AMBER Archive (2007) - Nov 2007 By DateMost recent messages
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Starting: Thu Nov 01 2007 - 02:29:26 CST
Ending: Fri Nov 30 2007 - 15:12:42 CST
- Re: AMBER: antechamber fails with large molecules Francesco Pietra (Thu Nov 01 2007 - 02:29:26 CST)
- AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Thu Nov 01 2007 - 04:43:54 CST)
- RE: AMBER: &dipoles output in QM/MM simulations Ross Walker (Thu Nov 01 2007 - 11:12:52 CST)
- AMBER: Improper torsion terms Pavan G (Thu Nov 01 2007 - 18:24:46 CST)
- Re: AMBER: antechamber fails with large molecules Junmei Wang (Fri Nov 02 2007 - 00:16:41 CST)
- Re: AMBER:antechamber fails with large molecules Junmei Wang (Fri Nov 02 2007 - 00:29:11 CST)
- Re: AMBER: antechamber fails with large molecules Ilyas Yildirim (Fri Nov 02 2007 - 02:24:26 CST)
- Re: AMBER: antechamber fails with large molecules Eddie Men (Fri Nov 02 2007 - 02:50:57 CST)
- Re: AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Fri Nov 02 2007 - 03:07:04 CST)
- Re: AMBER: antechamber fails with large molecules Ilyas Yildirim (Fri Nov 02 2007 - 03:10:33 CST)
- Re: AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Fri Nov 02 2007 - 04:59:01 CST)
- Re: AMBER: &dipoles output in QM/MM simulations Eddie Men (Fri Nov 02 2007 - 06:01:10 CST)
- Re: AMBER: &dipoles output in QM/MM simulations Adrian Roitberg (Fri Nov 02 2007 - 07:06:28 CST)
- Re: AMBER: Improper torsion terms Bill Ross (Fri Nov 02 2007 - 10:41:00 CST)
- Re: AMBER: antechamber fails with large molecules Francesco Pietra (Fri Nov 02 2007 - 11:07:52 CST)
- AMBER: Compiling single programs Francesco Pietra (Fri Nov 02 2007 - 11:44:09 CST)
- Re: AMBER: Compiling single programs Mark Williamson (Fri Nov 02 2007 - 11:58:32 CST)
- Re: AMBER: Compiling single programs Adrian Roitberg (Fri Nov 02 2007 - 12:08:44 CST)
- RE: AMBER: &dipoles output in QM/MM simulations Ross Walker (Fri Nov 02 2007 - 12:42:54 CST)
- AMBER: Failure to recompile antechamber Francesco Pietra (Fri Nov 02 2007 - 17:05:45 CST)
- Re: AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Sat Nov 03 2007 - 00:33:58 CST)
- Re: AMBER: antechamber fails with large molecules Ilyas Yildirim (Sat Nov 03 2007 - 02:38:03 CST)
- Re: AMBER: antechamber fails with large molecules Francesco Pietra (Sat Nov 03 2007 - 08:01:41 CST)
- AMBER: error with amber9 production run. Vijay Singh (Sat Nov 03 2007 - 08:10:52 CST)
- Re: AMBER: antechamber fails with large molecules Ilyas Yildirim (Sat Nov 03 2007 - 10:47:49 CST)
- Re: AMBER: antechamber fails with large molecules FyD (Sun Nov 04 2007 - 06:29:09 CST)
- AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ? sychen (Sun Nov 04 2007 - 06:46:09 CST)
- AMBER: dihedral driver fatima.chami_at_durham.ac.uk (Sun Nov 04 2007 - 06:51:22 CST)
- Re: AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ? Jiri Sponer (Sun Nov 04 2007 - 07:01:02 CST)
- RE: AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ? Catein Catherine (Sun Nov 04 2007 - 23:20:48 CST)
- AMBER: paper request Miguel Ortiz-Lombardía (Mon Nov 05 2007 - 03:01:08 CST)
- Re: AMBER: paper request FyD (Mon Nov 05 2007 - 03:13:38 CST)
- Re: AMBER: paper request Miguel Ortiz-Lombardía (Mon Nov 05 2007 - 04:14:09 CST)
- AMBER: "Atom valence violated" from LEaP Francesco Pietra (Mon Nov 05 2007 - 05:00:28 CST)
- AMBER: Fe bonds in HEME ! Pradipta Bandyopadhyay (Mon Nov 05 2007 - 05:50:58 CST)
- AMBER: ptraj frames maximum Hannes Wallnoefer (Mon Nov 05 2007 - 08:19:25 CST)
- Re: AMBER: ptraj frames maximum David A. Case (Mon Nov 05 2007 - 09:34:20 CST)
- AMBER: DUMBFREQ Steve Seibold (Mon Nov 05 2007 - 09:52:19 CST)
- AMBER: ptraj hbond mask Lars Skjærven (Mon Nov 05 2007 - 10:00:03 CST)
- Re: AMBER: RED-vIII fails Jesper Soerensen (Mon Nov 05 2007 - 10:01:21 CST)
- Re: AMBER: ptraj frames maximum Hannes Wallnoefer (Mon Nov 05 2007 - 10:07:00 CST)
- Re: AMBER: ptraj frames maximum David A. Case (Mon Nov 05 2007 - 10:37:11 CST)
- Re: Re: AMBER: AMBER 9 - Force Field Options - Question cgji (Mon Nov 05 2007 - 11:19:58 CST)
- Re: Re: AMBER: AMBER 9 - Force Field Options - Question Carlos Simmerling (Mon Nov 05 2007 - 11:39:01 CST)
- Re: AMBER: RED-vIII fails FyD (Mon Nov 05 2007 - 12:27:33 CST)
- AMBER: umbrella sampling and WHAM Allen, Thomas W., Ph.D. [RO BIOCHM] (Mon Nov 05 2007 - 14:03:31 CST)
- AMBER: Parallel test error with shared libraries Joe Nolan (Mon Nov 05 2007 - 15:05:27 CST)
- Re: AMBER: ptraj frames maximum Thomas Cheatham (Mon Nov 05 2007 - 17:54:37 CST)
- AMBER: Request reg parameter for vitamin e Rama krishnan (Tue Nov 06 2007 - 01:11:47 CST)
- AMBER: Request reg parameter for vitamin e Rama krishnan (Tue Nov 06 2007 - 01:13:51 CST)
- AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8? ming hui (Tue Nov 06 2007 - 02:30:17 CST)
- AMBER: Energy minimization problem of -SO3H group Takao Kobayashi (Tue Nov 06 2007 - 04:17:35 CST)
- Re: AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8? Carlos Simmerling (Tue Nov 06 2007 - 05:49:13 CST)
- AMBER: Question dykyy (Tue Nov 06 2007 - 07:12:46 CST)
- AMBER: Minimum energy tolerance gradient setting for minimization Sandhya Tiwari (Tue Nov 06 2007 - 08:13:52 CST)
- Re: AMBER: Minimum energy tolerance gradient setting for minimization David A. Case (Tue Nov 06 2007 - 10:03:18 CST)
- AMBER: Antechamber snoze pa (Tue Nov 06 2007 - 10:02:39 CST)
- Re: AMBER: Antechamber David Mobley (Tue Nov 06 2007 - 11:15:33 CST)
- Re: AMBER: Antechamber Ilyas Yildirim (Tue Nov 06 2007 - 11:36:35 CST)
- Re: AMBER: Antechamber snoze pa (Tue Nov 06 2007 - 13:04:05 CST)
- Re: AMBER: Antechamber David Mobley (Tue Nov 06 2007 - 14:41:17 CST)
- Re: AMBER: Antechamber Ilyas Yildirim (Tue Nov 06 2007 - 15:03:13 CST)
- Re: AMBER: Energy minimization problem of -SO3H group David A. Case (Tue Nov 06 2007 - 23:12:08 CST)
- Re: AMBER: Question David A. Case (Tue Nov 06 2007 - 23:18:33 CST)
- Re: AMBER: Energy minimization problem of -SO3H group Eddie Men (Tue Nov 06 2007 - 23:52:09 CST)
- AMBER: calculating charges to modified 4GA unit nag raj (Wed Nov 07 2007 - 05:26:51 CST)
- AMBER: AMBER 9 - visualization of MD trajectory by MOE dinko.x.ziher_at_gsk.com (Wed Nov 07 2007 - 06:45:41 CST)
- AMBER: LEaP bond problem Beale, John (Wed Nov 07 2007 - 06:57:30 CST)
- Re: AMBER: calculating charges to modified 4GA unit FyD (Wed Nov 07 2007 - 07:21:03 CST)
- Re: AMBER: calculating charges to modified 4GA unit Austin B. Yongye (Wed Nov 07 2007 - 08:26:57 CST)
- Re: AMBER: calculating charges to modified 4GA unit Karl Kirschner (Wed Nov 07 2007 - 07:37:42 CST)
- AMBER: divcon on AIX using xlf 10.1 Joachim Hein (Wed Nov 07 2007 - 10:23:14 CST)
- Re: AMBER: LEaP bond problem David A. Case (Wed Nov 07 2007 - 10:39:49 CST)
- AMBER: (no subject) Biman Jana (Wed Nov 07 2007 - 11:09:00 CST)
- AMBER: TIP5P water Simulation Biman Jana (Wed Nov 07 2007 - 11:12:42 CST)
- Re: AMBER: (no subject) David A. Case (Wed Nov 07 2007 - 11:11:43 CST)
- Re: AMBER: ptraj hbond mask Thomas Cheatham III (Wed Nov 07 2007 - 15:00:40 CST)
- AMBER: MD simulations with Pt atom - how to keep square planar geometry? Pablo Englebienne (Wed Nov 07 2007 - 20:21:21 CST)
- Re: AMBER: calculating charges to modified 4GA unit nag raj (Wed Nov 07 2007 - 21:04:53 CST)
- Re: AMBER: calculating charges to modified 4GA unit nag raj (Wed Nov 07 2007 - 21:04:53 CST)
- AMBER: make test.parallel Francesco Pietra (Thu Nov 08 2007 - 02:33:21 CST)
- Re: AMBER: make test.parallel David A. Case (Thu Nov 08 2007 - 09:58:39 CST)
- Re: AMBER: MD simulations with Pt atom - how to keep square planar geometry? gsciaini_at_qi.fcen.uba.ar (Thu Nov 08 2007 - 10:09:31 CST)
- AMBER: divcon san_amber roy (Thu Nov 08 2007 - 11:19:41 CST)
- Re: AMBER: make test.parallel Francesco Pietra (Thu Nov 08 2007 - 11:30:36 CST)
- Re: AMBER: MD simulations with Pt atom - how to keep square planar geometry? Pablo Englebienne (Thu Nov 08 2007 - 11:44:43 CST)
- Re: AMBER: divcon Pablo Englebienne (Thu Nov 08 2007 - 11:50:25 CST)
- AMBER: xleap patch for xorg-7.3 ?? M. L. Dodson (Thu Nov 08 2007 - 13:04:05 CST)
- Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) sanket deshmukh (Thu Nov 08 2007 - 13:29:35 CST)
- Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) David A. Case (Thu Nov 08 2007 - 14:16:57 CST)
- AMBER: thermodynamic integration Cooper, Matthew (Thu Nov 08 2007 - 15:14:25 CST)
- Re: AMBER: thermodynamic integration Ilyas Yildirim (Thu Nov 08 2007 - 16:42:04 CST)
- Re: AMBER: thermodynamic integration David A. Case (Thu Nov 08 2007 - 19:49:49 CST)
- Re: AMBER: xleap patch for xorg-7.3 ?? David A. Case (Thu Nov 08 2007 - 20:03:39 CST)
- Re: AMBER: divcon David A. Case (Thu Nov 08 2007 - 20:06:55 CST)
- Re: AMBER: How can i calculate generalized order parameters using ptraj. David A. Case (Thu Nov 08 2007 - 20:23:34 CST)
- RE: AMBER: thermodynamic integration Cooper, Matthew (Fri Nov 09 2007 - 08:03:32 CST)
- Re: AMBER: xleap patch for xorg-7.3 ?? Xuebin Qiao (Fri Nov 09 2007 - 08:26:38 CST)
- RE: AMBER: thermodynamic integration Cooper, Matthew (Fri Nov 09 2007 - 08:32:52 CST)
- Re: AMBER: make test.parallel Gustavo Seabra (Fri Nov 09 2007 - 10:28:23 CST)
- Re: AMBER: thermodynamic integration David A. Case (Fri Nov 09 2007 - 12:27:48 CST)
- Re: AMBER: heical content in simulations Scott Pendley (Fri Nov 09 2007 - 14:25:18 CST)
- AMBER: RESP question Eddie Men (Fri Nov 09 2007 - 18:33:16 CST)
- Re: AMBER: RESP question Gustavo Seabra (Fri Nov 09 2007 - 23:01:09 CST)
- AMBER: TIP5P water simulation using AMBER7 Biman Jana (Sat Nov 10 2007 - 08:57:20 CST)
- Re: AMBER: TIP5P water simulation using AMBER7 Carlos Simmerling (Sat Nov 10 2007 - 09:00:36 CST)
- AMBER: addles Peter Varnai (Sat Nov 10 2007 - 10:40:21 CST)
- AMBER: replica exchange problems with ifort >10.0.023 Peter Varnai (Sat Nov 10 2007 - 10:44:30 CST)
- Re: AMBER:antechamber fails with large molecules Francesco Pietra (Sun Nov 11 2007 - 05:13:56 CST)
- Re: AMBER:antechamber fails with large molecules Francesco Pietra (Sun Nov 11 2007 - 05:13:56 CST)
- Re: AMBER: TIP5P water simulation using AMBER7 Biman Jana (Sun Nov 11 2007 - 08:21:56 CST)
- Re: AMBER: TIP5P water simulation using AMBER7 Carlos Simmerling (Sun Nov 11 2007 - 08:25:50 CST)
- Re: AMBER: TIP5P water simulation using AMBER7 Adrian Roitberg (Sun Nov 11 2007 - 10:29:11 CST)
- Re: AMBER: TIP5P water simulation using AMBER7 David A. Case (Sun Nov 11 2007 - 16:04:08 CST)
- AMBER: invalid digit '*' in the input file rebeca_at_mmb.pcb.ub.es (Mon Nov 12 2007 - 08:06:16 CST)
- Re: AMBER: invalid digit '*' in the input file Martin Klefas-Stennett (Mon Nov 12 2007 - 08:31:08 CST)
- Re: AMBER: invalid digit '*' in the input file Chris Moth (Mon Nov 12 2007 - 08:40:26 CST)
- Re: AMBER: invalid digit '*' in the input file rebeca_at_mmb.pcb.ub.es (Mon Nov 12 2007 - 08:56:26 CST)
- RE: AMBER: invalid digit '*' in the input file Hayden Eastwood (Mon Nov 12 2007 - 09:10:03 CST)
- Re: AMBER: invalid digit '*' in the input file Adrian Roitberg (Mon Nov 12 2007 - 09:17:43 CST)
- Re: AMBER: amber9 installation problem Madjid Taghdir (Mon Nov 12 2007 - 02:38:57 CST)
- AMBER: restrain center of mass of one domain Wei Chen (Mon Nov 12 2007 - 17:14:11 CST)
- AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hopkins, Robert (Mon Nov 12 2007 - 17:32:20 CST)
- RE: AMBER: invalid digit '*' in the input file Yong Duan (Mon Nov 12 2007 - 19:07:26 CST)
- AMBER: Parallel scaling priya priya (Tue Nov 13 2007 - 04:35:20 CST)
- AMBER: gb minimization using nab Guillaume Renvez (Tue Nov 13 2007 - 05:06:13 CST)
- Re: AMBER: Parallel scaling Carlos Simmerling (Tue Nov 13 2007 - 05:07:53 CST)
- AMBER: Protein containing iron. Syed Tarique Moin (Tue Nov 13 2007 - 05:16:48 CST)
- Re: AMBER: Parallel scaling priya priya (Tue Nov 13 2007 - 05:26:23 CST)
- Re: AMBER: gb minimization using nab Andreas Svrcek-Seiler (Tue Nov 13 2007 - 05:58:05 CST)
- AMBER: Parallel Amber compilation problems !! Sampath Koppole (Tue Nov 13 2007 - 08:05:28 CST)
- Re: AMBER: gb minimization using nab Guillaume Renvez (Tue Nov 13 2007 - 08:49:48 CST)
- AMBER: Problem with xLeap alfredoq_at_mail.fcq.unc.edu.ar (Tue Nov 13 2007 - 09:34:46 CST)
- Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine David A. Case (Tue Nov 13 2007 - 09:54:38 CST)
- Re: AMBER: Problem with xLeap David A. Case (Tue Nov 13 2007 - 10:08:24 CST)
- RE: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hu, Shaowen (JSC-SK)[USRA] (Tue Nov 13 2007 - 10:13:18 CST)
- Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine David A. Case (Tue Nov 13 2007 - 10:28:52 CST)
- Re: AMBER: thermodynamic integration Thomas Steinbrecher (Tue Nov 13 2007 - 10:36:15 CST)
- AMBER: 2 double bond in AMBER ffield ABEL Stephane 984007 (Tue Nov 13 2007 - 11:00:08 CST)
- Re: AMBER: Problem with xLeap alfredoq_at_mail.fcq.unc.edu.ar (Tue Nov 13 2007 - 11:07:40 CST)
- Re: AMBER: Problem with xLeap David A. Case (Tue Nov 13 2007 - 11:55:24 CST)
- Re: AMBER: Problem with xLeap alfredoq_at_mail.fcq.unc.edu.ar (Tue Nov 13 2007 - 12:11:31 CST)
- RE: AMBER: Parallel Amber compilation problems !! Ross Walker (Tue Nov 13 2007 - 12:33:25 CST)
- RE: AMBER: Protein containing iron. Ross Walker (Tue Nov 13 2007 - 12:37:40 CST)
- AMBER: amber9 leap installation error on sgi_altix wei zhang (Tue Nov 13 2007 - 16:02:48 CST)
- RE: AMBER: amber9 leap installation error on sgi_altix Ross Walker (Tue Nov 13 2007 - 16:50:53 CST)
- Re: AMBER: amber9 leap installation error on sgi_altix David A. Case (Tue Nov 13 2007 - 17:27:55 CST)
- RE: AMBER: Parallel Amber compilation problems !! Sampath Koppole (Wed Nov 14 2007 - 03:22:15 CST)
- Re: AMBER: amber9 leap installation error on sgi_altix wei zhang (Wed Nov 14 2007 - 10:05:26 CST)
- [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] M. L. Dodson (Wed Nov 14 2007 - 12:51:35 CST)
- AMBER: Bug report: iwrap failure in PMEMD with netCDF Myunggi Yi (Wed Nov 14 2007 - 13:18:18 CST)
- Re: AMBER: Bug report: iwrap failure in PMEMD with netCDF Robert Duke (Wed Nov 14 2007 - 13:52:16 CST)
- AMBER: Error when doing a TI simulation: "vlimit exceeded ming hui (Wed Nov 14 2007 - 19:10:07 CST)
- Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] Xuebin Qiao (Thu Nov 15 2007 - 00:59:58 CST)
- Re: AMBER: Error when doing a TI simulation: "vlimit exceeded Thomas Steinbrecher (Thu Nov 15 2007 - 11:06:03 CST)
- Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] M. L. Dodson (Thu Nov 15 2007 - 11:28:28 CST)
- Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] Lili Peng (Thu Nov 15 2007 - 16:38:57 CST)
- AMBER: &shf setup McElheny, Dan (Thu Nov 15 2007 - 17:39:42 CST)
- Re: AMBER: Error when doing a TI simulation: "vlimit exceeded ming hui (Thu Nov 15 2007 - 18:48:05 CST)
- Re: AMBER: Error when doing a TI simulation: "vlimit exceeded Thomas Steinbrecher (Thu Nov 15 2007 - 19:18:54 CST)
- Re: AMBER: Error when doing a TI simulation: "vlimit exceeded ming hui (Thu Nov 15 2007 - 19:26:43 CST)
- Re: AMBER: Error when doing a TI simulation: "vlimit exceeded Thomas Steinbrecher (Thu Nov 15 2007 - 19:52:47 CST)
- AMBER: Understading of mdcrd file and pdb file.. Vijay Manickam Achari (Thu Nov 15 2007 - 23:02:08 CST)
- Re: AMBER: Understading of mdcrd file and pdb file.. David A. Case (Fri Nov 16 2007 - 00:23:30 CST)
- Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] David A. Case (Fri Nov 16 2007 - 00:12:45 CST)
- AMBER: [chirality.c] Atom did not match Francesco Pietra (Fri Nov 16 2007 - 11:09:10 CST)
- Re: AMBER: [chirality.c] Atom did not match Jojart Balazs (Fri Nov 16 2007 - 11:48:51 CST)
- AMBER: xleap heme iron coordination error Robyn Ayscue (Fri Nov 16 2007 - 13:33:35 CST)
- Re: AMBER: xleap heme iron coordination error David A. Case (Fri Nov 16 2007 - 13:47:53 CST)
- Re: AMBER: [chirality.c] Atom did not match Francesco Pietra (Fri Nov 16 2007 - 13:38:20 CST)
- AMBER: antechamber --> sander problem Yamada, Takahiro (Fri Nov 16 2007 - 14:18:18 CST)
- Re: AMBER: antechamber --> sander problem David A. Case (Fri Nov 16 2007 - 15:17:50 CST)
- AMBER: chem shift format McElheny, Dan (Fri Nov 16 2007 - 15:46:57 CST)
- AMBER: Fwd: [chirality.c] Atom did not match Francesco Pietra (Fri Nov 16 2007 - 15:59:40 CST)
- AMBER: five-coordinated phosphorus Smooth Cutie (Fri Nov 16 2007 - 17:48:40 CST)
- Re: AMBER: chem shift format David A. Case (Fri Nov 16 2007 - 18:00:27 CST)
- Re: AMBER: &shf setup David A. Case (Fri Nov 16 2007 - 17:59:19 CST)
- Re: AMBER: Fwd: [chirality.c] Atom did not match David A. Case (Fri Nov 16 2007 - 18:03:33 CST)
- AMBER: How to calculate S2 from P2 using ptraj ? brmeher_at_iitg.ernet.in (Sat Nov 17 2007 - 00:34:11 CST)
- AMBER: How to calculate S2 from P2 using ptraj ? brmeher_at_iitg.ernet.in (Sat Nov 17 2007 - 00:40:31 CST)
- Re: AMBER: Fwd: [chirality.c] Atom did not match Francesco Pietra (Sat Nov 17 2007 - 04:56:01 CST)
- AMBER: five-coordinated phosphorus Yubo Fan (Sat Nov 17 2007 - 08:19:06 CST)
- AMBER: question with ptraj loop Vijay Singh (Sat Nov 17 2007 - 10:06:53 CST)
- Fwd: Re: AMBER: Fwd: [chirality.c] Atom did not match Francesco Pietra (Sat Nov 17 2007 - 10:16:09 CST)
- Re: AMBER: Fwd: [chirality.c] Atom did not match David A. Case (Sat Nov 17 2007 - 10:53:01 CST)
- AMBER: Puzzle with WAT Francesco Pietra (Sat Nov 17 2007 - 12:14:38 CST)
- AMBER: EXCEEDED MAXLESADJ in sander.LES.MPI (amber9) Alessandro Nascimento (Sat Nov 17 2007 - 15:24:58 CST)
- Re: AMBER: EXCEEDED MAXLESADJ in sander.LES.MPI (amber9) Carlos Simmerling (Sat Nov 17 2007 - 15:51:09 CST)
- Re: AMBER: Puzzle with WAT Bill Ross (Sat Nov 17 2007 - 18:00:06 CST)
- Re: AMBER: Puzzle with WAT Francesco Pietra (Sun Nov 18 2007 - 02:09:27 CST)
- AMBER: Atom types for polyunsaturated lipids ABEL Stephane 984007 (Sun Nov 18 2007 - 11:14:14 CST)
- AMBER: R.E.D.-III bug fixes FyD (Sun Nov 18 2007 - 11:22:47 CST)
- Re: AMBER: Puzzle with WAT Bill Ross (Sun Nov 18 2007 - 12:55:15 CST)
- RE : AMBER: Atom types for polyunsaturated lipids ABEL Stephane 984007 (Sun Nov 18 2007 - 13:40:24 CST)
- Re: AMBER: Understading of mdcrd file and pdb file.. Vijay Manickam Achari (Sun Nov 18 2007 - 23:27:19 CST)
- AMBER: Missing BELE for MM in 1 backy (Mon Nov 19 2007 - 06:19:09 CST)
- RE: Re: AMBER: Fwd: [chirality.c] Atom did not match Steve Spronk (Mon Nov 19 2007 - 07:28:07 CST)
- RE: Re: AMBER: Fwd: [chirality.c] Atom did not match Steve Spronk (Mon Nov 19 2007 - 07:31:42 CST)
- Re: AMBER: How to calculate S2 from P2 using ptraj ? David A. Case (Mon Nov 19 2007 - 12:04:48 CST)
- AMBER: Solvation free energy Mike Wykes (Mon Nov 19 2007 - 12:08:23 CST)
- Re: AMBER: Solvation free energy Thomas Steinbrecher (Mon Nov 19 2007 - 12:21:23 CST)
- AMBER: pmemd with openmpi Myunggi Yi (Mon Nov 19 2007 - 13:25:48 CST)
- Re: AMBER: pmemd with openmpi Francesco Pietra (Mon Nov 19 2007 - 14:31:56 CST)
- Re: AMBER: pmemd with openmpi Myunggi Yi (Mon Nov 19 2007 - 15:40:41 CST)
- AMBER: newby question on converting xyz format to pdb format after energy minimization Mehmet Serkan Apaydin (Tue Nov 20 2007 - 15:02:42 CST)
- Re: AMBER: newby question on converting xyz format to pdb format after energy minimization Eddie Men (Tue Nov 20 2007 - 15:24:56 CST)
- Re: AMBER: newby question on converting xyz format to pdb format after energy minimization David A. Case (Tue Nov 20 2007 - 15:33:08 CST)
- AMBER: Implicit/Explicit solvation Eddie Men (Wed Nov 21 2007 - 01:03:12 CST)
- RE: AMBER: Implicit/Explicit solvation Ross Walker (Wed Nov 21 2007 - 10:10:58 CST)
- Re: AMBER: Implicit/Explicit solvation David A. Case (Wed Nov 21 2007 - 10:46:19 CST)
- AMBER: Zinc-Histidine force field Mattia Mori - CERM (Wed Nov 21 2007 - 10:54:02 CST)
- RE: AMBER: Zinc-Histidine force field Ray Luo (Wed Nov 21 2007 - 11:30:21 CST)
- AMBER:How to calculate the free energy of a series of conformations huzehan19870731_at_126.com (Mon Nov 19 2007 - 21:18:41 CST)
- Re: AMBER:How to calculate the free energy of a series of conformations David A. Case (Wed Nov 21 2007 - 13:42:09 CST)
- AMBER: Problem with LEaP generating topology and coord files after double bond creation M. L. Dodson (Wed Nov 21 2007 - 14:45:17 CST)
- AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Wed Nov 21 2007 - 15:41:45 CST)
- AMBER: McElheny, Dan (Wed Nov 21 2007 - 16:04:26 CST)
- Re: AMBER: modifications to force field for Fe4S4 cubane David A. Case (Wed Nov 21 2007 - 16:30:30 CST)
- Re: AMBER:How to calculate the free energy of a series of conformations Carlos Simmerling (Wed Nov 21 2007 - 17:04:03 CST)
- Re: AMBER: Problem with LEaP generating topology and coord files after double bond creation David A. Case (Wed Nov 21 2007 - 19:08:08 CST)
- AMBER: Atom type definition Xioling Chuang (Thu Nov 22 2007 - 03:03:29 CST)
- AMBER: BELLY issues Eddie Men (Thu Nov 22 2007 - 04:03:52 CST)
- Re: AMBER: Zinc-Histidine force field Mattia Mori - CERM (Thu Nov 22 2007 - 06:06:20 CST)
- AMBER: RE: FF94 or FF99? Patel, Bhavesh H (Thu Nov 22 2007 - 08:34:55 CST)
- AMBER: Pressure Variation for NPT simulation of TIP5P water Biman Jana (Thu Nov 22 2007 - 08:50:16 CST)
- Re: AMBER: RE: FF94 or FF99? Adrian Roitberg (Thu Nov 22 2007 - 09:20:22 CST)
- Re: AMBER: RE: FF94 or FF99? Jerome.GOLEBIOWSKI_at_unice.fr (Thu Nov 22 2007 - 09:57:33 CST)
- Re: AMBER: Pressure Variation for NPT simulation of TIP5P water David A. Case (Thu Nov 22 2007 - 11:34:34 CST)
- RE: AMBER: Zinc-Histidine force field Ray Luo (Thu Nov 22 2007 - 13:01:30 CST)
- Re: AMBER: Zinc-Histidine force field Mattia Mori - CERM (Thu Nov 22 2007 - 13:12:43 CST)
- AMBER: Pre-ABMER Installation Prob w/ MPICH2 Joseph Maxwell (Thu Nov 22 2007 - 13:55:18 CST)
- AMBER: BELLY Eddie Men (Thu Nov 22 2007 - 15:16:39 CST)
- Re: AMBER: BELLY Eddie Men (Thu Nov 22 2007 - 16:30:38 CST)
- Re: AMBER: RE: FF94 or FF99? Carlos Simmerling (Thu Nov 22 2007 - 18:13:16 CST)
- Re: AMBER: RE: FF94 or FF99? Ilyas Yildirim (Thu Nov 22 2007 - 18:29:08 CST)
- AMBER: frcmod file and NONB for dummy atoms Ilyas Yildirim (Thu Nov 22 2007 - 18:48:31 CST)
- AMBER: About TER records Francesco Pietra (Fri Nov 23 2007 - 02:15:05 CST)
- AMBER: connecting a non standard residue to the rest of an enzyme Boutheïna Kerkeni (Fri Nov 23 2007 - 07:43:36 CST)
- AMBER: Fwd: About TER records Francesco Pietra (Fri Nov 23 2007 - 09:23:41 CST)
- Re: AMBER: Fwd: About TER records Ilyas Yildirim (Fri Nov 23 2007 - 09:41:47 CST)
- Re: AMBER: Pre-ABMER Installation Prob w/ MPICH2 jantonioms J. A. Mondragon S (Fri Nov 23 2007 - 11:36:12 CST)
- Re: AMBER: About TER records David A. Case (Fri Nov 23 2007 - 12:35:46 CST)
- Re: AMBER: connecting a non standard residue to the rest of an enzyme David A. Case (Fri Nov 23 2007 - 12:39:13 CST)
- Re: AMBER: RE: FF94 or FF99? David A. Case (Fri Nov 23 2007 - 12:51:18 CST)
- Re: AMBER: frcmod file and NONB for dummy atoms David A. Case (Fri Nov 23 2007 - 12:58:46 CST)
- Re: AMBER: RE: FF94 or FF99? Ilyas Yildirim (Fri Nov 23 2007 - 17:29:15 CST)
- Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) sanket deshmukh (Fri Nov 23 2007 - 17:30:11 CST)
- Re: AMBER: frcmod file and NONB for dummy atoms Ilyas Yildirim (Fri Nov 23 2007 - 20:26:37 CST)
- AMBER: antechamber problem David A. Case (Fri Nov 23 2007 - 20:40:21 CST)
- AMBER: Hello Eddie Men (Fri Nov 23 2007 - 20:44:05 CST)
- Re: AMBER: Hello Carlos Simmerling (Fri Nov 23 2007 - 21:01:13 CST)
- Re: AMBER: RE: FF94 or FF99? Jiri Sponer (Sat Nov 24 2007 - 04:53:24 CST)
- AMBER: Pressure Variation for NPT simulation of TIP5P water (fwd) Biman Jana (Sat Nov 24 2007 - 07:22:39 CST)
- Re: AMBER: Pressure Variation for NPT simulation of TIP5P water (fwd) David A. Case (Sat Nov 24 2007 - 11:36:44 CST)
- Re: AMBER: Fwd: About TER records Francesco Pietra (Sat Nov 24 2007 - 12:29:15 CST)
- Re: AMBER: Hello Eddie Men (Sat Nov 24 2007 - 12:47:11 CST)
- Re: AMBER: Hello Carlos Simmerling (Sat Nov 24 2007 - 12:55:46 CST)
- Re: AMBER: Fwd: About TER records Francesco Pietra (Sat Nov 24 2007 - 15:27:11 CST)
- Re: AMBER: About TER records Francesco Pietra (Sat Nov 24 2007 - 15:34:59 CST)
- Re: AMBER: Hello David A. Case (Sun Nov 25 2007 - 00:14:23 CST)
- AMBER: solvatebox vs solvateoct Francesco Pietra (Sun Nov 25 2007 - 12:27:06 CST)
- AMBER: question about ntx=5 Wei Chen (Sun Nov 25 2007 - 13:21:44 CST)
- RE: AMBER: umbrella sampling Jardas sucuriba (Sun Nov 25 2007 - 13:32:28 CST)
- Re: AMBER: umbrella sampling Carlos Simmerling (Sun Nov 25 2007 - 13:52:57 CST)
- Re: AMBER: question about ntx=5 David A. Case (Sun Nov 25 2007 - 18:27:30 CST)
- Re: AMBER: question about ntx=5 Wei Chen (Sun Nov 25 2007 - 19:21:52 CST)
- AMBER: Weird restart file with ioutfm=0, iwrap=1 and ntwprt >0 Hai Long (Mon Nov 26 2007 - 11:41:18 CST)
- AMBER: LJ parameters for alkynes David Mobley (Mon Nov 26 2007 - 12:07:37 CST)
- AMBER: Polarizable potentials Denis Courtier (Mon Nov 26 2007 - 12:49:33 CST)
- AMBER: Value of taup for bulk TIP5P water simulation(amber7) Biman Jana (Mon Nov 26 2007 - 13:25:37 CST)
- AMBER: Restrained MD (amber9) Vincent Bisetty (Mon Nov 26 2007 - 16:52:28 CST)
- Re: AMBER: Restrained MD (amber9) David A. Case (Mon Nov 26 2007 - 17:49:43 CST)
- Re: AMBER: Polarizable potentials David A. Case (Mon Nov 26 2007 - 20:23:05 CST)
- AMBER: restraints to individual atoms Eddie Men (Mon Nov 26 2007 - 21:02:11 CST)
- AMBER: Extra-term to the Energy function !! Sampath Koppole (Tue Nov 27 2007 - 02:57:54 CST)
- Re: AMBER: Extra-term to the Energy function !! Carlos Simmerling (Tue Nov 27 2007 - 05:12:13 CST)
- AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Tue Nov 27 2007 - 05:26:22 CST)
- Re: AMBER: Extra-term to the Energy function !! Sampath Koppole (Tue Nov 27 2007 - 05:31:22 CST)
- AMBER: Xleap and Hydrogens Shozeb Haider (Tue Nov 27 2007 - 08:38:56 CST)
- Re: AMBER: modifications to force field for Fe4S4 cubane Ilyas Yildirim (Tue Nov 27 2007 - 09:02:21 CST)
- Re: AMBER: Xleap and Hydrogens Ilyas Yildirim (Tue Nov 27 2007 - 09:08:29 CST)
- AMBER: antechamber: read in charges fatima.chami_at_durham.ac.uk (Tue Nov 27 2007 - 09:40:13 CST)
- Re: AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Tue Nov 27 2007 - 09:23:39 CST)
- Re: AMBER: Xleap and Hydrogens Marius Retegan (Tue Nov 27 2007 - 09:43:36 CST)
- Re: AMBER: restraints to individual atoms Gustavo Seabra (Tue Nov 27 2007 - 10:34:14 CST)
- Re: AMBER: Xleap and Hydrogens David A. Case (Tue Nov 27 2007 - 10:40:05 CST)
- Re: AMBER: question about ntx=5 David A. Case (Tue Nov 27 2007 - 10:49:33 CST)
- Re: AMBER: Xleap and Hydrogens Bill Ross (Tue Nov 27 2007 - 11:11:35 CST)
- AMBER: predictive NOE generation Seth Lilavivat (Tue Nov 27 2007 - 11:41:08 CST)
- AMBER: Polarizable Potential Denis Courtier (Tue Nov 27 2007 - 11:40:34 CST)
- RE: AMBER: restraints to individual atoms Ross Walker (Tue Nov 27 2007 - 11:05:44 CST)
- AMBER: Re: antechamber problem Junmei Wang (Tue Nov 27 2007 - 11:38:17 CST)
- Re: AMBER: antechamber: read in charges Junmei Wang (Tue Nov 27 2007 - 11:50:11 CST)
- AMBER: RE: Amber9 compile problem Ross Walker (Tue Nov 27 2007 - 11:24:22 CST)
- Re: AMBER: predictive NOE generation Nicolas Lux Fawzi (Tue Nov 27 2007 - 12:26:48 CST)
- Re: AMBER: modifications to force field for Fe4S4 cubane Ilyas Yildirim (Tue Nov 27 2007 - 13:29:58 CST)
- Re: AMBER: modifications to force field for Fe4S4 cubane David A. Case (Tue Nov 27 2007 - 15:10:40 CST)
- Re: AMBER: [SOLVED] Problem with LEaP generating topology and coord files after double bond creation M. L. Dodson (Tue Nov 27 2007 - 15:45:44 CST)
- AMBER: Would amber work with Linspire 6.0? Campbell, Patrick (Tue Nov 27 2007 - 17:01:02 CST)
- AMBER: QMMM simulations Pankaj R. Daga (Tue Nov 27 2007 - 17:20:51 CST)
- RE: AMBER: QMMM simulations Ross Walker (Tue Nov 27 2007 - 18:41:11 CST)
- RE: AMBER: Would amber work with Linspire 6.0? Ross Walker (Tue Nov 27 2007 - 18:36:02 CST)
- Re: AMBER: Would amber work with Linspire 6.0? Peter Gannett (Tue Nov 27 2007 - 21:20:19 CST)
- AMBER: bondi radii problems Eddie Men (Tue Nov 27 2007 - 21:31:19 CST)
- Re: AMBER: Would amber work with Linspire 6.0? Christophe Guilbert (Tue Nov 27 2007 - 21:35:35 CST)
- Re: AMBER: restraints to individual atoms Eddie Men (Tue Nov 27 2007 - 21:54:30 CST)
- AMBER: PB warning in pb_miccg(): CG maxitn exceeded! Eddie Men (Tue Nov 27 2007 - 22:35:17 CST)
- AMBER: Error reading radii of Cu during ESP caculation. Syed Tarique Moin (Wed Nov 28 2007 - 05:27:53 CST)
- Re: AMBER: Error reading radii of Cu during ESP caculation. FyD (Wed Nov 28 2007 - 06:19:35 CST)
- Re: AMBER: Re: antechamber problem sanket deshmukh (Wed Nov 28 2007 - 08:05:37 CST)
- AMBER: Polarizable potential Denis Courtier (Wed Nov 28 2007 - 08:32:49 CST)
- AMBER: radial distribution by Ptraj Esther Brugger (Wed Nov 28 2007 - 08:35:49 CST)
- AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Francesco Pietra (Wed Nov 28 2007 - 09:01:37 CST)
- Re: AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Wed Nov 28 2007 - 09:36:38 CST)
- Re: AMBER: Polarizable potential David A. Case (Wed Nov 28 2007 - 10:19:06 CST)
- Re: AMBER: bondi radii problems David A. Case (Wed Nov 28 2007 - 10:32:21 CST)
- AMBER: (no subject) Gabriele Viliani (Wed Nov 28 2007 - 10:56:32 CST)
- Re: AMBER: (no subject) David A. Case (Wed Nov 28 2007 - 11:09:04 CST)
- Re: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated M. L. Dodson (Wed Nov 28 2007 - 11:31:04 CST)
- AMBER: leaprc.ff02polEP.r1into xleap Denis Courtier (Wed Nov 28 2007 - 11:44:21 CST)
- Re: AMBER: addles David A. Case (Wed Nov 28 2007 - 11:46:57 CST)
- Re: AMBER: [SOLVED] Problem with LEaP generating topology and coord files after double bond creation M. L. Dodson (Wed Nov 28 2007 - 12:33:38 CST)
- Re: AMBER: bondi radii problems Eddie Men (Wed Nov 28 2007 - 12:45:34 CST)
- Re: AMBER: antechamber: read in charges fatima.chami_at_durham.ac.uk (Wed Nov 28 2007 - 12:52:41 CST)
- Re: AMBER: leaprc.ff02polEP.r1into xleap David A. Case (Wed Nov 28 2007 - 12:58:30 CST)
- RE: AMBER: leaprc.ff02polEP.r1into xleap Ross Walker (Wed Nov 28 2007 - 12:38:47 CST)
- AMBER: [Fwd: Re: BOUNCE amber@scripps.edu: Non-member submission from [Taufik Al-Sarraj <taufik.alsarraj@utoronto.ca>]] Taufik Al-Sarraj (Wed Nov 28 2007 - 12:23:27 CST)
- Re: AMBER: Weird restart file with ioutfm=0, iwrap=1 and ntwprt >0 David A. Case (Wed Nov 28 2007 - 13:27:52 CST)
- AMBER: Calculating dipole moments Austin B. Yongye (Wed Nov 28 2007 - 13:33:41 CST)
- Re: AMBER: antechamber: read in charges Junmei Wang (Wed Nov 28 2007 - 14:58:36 CST)
- Re: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Gustavo Seabra (Wed Nov 28 2007 - 15:04:32 CST)
- Re: AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Wed Nov 28 2007 - 15:31:02 CST)
- AMBER: questions about smd of amber 9 WANG,YING (Wed Nov 28 2007 - 15:29:41 CST)
- RE: AMBER: Calculating dipole moments Ross Walker (Wed Nov 28 2007 - 15:57:12 CST)
- Re: AMBER: questions about smd of amber 9 Wei Chen (Wed Nov 28 2007 - 16:35:10 CST)
- Re: AMBER: questions about smd of amber 9 WANG,YING (Wed Nov 28 2007 - 20:14:21 CST)
- AMBER: Error in installing amber8 on Ubuntu tri nam Vo (Wed Nov 28 2007 - 22:24:24 CST)
- Re: AMBER: Error reading radii of Cu during ESP caculation. Syed Tarique Moin (Thu Nov 29 2007 - 00:26:39 CST)
- AMBER: About RAMD Francesco Pietra (Thu Nov 29 2007 - 01:26:45 CST)
- Re: AMBER: Error reading radii of Cu during ESP caculation. FyD (Thu Nov 29 2007 - 02:07:07 CST)
- AMBER: ele vs van der Waals backy (Thu Nov 29 2007 - 03:14:19 CST)
- AMBER: Error in reading number of frame in PTRAJ Vijay Manickam Achari (Thu Nov 29 2007 - 03:20:12 CST)
- Re: AMBER: About RAMD Alessandro Nascimento (Thu Nov 29 2007 - 04:54:02 CST)
- Re: AMBER: leaprc.ff02polEP.r1into xleap Denis Courtier (Thu Nov 29 2007 - 05:01:38 CST)
- AMBER: vlimit exceeded, polarizable force field Denis Courtier (Thu Nov 29 2007 - 05:43:45 CST)
- Re: AMBER: vlimit exceeded, polarizable force field Denis Courtier (Thu Nov 29 2007 - 07:33:22 CST)
- RE: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Steve Spronk (Thu Nov 29 2007 - 08:44:33 CST)
- Re: AMBER: questions about smd of amber 9 Gustavo Seabra (Thu Nov 29 2007 - 08:53:24 CST)
- Re: AMBER: leaprc.ff02polEP.r1into xleap David A. Case (Thu Nov 29 2007 - 09:40:04 CST)
- RE: AMBER: Calculating dipole moments Austin B. Yongye (Thu Nov 29 2007 - 09:40:51 CST)
- RE: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Francesco Pietra (Thu Nov 29 2007 - 09:44:33 CST)
- RE: AMBER: Error in installing amber8 on Ubuntu Ross Walker (Thu Nov 29 2007 - 09:44:10 CST)
- RE: AMBER: leaprc.ff02polEP.r1into xleap Ross Walker (Thu Nov 29 2007 - 09:54:13 CST)
- RE: AMBER: vlimit exceeded, polarizable force field Ross Walker (Thu Nov 29 2007 - 10:02:24 CST)
- RE: AMBER: Calculating dipole moments Ross Walker (Thu Nov 29 2007 - 10:08:50 CST)
- Re: AMBER: questions about smd of amber 9 Wei Chen (Thu Nov 29 2007 - 10:28:34 CST)
- Re: AMBER: questions about smd of amber 9 Adrian Roitberg (Thu Nov 29 2007 - 10:56:15 CST)
- AMBER: problems with restart of smd simulation w/ jar=1 & nmr=1 Wei Chen (Thu Nov 29 2007 - 11:15:51 CST)
- AMBER: DNA on Si surface Taufik Al-Sarraj (Thu Nov 29 2007 - 17:20:12 CST)
- AMBER: Re: Calculating Energies with imin=5 Pavan G (Fri Nov 30 2007 - 06:24:18 CST)
- Re: AMBER: Re: Calculating Energies with imin=5 Carlos Simmerling (Fri Nov 30 2007 - 06:32:04 CST)
- AMBER: angle between vectors Mag. rer. nat. Hannes Wallnöfer (Fri Nov 30 2007 - 06:45:02 CST)
- Re: AMBER: Re: Calculating Energies with imin=5 Pavan G (Fri Nov 30 2007 - 06:55:14 CST)
- Re: AMBER: Re: Calculating Energies with imin=5 Chris Moth (Fri Nov 30 2007 - 08:11:40 CST)
- AMBER: Group input for restrained atoms Francesco Pietra (Fri Nov 30 2007 - 10:28:50 CST)
- Re: AMBER: Re: Calculating Energies with imin=5 Pavan G (Fri Nov 30 2007 - 10:35:02 CST)
- Re: AMBER: Group input for restrained atoms Pavan G (Fri Nov 30 2007 - 10:43:23 CST)
- Re: AMBER: angle between vectors Ilyas Yildirim (Fri Nov 30 2007 - 11:28:59 CST)
- Re: AMBER: Re: Calculating Energies with imin=5 Chris Moth (Fri Nov 30 2007 - 11:49:46 CST)
- Re: AMBER: Group input for restrained atoms Francesco Pietra (Fri Nov 30 2007 - 15:12:42 CST)
Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:10 CST
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