Amber Archive Nov 2007 by thread
- Re: AMBER: antechamber fails with large molecules Francesco Pietra (Thu Nov 01 2007 - 01:29:26 PDT)
- AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Thu Nov 01 2007 - 03:43:54 PDT)
- AMBER: Improper torsion terms Pavan G (Thu Nov 01 2007 - 17:24:46 PDT)
- Re: AMBER:antechamber fails with large molecules Junmei Wang (Thu Nov 01 2007 - 23:29:11 PDT)
- Re: AMBER: Improper torsion terms Bill Ross (Fri Nov 02 2007 - 09:41:00 PDT)
- AMBER: Compiling single programs Francesco Pietra (Fri Nov 02 2007 - 10:44:09 PDT)
- AMBER: error with amber9 production run. Vijay Singh (Sat Nov 03 2007 - 07:10:52 PDT)
- AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ? sychen (Sun Nov 04 2007 - 04:46:09 PST)
- AMBER: dihedral driver fatima.chami.durham.ac.uk (Sun Nov 04 2007 - 04:51:22 PST)
- AMBER: paper request Miguel Ortiz-Lombardía (Mon Nov 05 2007 - 01:01:08 PST)
- AMBER: "Atom valence violated" from LEaP Francesco Pietra (Mon Nov 05 2007 - 03:00:28 PST)
- AMBER: Fe bonds in HEME ! Pradipta Bandyopadhyay (Mon Nov 05 2007 - 03:50:58 PST)
- AMBER: ptraj frames maximum Hannes Wallnoefer (Mon Nov 05 2007 - 06:19:25 PST)
- AMBER: DUMBFREQ Steve Seibold (Mon Nov 05 2007 - 07:52:19 PST)
- AMBER: ptraj hbond mask Lars Skjærven (Mon Nov 05 2007 - 08:00:03 PST)
- Re: AMBER: RED-vIII fails Jesper Soerensen (Mon Nov 05 2007 - 08:01:21 PST)
- Re: Re: AMBER: AMBER 9 - Force Field Options - Question cgji (Mon Nov 05 2007 - 09:19:58 PST)
- AMBER: umbrella sampling and WHAM Allen, Thomas W., Ph.D. [RO BIOCHM] (Mon Nov 05 2007 - 12:03:31 PST)
- AMBER: Parallel test error with shared libraries Joe Nolan (Mon Nov 05 2007 - 13:05:27 PST)
- AMBER: Request reg parameter for vitamin e Rama krishnan (Mon Nov 05 2007 - 23:13:51 PST)
- AMBER: Request reg parameter for vitamin e Rama krishnan (Mon Nov 05 2007 - 23:11:47 PST)
- AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8? ming hui (Tue Nov 06 2007 - 00:30:17 PST)
- AMBER: Energy minimization problem of -SO3H group Takao Kobayashi (Tue Nov 06 2007 - 02:17:35 PST)
- AMBER: Question dykyy (Tue Nov 06 2007 - 05:12:46 PST)
- AMBER: Minimum energy tolerance gradient setting for minimization Sandhya Tiwari (Tue Nov 06 2007 - 06:13:52 PST)
- AMBER: Antechamber snoze pa (Tue Nov 06 2007 - 08:02:39 PST)
- AMBER: calculating charges to modified 4GA unit nag raj (Wed Nov 07 2007 - 03:26:51 PST)
- AMBER: AMBER 9 - visualization of MD trajectory by MOE dinko.x.ziher.gsk.com (Wed Nov 07 2007 - 04:45:41 PST)
- AMBER: LEaP bond problem Beale, John (Wed Nov 07 2007 - 04:57:30 PST)
- AMBER: divcon on AIX using xlf 10.1 Joachim Hein (Wed Nov 07 2007 - 08:23:14 PST)
- AMBER: (no subject) Biman Jana (Wed Nov 07 2007 - 09:09:00 PST)
- AMBER: TIP5P water Simulation Biman Jana (Wed Nov 07 2007 - 09:12:42 PST)
- AMBER: MD simulations with Pt atom - how to keep square planar geometry? Pablo Englebienne (Wed Nov 07 2007 - 18:21:21 PST)
- AMBER: make test.parallel Francesco Pietra (Thu Nov 08 2007 - 00:33:21 PST)
- AMBER: divcon san_amber roy (Thu Nov 08 2007 - 09:19:41 PST)
- AMBER: xleap patch for xorg-7.3 ?? M. L. Dodson (Thu Nov 08 2007 - 11:04:05 PST)
- Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) sanket deshmukh (Thu Nov 08 2007 - 11:29:35 PST)
- AMBER: thermodynamic integration Cooper, Matthew (Thu Nov 08 2007 - 13:14:25 PST)
- Re: AMBER: How can i calculate generalized order parameters using ptraj. David A. Case (Thu Nov 08 2007 - 18:23:34 PST)
- Re: AMBER: heical content in simulations Scott Pendley (Fri Nov 09 2007 - 12:25:18 PST)
- AMBER: RESP question Eddie Men (Fri Nov 09 2007 - 16:33:16 PST)
- AMBER: TIP5P water simulation using AMBER7 Biman Jana (Sat Nov 10 2007 - 06:57:20 PST)
- AMBER: addles Peter Varnai (Sat Nov 10 2007 - 08:40:21 PST)
- AMBER: replica exchange problems with ifort >10.0.023 Peter Varnai (Sat Nov 10 2007 - 08:44:30 PST)
- AMBER: invalid digit '*' in the input file rebeca.mmb.pcb.ub.es (Mon Nov 12 2007 - 06:06:16 PST)
- Re: AMBER: amber9 installation problem Madjid Taghdir (Mon Nov 12 2007 - 00:38:57 PST)
- AMBER: restrain center of mass of one domain Wei Chen (Mon Nov 12 2007 - 15:14:11 PST)
- AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hopkins, Robert (Mon Nov 12 2007 - 15:32:20 PST)
- AMBER: Parallel scaling priya priya (Tue Nov 13 2007 - 02:35:20 PST)
- AMBER: gb minimization using nab Guillaume Renvez (Tue Nov 13 2007 - 03:06:13 PST)
- AMBER: Protein containing iron. Syed Tarique Moin (Tue Nov 13 2007 - 03:16:48 PST)
- AMBER: Parallel Amber compilation problems !! Sampath Koppole (Tue Nov 13 2007 - 06:05:28 PST)
- AMBER: 2 double bond in AMBER ffield ABEL Stephane 984007 (Tue Nov 13 2007 - 09:00:08 PST)
- AMBER: amber9 leap installation error on sgi_altix wei zhang (Tue Nov 13 2007 - 14:02:48 PST)
- [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] M. L. Dodson (Wed Nov 14 2007 - 10:51:35 PST)
- AMBER: Bug report: iwrap failure in PMEMD with netCDF Myunggi Yi (Wed Nov 14 2007 - 11:18:18 PST)
- AMBER: Error when doing a TI simulation: "vlimit exceeded ming hui (Wed Nov 14 2007 - 17:10:07 PST)
- AMBER: &shf setup McElheny, Dan (Thu Nov 15 2007 - 15:39:42 PST)
- AMBER: Understading of mdcrd file and pdb file.. Vijay Manickam Achari (Thu Nov 15 2007 - 21:02:08 PST)
- AMBER: [chirality.c] Atom did not match Francesco Pietra (Fri Nov 16 2007 - 09:09:10 PST)
- AMBER: xleap heme iron coordination error Robyn Ayscue (Fri Nov 16 2007 - 11:33:35 PST)
- AMBER: antechamber --> sander problem Yamada, Takahiro (Fri Nov 16 2007 - 12:18:18 PST)
- AMBER: chem shift format McElheny, Dan (Fri Nov 16 2007 - 13:46:57 PST)
- AMBER: Fwd: [chirality.c] Atom did not match Francesco Pietra (Fri Nov 16 2007 - 13:59:40 PST)
- AMBER: five-coordinated phosphorus Smooth Cutie (Fri Nov 16 2007 - 15:48:40 PST)
- AMBER: How to calculate S2 from P2 using ptraj ? brmeher.iitg.ernet.in (Fri Nov 16 2007 - 22:34:11 PST)
- AMBER: How to calculate S2 from P2 using ptraj ? brmeher.iitg.ernet.in (Fri Nov 16 2007 - 22:40:31 PST)
- AMBER: five-coordinated phosphorus Yubo Fan (Sat Nov 17 2007 - 06:19:06 PST)
- AMBER: question with ptraj loop Vijay Singh (Sat Nov 17 2007 - 08:06:53 PST)
- Fwd: Re: AMBER: Fwd: [chirality.c] Atom did not match Francesco Pietra (Sat Nov 17 2007 - 08:16:09 PST)
- AMBER: Puzzle with WAT Francesco Pietra (Sat Nov 17 2007 - 10:14:38 PST)
- AMBER: EXCEEDED MAXLESADJ in sander.LES.MPI (amber9) Alessandro Nascimento (Sat Nov 17 2007 - 13:24:58 PST)
- Re: AMBER: Puzzle with WAT Bill Ross (Sat Nov 17 2007 - 16:00:06 PST)
- AMBER: Atom types for polyunsaturated lipids ABEL Stephane 984007 (Sun Nov 18 2007 - 09:14:14 PST)
- AMBER: R.E.D.-III bug fixes FyD (Sun Nov 18 2007 - 09:22:47 PST)
- AMBER: Missing BELE for MM in 1 backy (Mon Nov 19 2007 - 04:19:09 PST)
- AMBER: Solvation free energy Mike Wykes (Mon Nov 19 2007 - 10:08:23 PST)
- AMBER: pmemd with openmpi Myunggi Yi (Mon Nov 19 2007 - 11:25:48 PST)
- AMBER: newby question on converting xyz format to pdb format after energy minimization Mehmet Serkan Apaydin (Tue Nov 20 2007 - 13:02:42 PST)
- AMBER: Implicit/Explicit solvation Eddie Men (Tue Nov 20 2007 - 23:03:12 PST)
- AMBER: Zinc-Histidine force field Mattia Mori - CERM (Wed Nov 21 2007 - 08:54:02 PST)
- AMBER:How to calculate the free energy of a series of conformations huzehan19870731.126.com (Mon Nov 19 2007 - 19:18:41 PST)
- AMBER: Problem with LEaP generating topology and coord files after double bond creation M. L. Dodson (Wed Nov 21 2007 - 12:45:17 PST)
- AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Wed Nov 21 2007 - 13:41:45 PST)
- AMBER: McElheny, Dan (Wed Nov 21 2007 - 14:04:26 PST)
- AMBER: Atom type definition Xioling Chuang (Thu Nov 22 2007 - 01:03:29 PST)
- AMBER: BELLY issues Eddie Men (Thu Nov 22 2007 - 02:03:52 PST)
- AMBER: RE: FF94 or FF99? Patel, Bhavesh H (Thu Nov 22 2007 - 06:34:55 PST)
- AMBER: Pressure Variation for NPT simulation of TIP5P water Biman Jana (Thu Nov 22 2007 - 06:50:16 PST)
- AMBER: Pre-ABMER Installation Prob w/ MPICH2 Joseph Maxwell (Thu Nov 22 2007 - 11:55:18 PST)
- AMBER: frcmod file and NONB for dummy atoms Ilyas Yildirim (Thu Nov 22 2007 - 16:48:31 PST)
- AMBER: About TER records Francesco Pietra (Fri Nov 23 2007 - 00:15:05 PST)
- AMBER: connecting a non standard residue to the rest of an enzyme Boutheïna Kerkeni (Fri Nov 23 2007 - 05:43:36 PST)
- AMBER: Fwd: About TER records Francesco Pietra (Fri Nov 23 2007 - 07:23:41 PST)
- AMBER: Hello Eddie Men (Fri Nov 23 2007 - 18:44:05 PST)
- AMBER: Pressure Variation for NPT simulation of TIP5P water (fwd) Biman Jana (Sat Nov 24 2007 - 05:22:39 PST)
- AMBER: solvatebox vs solvateoct Francesco Pietra (Sun Nov 25 2007 - 10:27:06 PST)
- AMBER: question about ntx=5 Wei Chen (Sun Nov 25 2007 - 11:21:44 PST)
- AMBER: Weird restart file with ioutfm=0, iwrap=1 and ntwprt >0 Hai Long (Mon Nov 26 2007 - 09:41:18 PST)
- AMBER: LJ parameters for alkynes David Mobley (Mon Nov 26 2007 - 10:07:37 PST)
- AMBER: Polarizable potentials Denis Courtier (Mon Nov 26 2007 - 10:49:33 PST)
- AMBER: Value of taup for bulk TIP5P water simulation(amber7) Biman Jana (Mon Nov 26 2007 - 11:25:37 PST)
- AMBER: Restrained MD (amber9) Vincent Bisetty (Mon Nov 26 2007 - 14:52:28 PST)
- AMBER: restraints to individual atoms Eddie Men (Mon Nov 26 2007 - 19:02:11 PST)
- AMBER: Extra-term to the Energy function !! Sampath Koppole (Tue Nov 27 2007 - 00:57:54 PST)
- AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Tue Nov 27 2007 - 03:26:22 PST)
- AMBER: Xleap and Hydrogens Shozeb Haider (Tue Nov 27 2007 - 06:38:56 PST)
- AMBER: antechamber: read in charges fatima.chami.durham.ac.uk (Tue Nov 27 2007 - 07:40:13 PST)
- AMBER: predictive NOE generation Seth Lilavivat (Tue Nov 27 2007 - 09:41:08 PST)
- AMBER: Polarizable Potential Denis Courtier (Tue Nov 27 2007 - 09:40:34 PST)
- AMBER: Re: antechamber problem Junmei Wang (Tue Nov 27 2007 - 09:38:17 PST)
- AMBER: RE: Amber9 compile problem Ross Walker (Tue Nov 27 2007 - 09:24:22 PST)
- Re: AMBER: [SOLVED] Problem with LEaP generating topology and coord files after double bond creation M. L. Dodson (Tue Nov 27 2007 - 13:45:44 PST)
- AMBER: Would amber work with Linspire 6.0? Campbell, Patrick (Tue Nov 27 2007 - 15:01:02 PST)
- AMBER: QMMM simulations Pankaj R. Daga (Tue Nov 27 2007 - 15:20:51 PST)
- AMBER: bondi radii problems Eddie Men (Tue Nov 27 2007 - 19:31:19 PST)
- AMBER: PB warning in pb_miccg(): CG maxitn exceeded! Eddie Men (Tue Nov 27 2007 - 20:35:17 PST)
- AMBER: Error reading radii of Cu during ESP caculation. Syed Tarique Moin (Wed Nov 28 2007 - 03:27:53 PST)
- AMBER: Polarizable potential Denis Courtier (Wed Nov 28 2007 - 06:32:49 PST)
- AMBER: radial distribution by Ptraj Esther Brugger (Wed Nov 28 2007 - 06:35:49 PST)
- AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Francesco Pietra (Wed Nov 28 2007 - 07:01:37 PST)
- AMBER: (no subject) Gabriele Viliani (Wed Nov 28 2007 - 08:56:32 PST)
- AMBER: leaprc.ff02polEP.r1into xleap Denis Courtier (Wed Nov 28 2007 - 09:44:21 PST)
- 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 - 10:23:27 PST)
- AMBER: Calculating dipole moments Austin B. Yongye (Wed Nov 28 2007 - 11:33:41 PST)
- AMBER: questions about smd of amber 9 WANG,YING (Wed Nov 28 2007 - 13:29:41 PST)
- AMBER: Error in installing amber8 on Ubuntu tri nam Vo (Wed Nov 28 2007 - 20:24:24 PST)
- AMBER: About RAMD Francesco Pietra (Wed Nov 28 2007 - 23:26:45 PST)
- AMBER: ele vs van der Waals backy (Thu Nov 29 2007 - 01:14:19 PST)
- AMBER: Error in reading number of frame in PTRAJ Vijay Manickam Achari (Thu Nov 29 2007 - 01:20:12 PST)
- AMBER: vlimit exceeded, polarizable force field Denis Courtier (Thu Nov 29 2007 - 03:43:45 PST)
- AMBER: problems with restart of smd simulation w/ jar=1 & nmr=1 Wei Chen (Thu Nov 29 2007 - 09:15:51 PST)
- AMBER: Re: Calculating Energies with imin=5 Pavan G (Fri Nov 30 2007 - 04:24:18 PST)
- AMBER: angle between vectors Mag. rer. nat. Hannes Wallnöfer (Fri Nov 30 2007 - 04:45:02 PST)
- AMBER: Group input for restrained atoms Francesco Pietra (Fri Nov 30 2007 - 08:28:50 PST)
- Last message date: Sun Dec 02 2007 - 06:07:41 PST
- Archived on: Mon Feb 03 2025 - 05:53:35 PST
