zhong (Sat Aug 25 2007 - 04:49:09 CDT)
Re: AMBER: SMD simulation Qiang Zhong (Sat Aug 25 2007 - 04:49:09 CDT)
AMBER: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sat Aug 25 2007 - 12:54:12 CDT)
Re: AMBER: SCC convergence failure in QM-MM DFTB Adrian Roitberg (Sat Aug 25 2007 - 13:10:35 CDT)
AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 02:26:42 CDT)
AMBER: personal computer configuration for parallel computing emine cebe (Sun Aug 26 2007 - 06:36:28 CDT)
AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 09:34:57 CDT)
Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB M. L. Dodson (Sun Aug 26 2007 - 10:42:14 CDT)
Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 11:28:14 CDT)
Fwd: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Mon Aug 27 2007 - 01:24:33 CDT)
Re: AMBER: NETCDF Geoff Wood (Mon Aug 27 2007 - 02:18:48 CDT)
Re: AMBER: Prepin error (?) in xleap David A. Case (Mon Aug 27 2007 - 10:58:20 CDT)
Re: AMBER: SCC convergence failure in QM-MM DFTB Gustavo Seabra (Mon Aug 27 2007 - 12:20:37 CDT)
AMBER: metalloprotein dynamics Sally Pias (Mon Aug 27 2007 - 12:55:51 CDT)
AMBER: generating a .rst file from an .mdcrd file Thomas Pochapsky (Mon Aug 27 2007 - 13:41:56 CDT)
AMBER: Add hydrogen and charge calculation snoze pa (Mon Aug 27 2007 - 14:06:44 CDT)
Re: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Gustavo Seabra (Mon Aug 27 2007 - 14:12:23 CDT)
Re: AMBER: generating a .rst file from an .mdcrd file Gustavo Seabra (Mon Aug 27 2007 - 14:15:23 CDT)
Re: AMBER: Add hydrogen and charge calculation Chris Moth (Mon Aug 27 2007 - 15:33:25 CDT)
Re: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Gustavo Seabra (Mon Aug 27 2007 - 15:50:40 CDT)
Re: AMBER: Prepin error (?) in xleap Lili Peng (Mon Aug 27 2007 - 16:38:30 CDT)
Re: AMBER: Prepin error (?) in xleap Junmei Wang (Mon Aug 27 2007 - 17:17:53 CDT)
Re: AMBER: Prepin error (?) in xleap David A. Case (Mon Aug 27 2007 - 17:29:49 CDT)
Re: AMBER: Add hydrogen and charge calculation snoze pa (Mon Aug 27 2007 - 23:07:55 CDT)
AMBER: QM/MM in reaction pathways? Qiang Zhong (Tue Aug 28 2007 - 02:51:30 CDT)
Re: AMBER: QM/MM in reaction pathways? Gustavo Seabra (Tue Aug 28 2007 - 09:55:20 CDT)
AMBER: protocols for high pressure simulation brmeher_at_iitg.ernet.in (Tue Aug 28 2007 - 10:23:00 CDT)
RE: AMBER: QM/MM in reaction pathways? Ross Walker (Tue Aug 28 2007 - 10:21:40 CDT)
Re: AMBER: protocols for high pressure simulation David A. Case (Tue Aug 28 2007 - 10:41:58 CDT)
AMBER: heating up system Francesco Pietra (Tue Aug 28 2007 - 11:16:57 CDT)
Re: AMBER: heating up system Adrian Roitberg (Tue Aug 28 2007 - 13:45:26 CDT)
RE: AMBER: QM/MM in reaction pathways? Qiang Zhong (Tue Aug 28 2007 - 19:52:21 CDT)
AMBER: energy minimization parameter Qiang Zhong (Wed Aug 29 2007 - 02:54:12 CDT)
Re: AMBER: energy minimization parameter Lorenzo Gontrani (Wed Aug 29 2007 - 02:54:58 CDT)
AMBER: refinement of NMR struture using AMBER Prem Prakash Pathak (Wed Aug 29 2007 - 05:57:11 CDT)
Re: AMBER: How to perform MD simulation in NVT ensemble? WANG,YING (Wed Aug 29 2007 - 08:50:30 CDT)
Re: AMBER: How to perform MD simulation in NVT ensemble? Gustavo Seabra (Wed Aug 29 2007 - 09:53:11 CDT)
AMBER: Criteria for classical md being OK to move to QM-MM Francesco Pietra (Wed Aug 29 2007 - 11:51:15 CDT)
Re: AMBER: Criteria for classical md being OK to move to QM-MM M. L. Dodson (Wed Aug 29 2007 - 12:11:29 CDT)
Re: AMBER: Criteria for classical md being OK to move to QM-MM Francesco Pietra (Wed Aug 29 2007 - 12:40:36 CDT)
Re: AMBER: Criteria for classical md being OK to move to QM-MM Gustavo Seabra (Wed Aug 29 2007 - 13:13:05 CDT)
Re: AMBER: Criteria for classical md being OK to move to QM-MM M. L. Dodson (Wed Aug 29 2007 - 13:24:43 CDT)
RE: AMBER: Criteria for classical md being OK to move to QM-MM Ross Walker (Wed Aug 29 2007 - 13:40:30 CDT)
AMBER: Schedule for QM-MM with Amber9/Amber10 Francesco Pietra (Thu Aug 30 2007 - 01:30:10 CDT)
AMBER: Dihedrals in Sander Martin Stennett (Thu Aug 30 2007 - 03:36:17 CDT)
AMBER: RDF unit cell volume BJÖRN KARLSSON (Thu Aug 30 2007 - 03:14:20 CDT)
AMBER: AMBER at WESTGRID Eduardo Mendez-Villuendas (Thu Aug 30 2007 - 06:49:07 CDT)
Re: AMBER: AMBER at WESTGRID Gustavo Seabra (Thu Aug 30 2007 - 07:35:49 CDT)
AMBER: bad atom type:F Emilia Wu (Thu Aug 30 2007 - 07:36:14 CDT)
AMBER: Beale, John (Thu Aug 30 2007 - 08:05:11 CDT)
AMBER: Fwd: Schedule for QM-MM with Amber9/Amber10 Francesco Pietra (Thu Aug 30 2007 - 08:17:41 CDT)
Re: AMBER: bad atom type:F David A. Case (Thu Aug 30 2007 - 10:35:00 CDT)
AMBER: Connecting two ethanes in LEaP Kliman, Michal (Thu Aug 30 2007 - 15:53:46 CDT)
AMBER: Squished dimer during transition from NVT to NPT Katrina Lexa (Thu Aug 30 2007 - 16:02:20 CDT)
AMBER: Scaling for octahedral versus rectilinear boxes David Cerutti (Fri Aug 31 2007 - 00:32:49 CDT)
Re: AMBER: Scaling for octahedral versus rectilinear boxes Robert Duke (Fri Aug 31 2007 - 07:40:48 CDT)
Re: AMBER: Scaling for octahedral versus rectilinear boxes David Cerutti (Fri Aug 31 2007 - 08:27:38 CDT)
AMBER: Confusion about Langevin dymamics Hayden Eastwood (Fri Aug 31 2007 - 08:46:28 CDT)
Re: AMBER: Confusion about Langevin dymamics Carlos Simmerling (Fri Aug 31 2007 - 08:52:02 CDT)
AMBER: antechamber question Beale, John (Fri Aug 31 2007 - 09:07:56 CDT)
Re: AMBER: Scaling for octahedral versus rectilinear boxes Robert Duke (Fri Aug 31 2007 - 09:23:11 CDT)
Re: AMBER: Confusion about Langevin dymamics David A. Case (Fri Aug 31 2007 - 09:53:47 CDT)
Re: AMBER: Confusion about Langevin dymamics David Mobley (Fri Aug 31 2007 - 11:05:13 CDT)
Re: AMBER: Connecting two ethanes in LEaP David A. Case (Fri Aug 31 2007 - 11:18:18 CDT)
Re: AMBER: Melinda Layten (Fri Aug 31 2007 - 12:19:21 CDT)
Re: AMBER: Prepin error (?) in xleap Lili Peng (Thu Aug 30 2007 - 15:48:34 CDT)
Re: AMBER: Schedule for QM-MM with Amber9/Amber10 Gustavo Seabra (Fri Aug 31 2007 - 12:41:18 CDT)
AMBER: Converting AMBER-format force fields for tinker Aaron Virshup (Fri Aug 31 2007 - 14:04:12 CDT)
AMBER: Measuring Bond Angle over simulation Seth Lilavivat (Fri Aug 31 2007 - 14:25:20 CDT)
Re: AMBER: Measuring Bond Angle over simulation Carlos Simmerling (Fri Aug 31 2007 - 14:34:13 CDT)
Re: AMBER: antechamber question Junmei Wang (Fri Aug 31 2007 - 15:07:09 CDT)
Re: AMBER: Prepin error (?) in xleap Junmei Wang (Fri Aug 31 2007 - 15:22:07 CDT)
AMBER: modified leaprc for glycoproteins Irene Newhouse (Fri Aug 31 2007 - 15:53:05 CDT)
AMBER: Using ntr=1 in xleap Lili Peng (Fri Aug 31 2007 - 16:27:44 CDT)
Re: AMBER: Using ntr=1 in xleap David A. Case (Fri Aug 31 2007 - 17:52:13 CDT)
Re: AMBER: modified leaprc for glycoproteins David A. Case (Fri Aug 31 2007 - 16:42:03 CDT)
Re: AMBER: Using ntr=1 in xleap Carlos Simmerling (Fri Aug 31 2007 - 16:49:14 CDT)
RE: AMBER: modified leaprc for glycoproteins Irene Newhouse (Fri Aug 31 2007 - 20:14:32 CDT)

Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:09 CST

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