Amber Archive Aug 2007 by author
477 messages
:
Starting
Sun Aug 05 2007 - 06:07:07 PDT,
Ending
Sun Sep 02 2007 - 06:07:39 PDT
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Aaron Virshup
AMBER: Converting AMBER-format force fields for tinker
(Fri Aug 31 2007 - 12:04:12 PDT)
Adrian Roitberg
Re: AMBER: heating up system
(Tue Aug 28 2007 - 11:45:26 PDT)
Re: AMBER: SCC convergence failure in QM-MM DFTB
(Sat Aug 25 2007 - 11:10:35 PDT)
Re: AMBER: SMD simulation
(Fri Aug 24 2007 - 05:43:35 PDT)
Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj).
(Thu Aug 23 2007 - 06:32:28 PDT)
Andreas Svrcek-Seiler
Re: AMBER: What is the best computer for running AMBER simulations?
(Thu Aug 16 2007 - 15:51:06 PDT)
RE: AMBER: Any experience on Dell two quad core system?
(Mon Aug 13 2007 - 13:46:58 PDT)
Re: AMBER: Any experience on Dell two quad core system?
(Mon Aug 13 2007 - 10:21:39 PDT)
RE: AMBER: Any experience on Dell two quad core system?
(Mon Aug 13 2007 - 08:12:15 PDT)
Re: AMBER: Any experience on Dell two quad core system?
(Thu Aug 02 2007 - 21:18:42 PDT)
Andrew Borgert
AMBER: Integrating the alpha-helix bias correction into ff94
(Mon Aug 06 2007 - 12:18:58 PDT)
Anju Sharma
AMBER: How to carry out drug-dna complex simulations
(Tue Aug 14 2007 - 01:50:04 PDT)
Re: AMBER: Problem while carrying out minimisation of drug molecule using sander
(Mon Aug 06 2007 - 22:32:43 PDT)
AMBER: Problem while carrying out minimisation of drug molecule using sander
(Sun Aug 05 2007 - 20:51:11 PDT)
Re: AMBER: Problem with antechamber
(Thu Aug 02 2007 - 02:03:36 PDT)
AMBER: Problem with antechamber
(Wed Aug 01 2007 - 23:34:39 PDT)
Re: AMBER: Problem while saving .top and .crd files.
(Wed Aug 01 2007 - 22:25:19 PDT)
anna duraj
AMBER: docking ability
(Wed Aug 15 2007 - 10:34:37 PDT)
Re: AMBER: Problem with Antechamber and point charges
(Fri Aug 03 2007 - 12:47:17 PDT)
AMBER: Problem with Antechamber and point charges
(Wed Aug 01 2007 - 12:40:44 PDT)
Antonio Morreale
Re: AMBER: MM_PBSA No radius found for Br!!
(Mon Aug 13 2007 - 04:39:52 PDT)
Balvinder Singh
RE: AMBER: Building parallel Amber 9.0
(Wed Aug 15 2007 - 21:02:38 PDT)
RE: AMBER: Building parallel Amber 9.0
(Wed Aug 15 2007 - 20:53:44 PDT)
Beale, John
AMBER: antechamber question
(Fri Aug 31 2007 - 07:07:56 PDT)
AMBER:
(Thu Aug 30 2007 - 06:05:11 PDT)
AMBER: articles
(Fri Aug 24 2007 - 06:02:05 PDT)
AMBER:
(Mon Aug 20 2007 - 08:41:06 PDT)
AMBER: MPI
(Fri Aug 17 2007 - 05:00:33 PDT)
AMBER: Building parallel Amber 9.0
(Wed Aug 15 2007 - 05:21:56 PDT)
AMBER: Force Field Parameters
(Thu Aug 02 2007 - 09:46:16 PDT)
Benjamin Juhl
Re: AMBER: Machine environment to install AMBER 8
(Tue Aug 14 2007 - 03:49:13 PDT)
Re: AMBER: Machine environment to install AMBER 8
(Tue Aug 14 2007 - 02:10:16 PDT)
Re: AMBER: Machine environment to install AMBER 8
(Tue Aug 14 2007 - 01:28:09 PDT)
Re: AMBER: how to combine two molecules
(Fri Aug 10 2007 - 02:11:07 PDT)
Bertrand Russell
Re: AMBER: Machine environment to install AMBER 8
(Tue Aug 14 2007 - 23:34:02 PDT)
Re: AMBER: Machine environment to install AMBER 8
(Tue Aug 14 2007 - 02:50:07 PDT)
Re: AMBER: Machine environment to install AMBER 8
(Tue Aug 14 2007 - 02:21:07 PDT)
Bill Ross
Re: AMBER: Cygwin error
(Thu Aug 09 2007 - 13:42:48 PDT)
Re: AMBER: Cygwin error
(Wed Aug 08 2007 - 15:29:24 PDT)
Re: AMBER: Cygwin error
(Wed Aug 08 2007 - 14:43:49 PDT)
Re: AMBER: Problem with antechamber
(Thu Aug 02 2007 - 13:14:37 PDT)
BJÖRN KARLSSON
AMBER: RDF unit cell volume
(Thu Aug 30 2007 - 01:14:20 PDT)
brmeher.iitg.ernet.in
AMBER: protocols for high pressure simulation
(Tue Aug 28 2007 - 08:23:00 PDT)
Carlos Simmerling
Re: AMBER: Using ntr=1 in xleap
(Fri Aug 31 2007 - 14:49:14 PDT)
Re: AMBER: Measuring Bond Angle over simulation
(Fri Aug 31 2007 - 12:34:13 PDT)
Re: AMBER: Confusion about Langevin dymamics
(Fri Aug 31 2007 - 06:52:02 PDT)
Re: AMBER: Distance restraints between center of mass of two molecules
(Wed Aug 15 2007 - 14:17:33 PDT)
Re: AMBER: Distance restraints between center of mass of two molecules
(Wed Aug 15 2007 - 08:52:27 PDT)
Re: AMBER: Distance restraints between center of mass of two molecules
(Wed Aug 15 2007 - 07:54:40 PDT)
Re: AMBER: torsional restraints in a solvated MD simulation.
(Tue Aug 14 2007 - 13:41:52 PDT)
Re: AMBER: regarding implicit simulation
(Tue Aug 14 2007 - 04:22:24 PDT)
Re: AMBER: imin=5 and inptraj
(Sat Aug 11 2007 - 14:23:29 PDT)
Re: AMBER: How to couple only one residue to the temperature bath?
(Fri Aug 10 2007 - 15:43:29 PDT)
Re: AMBER: How to couple only one residue to the temperature bath?
(Fri Aug 10 2007 - 08:55:02 PDT)
Re: AMBER: Implicit solvent simulation is too slow.
(Fri Aug 10 2007 - 06:07:50 PDT)
Re: AMBER: Problem while carrying out minimisation of drug molecule using sander
(Tue Aug 07 2007 - 03:57:53 PDT)
Re: AMBER: Integrating the alpha-helix bias correction into ff94
(Mon Aug 06 2007 - 12:42:17 PDT)
Re: AMBER: (no subject)
(Sat Aug 04 2007 - 03:55:29 PDT)
Re: AMBER: Problem with Antechamber and point charges
(Fri Aug 03 2007 - 12:55:43 PDT)
Re: AMBER: planarity restraints for NA
(Thu Aug 02 2007 - 07:17:32 PDT)
Re: AMBER: planarity restraints for NA
(Thu Aug 02 2007 - 06:17:56 PDT)
Re: AMBER: (no subject)
(Thu Aug 02 2007 - 05:48:36 PDT)
Re: AMBER: neutral terminals
(Thu Aug 02 2007 - 05:04:15 PDT)
Re: AMBER: Problem with Antechamber and point charges
(Wed Aug 01 2007 - 12:52:53 PDT)
Cenk Andac
Re: AMBER: Force field for RNA with U-turn motif
(Wed Aug 22 2007 - 11:31:04 PDT)
Re: AMBER: Force field for RNA with U-turn motif
(Wed Aug 22 2007 - 09:08:29 PDT)
AMBER: Force field for RNA with U-turn motif
(Tue Aug 21 2007 - 06:52:48 PDT)
Chng Choon-Peng
Re: AMBER: heical content in simulations
(Tue Aug 07 2007 - 01:19:26 PDT)
Chris Moth
Re: AMBER: Add hydrogen and charge calculation
(Mon Aug 27 2007 - 13:33:25 PDT)
AMBER: NETCDF
(Fri Aug 24 2007 - 06:03:37 PDT)
Re: AMBER: NETCDF
(Fri Aug 24 2007 - 05:58:34 PDT)
Re: AMBER: How to perform MD simulation in NVT ensemble?
(Thu Aug 23 2007 - 10:07:30 PDT)
Re: AMBER: imin=5 and inptraj
(Sat Aug 11 2007 - 14:37:11 PDT)
Christopher Gaughan
AMBER: restrained md and mm pbsa
(Thu Aug 02 2007 - 07:15:17 PDT)
David A. Case
Re: AMBER: modified leaprc for glycoproteins
(Fri Aug 31 2007 - 14:42:03 PDT)
Re: AMBER: Using ntr=1 in xleap
(Fri Aug 31 2007 - 15:52:13 PDT)
Re: AMBER: Connecting two ethanes in LEaP
(Fri Aug 31 2007 - 09:18:18 PDT)
Re: AMBER: Confusion about Langevin dymamics
(Fri Aug 31 2007 - 07:53:47 PDT)
Re: AMBER: bad atom type:F
(Thu Aug 30 2007 - 08:35:00 PDT)
Re: AMBER: protocols for high pressure simulation
(Tue Aug 28 2007 - 08:41:58 PDT)
Re: AMBER: Prepin error (?) in xleap
(Mon Aug 27 2007 - 15:29:49 PDT)
Re: AMBER: Prepin error (?) in xleap
(Mon Aug 27 2007 - 08:58:20 PDT)
Re: AMBER: Prepin error (?) in xleap
(Thu Aug 23 2007 - 17:28:29 PDT)
Re: AMBER: How to use AMBER Parameter Database ?
(Thu Aug 23 2007 - 09:53:55 PDT)
Re: AMBER: Regarding free energy calculation and covalent bond
(Thu Aug 23 2007 - 09:52:17 PDT)
Re: AMBER: Ca(2+) parameter
(Thu Aug 23 2007 - 08:04:01 PDT)
Re: AMBER: xLeap "Could not find type" error
(Wed Aug 22 2007 - 08:45:02 PDT)
Re: AMBER: xLeap "Could not find type" error
(Wed Aug 22 2007 - 08:15:25 PDT)
Re: AMBER: xLeap "Could not find type" error
(Tue Aug 21 2007 - 17:40:09 PDT)
Re: AMBER:
(Mon Aug 20 2007 - 17:31:21 PDT)
Re: AMBER: charges in PBSA calculation
(Sun Aug 19 2007 - 17:57:14 PDT)
AMBER: question about a 20 kDa protein
(Sat Aug 18 2007 - 09:07:09 PDT)
Re: AMBER: Thermodynamic Integration for a CHARGED molecule
(Fri Aug 17 2007 - 08:46:38 PDT)
Re: AMBER: What is the best computer for running AMBER simulations?
(Thu Aug 16 2007 - 16:42:54 PDT)
Re: AMBER: Missplaced TERs
(Thu Aug 16 2007 - 11:53:10 PDT)
Re: AMBER: EXTRA_PTS: frtype 2 Should not be here
(Thu Aug 16 2007 - 09:33:52 PDT)
Re: AMBER: antechamber, how does it work
(Thu Aug 16 2007 - 08:40:16 PDT)
Re: AMBER: Normal Mode Analysis
(Wed Aug 15 2007 - 15:56:46 PDT)
Re: AMBER: EXTRA_PTS: frtype 2 Should not be here
(Wed Aug 15 2007 - 10:34:49 PDT)
Re: AMBER: antechamber, how does it work
(Wed Aug 15 2007 - 10:07:22 PDT)
Re: AMBER: torsional restraints in a solvated MD simulation.
(Tue Aug 14 2007 - 13:50:31 PDT)
Re: AMBER:
(Tue Aug 14 2007 - 08:27:48 PDT)
Re: AMBER: How to carry out drug-dna complex simulations
(Tue Aug 14 2007 - 08:18:47 PDT)
Re: AMBER: Using TLEAP to set up MD in the crystal lattice space?
(Mon Aug 13 2007 - 18:26:24 PDT)
Re: AMBER: setbox command error
(Mon Aug 13 2007 - 13:38:30 PDT)
Re: AMBER: how to combine two molecules
(Mon Aug 13 2007 - 09:43:57 PDT)
Re: AMBER: hybridization in Amber, pertaining to resonant structures, ions
(Sat Aug 11 2007 - 13:35:15 PDT)
Re: AMBER: NVE energy and temperature drift
(Sat Aug 11 2007 - 13:28:30 PDT)
Re: AMBER: Citation for Langevin thermostat?
(Sat Aug 11 2007 - 12:47:59 PDT)
Re: AMBER: Binary file curiosities
(Mon Aug 06 2007 - 08:03:07 PDT)
Re: AMBER: Problem while carrying out minimisation of drug molecule using sander
(Mon Aug 06 2007 - 07:35:25 PDT)
Re: AMBER: nucleic acid electrostatic energy
(Sat Aug 04 2007 - 08:28:36 PDT)
Re: AMBER: Binary file curiosities
(Fri Aug 03 2007 - 16:21:25 PDT)
Re: AMBER: Antechamber formal charges with Gasteiger method
(Fri Aug 03 2007 - 13:17:11 PDT)
Re: AMBER: bug in nonbond_list.f (nee ew_setup.f)
(Fri Aug 03 2007 - 08:14:27 PDT)
Re: AMBER: unable to save prmtop/inpcrd for chcl3box
(Fri Aug 03 2007 - 07:58:03 PDT)
Re: AMBER: Information about Amber 9
(Fri Aug 03 2007 - 07:53:22 PDT)
Re: AMBER: Problem generating .prepin file in Antechamber
(Thu Aug 02 2007 - 13:53:03 PDT)
Re: AMBER: edit.out amber version 9
(Thu Aug 02 2007 - 12:00:22 PDT)
Re: AMBER: Problem with antechamber
(Thu Aug 02 2007 - 08:07:30 PDT)
Re: AMBER: bugfix for impropers in parmchk
(Wed Aug 01 2007 - 22:04:20 PDT)
Re: AMBER: problem compiling Amber9 on 64-machine
(Wed Aug 01 2007 - 09:43:21 PDT)
Re: AMBER: problem compiling Amber9 on 64-machine
(Wed Aug 01 2007 - 09:36:37 PDT)
Re: AMBER: problem compiling Amber9 on 64-machine
(Wed Aug 01 2007 - 07:50:30 PDT)
David Cerutti
Re: AMBER: Scaling for octahedral versus rectilinear boxes
(Fri Aug 31 2007 - 06:27:38 PDT)
AMBER: Scaling for octahedral versus rectilinear boxes
(Thu Aug 30 2007 - 22:32:49 PDT)
Re: AMBER: Octahedral box orientation
(Tue Aug 21 2007 - 17:07:32 PDT)
AMBER: Octahedral box orientation
(Tue Aug 21 2007 - 06:08:38 PDT)
Re: AMBER: Any experience on Dell two quad core system?
(Tue Aug 14 2007 - 08:05:34 PDT)
AMBER: Using TLEAP to set up MD in the crystal lattice space?
(Mon Aug 13 2007 - 14:09:51 PDT)
Re: AMBER: Any experience on Dell two quad core system?
(Mon Aug 13 2007 - 13:59:58 PDT)
David LeBard
Re: AMBER: What is the best computer for running AMBER simulations?
(Thu Aug 16 2007 - 15:17:42 PDT)
Re: AMBER: Binary file curiosities
(Sat Aug 04 2007 - 14:34:23 PDT)
AMBER: Binary file curiosities
(Fri Aug 03 2007 - 15:59:45 PDT)
David Mobley
Re: AMBER: Confusion about Langevin dymamics
(Fri Aug 31 2007 - 09:05:13 PDT)
Re: AMBER: Entropy in MM_PBSA
(Fri Aug 24 2007 - 09:31:28 PDT)
Re: AMBER: Thermodynamic Integration for a CHARGED molecule
(Fri Aug 17 2007 - 06:56:33 PDT)
Dilip Dagade
Re: AMBER: EXTRA_PTS: frtype 2 Should not be here
(Thu Aug 16 2007 - 09:52:56 PDT)
Re: AMBER: EXTRA_PTS: frtype 2 Should not be here
(Wed Aug 15 2007 - 21:39:37 PDT)
AMBER: EXTRA_PTS: frtype 2 Should not be here
(Wed Aug 15 2007 - 09:50:57 PDT)
Eduardo Mendez-Villuendas
AMBER: AMBER at WESTGRID
(Thu Aug 30 2007 - 04:49:07 PDT)
Emilia Wu
AMBER: bad atom type:F
(Thu Aug 30 2007 - 05:36:14 PDT)
emine cebe
AMBER: personal computer configuration for parallel computing
(Sun Aug 26 2007 - 04:36:28 PDT)
fatima.chami.durham.ac.uk
Re: AMBER: problem compiling Amber9 on 64-machine
(Wed Aug 01 2007 - 08:55:26 PDT)
Re: AMBER: problem compiling Amber9 on 64-machine
(Wed Aug 01 2007 - 08:52:13 PDT)
AMBER: problem compiling Amber9 on 64-machine
(Wed Aug 01 2007 - 04:03:48 PDT)
Francesco Pietra
AMBER: Fwd: Schedule for QM-MM with Amber9/Amber10
(Thu Aug 30 2007 - 06:17:41 PDT)
AMBER: Schedule for QM-MM with Amber9/Amber10
(Wed Aug 29 2007 - 23:30:10 PDT)
Re: AMBER: Criteria for classical md being OK to move to QM-MM
(Wed Aug 29 2007 - 10:40:36 PDT)
AMBER: Criteria for classical md being OK to move to QM-MM
(Wed Aug 29 2007 - 09:51:15 PDT)
AMBER: heating up system
(Tue Aug 28 2007 - 09:16:57 PDT)
Fwd: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB
(Sun Aug 26 2007 - 23:24:33 PDT)
Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB
(Sun Aug 26 2007 - 09:28:14 PDT)
AMBER: Fwd: SCC convergence failure in QM-MM DFTB
(Sun Aug 26 2007 - 07:34:57 PDT)
AMBER: Fwd: SCC convergence failure in QM-MM DFTB
(Sun Aug 26 2007 - 00:26:42 PDT)
AMBER: SCC convergence failure in QM-MM DFTB
(Sat Aug 25 2007 - 10:54:12 PDT)
RE: AMBER: solvateCap minin and mdin for qm-mm dftb
(Fri Aug 24 2007 - 14:37:12 PDT)
Re: AMBER: solvateCap minin and mdin for qm-mm dftb
(Fri Aug 24 2007 - 13:42:50 PDT)
RE: AMBER: solvateCap minin and mdin for qm-mm dftb
(Fri Aug 24 2007 - 10:28:32 PDT)
Re: AMBER: solvateCap minin and mdin for qm-mm dftb
(Fri Aug 24 2007 - 09:01:31 PDT)
AMBER: solvateCap minin and mdin for qm-mm dftb
(Fri Aug 24 2007 - 03:19:30 PDT)
Re: AMBER: Thermodynamic Integration for conformational changes?
(Tue Aug 21 2007 - 23:53:15 PDT)
AMBER: Thermodynamic Integration for conformational changes?
(Tue Aug 21 2007 - 09:57:47 PDT)
AMBER: CRESP charges in antechamber prepin
(Mon Aug 20 2007 - 00:23:24 PDT)
AMBER: DFTB email address
(Sat Aug 18 2007 - 00:14:53 PDT)
Re: AMBER: about parallelization in QM-MM
(Thu Aug 16 2007 - 23:41:02 PDT)
Re: AMBER: antechamber, how does it work
(Thu Aug 16 2007 - 10:25:35 PDT)
Re: AMBER: antechamber, how does it work
(Wed Aug 15 2007 - 22:53:34 PDT)
Re: AMBER: antechamber, how does it work
(Wed Aug 15 2007 - 14:53:55 PDT)
Re: AMBER: antechamber, how does it work
(Wed Aug 15 2007 - 09:08:37 PDT)
Re: AMBER: antechamber, how does it work
(Wed Aug 15 2007 - 08:05:31 PDT)
Re: AMBER: antechamber, how does it work
(Wed Aug 15 2007 - 07:25:12 PDT)
AMBER: antechamber, how does it work
(Wed Aug 15 2007 - 01:43:45 PDT)
AMBER: Parallelizin antechamber?
(Tue Aug 14 2007 - 06:29:11 PDT)
RE: AMBER: Failure to SCF convergence & parallelization and memory
(Sun Aug 12 2007 - 00:37:33 PDT)
AMBER: Neutralize charges for simulated annealing?
(Sat Aug 11 2007 - 15:35:30 PDT)
AMBER: Failure to SCF convergence
(Sat Aug 11 2007 - 09:56:53 PDT)
AMBER: Positive EPtot in QM-MM
(Tue Aug 07 2007 - 07:34:35 PDT)
Re: AMBER: Fwd: QM region + cutoff larger that box
(Mon Aug 06 2007 - 08:07:09 PDT)
RE: AMBER: Fwd: QM region + cutoff larger that box
(Sun Aug 05 2007 - 23:28:13 PDT)
Re: AMBER: Fwd: QM region + cutoff larger that box
(Sat Aug 04 2007 - 09:42:33 PDT)
AMBER: Fwd: QM region + cutoff larger that box
(Sat Aug 04 2007 - 07:33:35 PDT)
AMBER: Fwd: QM region + cutoff larger that box
(Sat Aug 04 2007 - 01:32:40 PDT)
AMBER: Fwd: unable to save prmtop/inpcrd for chcl3box
(Fri Aug 03 2007 - 05:24:24 PDT)
AMBER: unable to save prmtop/inpcrd for chcl3box
(Fri Aug 03 2007 - 03:09:03 PDT)
AMBER: Calculating cumulative average
(Thu Aug 02 2007 - 10:00:10 PDT)
Fwd: RE: AMBER: Average potential energies and conformer ratios
(Wed Aug 01 2007 - 06:58:02 PDT)
Geoff Wood
Re: AMBER: NETCDF
(Mon Aug 27 2007 - 00:18:48 PDT)
AMBER: NETCDF
(Fri Aug 24 2007 - 03:43:11 PDT)
Greg Gannon
AMBER: edit.out amber version 9
(Thu Aug 02 2007 - 11:21:31 PDT)
gurpreet singh
AMBER: regarding implicit simulation
(Mon Aug 13 2007 - 23:21:35 PDT)
Re: AMBER: (no subject)
(Thu Aug 02 2007 - 01:39:07 PDT)
Re: AMBER: Problem with antechamber
(Thu Aug 02 2007 - 01:24:18 PDT)
Gustavo Seabra
Re: AMBER: Schedule for QM-MM with Amber9/Amber10
(Fri Aug 31 2007 - 10:41:18 PDT)
Re: AMBER: AMBER at WESTGRID
(Thu Aug 30 2007 - 05:35:49 PDT)
Re: AMBER: Criteria for classical md being OK to move to QM-MM
(Wed Aug 29 2007 - 11:13:05 PDT)
Re: AMBER: How to perform MD simulation in NVT ensemble?
(Wed Aug 29 2007 - 07:53:11 PDT)
Re: AMBER: QM/MM in reaction pathways?
(Tue Aug 28 2007 - 07:55:20 PDT)
Re: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB
(Mon Aug 27 2007 - 13:50:40 PDT)
Re: AMBER: generating a .rst file from an .mdcrd file
(Mon Aug 27 2007 - 12:15:23 PDT)
Re: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB
(Mon Aug 27 2007 - 12:12:23 PDT)
Re: AMBER: SCC convergence failure in QM-MM DFTB
(Mon Aug 27 2007 - 10:20:37 PDT)
Re: AMBER: How to perform MD simulation in NVT ensemble?
(Fri Aug 24 2007 - 19:21:59 PDT)
Re: AMBER: ow to split MDCRD file using ptraj
(Fri Aug 24 2007 - 19:17:27 PDT)
Re: AMBER: Thermodynamic Integration for conformational changes?
(Tue Aug 21 2007 - 20:41:23 PDT)
Re: AMBER: Thermodynamic Integration for conformational changes?
(Tue Aug 21 2007 - 20:33:36 PDT)
Re: AMBER: antechamber, how does it work
(Wed Aug 15 2007 - 07:15:48 PDT)
Re: AMBER: Building parallel Amber 9.0
(Wed Aug 15 2007 - 06:46:59 PDT)
Re: AMBER: Cygwin error
(Thu Aug 09 2007 - 14:40:14 PDT)
Re: AMBER: Cygwin error
(Thu Aug 09 2007 - 13:30:19 PDT)
Re: AMBER: Cygwin error
(Thu Aug 09 2007 - 12:08:27 PDT)
Re: AMBER: Cygwin error
(Wed Aug 08 2007 - 16:36:29 PDT)
Re: AMBER: Cygwin error
(Wed Aug 08 2007 - 15:21:01 PDT)
RE: AMBER: Fwd: QM region + cutoff larger that box
(Mon Aug 06 2007 - 08:38:19 PDT)
RE: AMBER: Fwd: QM region + cutoff larger that box
(Sat Aug 04 2007 - 08:33:12 PDT)
RE: AMBER: (no subject)
(Thu Aug 02 2007 - 13:19:05 PDT)
Hans Martin Senn
AMBER: GAFF atom typing for flavin
(Sat Aug 04 2007 - 09:15:30 PDT)
Hayden Eastwood
AMBER: Confusion about Langevin dymamics
(Fri Aug 31 2007 - 06:46:28 PDT)
Hu, Shaowen (JSC-SK)[USRA]
AMBER: force field for irregulate DNA ends
(Sat Aug 04 2007 - 11:20:42 PDT)
RE: AMBER: planarity restraints for NA
(Thu Aug 02 2007 - 11:49:15 PDT)
Ilyas Yildirim
Re: AMBER: command tleap is not normal
(Tue Aug 21 2007 - 01:50:35 PDT)
Re: AMBER: Any experience on Dell two quad core system?
(Mon Aug 13 2007 - 17:39:01 PDT)
RE: AMBER: Any experience on Dell two quad core system?
(Mon Aug 13 2007 - 12:25:22 PDT)
Re: AMBER: Any experience on Dell two quad core system?
(Fri Aug 03 2007 - 09:35:26 PDT)
Re: AMBER: Any experience on Dell two quad core system?
(Thu Aug 02 2007 - 21:23:17 PDT)
AMBER: Any experience on Dell two quad core system?
(Thu Aug 02 2007 - 17:33:40 PDT)
In Hee Park
Re: AMBER: MPI Quiescence problem in REMD
(Thu Aug 16 2007 - 15:56:37 PDT)
Irene Newhouse
RE: AMBER: modified leaprc for glycoproteins
(Fri Aug 31 2007 - 18:14:32 PDT)
AMBER: modified leaprc for glycoproteins
(Fri Aug 31 2007 - 13:53:05 PDT)
Jena M
AMBER: neutral terminals
(Wed Aug 01 2007 - 17:15:46 PDT)
Jiri Sponer
Re: AMBER: Force field for RNA with U-turn motif
(Wed Aug 22 2007 - 09:33:46 PDT)
Jiten
Re: AMBER: bugfix for impropers in parmchk
(Wed Aug 01 2007 - 23:23:20 PDT)
Re: AMBER: bugfix for impropers in parmchk
(Wed Aug 01 2007 - 21:02:24 PDT)
jitrayut jitonnom
Re: AMBER: protonation of His residue!
(Thu Aug 23 2007 - 20:52:51 PDT)
Re: AMBER: Error in MMPBSA Calculation
(Tue Aug 21 2007 - 00:11:52 PDT)
Jones de Andrade
AMBER: Performance of polarizable model simulations
(Wed Aug 22 2007 - 21:17:52 PDT)
Jose Gallego
AMBER: short 2'OH-OP contacts in RNA
(Fri Aug 10 2007 - 09:22:35 PDT)
Junmei Wang
Re: AMBER: Prepin error (?) in xleap
(Fri Aug 31 2007 - 13:22:07 PDT)
Re: AMBER: antechamber question
(Fri Aug 31 2007 - 13:07:09 PDT)
Re: AMBER: Prepin error (?) in xleap
(Mon Aug 27 2007 - 15:17:53 PDT)
Re: AMBER: antechamber, how does it work
(Wed Aug 15 2007 - 06:33:36 PDT)
Re: AMBER: Parallelizin antechamber?
(Wed Aug 15 2007 - 06:41:45 PDT)
Kailee
AMBER: compile amber8 with mpich2
(Tue Aug 07 2007 - 06:18:14 PDT)
Karen Callahan
AMBER: hybridization in Amber, pertaining to resonant structures, ions
(Mon Aug 06 2007 - 21:13:27 PDT)
Katrina Lexa
AMBER: Squished dimer during transition from NVT to NPT
(Thu Aug 30 2007 - 14:02:20 PDT)
Kliman, Michal
AMBER: Connecting two ethanes in LEaP
(Thu Aug 30 2007 - 13:53:46 PDT)
Kresimir Sikic
AMBER: Normal Mode Analysis
(Mon Aug 13 2007 - 08:12:59 PDT)
Lili Peng
AMBER: Using ntr=1 in xleap
(Fri Aug 31 2007 - 14:27:44 PDT)
Re: AMBER: Prepin error (?) in xleap
(Thu Aug 30 2007 - 13:48:34 PDT)
Re: AMBER: Prepin error (?) in xleap
(Mon Aug 27 2007 - 14:38:30 PDT)
Re: AMBER: Prepin error (?) in xleap
(Fri Aug 24 2007 - 12:26:17 PDT)
Re: AMBER: Prepin error (?) in xleap
(Fri Aug 24 2007 - 12:19:07 PDT)
Re: AMBER: articles
(Fri Aug 24 2007 - 12:10:12 PDT)
AMBER: Prepin error (?) in xleap
(Thu Aug 23 2007 - 14:04:03 PDT)
AMBER: Running Gaussian to get .out files
(Wed Aug 22 2007 - 13:27:25 PDT)
Re: AMBER: xLeap "Could not find type" error
(Tue Aug 21 2007 - 18:17:44 PDT)
AMBER: xLeap "Could not find type" error
(Tue Aug 21 2007 - 12:28:46 PDT)
Re: AMBER: What is the best computer for running AMBER simulations?
(Thu Aug 16 2007 - 21:50:42 PDT)
AMBER: What is the best computer for running AMBER simulations?
(Thu Aug 16 2007 - 14:37:03 PDT)
Re: AMBER: Cygwin error
(Thu Aug 09 2007 - 12:16:20 PDT)
Re: AMBER: Cygwin error
(Thu Aug 09 2007 - 12:06:03 PDT)
Re: AMBER: Cygwin error
(Thu Aug 09 2007 - 11:13:27 PDT)
Re: AMBER: Cygwin error
(Wed Aug 08 2007 - 16:04:31 PDT)
Re: AMBER: Cygwin error
(Wed Aug 08 2007 - 15:13:54 PDT)
Re: AMBER: Cygwin error
(Wed Aug 08 2007 - 14:56:00 PDT)
AMBER: Cygwin error
(Wed Aug 08 2007 - 14:33:22 PDT)
Re: AMBER: Problem generating .prepin file in Antechamber
(Thu Aug 02 2007 - 12:15:41 PDT)
AMBER: Problem generating .prepin file in Antechamber
(Thu Aug 02 2007 - 12:07:11 PDT)
Lillian chong
Re: AMBER: setting dimensions of truncated octahedron
(Sun Aug 05 2007 - 06:25:01 PDT)
AMBER: setting dimensions of truncated octahedron
(Sat Aug 04 2007 - 13:34:59 PDT)
linfu
Re: Re: AMBER: about shake
(Wed Aug 08 2007 - 18:10:05 PDT)
Re: AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA
(Wed Aug 08 2007 - 06:33:58 PDT)
AMBER: about shake
(Tue Aug 07 2007 - 18:36:59 PDT)
Lorenzo Gontrani
Re: AMBER: energy minimization parameter
(Wed Aug 29 2007 - 00:54:58 PDT)
Lycourgos Chiniadis
AMBER: Information about Amber 9
(Thu Aug 02 2007 - 22:11:17 PDT)
M. L. Dodson
Re: AMBER: Criteria for classical md being OK to move to QM-MM
(Wed Aug 29 2007 - 11:24:43 PDT)
Re: AMBER: Criteria for classical md being OK to move to QM-MM
(Wed Aug 29 2007 - 10:11:29 PDT)
Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB
(Sun Aug 26 2007 - 08:42:14 PDT)
Re: AMBER: solvateCap minin and mdin for qm-mm dftb
(Fri Aug 24 2007 - 13:59:04 PDT)
Re: AMBER: solvateCap minin and mdin for qm-mm dftb
(Fri Aug 24 2007 - 09:17:37 PDT)
Re: AMBER: solvateCap minin and mdin for qm-mm dftb
(Fri Aug 24 2007 - 06:11:06 PDT)
Re: AMBER: Parallelizin antechamber?
(Tue Aug 14 2007 - 07:29:16 PDT)
Re: AMBER: Any experience on Dell two quad core system?
(Mon Aug 13 2007 - 10:37:47 PDT)
Re: AMBER: Any experience on Dell two quad core system?
(Mon Aug 13 2007 - 08:59:11 PDT)
Re: AMBER: Fwd: QM region + cutoff larger that box
(Mon Aug 06 2007 - 08:29:43 PDT)
Re: AMBER: Fwd: QM region + cutoff larger that box
(Mon Aug 06 2007 - 05:58:56 PDT)
Re: AMBER: Fwd: QM region + cutoff larger that box
(Sat Aug 04 2007 - 07:51:22 PDT)
Re: AMBER: Fwd: QM region + cutoff larger that box
(Sat Aug 04 2007 - 07:32:17 PDT)
M. Maeda
Re: AMBER: Machine environment to install AMBER 8
(Tue Aug 14 2007 - 22:17:03 PDT)
Re: AMBER: Machine environment to install AMBER 8
(Tue Aug 14 2007 - 02:45:53 PDT)
Re: AMBER: Machine environment to install AMBER 8
(Tue Aug 14 2007 - 02:19:37 PDT)
Re: AMBER: Machine environment to install AMBER 8
(Tue Aug 14 2007 - 01:54:03 PDT)
AMBER: Machine environment to install AMBER 8
(Mon Aug 13 2007 - 23:03:07 PDT)
Re: AMBER: program bug?
(Wed Aug 08 2007 - 19:37:13 PDT)
Marc Baaden
AMBER: Citation for Langevin thermostat?
(Sat Aug 11 2007 - 00:13:28 PDT)
Mark Williamson
Re: AMBER: MPI
(Fri Aug 17 2007 - 05:58:00 PDT)
Re: AMBER: Cygwin error
(Wed Aug 08 2007 - 15:02:15 PDT)
Martin Stennett
AMBER: Dihedrals in Sander
(Thu Aug 30 2007 - 01:36:17 PDT)
Re: AMBER: TEST_FAILURES
(Mon Aug 20 2007 - 05:56:36 PDT)
Melinda Layten
Re: AMBER:
(Fri Aug 31 2007 - 10:19:21 PDT)
Michael Lerner
AMBER: ptraj hydrogen bonding defaults
(Fri Aug 17 2007 - 15:26:09 PDT)
Re: AMBER: How to couple only one residue to the temperature bath?
(Fri Aug 10 2007 - 14:35:38 PDT)
AMBER: How to couple only one residue to the temperature bath?
(Fri Aug 10 2007 - 07:45:10 PDT)
ming hui
AMBER: Thermodynamic Integration for a CHARGED molecule
(Fri Aug 17 2007 - 02:12:38 PDT)
msubhamoy.ibab.ac.in
AMBER: Error in MMPBSA Calculation
(Mon Aug 20 2007 - 22:53:17 PDT)
AMBER: mmpbsa calculation
(Mon Aug 20 2007 - 02:53:42 PDT)
AMBER: MMPBSA NOT Getting results
(Tue Aug 14 2007 - 01:26:57 PDT)
AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA
(Wed Aug 08 2007 - 06:08:04 PDT)
AMBER:
(Wed Aug 08 2007 - 06:01:00 PDT)
nag raj
AMBER: Regarding free energy calculation and covalent bond
(Mon Aug 20 2007 - 21:07:04 PDT)
Neha Gandhi
AMBER: Parse charges for small molecules
(Wed Aug 22 2007 - 21:50:38 PDT)
Re: AMBER: charges in PBSA calculation
(Sun Aug 19 2007 - 16:01:47 PDT)
AMBER: charges in PBSA calculation
(Sat Aug 18 2007 - 19:20:16 PDT)
neville forlemu
Re: AMBER: bug in nonbond_list.f (nee ew_setup.f)
(Wed Aug 08 2007 - 11:35:51 PDT)
Nikola Trbovic
Re: AMBER: NVE energy and temperature drift
(Sat Aug 11 2007 - 14:33:09 PDT)
Re: AMBER: imin=5 and inptraj
(Sat Aug 11 2007 - 14:31:40 PDT)
AMBER: imin=5 and inptraj
(Sat Aug 11 2007 - 13:11:08 PDT)
RE: AMBER: NVE energy and temperature drift
(Thu Aug 09 2007 - 17:11:07 PDT)
Re: AMBER: NVE energy and temperature drift
(Thu Aug 09 2007 - 15:50:45 PDT)
AMBER: NVE energy and temperature drift
(Thu Aug 09 2007 - 13:24:11 PDT)
Pan, Yongmei
AMBER: unsubscribe
(Mon Aug 13 2007 - 10:35:12 PDT)
Pankaj R. Daga
AMBER: Molsurf error
(Fri Aug 17 2007 - 10:46:54 PDT)
Prashanth Athri
Re: AMBER: Force Field Parameters
(Thu Aug 02 2007 - 10:39:10 PDT)
Prem Prakash Pathak
AMBER: refinement of NMR struture using AMBER
(Wed Aug 29 2007 - 03:57:11 PDT)
Re: AMBER: What is the best computer for running AMBER simulations?
(Sat Aug 18 2007 - 02:36:00 PDT)
AMBER: force field for hydrogels
(Thu Aug 02 2007 - 23:03:48 PDT)
priya priya
AMBER: ow to split MDCRD file using ptraj
(Fri Aug 24 2007 - 00:34:27 PDT)
AMBER: Unable to open MDCRD file using vmd
(Thu Aug 23 2007 - 08:04:19 PDT)
Re: AMBER: setbox command error
(Tue Aug 14 2007 - 01:58:40 PDT)
Re: AMBER: setbox command error
(Mon Aug 13 2007 - 23:42:45 PDT)
AMBER: setbox command error
(Mon Aug 13 2007 - 09:18:16 PDT)
Re: AMBER: heical content in simulations
(Tue Aug 07 2007 - 01:41:16 PDT)
AMBER: heical content in simulations
(Tue Aug 07 2007 - 00:58:12 PDT)
AMBER: Specific heat graph is a straight line
(Mon Aug 06 2007 - 06:33:52 PDT)
Qiang Zhong
AMBER: energy minimization parameter
(Wed Aug 29 2007 - 00:54:12 PDT)
RE: AMBER: QM/MM in reaction pathways?
(Tue Aug 28 2007 - 17:52:21 PDT)
AMBER: QM/MM in reaction pathways?
(Tue Aug 28 2007 - 00:51:30 PDT)
Re: AMBER: SMD simulation
(Sat Aug 25 2007 - 02:49:09 PDT)
AMBER: SMD simulation
(Fri Aug 24 2007 - 03:33:41 PDT)
AMBER: QM/MM in reaction pathways?
(Fri Aug 24 2007 - 01:00:50 PDT)
AMBER: protonation of His residue!
(Thu Aug 23 2007 - 19:39:51 PDT)
AMBER: Ca(2+) parameter
(Thu Aug 23 2007 - 04:01:24 PDT)
AMBER: How to use AMBER Parameter Database ?
(Wed Aug 22 2007 - 01:53:04 PDT)
AMBER: Tutorial of document about QM/MM in reaction pathways?
(Tue Aug 21 2007 - 07:06:53 PDT)
AMBER: How to use AMBER Parameter Database ?
(Tue Aug 21 2007 - 05:36:46 PDT)
AMBER: command tleap is not normal
(Tue Aug 21 2007 - 01:12:44 PDT)
AMBER: $tleap is not normal
(Mon Aug 20 2007 - 18:34:00 PDT)
Re: AMBER: TEST_FAILURES
(Mon Aug 20 2007 - 17:43:23 PDT)
AMBER: TEST_FAILURES
(Mon Aug 20 2007 - 05:59:28 PDT)
AMBER: Tutorial about SMD?
(Tue Aug 14 2007 - 03:19:09 PDT)
Rafi Ahmad
RE: AMBER: MMPBSA NOT Getting results
(Tue Aug 14 2007 - 01:34:35 PDT)
Rajendra P. OJHA
RE: AMBER: Building parallel Amber 9.0
(Wed Aug 15 2007 - 08:44:10 PDT)
RE: AMBER: Building parallel Amber 9.0
(Wed Aug 15 2007 - 08:41:25 PDT)
Raviprasad Aduri
Re: AMBER: Force Field Parameters
(Thu Aug 02 2007 - 12:49:37 PDT)
Ray Luo
Re: AMBER: charges in PBSA calculation
(Sun Aug 19 2007 - 06:32:19 PDT)
Robert Duke
Re: AMBER: Scaling for octahedral versus rectilinear boxes
(Fri Aug 31 2007 - 07:23:11 PDT)
Re: AMBER: Scaling for octahedral versus rectilinear boxes
(Fri Aug 31 2007 - 05:40:48 PDT)
Re: AMBER: Any experience on Dell two quad core system?
(Tue Aug 14 2007 - 09:13:07 PDT)
Re: AMBER: NVE energy and temperature drift
(Thu Aug 09 2007 - 19:15:19 PDT)
Re: AMBER: NVE energy and temperature drift
(Thu Aug 09 2007 - 16:43:42 PDT)
Re: AMBER: NVE energy and temperature drift
(Thu Aug 09 2007 - 15:15:58 PDT)
Ross Walker
RE: AMBER: Criteria for classical md being OK to move to QM-MM
(Wed Aug 29 2007 - 11:40:30 PDT)
RE: AMBER: QM/MM in reaction pathways?
(Tue Aug 28 2007 - 08:21:40 PDT)
RE: AMBER: solvateCap minin and mdin for qm-mm dftb
(Fri Aug 24 2007 - 14:05:24 PDT)
RE: AMBER: PM6?
(Fri Aug 24 2007 - 13:19:22 PDT)
RE: AMBER: solvateCap minin and mdin for qm-mm dftb
(Fri Aug 24 2007 - 09:57:55 PDT)
RE: AMBER: PM6?
(Fri Aug 24 2007 - 09:36:26 PDT)
RE: AMBER: SMD simulation
(Fri Aug 24 2007 - 06:12:43 PDT)
RE: AMBER: solvateCap minin and mdin for qm-mm dftb
(Fri Aug 24 2007 - 06:10:54 PDT)
RE: AMBER: Unable to open MDCRD file using vmd
(Thu Aug 23 2007 - 13:40:27 PDT)
RE: AMBER: how to include mpirun in this script
(Tue Aug 21 2007 - 11:45:23 PDT)
RE: AMBER: $tleap is not normal
(Mon Aug 20 2007 - 19:51:16 PDT)
RE: AMBER: about parallelization in QM-MM
(Fri Aug 17 2007 - 11:45:08 PDT)
RE: AMBER: about parallelization in QM-MM
(Fri Aug 17 2007 - 09:58:54 PDT)
RE: AMBER: Building parallel Amber 9.0
(Wed Aug 15 2007 - 10:43:28 PDT)
RE: AMBER: Building parallel Amber 9.0
(Wed Aug 15 2007 - 07:26:36 PDT)
RE: AMBER: Failure to SCF convergence & parallelization and memory
(Mon Aug 13 2007 - 10:16:25 PDT)
RE: AMBER: Failure to SCF convergence
(Sat Aug 11 2007 - 16:14:54 PDT)
RE: AMBER: vlimit exceeded for the step
(Fri Aug 10 2007 - 13:04:10 PDT)
RE: AMBER: Implicit solvent simulation is too slow.
(Fri Aug 10 2007 - 08:56:32 PDT)
RE: AMBER: Cygwin error
(Thu Aug 09 2007 - 11:52:36 PDT)
AMBER: RE: Problem loading pdf into tleap
(Wed Aug 08 2007 - 10:29:19 PDT)
AMBER: RE: TUTORIAL B1 file polyAT_vac.prmtop
(Wed Aug 08 2007 - 07:52:39 PDT)
RE: AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA
(Wed Aug 08 2007 - 07:49:11 PDT)
RE: AMBER: Problem with minimization
(Tue Aug 07 2007 - 06:57:18 PDT)
AMBER: RE: tutorial file polyAT_vac.prmtop
(Sun Aug 05 2007 - 20:09:46 PDT)
RE: AMBER: (no subject)
(Sat Aug 04 2007 - 08:30:36 PDT)
RE: AMBER: Any experience on Dell two quad core system?
(Fri Aug 03 2007 - 09:28:57 PDT)
RE: AMBER: Problem with antechamber
(Thu Aug 02 2007 - 08:22:52 PDT)
RE: AMBER: Problem while saving .top and .crd files.
(Thu Aug 02 2007 - 07:54:21 PDT)
RE: AMBER: problem compiling Amber9 on 64-machine
(Wed Aug 01 2007 - 09:10:17 PDT)
S.Sundar Raman
Re: AMBER: problem compiling Amber9 on 64-machine
(Wed Aug 01 2007 - 22:03:32 PDT)
Re: AMBER: problem compiling Amber9 on 64-machine
(Wed Aug 01 2007 - 08:46:10 PDT)
Sally Pias
AMBER: metalloprotein dynamics
(Mon Aug 27 2007 - 10:55:51 PDT)
Sandeep Kaushik
AMBER: NAN and vlimit exceeded errors in restrained MD.. using IBELLY
(Thu Aug 16 2007 - 22:44:17 PDT)
saurabh agrawal
Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj).
(Wed Aug 22 2007 - 03:25:53 PDT)
AMBER: How to delete particular frame from mdcrd file (not with ptraj).
(Wed Aug 22 2007 - 02:48:52 PDT)
Scott Brozell
Re: AMBER: docking ability
(Sun Aug 19 2007 - 11:19:08 PDT)
Re: AMBER: How to carry out drug-dna complex simulations
(Sun Aug 19 2007 - 11:06:22 PDT)
Re: AMBER: MM_PBSA No radius found for Br!!
(Sun Aug 19 2007 - 10:40:20 PDT)
Re: AMBER: compile amber8 with mpich2
(Wed Aug 08 2007 - 19:46:22 PDT)
Re: AMBER: Antechamber formal charges with Gasteiger method
(Sat Aug 04 2007 - 12:42:43 PDT)
Re: AMBER: Antechamber formal charges with Gasteiger method
(Thu Aug 02 2007 - 18:44:28 PDT)
Seongeun Yang
AMBER: Using charmm force field in amber
(Sat Aug 11 2007 - 01:44:44 PDT)
Sergey Samsonov
AMBER: MM-PBSA calculations of entropy within the sphere
(Wed Aug 22 2007 - 06:49:25 PDT)
AMBER: Entropy in MM_PBSA
(Mon Aug 20 2007 - 08:01:37 PDT)
Servaas Michielssens
AMBER: vector corrplane
(Thu Aug 02 2007 - 08:25:45 PDT)
Seth Hayik
Re: AMBER: antechamber, how does it work
(Wed Aug 15 2007 - 08:10:22 PDT)
Seth Lilavivat
AMBER: Measuring Bond Angle over simulation
(Fri Aug 31 2007 - 12:25:20 PDT)
Re: AMBER: planarity restraints for NA
(Thu Aug 02 2007 - 12:29:42 PDT)
Re: AMBER: planarity restraints for NA
(Thu Aug 02 2007 - 10:01:39 PDT)
Re: AMBER: planarity restraints for NA
(Thu Aug 02 2007 - 07:07:23 PDT)
AMBER: planarity restraints for NA
(Thu Aug 02 2007 - 06:12:18 PDT)
SeungPyo Hong
Re: AMBER: Implicit solvent simulation is too slow.
(Fri Aug 10 2007 - 07:04:28 PDT)
AMBER: Implicit solvent simulation is too slow.
(Fri Aug 10 2007 - 05:42:11 PDT)
snoze pa
Re: AMBER: Add hydrogen and charge calculation
(Mon Aug 27 2007 - 21:07:55 PDT)
AMBER: Add hydrogen and charge calculation
(Mon Aug 27 2007 - 12:06:44 PDT)
Steve Seibold
RE: AMBER: Missplaced TERs
(Thu Aug 16 2007 - 12:47:38 PDT)
AMBER: Missplaced TERs
(Thu Aug 16 2007 - 11:35:26 PDT)
AMBER:
(Fri Aug 10 2007 - 13:17:47 PDT)
Steve Spronk
AMBER: Running Gaussian to get .out files
(Fri Aug 24 2007 - 07:08:13 PDT)
RE: AMBER: How to delete particular frame from mdcrd file (not with ptraj).
(Thu Aug 23 2007 - 06:25:50 PDT)
RE: AMBER: Running Gaussian to get .out files
(Thu Aug 23 2007 - 06:05:25 PDT)
AMBER: Bug in ptraj mask processing?
(Wed Aug 15 2007 - 12:18:15 PDT)
Steven Winfield
[Fwd: Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj).]
(Thu Aug 23 2007 - 06:31:49 PDT)
Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj).
(Wed Aug 22 2007 - 03:12:16 PDT)
Re: AMBER: setbox command error
(Tue Aug 14 2007 - 02:00:39 PDT)
Re: AMBER: setbox command error
(Tue Aug 14 2007 - 00:45:08 PDT)
Re: AMBER: about shake
(Wed Aug 08 2007 - 08:59:45 PDT)
Sudha Mani Karra
Re: AMBER: Distance restraints between center of mass of two molecules
(Wed Aug 15 2007 - 14:02:55 PDT)
Re: AMBER: Distance restraints between center of mass of two molecules
(Wed Aug 15 2007 - 08:40:37 PDT)
AMBER: Distance restraints between center of mass of two molecules
(Wed Aug 15 2007 - 07:38:06 PDT)
AMBER: vlimit exceeded for the step
(Fri Aug 10 2007 - 12:31:08 PDT)
Syed Tarique Moin
AMBER: how to include mpirun in this script
(Tue Aug 21 2007 - 03:50:12 PDT)
AMBER: Problem with minimization
(Tue Aug 07 2007 - 06:11:32 PDT)
Re: AMBER: (no subject)
(Sat Aug 04 2007 - 07:07:23 PDT)
RE: AMBER: (no subject)
(Fri Aug 03 2007 - 23:11:51 PDT)
Re: AMBER: (no subject)
(Thu Aug 02 2007 - 05:36:21 PDT)
AMBER: (no subject)
(Wed Aug 01 2007 - 23:50:59 PDT)
AMBER: how to calculate the ps/day of md simulation using using my cluster system in amber7
(Wed Aug 01 2007 - 02:36:31 PDT)
Thomas Cheatham
Re: AMBER: ptraj hydrogen bonding defaults
(Fri Aug 17 2007 - 19:33:55 PDT)
Re: AMBER: Using TLEAP to set up MD in the crystal lattice space?
(Mon Aug 13 2007 - 19:45:19 PDT)
Re: AMBER: setting dimensions of truncated octahedron
(Sat Aug 04 2007 - 15:38:15 PDT)
Thomas Cheatham III
Re: AMBER: antechamber, how does it work
(Wed Aug 15 2007 - 16:02:07 PDT)
Re: AMBER: NVE energy and temperature drift
(Thu Aug 09 2007 - 15:27:50 PDT)
Re: AMBER: Binary file curiosities
(Fri Aug 03 2007 - 16:32:55 PDT)
Thomas Patko
Re: AMBER: PM6?
(Fri Aug 24 2007 - 10:43:35 PDT)
Thomas Patko (CSULB)
AMBER: PM6?
(Fri Aug 24 2007 - 06:46:16 PDT)
Thomas Pochapsky
AMBER: generating a .rst file from an .mdcrd file
(Mon Aug 27 2007 - 11:41:56 PDT)
Re: AMBER:
(Fri Aug 10 2007 - 13:34:32 PDT)
Tiago Sobreira
AMBER: nucleic acid electrostatic energy
(Sat Aug 04 2007 - 06:45:46 PDT)
Tom Pochapsky
Re: AMBER: torsional restraints in a solvated MD simulation.
(Tue Aug 14 2007 - 18:04:24 PDT)
Re: AMBER: torsional restraints in a solvated MD simulation.
(Tue Aug 14 2007 - 16:15:06 PDT)
Re: AMBER: torsional restraints in a solvated MD simulation.
(Tue Aug 14 2007 - 16:11:27 PDT)
AMBER: torsional restraints in a solvated MD simulation.
(Tue Aug 14 2007 - 13:31:34 PDT)
tomas.kubar.marge.uochb.cas.cz
Re: AMBER: DFTB email address
(Sun Aug 19 2007 - 13:27:48 PDT)
Urszula Uciechowska
AMBER: MM_PBSA No radius found for Br!!
(Tue Aug 14 2007 - 08:53:32 PDT)
Re: AMBER: MM_PBSA No radius found for Br!!
(Tue Aug 14 2007 - 06:49:06 PDT)
AMBER: MM_PBSA No radius found for Br!!
(Mon Aug 13 2007 - 02:52:34 PDT)
Viv Kendon
Re: AMBER: Successful compile on Mac OSX + Intel compilers
(Fri Aug 03 2007 - 09:00:57 PDT)
AMBER: Successful compile on Mac OSX + Intel compilers
(Fri Aug 03 2007 - 05:28:56 PDT)
Vlad Cojocaru
Re: AMBER: Force field for RNA with U-turn motif
(Wed Aug 22 2007 - 01:07:24 PDT)
Re: AMBER: NVE energy and temperature drift
(Fri Aug 10 2007 - 02:10:51 PDT)
Re: AMBER: NVE energy and temperature drift
(Fri Aug 10 2007 - 02:03:15 PDT)
WANG,YING
Re: AMBER: How to perform MD simulation in NVT ensemble?
(Wed Aug 29 2007 - 06:50:30 PDT)
Re: AMBER: How to perform MD simulation in NVT ensemble?
(Thu Aug 23 2007 - 13:53:05 PDT)
AMBER: How to perform MD simulation in NVT ensemble?
(Thu Aug 23 2007 - 09:13:51 PDT)
Re: AMBER: xLeap "Could not find type" error
(Wed Aug 22 2007 - 08:46:58 PDT)
AMBER: xLeap "Could not find type" error
(Wed Aug 22 2007 - 07:04:37 PDT)
AMBER: a question about xleap
(Tue Aug 21 2007 - 12:16:48 PDT)
Re: AMBER: edit.out amber version 9
(Thu Aug 02 2007 - 13:33:49 PDT)
Wei Zhang
Re: AMBER: xLeap "Could not find type" error
(Wed Aug 22 2007 - 08:18:11 PDT)
Wenyong Tong
Re: AMBER: how to combine two molecules
(Mon Aug 13 2007 - 16:14:49 PDT)
Re: AMBER: how to combine two molecules
(Sat Aug 11 2007 - 18:48:48 PDT)
AMBER: how to combine two molecules
(Wed Aug 08 2007 - 22:34:33 PDT)
Ye Mei
Re: AMBER: Any experience on Dell two quad core system?
(Thu Aug 02 2007 - 20:57:00 PDT)
Yu Chen
Re: AMBER: What is the best computer for running AMBER simulations?
(Thu Aug 16 2007 - 20:44:49 PDT)
Last message date
:
Sun Sep 02 2007 - 06:07:39 PDT
Archived on
: Sun Dec 22 2024 - 05:53:38 PST
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