Amber Archive Nov 2007: by subject

Amber9 compile problem
- Ross Walker (Tue Nov 27 2007 - 09:24:22 PST)
AMBER:
- McElheny, Dan (Wed Nov 21 2007 - 14:04:26 PST)
AMBER: "Atom valence violated" from LEaP
- Francesco Pietra (Mon Nov 05 2007 - 03:00:28 PST)
AMBER: &dipoles output in QM/MM simulations
- Seongeun Yang (Fri Nov 02 2007 - 23:33:58 PDT)
- Ross Walker (Fri Nov 02 2007 - 11:42:54 PDT)
- Adrian Roitberg (Fri Nov 02 2007 - 06:06:28 PDT)
- Eddie Men (Fri Nov 02 2007 - 05:01:10 PDT)
- Seongeun Yang (Fri Nov 02 2007 - 03:59:01 PDT)
- Seongeun Yang (Fri Nov 02 2007 - 02:07:04 PDT)
- Ross Walker (Thu Nov 01 2007 - 10:12:52 PDT)
- Seongeun Yang (Thu Nov 01 2007 - 03:43:54 PDT)
AMBER: &shf setup
- David A. Case (Fri Nov 16 2007 - 15:59:19 PST)
- McElheny, Dan (Thu Nov 15 2007 - 15:39:42 PST)
AMBER: (no subject)
- David A. Case (Wed Nov 28 2007 - 09:09:04 PST)
- Gabriele Viliani (Wed Nov 28 2007 - 08:56:32 PST)
- David A. Case (Wed Nov 07 2007 - 09:11:43 PST)
- Biman Jana (Wed Nov 07 2007 - 09:09:00 PST)
AMBER: 2 double bond in AMBER ffield
- ABEL Stephane 984007 (Tue Nov 13 2007 - 09:00:08 PST)
AMBER: [chirality.c] Atom did not match
- Francesco Pietra (Fri Nov 16 2007 - 11:38:20 PST)
- Jojart Balazs (Fri Nov 16 2007 - 09:48:51 PST)
- Francesco Pietra (Fri Nov 16 2007 - 09:09:10 PST)
AMBER: [SOLVED] Problem with LEaP generating topology and coord files after double bond creation
- M. L. Dodson (Wed Nov 28 2007 - 10:33:38 PST)
- M. L. Dodson (Tue Nov 27 2007 - 13:45:44 PST)
AMBER: About RAMD
- Alessandro Nascimento (Thu Nov 29 2007 - 02:54:02 PST)
- Francesco Pietra (Wed Nov 28 2007 - 23:26:45 PST)
AMBER: About TER records
- Francesco Pietra (Sat Nov 24 2007 - 13:34:59 PST)
- David A. Case (Fri Nov 23 2007 - 10:35:46 PST)
- Francesco Pietra (Fri Nov 23 2007 - 00:15:05 PST)
AMBER: addles
- David A. Case (Wed Nov 28 2007 - 09:46:57 PST)
- Peter Varnai (Sat Nov 10 2007 - 08:40:21 PST)
AMBER: AMBER 9 - Force Field Options - Question
- Carlos Simmerling (Mon Nov 05 2007 - 09:39:01 PST)
- cgji (Mon Nov 05 2007 - 09:19:58 PST)
AMBER: AMBER 9 - visualization of MD trajectory by MOE
- dinko.x.ziher.gsk.com (Wed Nov 07 2007 - 04:45:41 PST)
AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels)
- sanket deshmukh (Fri Nov 23 2007 - 15:30:11 PST)
- David A. Case (Thu Nov 08 2007 - 12:16:57 PST)
- sanket deshmukh (Thu Nov 08 2007 - 11:29:35 PST)
AMBER: amber9 installation problem
- Madjid Taghdir (Mon Nov 12 2007 - 00:38:57 PST)
AMBER: amber9 leap installation error on sgi_altix
- wei zhang (Wed Nov 14 2007 - 08:05:26 PST)
- David A. Case (Tue Nov 13 2007 - 15:27:55 PST)
- Ross Walker (Tue Nov 13 2007 - 14:50:53 PST)
- wei zhang (Tue Nov 13 2007 - 14:02:48 PST)
AMBER: angle between vectors
- Ilyas Yildirim (Fri Nov 30 2007 - 09:28:59 PST)
- Mag. rer. nat. Hannes Wallnöfer (Fri Nov 30 2007 - 04:45:02 PST)
AMBER: Antechamber
- Ilyas Yildirim (Tue Nov 06 2007 - 13:03:13 PST)
- David Mobley (Tue Nov 06 2007 - 12:41:17 PST)
- snoze pa (Tue Nov 06 2007 - 11:04:05 PST)
- Ilyas Yildirim (Tue Nov 06 2007 - 09:36:35 PST)
- David Mobley (Tue Nov 06 2007 - 09:15:33 PST)
- snoze pa (Tue Nov 06 2007 - 08:02:39 PST)
AMBER: antechamber --> sander problem
- David A. Case (Fri Nov 16 2007 - 13:17:50 PST)
- Yamada, Takahiro (Fri Nov 16 2007 - 12:18:18 PST)
AMBER: antechamber fails with large molecules
- FyD (Sun Nov 04 2007 - 04:29:09 PST)
- Ilyas Yildirim (Sat Nov 03 2007 - 09:47:49 PDT)
- Francesco Pietra (Sat Nov 03 2007 - 07:01:41 PDT)
- Ilyas Yildirim (Sat Nov 03 2007 - 01:38:03 PDT)
- Francesco Pietra (Fri Nov 02 2007 - 10:07:52 PDT)
- Ilyas Yildirim (Fri Nov 02 2007 - 02:10:33 PDT)
- Eddie Men (Fri Nov 02 2007 - 01:50:57 PDT)
- Ilyas Yildirim (Fri Nov 02 2007 - 01:24:26 PDT)
- Junmei Wang (Thu Nov 01 2007 - 23:16:41 PDT)
- Francesco Pietra (Thu Nov 01 2007 - 01:29:26 PDT)
AMBER: antechamber problem
- David A. Case (Fri Nov 23 2007 - 18:40:21 PST)
AMBER: antechamber: read in charges
- Junmei Wang (Wed Nov 28 2007 - 12:58:36 PST)
- fatima.chami.durham.ac.uk (Wed Nov 28 2007 - 10:52:41 PST)
- Junmei Wang (Tue Nov 27 2007 - 09:50:11 PST)
- fatima.chami.durham.ac.uk (Tue Nov 27 2007 - 07:40:13 PST)
AMBER: Atom type definition
- Xioling Chuang (Thu Nov 22 2007 - 01:03:29 PST)
AMBER: Atom types for polyunsaturated lipids
- ABEL Stephane 984007 (Sun Nov 18 2007 - 09:14:14 PST)
AMBER: BELLY
- Eddie Men (Thu Nov 22 2007 - 14:30:38 PST)
- Eddie Men (Thu Nov 22 2007 - 13:16:39 PST)
AMBER: BELLY issues
- Eddie Men (Thu Nov 22 2007 - 02:03:52 PST)
AMBER: bondi radii problems
- Eddie Men (Wed Nov 28 2007 - 10:45:34 PST)
- David A. Case (Wed Nov 28 2007 - 08:32:21 PST)
- Eddie Men (Tue Nov 27 2007 - 19:31:19 PST)
AMBER: Bug report: iwrap failure in PMEMD with netCDF
- Robert Duke (Wed Nov 14 2007 - 11:52:16 PST)
- Myunggi Yi (Wed Nov 14 2007 - 11:18:18 PST)
AMBER: calculating charges to modified 4GA unit
- nag raj (Wed Nov 07 2007 - 19:04:53 PST)
- nag raj (Wed Nov 07 2007 - 19:04:53 PST)
- Karl Kirschner (Wed Nov 07 2007 - 05:37:42 PST)
- Austin B. Yongye (Wed Nov 07 2007 - 06:26:57 PST)
- FyD (Wed Nov 07 2007 - 05:21:03 PST)
- nag raj (Wed Nov 07 2007 - 03:26:51 PST)
AMBER: Calculating dipole moments
- Ross Walker (Thu Nov 29 2007 - 08:08:50 PST)
- Austin B. Yongye (Thu Nov 29 2007 - 07:40:51 PST)
- Ross Walker (Wed Nov 28 2007 - 13:57:12 PST)
- Austin B. Yongye (Wed Nov 28 2007 - 11:33:41 PST)
AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8?
- Carlos Simmerling (Tue Nov 06 2007 - 03:49:13 PST)
- ming hui (Tue Nov 06 2007 - 00:30:17 PST)
AMBER: chem shift format
- David A. Case (Fri Nov 16 2007 - 16:00:27 PST)
- McElheny, Dan (Fri Nov 16 2007 - 13:46:57 PST)
AMBER: Compiling single programs
- Adrian Roitberg (Fri Nov 02 2007 - 11:08:44 PDT)
- Mark Williamson (Fri Nov 02 2007 - 10:58:32 PDT)
- Francesco Pietra (Fri Nov 02 2007 - 10:44:09 PDT)
AMBER: connecting a non standard residue to the rest of an enzyme
- David A. Case (Fri Nov 23 2007 - 10:39:13 PST)
- Boutheïna Kerkeni (Fri Nov 23 2007 - 05:43:36 PST)
AMBER: dihedral driver
- fatima.chami.durham.ac.uk (Sun Nov 04 2007 - 04:51:22 PST)
AMBER: divcon
- David A. Case (Thu Nov 08 2007 - 18:06:55 PST)
- Pablo Englebienne (Thu Nov 08 2007 - 09:50:25 PST)
- san_amber roy (Thu Nov 08 2007 - 09:19:41 PST)
AMBER: divcon on AIX using xlf 10.1
- Joachim Hein (Wed Nov 07 2007 - 08:23:14 PST)
AMBER: DNA on Si surface
- Taufik Al-Sarraj (Thu Nov 29 2007 - 15:20:12 PST)
AMBER: DUMBFREQ
- Steve Seibold (Mon Nov 05 2007 - 07:52:19 PST)
AMBER: ele vs van der Waals
- backy (Thu Nov 29 2007 - 01:14:19 PST)
AMBER: Energy minimization problem of -SO3H group
- Eddie Men (Tue Nov 06 2007 - 21:52:09 PST)
- David A. Case (Tue Nov 06 2007 - 21:12:08 PST)
- Takao Kobayashi (Tue Nov 06 2007 - 02:17:35 PST)
AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated
- Francesco Pietra (Thu Nov 29 2007 - 07:44:33 PST)
- Steve Spronk (Thu Nov 29 2007 - 06:44:33 PST)
- Gustavo Seabra (Wed Nov 28 2007 - 13:04:32 PST)
- M. L. Dodson (Wed Nov 28 2007 - 09:31:04 PST)
- Francesco Pietra (Wed Nov 28 2007 - 07:01:37 PST)
AMBER: Error in installing amber8 on Ubuntu
- Ross Walker (Thu Nov 29 2007 - 07:44:10 PST)
- tri nam Vo (Wed Nov 28 2007 - 20:24:24 PST)
AMBER: Error in reading number of frame in PTRAJ
- Vijay Manickam Achari (Thu Nov 29 2007 - 01:20:12 PST)
AMBER: Error reading radii of Cu during ESP caculation.
- FyD (Thu Nov 29 2007 - 00:07:07 PST)
- Syed Tarique Moin (Wed Nov 28 2007 - 22:26:39 PST)
- FyD (Wed Nov 28 2007 - 04:19:35 PST)
- Syed Tarique Moin (Wed Nov 28 2007 - 03:27:53 PST)
AMBER: Error when doing a TI simulation: "vlimit exceeded
- Thomas Steinbrecher (Thu Nov 15 2007 - 17:52:47 PST)
- ming hui (Thu Nov 15 2007 - 17:26:43 PST)
- Thomas Steinbrecher (Thu Nov 15 2007 - 17:18:54 PST)
- ming hui (Thu Nov 15 2007 - 16:48:05 PST)
- Thomas Steinbrecher (Thu Nov 15 2007 - 09:06:03 PST)
- ming hui (Wed Nov 14 2007 - 17:10:07 PST)
AMBER: error with amber9 production run.
- Vijay Singh (Sat Nov 03 2007 - 07:10:52 PDT)
AMBER: EXCEEDED MAXLESADJ in sander.LES.MPI (amber9)
- Carlos Simmerling (Sat Nov 17 2007 - 13:51:09 PST)
- Alessandro Nascimento (Sat Nov 17 2007 - 13:24:58 PST)
AMBER: Extra-term to the Energy function !!
- Sampath Koppole (Tue Nov 27 2007 - 03:31:22 PST)
- Carlos Simmerling (Tue Nov 27 2007 - 03:12:13 PST)
- Sampath Koppole (Tue Nov 27 2007 - 00:57:54 PST)
AMBER: Failure to recompile antechamber
- Francesco Pietra (Fri Nov 02 2007 - 16:05:45 PDT)
AMBER: Fe bonds in HEME !
- Pradipta Bandyopadhyay (Mon Nov 05 2007 - 03:50:58 PST)
AMBER: five-coordinated phosphorus
- Yubo Fan (Sat Nov 17 2007 - 06:19:06 PST)
- Smooth Cutie (Fri Nov 16 2007 - 15:48:40 PST)
AMBER: frcmod file and NONB for dummy atoms
- Ilyas Yildirim (Fri Nov 23 2007 - 18:26:37 PST)
- David A. Case (Fri Nov 23 2007 - 10:58:46 PST)
- Ilyas Yildirim (Thu Nov 22 2007 - 16:48:31 PST)
AMBER: Fwd: [chirality.c] Atom did not match
- Steve Spronk (Mon Nov 19 2007 - 05:31:42 PST)
- Steve Spronk (Mon Nov 19 2007 - 05:28:07 PST)
- David A. Case (Sat Nov 17 2007 - 08:53:01 PST)
- Francesco Pietra (Sat Nov 17 2007 - 08:16:09 PST)
- Francesco Pietra (Sat Nov 17 2007 - 02:56:01 PST)
- David A. Case (Fri Nov 16 2007 - 16:03:33 PST)
- Francesco Pietra (Fri Nov 16 2007 - 13:59:40 PST)
AMBER: Fwd: About TER records
- Francesco Pietra (Sat Nov 24 2007 - 13:27:11 PST)
- Francesco Pietra (Sat Nov 24 2007 - 10:29:15 PST)
- Ilyas Yildirim (Fri Nov 23 2007 - 07:41:47 PST)
- Francesco Pietra (Fri Nov 23 2007 - 07:23:41 PST)
AMBER: gb minimization using nab
- Guillaume Renvez (Tue Nov 13 2007 - 06:49:48 PST)
- Andreas Svrcek-Seiler (Tue Nov 13 2007 - 03:58:05 PST)
- Guillaume Renvez (Tue Nov 13 2007 - 03:06:13 PST)
AMBER: Group input for restrained atoms
- Francesco Pietra (Fri Nov 30 2007 - 13:12:42 PST)
- Pavan G (Fri Nov 30 2007 - 08:43:23 PST)
- Francesco Pietra (Fri Nov 30 2007 - 08:28:50 PST)
AMBER: heical content in simulations
- Scott Pendley (Fri Nov 09 2007 - 12:25:18 PST)
AMBER: Hello
- David A. Case (Sat Nov 24 2007 - 22:14:23 PST)
- Carlos Simmerling (Sat Nov 24 2007 - 10:55:46 PST)
- Eddie Men (Sat Nov 24 2007 - 10:47:11 PST)
- Carlos Simmerling (Fri Nov 23 2007 - 19:01:13 PST)
- Eddie Men (Fri Nov 23 2007 - 18:44:05 PST)
AMBER: How can i calculate generalized order parameters using ptraj.
- David A. Case (Thu Nov 08 2007 - 18:23:34 PST)
AMBER: How to calculate S2 from P2 using ptraj ?
- David A. Case (Mon Nov 19 2007 - 10:04:48 PST)
- brmeher.iitg.ernet.in (Fri Nov 16 2007 - 22:40:31 PST)
- brmeher.iitg.ernet.in (Fri Nov 16 2007 - 22:34:11 PST)
AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ?
- Catein Catherine (Sun Nov 04 2007 - 21:20:48 PST)
- Jiri Sponer (Sun Nov 04 2007 - 05:01:02 PST)
- sychen (Sun Nov 04 2007 - 04:46:09 PST)
AMBER: Implicit/Explicit solvation
- David A. Case (Wed Nov 21 2007 - 08:46:19 PST)
- Ross Walker (Wed Nov 21 2007 - 08:10:58 PST)
- Eddie Men (Tue Nov 20 2007 - 23:03:12 PST)
AMBER: Improper torsion terms
- Bill Ross (Fri Nov 02 2007 - 09:41:00 PDT)
- Pavan G (Thu Nov 01 2007 - 17:24:46 PDT)
AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine
- David A. Case (Tue Nov 13 2007 - 08:28:52 PST)
- Hu, Shaowen (JSC-SK)[USRA] (Tue Nov 13 2007 - 08:13:18 PST)
- David A. Case (Tue Nov 13 2007 - 07:54:38 PST)
- Hopkins, Robert (Mon Nov 12 2007 - 15:32:20 PST)
AMBER: invalid digit '*' in the input file
- Yong Duan (Mon Nov 12 2007 - 17:07:26 PST)
- Adrian Roitberg (Mon Nov 12 2007 - 07:17:43 PST)
- Hayden Eastwood (Mon Nov 12 2007 - 07:10:03 PST)
- rebeca.mmb.pcb.ub.es (Mon Nov 12 2007 - 06:56:26 PST)
- Chris Moth (Mon Nov 12 2007 - 06:40:26 PST)
- Martin Klefas-Stennett (Mon Nov 12 2007 - 06:31:08 PST)
- rebeca.mmb.pcb.ub.es (Mon Nov 12 2007 - 06:06:16 PST)
AMBER: LEaP bond problem
- David A. Case (Wed Nov 07 2007 - 08:39:49 PST)
- Beale, John (Wed Nov 07 2007 - 04:57:30 PST)
AMBER: leaprc.ff02polEP.r1into xleap
- Ross Walker (Thu Nov 29 2007 - 07:54:13 PST)
- David A. Case (Thu Nov 29 2007 - 07:40:04 PST)
- Denis Courtier (Thu Nov 29 2007 - 03:01:38 PST)
- David A. Case (Wed Nov 28 2007 - 10:58:30 PST)
- Ross Walker (Wed Nov 28 2007 - 10:38:47 PST)
- Denis Courtier (Wed Nov 28 2007 - 09:44:21 PST)
AMBER: LJ parameters for alkynes
- David Mobley (Mon Nov 26 2007 - 10:07:37 PST)
AMBER: make test.parallel
- Gustavo Seabra (Fri Nov 09 2007 - 08:28:23 PST)
- Francesco Pietra (Thu Nov 08 2007 - 09:30:36 PST)
- David A. Case (Thu Nov 08 2007 - 07:58:39 PST)
- Francesco Pietra (Thu Nov 08 2007 - 00:33:21 PST)
AMBER: MD simulations with Pt atom - how to keep square planar geometry?
- Pablo Englebienne (Thu Nov 08 2007 - 09:44:43 PST)
- gsciaini.qi.fcen.uba.ar (Thu Nov 08 2007 - 08:09:31 PST)
- Pablo Englebienne (Wed Nov 07 2007 - 18:21:21 PST)
AMBER: Minimum energy tolerance gradient setting for minimization
- David A. Case (Tue Nov 06 2007 - 08:03:18 PST)
- Sandhya Tiwari (Tue Nov 06 2007 - 06:13:52 PST)
AMBER: Missing BELE for MM in 1
- backy (Mon Nov 19 2007 - 04:19:09 PST)
AMBER: modifications to force field for Fe4S4 cubane
- Boutheïna Kerkeni (Wed Nov 28 2007 - 13:31:02 PST)
- Boutheïna Kerkeni (Wed Nov 28 2007 - 07:36:38 PST)
- David A. Case (Tue Nov 27 2007 - 13:10:40 PST)
- Ilyas Yildirim (Tue Nov 27 2007 - 11:29:58 PST)
- Boutheïna Kerkeni (Tue Nov 27 2007 - 07:23:39 PST)
- Ilyas Yildirim (Tue Nov 27 2007 - 07:02:21 PST)
- Boutheïna Kerkeni (Tue Nov 27 2007 - 03:26:22 PST)
- David A. Case (Wed Nov 21 2007 - 14:30:30 PST)
- Boutheïna Kerkeni (Wed Nov 21 2007 - 13:41:45 PST)
AMBER: newby question on converting xyz format to pdb format after energy minimization
- David A. Case (Tue Nov 20 2007 - 13:33:08 PST)
- Eddie Men (Tue Nov 20 2007 - 13:24:56 PST)
- Mehmet Serkan Apaydin (Tue Nov 20 2007 - 13:02:42 PST)
AMBER: paper request
- Miguel Ortiz-Lombardía (Mon Nov 05 2007 - 02:14:09 PST)
- FyD (Mon Nov 05 2007 - 01:13:38 PST)
- Miguel Ortiz-Lombardía (Mon Nov 05 2007 - 01:01:08 PST)
AMBER: Parallel Amber compilation problems !!
- Sampath Koppole (Wed Nov 14 2007 - 01:22:15 PST)
- Ross Walker (Tue Nov 13 2007 - 10:33:25 PST)
- Sampath Koppole (Tue Nov 13 2007 - 06:05:28 PST)
AMBER: Parallel scaling
- priya priya (Tue Nov 13 2007 - 03:26:23 PST)
- Carlos Simmerling (Tue Nov 13 2007 - 03:07:53 PST)
- priya priya (Tue Nov 13 2007 - 02:35:20 PST)
AMBER: Parallel test error with shared libraries
- Joe Nolan (Mon Nov 05 2007 - 13:05:27 PST)
AMBER: PB warning in pb_miccg(): CG maxitn exceeded!
- Eddie Men (Tue Nov 27 2007 - 20:35:17 PST)
AMBER: pmemd with openmpi
- Myunggi Yi (Mon Nov 19 2007 - 13:40:41 PST)
- Francesco Pietra (Mon Nov 19 2007 - 12:31:56 PST)
- Myunggi Yi (Mon Nov 19 2007 - 11:25:48 PST)
AMBER: Polarizable potential
- David A. Case (Wed Nov 28 2007 - 08:19:06 PST)
- Denis Courtier (Wed Nov 28 2007 - 06:32:49 PST)
- Denis Courtier (Tue Nov 27 2007 - 09:40:34 PST)
AMBER: Polarizable potentials
- David A. Case (Mon Nov 26 2007 - 18:23:05 PST)
- Denis Courtier (Mon Nov 26 2007 - 10:49:33 PST)
AMBER: Pre-ABMER Installation Prob w/ MPICH2
- jantonioms J. A. Mondragon S (Fri Nov 23 2007 - 09:36:12 PST)
- Joseph Maxwell (Thu Nov 22 2007 - 11:55:18 PST)
AMBER: predictive NOE generation
- Nicolas Lux Fawzi (Tue Nov 27 2007 - 10:26:48 PST)
- Seth Lilavivat (Tue Nov 27 2007 - 09:41:08 PST)
AMBER: Pressure Variation for NPT simulation of TIP5P water
- David A. Case (Thu Nov 22 2007 - 09:34:34 PST)
- Biman Jana (Thu Nov 22 2007 - 06:50:16 PST)
AMBER: Pressure Variation for NPT simulation of TIP5P water (fwd)
- David A. Case (Sat Nov 24 2007 - 09:36:44 PST)
- Biman Jana (Sat Nov 24 2007 - 05:22:39 PST)
AMBER: Problem with LEaP generating topology and coord files after double bond creation
- David A. Case (Wed Nov 21 2007 - 17:08:08 PST)
- M. L. Dodson (Wed Nov 21 2007 - 12:45:17 PST)
AMBER: Problem with xLeap
- David A. Case (Tue Nov 13 2007 - 09:55:24 PST)
- alfredoq.mail.fcq.unc.edu.ar (Tue Nov 13 2007 - 10:11:31 PST)
- alfredoq.mail.fcq.unc.edu.ar (Tue Nov 13 2007 - 09:07:40 PST)
- David A. Case (Tue Nov 13 2007 - 08:08:24 PST)
- alfredoq.mail.fcq.unc.edu.ar (Tue Nov 13 2007 - 07:34:46 PST)
AMBER: problems with restart of smd simulation w/ jar=1 & nmr=1
- Wei Chen (Thu Nov 29 2007 - 09:15:51 PST)
AMBER: Protein containing iron.
- Ross Walker (Tue Nov 13 2007 - 10:37:40 PST)
- Syed Tarique Moin (Tue Nov 13 2007 - 03:16:48 PST)
AMBER: ptraj frames maximum
- Thomas Cheatham (Mon Nov 05 2007 - 15:54:37 PST)
- David A. Case (Mon Nov 05 2007 - 08:37:11 PST)
- Hannes Wallnoefer (Mon Nov 05 2007 - 08:07:00 PST)
- David A. Case (Mon Nov 05 2007 - 07:34:20 PST)
- Hannes Wallnoefer (Mon Nov 05 2007 - 06:19:25 PST)
AMBER: ptraj hbond mask
- Thomas Cheatham III (Wed Nov 07 2007 - 13:00:40 PST)
- Lars Skjærven (Mon Nov 05 2007 - 08:00:03 PST)
AMBER: Puzzle with WAT
- Bill Ross (Sun Nov 18 2007 - 10:55:15 PST)
- Francesco Pietra (Sun Nov 18 2007 - 00:09:27 PST)
- Bill Ross (Sat Nov 17 2007 - 16:00:06 PST)
- Francesco Pietra (Sat Nov 17 2007 - 10:14:38 PST)
AMBER: QMMM simulations
- Ross Walker (Tue Nov 27 2007 - 16:41:11 PST)
- Pankaj R. Daga (Tue Nov 27 2007 - 15:20:51 PST)
AMBER: Question
- David A. Case (Tue Nov 06 2007 - 21:18:33 PST)
- dykyy (Tue Nov 06 2007 - 05:12:46 PST)
AMBER: question about ntx=5
- David A. Case (Tue Nov 27 2007 - 08:49:33 PST)
- Wei Chen (Sun Nov 25 2007 - 17:21:52 PST)
- David A. Case (Sun Nov 25 2007 - 16:27:30 PST)
- Wei Chen (Sun Nov 25 2007 - 11:21:44 PST)
AMBER: question with ptraj loop
- Vijay Singh (Sat Nov 17 2007 - 08:06:53 PST)
AMBER: questions about smd of amber 9
- Adrian Roitberg (Thu Nov 29 2007 - 08:56:15 PST)
- Wei Chen (Thu Nov 29 2007 - 08:28:34 PST)
- Gustavo Seabra (Thu Nov 29 2007 - 06:53:24 PST)
- WANG,YING (Wed Nov 28 2007 - 18:14:21 PST)
- Wei Chen (Wed Nov 28 2007 - 14:35:10 PST)
- WANG,YING (Wed Nov 28 2007 - 13:29:41 PST)
AMBER: R.E.D.-III bug fixes
- FyD (Sun Nov 18 2007 - 09:22:47 PST)
AMBER: radial distribution by Ptraj
- Esther Brugger (Wed Nov 28 2007 - 06:35:49 PST)
AMBER: RED-vIII fails
- FyD (Mon Nov 05 2007 - 10:27:33 PST)
- Jesper Soerensen (Mon Nov 05 2007 - 08:01:21 PST)
AMBER: replica exchange problems with ifort >10.0.023
- Peter Varnai (Sat Nov 10 2007 - 08:44:30 PST)
AMBER: Request reg parameter for vitamin e
- Rama krishnan (Mon Nov 05 2007 - 23:11:47 PST)
- Rama krishnan (Mon Nov 05 2007 - 23:13:51 PST)
AMBER: RESP question
- Gustavo Seabra (Fri Nov 09 2007 - 21:01:09 PST)
- Eddie Men (Fri Nov 09 2007 - 16:33:16 PST)
AMBER: restrain center of mass of one domain
- Wei Chen (Mon Nov 12 2007 - 15:14:11 PST)
AMBER: Restrained MD (amber9)
- David A. Case (Mon Nov 26 2007 - 15:49:43 PST)
- Vincent Bisetty (Mon Nov 26 2007 - 14:52:28 PST)
AMBER: restraints to individual atoms
- Eddie Men (Tue Nov 27 2007 - 19:54:30 PST)
- Ross Walker (Tue Nov 27 2007 - 09:05:44 PST)
- Gustavo Seabra (Tue Nov 27 2007 - 08:34:14 PST)
- Eddie Men (Mon Nov 26 2007 - 19:02:11 PST)
AMBER: solvatebox vs solvateoct
- Francesco Pietra (Sun Nov 25 2007 - 10:27:06 PST)
AMBER: Solvation free energy
- Thomas Steinbrecher (Mon Nov 19 2007 - 10:21:23 PST)
- Mike Wykes (Mon Nov 19 2007 - 10:08:23 PST)
AMBER: thermodynamic integration
- Thomas Steinbrecher (Tue Nov 13 2007 - 08:36:15 PST)
- David A. Case (Fri Nov 09 2007 - 10:27:48 PST)
- Cooper, Matthew (Fri Nov 09 2007 - 06:32:52 PST)
- Cooper, Matthew (Fri Nov 09 2007 - 06:03:32 PST)
- David A. Case (Thu Nov 08 2007 - 17:49:49 PST)
- Ilyas Yildirim (Thu Nov 08 2007 - 14:42:04 PST)
- Cooper, Matthew (Thu Nov 08 2007 - 13:14:25 PST)
AMBER: TIP5P water Simulation
- Biman Jana (Wed Nov 07 2007 - 09:12:42 PST)
AMBER: TIP5P water simulation using AMBER7
- David A. Case (Sun Nov 11 2007 - 14:04:08 PST)
- Adrian Roitberg (Sun Nov 11 2007 - 08:29:11 PST)
- Carlos Simmerling (Sun Nov 11 2007 - 06:25:50 PST)
- Biman Jana (Sun Nov 11 2007 - 06:21:56 PST)
- Carlos Simmerling (Sat Nov 10 2007 - 07:00:36 PST)
- Biman Jana (Sat Nov 10 2007 - 06:57:20 PST)
AMBER: umbrella sampling
- Carlos Simmerling (Sun Nov 25 2007 - 11:52:57 PST)
- Jardas sucuriba (Sun Nov 25 2007 - 11:32:28 PST)
AMBER: umbrella sampling and WHAM
- Allen, Thomas W., Ph.D. [RO BIOCHM] (Mon Nov 05 2007 - 12:03:31 PST)
AMBER: Understading of mdcrd file and pdb file..
- Vijay Manickam Achari (Sun Nov 18 2007 - 21:27:19 PST)
- David A. Case (Thu Nov 15 2007 - 22:23:30 PST)
- Vijay Manickam Achari (Thu Nov 15 2007 - 21:02:08 PST)
AMBER: Value of taup for bulk TIP5P water simulation(amber7)
- Biman Jana (Mon Nov 26 2007 - 11:25:37 PST)
AMBER: vlimit exceeded, polarizable force field
- Ross Walker (Thu Nov 29 2007 - 08:02:24 PST)
- Denis Courtier (Thu Nov 29 2007 - 05:33:22 PST)
- Denis Courtier (Thu Nov 29 2007 - 03:43:45 PST)
AMBER: Weird restart file with ioutfm=0, iwrap=1 and ntwprt >0
- David A. Case (Wed Nov 28 2007 - 11:27:52 PST)
- Hai Long (Mon Nov 26 2007 - 09:41:18 PST)
AMBER: Would amber work with Linspire 6.0?
- Christophe Guilbert (Tue Nov 27 2007 - 19:35:35 PST)
- Peter Gannett (Tue Nov 27 2007 - 19:20:19 PST)
- Ross Walker (Tue Nov 27 2007 - 16:36:02 PST)
- Campbell, Patrick (Tue Nov 27 2007 - 15:01:02 PST)
AMBER: Xleap and Hydrogens
- Bill Ross (Tue Nov 27 2007 - 09:11:35 PST)
- David A. Case (Tue Nov 27 2007 - 08:40:05 PST)
- Marius Retegan (Tue Nov 27 2007 - 07:43:36 PST)
- Ilyas Yildirim (Tue Nov 27 2007 - 07:08:29 PST)
- Shozeb Haider (Tue Nov 27 2007 - 06:38:56 PST)
AMBER: xleap heme iron coordination error
- David A. Case (Fri Nov 16 2007 - 11:47:53 PST)
- Robyn Ayscue (Fri Nov 16 2007 - 11:33:35 PST)
AMBER: xleap patch for xorg-7.3 ??
- Xuebin Qiao (Fri Nov 09 2007 - 06:26:38 PST)
- David A. Case (Thu Nov 08 2007 - 18:03:39 PST)
- M. L. Dodson (Thu Nov 08 2007 - 11:04:05 PST)
AMBER: xleap patch for xorg-7.3 ??]
- David A. Case (Thu Nov 15 2007 - 22:12:45 PST)
- Lili Peng (Thu Nov 15 2007 - 14:38:57 PST)
- M. L. Dodson (Thu Nov 15 2007 - 09:28:28 PST)
- Xuebin Qiao (Wed Nov 14 2007 - 22:59:58 PST)
- M. L. Dodson (Wed Nov 14 2007 - 10:51:35 PST)
AMBER: Zinc-Histidine force field
- Mattia Mori - CERM (Thu Nov 22 2007 - 11:12:43 PST)
- Ray Luo (Thu Nov 22 2007 - 11:01:30 PST)
- Mattia Mori - CERM (Thu Nov 22 2007 - 04:06:20 PST)
- Ray Luo (Wed Nov 21 2007 - 09:30:21 PST)
- Mattia Mori - CERM (Wed Nov 21 2007 - 08:54:02 PST)
AMBER:antechamber fails with large molecules
- Francesco Pietra (Sun Nov 11 2007 - 03:13:56 PST)
- Junmei Wang (Thu Nov 01 2007 - 23:29:11 PDT)
AMBER:How to calculate the free energy of a series of conformations
- Carlos Simmerling (Wed Nov 21 2007 - 15:04:03 PST)
- David A. Case (Wed Nov 21 2007 - 11:42:09 PST)
- huzehan19870731.126.com (Mon Nov 19 2007 - 19:18:41 PST)
antechamber problem
- sanket deshmukh (Wed Nov 28 2007 - 06:05:37 PST)
- Junmei Wang (Tue Nov 27 2007 - 09:38:17 PST)
BOUNCE amber.scripps.edu: Non-member submission from [Taufik Al-Sarraj <taufik.alsarraj@utoronto.ca>]]
- Taufik Al-Sarraj (Wed Nov 28 2007 - 10:23:27 PST)
Calculating Energies with imin=5
- Chris Moth (Fri Nov 30 2007 - 09:49:46 PST)
- Pavan G (Fri Nov 30 2007 - 08:35:02 PST)
- Chris Moth (Fri Nov 30 2007 - 06:11:40 PST)
- Pavan G (Fri Nov 30 2007 - 04:55:14 PST)
- Carlos Simmerling (Fri Nov 30 2007 - 04:32:04 PST)
- Pavan G (Fri Nov 30 2007 - 04:24:18 PST)
FF94 or FF99?
- Jiri Sponer (Sat Nov 24 2007 - 02:53:24 PST)
- Ilyas Yildirim (Fri Nov 23 2007 - 15:29:15 PST)
- David A. Case (Fri Nov 23 2007 - 10:51:18 PST)
- Ilyas Yildirim (Thu Nov 22 2007 - 16:29:08 PST)
- Carlos Simmerling (Thu Nov 22 2007 - 16:13:16 PST)
- Jerome.GOLEBIOWSKI.unice.fr (Thu Nov 22 2007 - 07:57:33 PST)
- Adrian Roitberg (Thu Nov 22 2007 - 07:20:22 PST)
- Patel, Bhavesh H (Thu Nov 22 2007 - 06:34:55 PST)
RE : AMBER: Atom types for polyunsaturated lipids
- ABEL Stephane 984007 (Sun Nov 18 2007 - 11:40:24 PST)

Amber Archive Nov 2007 by subject