AMBER Archive (2007) - Nov 2007 By ThreadMost recent messages
370 messages sorted by:
[ author ]
[ date ]
[ subject ]
About this archive
Starting: Thu Nov 01 2007 - 02:29:26 CST
Ending: Fri Nov 30 2007 - 15:12:42 CST
- AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Thu Nov 01 2007 - 04:43:54 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 - 00:29:11 CST)
- Re: AMBER: Improper torsion terms Bill Ross (Fri Nov 02 2007 - 10:41:00 CST)
- AMBER: Compiling single programs Francesco Pietra (Fri Nov 02 2007 - 11:44:09 CST)
- AMBER: error with amber9 production run. Vijay Singh (Sat Nov 03 2007 - 08:10:52 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)
- AMBER: paper request Miguel Ortiz-Lombardía (Mon Nov 05 2007 - 03:01:08 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)
- 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)
- 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)
- 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)
- 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)
- AMBER: Antechamber snoze pa (Tue Nov 06 2007 - 10:02:39 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)
- AMBER: divcon on AIX using xlf 10.1 Joachim Hein (Wed Nov 07 2007 - 10:23:14 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)
- AMBER: MD simulations with Pt atom - how to keep square planar geometry? Pablo Englebienne (Wed Nov 07 2007 - 20:21:21 CST)
- AMBER: make test.parallel Francesco Pietra (Thu Nov 08 2007 - 02:33:21 CST)
- AMBER: divcon san_amber roy (Thu Nov 08 2007 - 11:19:41 CST)
- AMBER: xleap patch for xorg-7.3 ?? M. L. Dodson (Thu Nov 08 2007 - 13:04:05 CST)
- AMBER: thermodynamic integration Cooper, Matthew (Thu Nov 08 2007 - 15:14:25 CST)
- AMBER: RESP question Eddie Men (Fri Nov 09 2007 - 18:33:16 CST)
- AMBER: TIP5P water simulation using AMBER7 Biman Jana (Sat Nov 10 2007 - 08:57:20 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)
- AMBER: invalid digit '*' in the input file rebeca_at_mmb.pcb.ub.es (Mon Nov 12 2007 - 08:06:16 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)
- 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)
- AMBER: Protein containing iron. Syed Tarique Moin (Tue Nov 13 2007 - 05:16:48 CST)
- AMBER: Parallel Amber compilation problems !! Sampath Koppole (Tue Nov 13 2007 - 08:05:28 CST)
- AMBER: 2 double bond in AMBER ffield ABEL Stephane 984007 (Tue Nov 13 2007 - 11:00:08 CST)
- AMBER: amber9 leap installation error on sgi_altix wei zhang (Tue Nov 13 2007 - 16:02:48 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)
- AMBER: Error when doing a TI simulation: "vlimit exceeded ming hui (Wed Nov 14 2007 - 19:10:07 CST)
- AMBER: &shf setup McElheny, Dan (Thu Nov 15 2007 - 17:39:42 CST)
- AMBER: Understading of mdcrd file and pdb file.. Vijay Manickam Achari (Thu Nov 15 2007 - 23:02:08 CST)
- AMBER: [chirality.c] Atom did not match Francesco Pietra (Fri Nov 16 2007 - 11:09:10 CST)
- AMBER: xleap heme iron coordination error Robyn Ayscue (Fri Nov 16 2007 - 13:33:35 CST)
- AMBER: antechamber --> sander problem Yamada, Takahiro (Fri Nov 16 2007 - 14:18:18 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)
- 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)
- 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)
- 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: Puzzle with WAT Bill Ross (Sat Nov 17 2007 - 18:00:06 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)
- AMBER: Missing BELE for MM in 1 backy (Mon Nov 19 2007 - 06:19:09 CST)
- AMBER: Solvation free energy Mike Wykes (Mon Nov 19 2007 - 12:08:23 CST)
- AMBER: pmemd with openmpi Myunggi Yi (Mon Nov 19 2007 - 13:25:48 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)
- AMBER: Implicit/Explicit solvation Eddie Men (Wed Nov 21 2007 - 01:03:12 CST)
- AMBER: Zinc-Histidine force field Mattia Mori - CERM (Wed Nov 21 2007 - 10:54:02 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)
- 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)
- 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)
- 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)
- AMBER: Pre-ABMER Installation Prob w/ MPICH2 Joseph Maxwell (Thu Nov 22 2007 - 13:55:18 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)
- AMBER: Hello Eddie Men (Fri Nov 23 2007 - 20:44:05 CST)
- AMBER: Pressure Variation for NPT simulation of TIP5P water (fwd) Biman Jana (Sat Nov 24 2007 - 07:22:39 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)
- 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)
- 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)
- AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Tue Nov 27 2007 - 05:26:22 CST)
- AMBER: Xleap and Hydrogens Shozeb Haider (Tue Nov 27 2007 - 08:38:56 CST)
- AMBER: antechamber: read in charges fatima.chami_at_durham.ac.uk (Tue Nov 27 2007 - 09:40:13 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)
- AMBER: Re: antechamber problem Junmei Wang (Tue Nov 27 2007 - 11:38:17 CST)
- AMBER: RE: Amber9 compile problem Ross Walker (Tue Nov 27 2007 - 11:24:22 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)
- AMBER: bondi radii problems Eddie Men (Tue Nov 27 2007 - 21:31:19 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)
- 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)
- AMBER: (no subject) Gabriele Viliani (Wed Nov 28 2007 - 10:56:32 CST)
- AMBER: leaprc.ff02polEP.r1into xleap Denis Courtier (Wed Nov 28 2007 - 11:44:21 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)
- AMBER: Calculating dipole moments Austin B. Yongye (Wed Nov 28 2007 - 13:33:41 CST)
- AMBER: questions about smd of amber 9 WANG,YING (Wed Nov 28 2007 - 15:29:41 CST)
- AMBER: Error in installing amber8 on Ubuntu tri nam Vo (Wed Nov 28 2007 - 22:24:24 CST)
- AMBER: About RAMD Francesco Pietra (Thu Nov 29 2007 - 01:26:45 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)
- AMBER: vlimit exceeded, polarizable force field Denis Courtier (Thu Nov 29 2007 - 05:43:45 CST)
- AMBER: problems with restart of smd simulation w/ jar=1 & nmr=1 Wei Chen (Thu Nov 29 2007 - 11:15:51 CST)
- AMBER: Re: Calculating Energies with imin=5 Pavan G (Fri Nov 30 2007 - 06:24:18 CST)
- AMBER: angle between vectors Mag. rer. nat. Hannes Wallnöfer (Fri Nov 30 2007 - 06:45:02 CST)
- AMBER: Group input for restrained atoms Francesco Pietra (Fri Nov 30 2007 - 10:28:50 CST)
Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:10 CST
370 messages sorted by:
[ author ]
[ date ]
[ subject ]
About this archive
|