Amber Archive Feb 2007 by author
432 messages
:
Starting
Sun Feb 04 2007 - 06:07:19 PST,
Ending
Sun Mar 04 2007 - 06:07:28 PST
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A Box
AMBER: Prepgen
(Wed Feb 14 2007 - 20:15:21 PST)
AMBER: LeaP: Mol2 files
(Tue Feb 13 2007 - 17:44:08 PST)
Adrian Roitberg
Re: AMBER: Sander slower on 16 processors than 8
(Thu Feb 22 2007 - 13:25:15 PST)
Re: AMBER: units in hessian matrix
(Thu Feb 15 2007 - 09:35:07 PST)
Re: AMBER: Protonation of Aspartate
(Thu Feb 08 2007 - 09:17:11 PST)
Akshay Patny
AMBER: Difference in Equilibration & Production MD in Amber
(Wed Feb 28 2007 - 12:33:56 PST)
RE: AMBER: Box dimensions
(Fri Feb 16 2007 - 08:34:40 PST)
AMBER: Density of a system in MD
(Thu Feb 15 2007 - 12:45:27 PST)
RE: AMBER: Membrane Simulation: NPT Issues
(Thu Feb 15 2007 - 08:54:02 PST)
RE: AMBER: Membrane Simulation: NPT Issues
(Mon Feb 12 2007 - 07:33:40 PST)
RE: AMBER: antechamber for topology file
(Wed Feb 07 2007 - 22:28:50 PST)
AMBER: Membrane Simulation: NPT Issues
(Wed Feb 07 2007 - 09:28:05 PST)
AMBER: Membrane Simulation: NPT issues
(Wed Feb 07 2007 - 10:29:36 PST)
AMBER: RESP Charges for Charged Carboxylate in Organic Ligand
(Fri Feb 02 2007 - 08:05:35 PST)
Alexander Rubinstein
AMBER: Energy calculation by Anal
(Thu Feb 08 2007 - 12:11:16 PST)
Alexander Steudle
AMBER: MAXGRP error message
(Mon Feb 05 2007 - 06:03:45 PST)
Amarda Shehu
Re: AMBER: equilibration in explicit solvent
(Thu Feb 08 2007 - 11:48:23 PST)
Re: AMBER: equilibration in explicit solvent
(Thu Feb 08 2007 - 09:37:39 PST)
Re: AMBER: equilibration in explicit solvent
(Sun Feb 04 2007 - 10:32:05 PST)
AMBER: equilibration in explicit solvent
(Sun Feb 04 2007 - 09:40:12 PST)
Amit Kumar
Re: AMBER: extracting coordinate from crd file
(Sat Feb 10 2007 - 07:31:35 PST)
AMBER: addions
(Sat Feb 03 2007 - 05:17:57 PST)
Andreas Svrcek-Seiler
Re: AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8
(Fri Feb 23 2007 - 03:02:52 PST)
Anju Sharma
Re: AMBER: hi
(Tue Feb 13 2007 - 20:44:45 PST)
Re: AMBER: hi
(Tue Feb 13 2007 - 20:50:16 PST)
Re: AMBER: hi
(Tue Feb 13 2007 - 20:48:36 PST)
AMBER: hi
(Tue Feb 13 2007 - 02:08:01 PST)
AMBER: Fwd: help me out...
(Mon Feb 12 2007 - 04:22:57 PST)
AMBER: help me out...
(Mon Feb 12 2007 - 04:21:00 PST)
AYTUG TUNCEL
Re: Re: AMBER: crd to pdb conversion
(Mon Feb 19 2007 - 07:04:58 PST)
AMBER: crd to pdb conversion
(Mon Feb 19 2007 - 05:27:34 PST)
Beale, John
AMBER: LEaP crashes
(Wed Feb 28 2007 - 08:29:16 PST)
RE: AMBER: Disulfide Bonds
(Wed Feb 28 2007 - 05:37:48 PST)
AMBER: Disulfide Bonds
(Wed Feb 28 2007 - 04:56:55 PST)
AMBER: PTRAJ problem
(Mon Feb 26 2007 - 10:26:21 PST)
AMBER: LEaP Problem
(Wed Feb 21 2007 - 05:11:13 PST)
AMBER: oops
(Tue Feb 20 2007 - 05:35:19 PST)
AMBER:
(Tue Feb 20 2007 - 05:02:24 PST)
AMBER: problems with bonding disulfide linkages
(Mon Feb 19 2007 - 12:39:10 PST)
AMBER: carbohydrate-peptide
(Mon Feb 19 2007 - 08:09:54 PST)
RE: AMBER: Lone Pairs
(Tue Feb 13 2007 - 06:33:44 PST)
AMBER: Lone Pairs
(Mon Feb 12 2007 - 10:52:48 PST)
AMBER: Calcium and peptides
(Thu Feb 08 2007 - 10:20:30 PST)
AMBER: Glycam
(Tue Feb 06 2007 - 05:07:22 PST)
bertrand russell
Re: AMBER: phe-phe molecule
(Mon Feb 26 2007 - 00:03:27 PST)
Re: AMBER: phe-phe molecule
(Sun Feb 25 2007 - 22:08:42 PST)
AMBER: getting same box dimension
(Sun Feb 25 2007 - 21:27:40 PST)
AMBER: Umbrella sampling - Tutorial
(Fri Feb 09 2007 - 23:35:31 PST)
Re: AMBER: calculating distance between two atoms
(Mon Feb 05 2007 - 04:22:16 PST)
AMBER: replacement of mutated atoms in protein structure
(Mon Feb 05 2007 - 02:42:37 PST)
AMBER: calculating distance between two atoms
(Fri Feb 02 2007 - 09:49:07 PST)
Bill Ross
Re: AMBER: extracting coordinate from crd file
(Sun Feb 11 2007 - 21:13:38 PST)
Carlos Simmerling
Re: AMBER: solvent accessible surface area (SASA)
(Wed Feb 28 2007 - 14:50:20 PST)
Re: AMBER: abnormal high temperature during NPT ensembles MD
(Tue Feb 27 2007 - 18:36:01 PST)
Re: AMBER: Error in running Replica Exchange MD with amber9
(Sat Feb 24 2007 - 12:27:01 PST)
Re: AMBER: Error in running Replica Exchange MD with amber9
(Fri Feb 23 2007 - 07:16:59 PST)
Re: AMBER: Sander slower on 16 processors than 8
(Thu Feb 22 2007 - 13:19:18 PST)
Re: AMBER: Error in running replica exchange MD
(Tue Feb 20 2007 - 06:26:24 PST)
Re: AMBER: Error in running replica exchange MD
(Tue Feb 20 2007 - 06:17:56 PST)
Re: AMBER: problems with bonding disulfide linkages
(Mon Feb 19 2007 - 12:45:28 PST)
Re: AMBER: MDGRAPE and AMBER
(Mon Feb 19 2007 - 06:23:58 PST)
Re: AMBER: REMD error on first exchange
(Mon Feb 19 2007 - 06:21:16 PST)
Re: AMBER: question about ADDLES module
(Fri Feb 16 2007 - 17:48:27 PST)
Re: AMBER: Torsion Restraint on Glycosidic Bond
(Fri Feb 16 2007 - 13:32:44 PST)
Re: AMBER: How to modify the velocity of a water molecule?
(Thu Feb 15 2007 - 18:58:54 PST)
Re: AMBER: Simulating a section of a molecule
(Thu Feb 15 2007 - 10:06:50 PST)
Re: AMBER: Best Force field for protein, DNA, and organic compounds?
(Wed Feb 14 2007 - 06:08:17 PST)
Re: AMBER: Best Force field for protein, DNA, and organic compounds?
(Wed Feb 14 2007 - 04:28:05 PST)
Re: AMBER: Help: 1 ns for implicit solvent (GB) calculations, enough?
(Wed Feb 14 2007 - 04:26:31 PST)
Re: AMBER: How precise is a MD simulation? Which strcutures should be reported?
(Wed Feb 14 2007 - 04:25:02 PST)
Re: AMBER: antechamber for topology file
(Wed Feb 07 2007 - 04:32:52 PST)
Re: AMBER: problem in xleap
(Tue Feb 06 2007 - 15:46:29 PST)
Re: AMBER: force fields
(Tue Feb 06 2007 - 04:50:42 PST)
Re: AMBER: equilibration in explicit solvent
(Mon Feb 05 2007 - 10:35:30 PST)
Re: AMBER: calculating distance between two atoms
(Mon Feb 05 2007 - 04:55:19 PST)
Re: AMBER: force fields
(Mon Feb 05 2007 - 04:49:29 PST)
Re: AMBER: angle command in Ptraj
(Sat Feb 03 2007 - 05:17:26 PST)
Re: AMBER: calculating distance between two atoms
(Fri Feb 02 2007 - 13:42:41 PST)
Catein Catherine
Re: AMBER: How precise is a MD simulation? Which strcutures should be reported?
(Tue Feb 13 2007 - 20:28:09 PST)
AMBER: Help: 1 ns for implicit solvent (GB) calculations, enough?
(Tue Feb 13 2007 - 20:18:23 PST)
AMBER: Best Force field for protein, DNA, and organic compounds?
(Tue Feb 13 2007 - 20:13:31 PST)
RE: AMBER: atomicfluct
(Tue Feb 13 2007 - 19:36:35 PST)
AMBER: atomicfluct
(Sun Feb 11 2007 - 21:45:40 PST)
Cenk Andac
Re: AMBER: Compiling Amber 8 on SuSE 10.2
(Wed Feb 07 2007 - 12:02:17 PST)
Chengwen Chen
AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9)
(Fri Feb 09 2007 - 00:25:00 PST)
Re: AMBER: some questions about minimization and MD of DNA duplex with sander
(Mon Feb 05 2007 - 21:43:29 PST)
Re: AMBER: some questions about minimization and MD of DNA duplex with sander
(Thu Feb 01 2007 - 21:40:11 PST)
Chris Moth
AMBER: units of mwcovar matrix befor conversion
(Thu Feb 22 2007 - 15:01:57 PST)
Re: AMBER: Fwd: help me out...
(Mon Feb 12 2007 - 07:08:24 PST)
AMBER: workaround for ibm xlf90 powerpc FORTRAN compiler: -q64 and -O3 yield Run.dhfr.min failure
(Thu Feb 01 2007 - 10:33:33 PST)
Chris-Kriton Skylaris
AMBER: AMBER question: Combining Gaff and ff99 forcefields for a single molecule
(Fri Feb 23 2007 - 01:54:00 PST)
Christopher Gaughan
AMBER: Replica Exchange
(Tue Feb 13 2007 - 13:20:08 PST)
Craig Gough
AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8
(Fri Feb 23 2007 - 00:47:36 PST)
AMBER: MDGRAPE and AMBER
(Mon Feb 19 2007 - 00:34:43 PST)
Daniel Oehme
AMBER: REMD error on first exchange
(Sun Feb 18 2007 - 18:31:57 PST)
Dave, Sonya
RE: AMBER: Simulating a section of a molecule
(Thu Feb 15 2007 - 15:10:06 PST)
AMBER: Simulating a section of a molecule
(Thu Feb 15 2007 - 08:59:53 PST)
RE: AMBER: How precise is a MD simulation?
(Wed Feb 14 2007 - 10:35:16 PST)
RE: AMBER: How precise is a MD simulation?
(Tue Feb 13 2007 - 12:01:23 PST)
AMBER: How precise is a MD simulation?
(Mon Feb 12 2007 - 16:00:07 PST)
RE: AMBER: simulating part of a molecule with homology modeling
(Mon Feb 12 2007 - 08:50:36 PST)
AMBER: simulating part of a molecule with homology modeling
(Sat Feb 10 2007 - 16:00:11 PST)
David A. Case
Re: AMBER: problem with atom restraints
(Wed Feb 28 2007 - 10:54:58 PST)
Re: AMBER: phe-phe molecule
(Wed Feb 28 2007 - 10:03:49 PST)
Re: AMBER: LEaP crashes
(Wed Feb 28 2007 - 10:03:29 PST)
Re: AMBER: getting same box dimension
(Mon Feb 26 2007 - 18:10:30 PST)
AMBER: Re: REMD with torsional restraints- Temperature swapping not occuring
(Mon Feb 26 2007 - 15:01:41 PST)
Re: AMBER: Modified nucleotides-ATOM TYPES
(Mon Feb 26 2007 - 06:21:16 PST)
Re: AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8
(Fri Feb 23 2007 - 08:35:34 PST)
Re: AMBER: LEaP Problem
(Thu Feb 22 2007 - 18:02:11 PST)
AMBER: [rsachdeva.imtech.res.in: Pls help - REMD with torsional restraints]
(Thu Feb 22 2007 - 18:03:47 PST)
Re: AMBER: Is this system too large?
(Thu Feb 22 2007 - 18:01:52 PST)
Re: AMBER: Amber/ANAL and psf files
(Wed Feb 21 2007 - 20:14:42 PST)
Re: AMBER: Is this system too large?
(Wed Feb 21 2007 - 16:05:39 PST)
Re: AMBER: carbohydrate-peptide
(Wed Feb 21 2007 - 16:04:59 PST)
Re: AMBER: Pseudo-CSA in Amber?
(Wed Feb 21 2007 - 16:04:32 PST)
Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa
(Sat Feb 17 2007 - 13:22:38 PST)
Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa
(Fri Feb 16 2007 - 17:22:05 PST)
Re: AMBER: Problem with dacdif when using cygwin
(Fri Feb 16 2007 - 11:44:00 PST)
Re: AMBER: Box dimensions
(Fri Feb 16 2007 - 08:54:48 PST)
Re: AMBER: implicit solvent free energy calcs
(Thu Feb 15 2007 - 12:19:53 PST)
Re: AMBER: units in hessian matrix
(Thu Feb 15 2007 - 10:07:03 PST)
Re: AMBER: units in hessian matrix
(Thu Feb 15 2007 - 09:31:01 PST)
Re: AMBER: NMR violations increase in explicite water
(Thu Feb 15 2007 - 08:40:12 PST)
Re: AMBER: Membrane Simulation: NPT Issues
(Wed Feb 14 2007 - 15:04:47 PST)
Re: AMBER: SANDER bug
(Wed Feb 14 2007 - 10:11:12 PST)
Re: AMBER: Box problems in vacuum minimization with sander.serial 8
(Tue Feb 13 2007 - 11:34:57 PST)
Re: AMBER: Lone Pairs
(Tue Feb 13 2007 - 08:00:21 PST)
Re: AMBER: amber9 possible failure tgtmd
(Mon Feb 12 2007 - 21:58:15 PST)
Re: AMBER: Lone Pairs
(Mon Feb 12 2007 - 13:24:48 PST)
Re: AMBER: quasiharnomic analysis
(Mon Feb 12 2007 - 08:31:36 PST)
Re: AMBER: connect atom
(Mon Feb 12 2007 - 08:28:57 PST)
Re: AMBER: reporting EPtot and EKtot separately for two molecules
(Mon Feb 12 2007 - 08:25:55 PST)
Re: AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9)
(Sat Feb 10 2007 - 22:57:27 PST)
Re: AMBER: extracting coordinate from crd file
(Sat Feb 10 2007 - 08:08:28 PST)
Re: AMBER: problem with sander
(Sat Feb 10 2007 - 02:08:01 PST)
Re: AMBER: assigning charges to a prepi file
(Thu Feb 08 2007 - 22:58:08 PST)
Re: AMBER: Compiling AMBER 8 on RHEL4 AMD64
(Thu Feb 08 2007 - 22:22:01 PST)
Re: AMBER: antechamber for topology file
(Wed Feb 07 2007 - 23:08:04 PST)
Re: AMBER: problem with AMBER8 installation
(Wed Feb 07 2007 - 10:10:51 PST)
Re: AMBER: trajectory problem
(Wed Feb 07 2007 - 09:52:59 PST)
Re: AMBER: MAXGRP error message
(Wed Feb 07 2007 - 09:43:33 PST)
Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel)
(Tue Feb 06 2007 - 16:22:03 PST)
Re: AMBER: Compile Amber9 for MVAPICH
(Tue Feb 06 2007 - 12:23:07 PST)
Re: AMBER: Tutorial for chemical shift calculation?
(Tue Feb 06 2007 - 08:25:40 PST)
Re: AMBER: Glycam
(Tue Feb 06 2007 - 08:04:21 PST)
Re: AMBER: equilibration in explicit solvent
(Sun Feb 04 2007 - 21:27:44 PST)
Re: AMBER: equilibration in explicit solvent
(Sun Feb 04 2007 - 10:21:18 PST)
Re: AMBER: addions
(Sun Feb 04 2007 - 09:33:37 PST)
Re: AMBER: iRED and corrired
(Fri Feb 02 2007 - 10:57:43 PST)
Re: AMBER: Example needed for addAtomType command
(Thu Feb 01 2007 - 14:30:03 PST)
Re: AMBER: xleap
(Thu Feb 01 2007 - 08:58:40 PST)
David Cerutti
AMBER: Deriving constraint forces on water molecules based on SETTLE moves
(Wed Feb 14 2007 - 16:08:45 PST)
Re: AMBER: Positive binding free energy!
(Tue Feb 13 2007 - 16:40:35 PST)
AMBER: Constraint virial
(Tue Feb 13 2007 - 02:22:20 PST)
AMBER: Still puzzled about this virial computation
(Thu Feb 01 2007 - 00:00:10 PST)
David J. Powers
RE: AMBER: Compiling Amber 7
(Sat Feb 10 2007 - 07:59:42 PST)
RE: AMBER: Compiling Amber 7
(Thu Feb 08 2007 - 11:27:41 PST)
AMBER: Compiling Amber 7
(Thu Feb 08 2007 - 07:13:00 PST)
David LeBard
Re: AMBER: read the data
(Fri Feb 16 2007 - 11:22:12 PST)
Re: AMBER: read the data
(Fri Feb 16 2007 - 11:00:10 PST)
Re: AMBER: read the data
(Fri Feb 16 2007 - 10:31:13 PST)
Re: AMBER: read the data
(Thu Feb 15 2007 - 13:18:08 PST)
David Mobley
AMBER: implicit solvent free energy calcs
(Thu Feb 15 2007 - 10:07:37 PST)
Re: AMBER: How precise is a MD simulation?
(Tue Feb 13 2007 - 12:19:13 PST)
Re: AMBER: How precise is a MD simulation?
(Tue Feb 13 2007 - 12:11:17 PST)
Re: AMBER: How precise is a MD simulation?
(Tue Feb 13 2007 - 11:36:17 PST)
deepti nayar
Re: AMBER: phe-phe molecule
(Mon Feb 26 2007 - 20:51:53 PST)
Re: AMBER: phe-phe molecule
(Sun Feb 25 2007 - 23:46:10 PST)
AMBER: phe-phe molecule
(Sun Feb 25 2007 - 22:01:26 PST)
AMBER: atom types
(Wed Feb 21 2007 - 21:43:38 PST)
AMBER: connect atom
(Mon Feb 12 2007 - 03:01:57 PST)
AMBER: assigning charges to a prepi file
(Thu Feb 08 2007 - 22:38:27 PST)
AMBER: phe-phe prep file
(Thu Feb 08 2007 - 22:09:15 PST)
Re: AMBER: antechamber for topology file
(Wed Feb 07 2007 - 22:55:35 PST)
Re: AMBER: antechamber for topology file
(Wed Feb 07 2007 - 22:07:22 PST)
AMBER: antechamber for topology file
(Wed Feb 07 2007 - 02:42:51 PST)
Re: AMBER: force fields
(Tue Feb 06 2007 - 00:20:05 PST)
Re: AMBER: force fields
(Tue Feb 06 2007 - 02:33:37 PST)
Re: AMBER: force fields
(Mon Feb 05 2007 - 21:37:05 PST)
AMBER: force fields
(Sun Feb 04 2007 - 23:05:09 PST)
AMBER: xleap
(Thu Feb 01 2007 - 00:04:09 PST)
ebright HMS
Re: AMBER: abnormal high temperature during NPT ensembles MD
(Wed Feb 28 2007 - 08:29:41 PST)
AMBER: abnormal high temperature during NPT ensembles MD
(Tue Feb 27 2007 - 15:13:29 PST)
Ed Pate
AMBER: IFVARI parameter
(Tue Feb 27 2007 - 13:22:43 PST)
AMBER: problem with atom restraints
(Sun Feb 25 2007 - 20:53:31 PST)
Esther Brugger
Re: AMBER: solvent accessible surface area (SASA)
(Wed Feb 28 2007 - 15:54:51 PST)
AMBER: solvent accessible surface area (SASA)
(Wed Feb 28 2007 - 10:38:55 PST)
Re: AMBER: read the data
(Sat Feb 17 2007 - 12:22:50 PST)
Re: AMBER: read the data
(Fri Feb 16 2007 - 11:01:27 PST)
Re: AMBER: read the data
(Fri Feb 16 2007 - 10:40:45 PST)
Re: AMBER: read the data
(Fri Feb 16 2007 - 08:54:06 PST)
Re: AMBER: read the data
(Thu Feb 15 2007 - 15:00:39 PST)
Re: AMBER: read the data
(Fri Feb 16 2007 - 09:43:39 PST)
AMBER: read the data
(Thu Feb 15 2007 - 11:53:45 PST)
AMBER: H-Bond
(Thu Feb 08 2007 - 09:06:57 PST)
Re: AMBER: side chain orientation
(Wed Feb 07 2007 - 07:23:55 PST)
AMBER: side chain orientation
(Tue Feb 06 2007 - 15:36:48 PST)
Re: AMBER: angle command in Ptraj
(Fri Feb 02 2007 - 16:36:01 PST)
AMBER: angle command in Ptraj
(Fri Feb 02 2007 - 16:20:34 PST)
Evan Kelly
AMBER: AM1-bcc
(Tue Feb 27 2007 - 16:26:22 PST)
AMBER: ptraj dipole calculation in QMMM simulation
(Fri Feb 09 2007 - 10:36:30 PST)
Fenghui Fan
RE: AMBER: Is this system too large?
(Wed Feb 21 2007 - 14:55:57 PST)
Re: AMBER: Is this system too large?
(Tue Feb 20 2007 - 20:53:26 PST)
Re: AMBER: How precise is a MD simulation?
(Mon Feb 12 2007 - 17:47:09 PST)
Re: AMBER: simulating part of a molecule with homology modeling
(Sat Feb 10 2007 - 20:26:41 PST)
Re: AMBER: side chain orientation
(Tue Feb 06 2007 - 16:11:47 PST)
Florian Haberl
Re: AMBER: read the data
(Thu Feb 15 2007 - 12:11:16 PST)
Franck Vendeix
Re: AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain?
(Fri Feb 16 2007 - 14:04:48 PST)
Re: AMBER: Umbrella sampling
(Wed Feb 14 2007 - 19:13:31 PST)
AMBER: Umbrella sampling
(Fri Feb 09 2007 - 06:37:35 PST)
Francois Theillet
Re: AMBER: iRED and corrired
(Fri Feb 02 2007 - 13:05:41 PST)
AMBER: iRED and corrired
(Fri Feb 02 2007 - 09:07:47 PST)
FyD
Re: AMBER: RESP calculation of modified nucleotides
(Sun Feb 25 2007 - 09:49:55 PST)
Re: AMBER: LeaP: Mol2 files
(Wed Feb 14 2007 - 09:47:40 PST)
Re: AMBER: Modified nucleotides
(Wed Feb 14 2007 - 04:30:50 PST)
Re: AMBER: antechamber for topology file
(Thu Feb 08 2007 - 00:10:29 PST)
Re: AMBER: antechamber for topology file
(Wed Feb 07 2007 - 05:28:58 PST)
Gabbar S. Daaku
AMBER: Re: reporting EPtot and EKtot separately for two molecules
(Mon Feb 12 2007 - 08:16:45 PST)
AMBER: reporting EPtot and EKtot separately for two molecules
(Mon Feb 12 2007 - 08:15:09 PST)
Gobind Singh Bisht
AMBER: format of .xyz files and pdb
(Wed Jan 31 2007 - 14:05:24 PST)
Gohlke.bioinformatik.uni-frankfurt.de
Re: AMBER: Comparison of normal modes with ptraj?
(Wed Feb 14 2007 - 05:08:38 PST)
Re: AMBER: iRED and corrired
(Sun Feb 04 2007 - 05:01:17 PST)
gurpreet singh
AMBER: Residence time of WATER
(Mon Feb 19 2007 - 00:33:59 PST)
AMBER: extracting coordinate from crd file
(Sat Feb 10 2007 - 02:05:20 PST)
AMBER: extracting coordinates from crd file
(Sat Feb 10 2007 - 00:40:44 PST)
Gustavo Seabra
Re: AMBER: Difference in Equilibration & Production MD in Amber
(Wed Feb 28 2007 - 12:54:13 PST)
Re: AMBER: Box dimensions
(Fri Feb 16 2007 - 08:19:39 PST)
Re: AMBER: How to place torsion restraint
(Tue Feb 13 2007 - 08:48:08 PST)
Re: AMBER: ptraj dipole calculation in QMMM simulation
(Fri Feb 09 2007 - 10:54:04 PST)
Re: AMBER: ab initio modeling using Amber
(Thu Feb 01 2007 - 20:07:45 PST)
Hans Lee
AMBER: quasiharnomic analysis
(Sun Feb 11 2007 - 13:12:52 PST)
Harald Lanig
AMBER: Comparison of normal modes with ptraj?
(Wed Feb 14 2007 - 02:10:19 PST)
HL Eastwood
AMBER: How do I make and enter new ff parameters into AMBER
(Fri Feb 02 2007 - 13:26:46 PST)
Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand
(Fri Feb 02 2007 - 09:41:50 PST)
Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand
(Fri Feb 02 2007 - 09:40:10 PST)
Holger Gohlke
Re: AMBER: iRED and corrired
(Mon Feb 05 2007 - 08:09:15 PST)
Hu, Shaowen \(JSC-SK\)[USRA]
RE: AMBER: Is this system too large?
(Fri Feb 23 2007 - 08:10:09 PST)
RE: AMBER: Is this system too large?
(Thu Feb 22 2007 - 07:58:01 PST)
RE: AMBER: Is this system too large?
(Wed Feb 21 2007 - 09:02:21 PST)
AMBER: Is this system too large?
(Tue Feb 20 2007 - 20:17:41 PST)
Ichinkhorloo Erdenebaatar
AMBER: SANDER bug
(Tue Feb 13 2007 - 17:19:21 PST)
Ilyas Yildirim
Re: Re: AMBER: crd to pdb conversion
(Mon Feb 19 2007 - 09:12:43 PST)
Re: AMBER: crd to pdb conversion
(Mon Feb 19 2007 - 05:35:16 PST)
Re: AMBER: Installing AMBER v9 in Linux
(Sat Feb 17 2007 - 23:30:34 PST)
Re: AMBER: read the data
(Fri Feb 16 2007 - 15:05:31 PST)
Re: AMBER: hi
(Wed Feb 14 2007 - 14:14:11 PST)
Re: AMBER: Modified nucleotides
(Tue Feb 13 2007 - 20:05:25 PST)
Re: AMBER: Modified nucleotides
(Mon Feb 12 2007 - 20:58:50 PST)
Re: AMBER: extracting coordinates from crd file
(Sat Feb 10 2007 - 00:59:04 PST)
AMBER: Heating the system prior to production run
(Fri Feb 09 2007 - 13:28:08 PST)
Re: AMBER: equilibration in explicit solvent
(Thu Feb 08 2007 - 12:16:10 PST)
Re: AMBER: side chain orientation
(Wed Feb 07 2007 - 10:00:37 PST)
Re: AMBER: Link to Modified NA bases files
(Mon Feb 05 2007 - 20:05:21 PST)
Re: AMBER: equilibration in explicit solvent
(Sun Feb 04 2007 - 21:13:48 PST)
j j
Re: AMBER: Box problems in vacuum minimization with sander.serial 8
(Tue Feb 13 2007 - 11:43:34 PST)
AMBER: Box problems in vacuum minimization with sander.serial 8
(Tue Feb 13 2007 - 11:05:16 PST)
jacopo.sgrignani.unifi.it
AMBER: ptraj hbond
(Sat Feb 03 2007 - 08:28:20 PST)
Jarrod Smith
RE: AMBER: Problems with QMMM tests on Altix
(Fri Feb 23 2007 - 11:34:53 PST)
AMBER: Problems with QMMM tests on Altix
(Thu Feb 22 2007 - 14:03:14 PST)
Jerome.GOLEBIOWSKI.unice.fr
Re: AMBER: Disulfide Bonds
(Wed Feb 28 2007 - 05:27:23 PST)
Re: AMBER: Umbrella sampling
(Mon Feb 12 2007 - 01:33:18 PST)
Ji-Lai Li
AMBER: How to modify the velocity of a water molecule?
(Thu Feb 15 2007 - 18:15:45 PST)
Jiri Sponer
AMBER: DNA and RNA computations
(Mon Feb 19 2007 - 10:16:53 PST)
jlalonde
AMBER: amber9 possible failure tgtmd
(Fri Feb 09 2007 - 08:19:19 PST)
Junmei Wang
RE: AMBER: AM1-bcc
(Tue Feb 27 2007 - 18:57:23 PST)
Kara Di Giorgio
Re: AMBER: Example needed for addAtomType command
(Thu Feb 01 2007 - 15:02:39 PST)
AMBER: Example needed for addAtomType command
(Thu Feb 01 2007 - 13:26:12 PST)
kkirschn.hamilton.edu
Re: AMBER: Glycam
(Tue Feb 06 2007 - 06:44:52 PST)
Kristina Furse
Re: AMBER: IFVARI parameter
(Tue Feb 27 2007 - 13:50:45 PST)
Lorenzo Gontrani
AMBER: H-bond ptraj dilemma
(Fri Feb 16 2007 - 07:46:54 PST)
Luis Gracia
Re: AMBER: Problems with QMMM tests on Altix
(Thu Feb 22 2007 - 14:35:14 PST)
M. L. Dodson
Re: AMBER: Solvate box
(Tue Feb 13 2007 - 19:33:49 PST)
Marie Brut
AMBER: units in hessian matrix
(Thu Feb 15 2007 - 08:52:01 PST)
Mark Williamson
Re: AMBER: Help!! I cannot perform the ambpdb
(Wed Feb 07 2007 - 12:25:19 PST)
Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel)
(Wed Feb 07 2007 - 09:45:29 PST)
Re: AMBER: Strange behavior on g95 compile.
(Wed Feb 07 2007 - 08:18:16 PST)
Re: AMBER: Help!! I cannot perform the ambpdb
(Wed Feb 07 2007 - 08:08:41 PST)
Markus Weingarth
AMBER: Calculate force constants
(Sun Feb 04 2007 - 14:13:28 PST)
Martin Stennett
Re: AMBER: Sander slower on 16 processors than 8
(Thu Feb 22 2007 - 13:58:57 PST)
Re: AMBER: Sander slower on 16 processors than 8
(Thu Feb 22 2007 - 13:10:40 PST)
AMBER: Strange behavior on g95 compile.
(Wed Feb 07 2007 - 08:00:23 PST)
AMBER: Problem with paralell installation
(Fri Feb 02 2007 - 00:22:25 PST)
MARY O'CONNOR
AMBER: Force fields for iron
(Mon Feb 05 2007 - 08:19:52 PST)
AMBER: How do I make and enter new ff parameters into AMBER
(Fri Feb 02 2007 - 11:35:20 PST)
mathew k varghese
Re: AMBER: RESP calculation of modified nucleotides
(Wed Feb 28 2007 - 00:55:58 PST)
AMBER: Modified nucleotides-ATOM TYPES
(Mon Feb 26 2007 - 01:13:59 PST)
Re: AMBER: RESP calculation of modified nucleotides
(Sun Feb 25 2007 - 19:17:34 PST)
AMBER: RESP calculation of modified nucleotides
(Fri Feb 23 2007 - 22:50:23 PST)
AMBER: Water density calculation
(Sun Feb 18 2007 - 22:51:57 PST)
Re: AMBER: Modified nucleotides
(Wed Feb 14 2007 - 21:09:56 PST)
Re: AMBER: Modified nucleotides
(Tue Feb 13 2007 - 19:47:08 PST)
AMBER: Modified nucleotides
(Mon Feb 12 2007 - 20:44:31 PST)
Michel Becker
AMBER: NMR violations increase in explicite water
(Wed Feb 14 2007 - 12:15:14 PST)
Miguel Ferreira
AMBER: interior dielectric constant
(Tue Feb 20 2007 - 09:22:31 PST)
AMBER: trajectory problem
(Tue Feb 06 2007 - 20:52:25 PST)
Mike Hanby
AMBER: Compile Amber9 for MVAPICH
(Tue Feb 06 2007 - 11:51:18 PST)
Mike Summers
AMBER: Pseudo-CSA in Amber?
(Mon Feb 19 2007 - 06:30:13 PST)
Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel)
(Tue Feb 06 2007 - 18:30:22 PST)
Re: AMBER: Tutorial for chemical shift calculation?
(Tue Feb 06 2007 - 10:36:05 PST)
AMBER: Tutorial for chemical shift calculation?
(Mon Feb 05 2007 - 17:04:48 PST)
Nevin Gerek
AMBER: compiling AMBER9 on Mac OS X Tiger (Intel)
(Tue Feb 06 2007 - 15:08:08 PST)
Nicolas Lux Fawzi
AMBER: ptraj bug? -- doesn't like restart files from REMD
(Thu Feb 22 2007 - 13:33:58 PST)
Pankaj R. Daga
Re: AMBER: problems with bonding disulfide linkages
(Mon Feb 19 2007 - 14:54:24 PST)
Peter Gannett
RE: AMBER: Installing AMBER v9 in Linux
(Mon Feb 19 2007 - 04:27:44 PST)
r. a.
AMBER: native contact analysis!
(Wed Feb 21 2007 - 18:52:37 PST)
Rafi Ahmad
RE: AMBER: Best Force field for protein, DNA, and organic compounds?
(Wed Feb 14 2007 - 05:35:28 PST)
RE: AMBER: atomicfluct
(Mon Feb 12 2007 - 00:32:37 PST)
Raviprasad Aduri
Re: AMBER: RESP calculation of modified nucleotides
(Wed Feb 28 2007 - 13:11:34 PST)
Re: AMBER: RESP calculation of modified nucleotides
(Mon Feb 26 2007 - 08:56:47 PST)
Re: AMBER: Modified nucleotides
(Wed Feb 14 2007 - 16:58:39 PST)
Re: AMBER: Modified nucleotides
(Tue Feb 13 2007 - 09:23:15 PST)
rebeca.mmb.pcb.ub.es
AMBER: contacts in ptraj (Amber 9)
(Wed Feb 21 2007 - 10:56:50 PST)
AMBER: Amber/ANAL and psf files
(Wed Feb 21 2007 - 08:24:33 PST)
Rima Chaudhuri
Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa
(Wed Feb 28 2007 - 14:25:54 PST)
AMBER: MD temperature and MM_pbsa temperature
(Fri Feb 23 2007 - 13:22:30 PST)
Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa
(Sat Feb 17 2007 - 12:10:38 PST)
AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa
(Fri Feb 16 2007 - 14:17:49 PST)
AMBER: Positive binding free energy!
(Tue Feb 13 2007 - 14:53:05 PST)
AMBER: Missing values for MM ELE (MM-PBSA)..help!!
(Wed Feb 07 2007 - 08:21:38 PST)
AMBER: Binding free energy calculation - MM-pbsa
(Wed Feb 07 2007 - 12:55:26 PST)
AMBER: Missing Value for MM ELE
(Tue Feb 06 2007 - 15:26:08 PST)
AMBER: MM-PBSA questions/clarifications
(Tue Feb 06 2007 - 10:51:08 PST)
Robert Duke
Re: AMBER: Sander slower on 16 processors than 8
(Thu Feb 22 2007 - 19:27:12 PST)
Re: AMBER: Still puzzled about this virial computation
(Thu Feb 01 2007 - 08:16:51 PST)
Re: AMBER: Still puzzled about this virial computation
(Thu Feb 01 2007 - 07:35:25 PST)
Ross Walker
RE: AMBER: Problems with QMMM tests on Altix
(Sat Feb 24 2007 - 10:02:24 PST)
RE: AMBER: SCF convergence issues
(Fri Feb 23 2007 - 15:35:47 PST)
RE: AMBER: SCF convergence issues
(Fri Feb 23 2007 - 11:00:21 PST)
RE: AMBER: Problems with QMMM tests on Altix
(Thu Feb 22 2007 - 18:12:55 PST)
RE: AMBER: Sander slower on 16 processors than 8
(Thu Feb 22 2007 - 17:47:55 PST)
RE: AMBER: Sander slower on 16 processors than 8
(Thu Feb 22 2007 - 14:15:07 PST)
RE: AMBER: Sander slower on 16 processors than 8
(Thu Feb 22 2007 - 14:10:57 PST)
RE: AMBER: Errors in amber9 parallel installation
(Thu Feb 22 2007 - 05:52:16 PST)
AMBER: RE: about ANTECHAMBER
(Tue Feb 20 2007 - 08:22:21 PST)
RE: AMBER: Installing AMBER v9 in Linux
(Mon Feb 19 2007 - 10:03:12 PST)
RE: AMBER: Installing AMBER v9 in Linux
(Mon Feb 19 2007 - 01:44:15 PST)
RE: AMBER: Installing AMBER v9 in Linux
(Sun Feb 18 2007 - 23:39:05 PST)
RE: AMBER: Installing AMBER v9 in Linux
(Sun Feb 18 2007 - 22:53:45 PST)
RE: AMBER: Installing AMBER v9 in Linux
(Sat Feb 17 2007 - 08:52:00 PST)
RE: AMBER: hi
(Wed Feb 14 2007 - 08:15:50 PST)
RE: AMBER: Solvate box
(Tue Feb 13 2007 - 08:26:51 PST)
RE: AMBER: hi
(Tue Feb 13 2007 - 08:16:56 PST)
RE: AMBER: help me out...
(Mon Feb 12 2007 - 07:11:03 PST)
RE: AMBER: Compiling Amber 7
(Sat Feb 10 2007 - 09:11:54 PST)
RE: AMBER: ptraj dipole calculation in QMMM simulation
(Fri Feb 09 2007 - 10:53:30 PST)
RE: AMBER: Compiling Amber 7
(Thu Feb 08 2007 - 08:30:30 PST)
RE: AMBER: Help!! I cannot perform the ambpdb
(Wed Feb 07 2007 - 07:21:13 PST)
RE: AMBER: problem with AMBER8 installation
(Wed Feb 07 2007 - 10:06:42 PST)
RE: AMBER: Strange behavior on g95 compile.
(Wed Feb 07 2007 - 08:17:37 PST)
RE: AMBER: some questions about minimization and MD of DNA duplex with sander
(Fri Feb 02 2007 - 09:23:02 PST)
RE: AMBER: Problem with paralell installation
(Fri Feb 02 2007 - 07:21:16 PST)
RE: AMBER: xleap
(Thu Feb 01 2007 - 08:18:19 PST)
rpaduri.chem.wayne.edu
Re: AMBER: RESP calculation of modified nucleotides
(Sat Feb 24 2007 - 13:49:10 PST)
sai vikram
AMBER: Protonation of Aspartate
(Thu Feb 08 2007 - 09:12:03 PST)
saurabh agrawal
AMBER: positive binding energy
(Mon Feb 05 2007 - 09:30:46 PST)
Scott Brozell
Re: AMBER: Problem with dacdif when using cygwin
(Fri Feb 16 2007 - 12:43:07 PST)
Re: AMBER: Problem with dacdif when using cygwin
(Fri Feb 16 2007 - 11:32:06 PST)
Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel)
(Wed Feb 07 2007 - 09:59:41 PST)
Scott Pendley
Re: AMBER: mm_pbsa Array reference error
(Fri Feb 02 2007 - 09:09:50 PST)
Re: AMBER: mm_pbsa Array reference error
(Thu Feb 01 2007 - 09:05:27 PST)
Sean Rathlef
Re: AMBER: Modified nucleotides
(Mon Feb 12 2007 - 21:55:20 PST)
Seongeun Yang
Re: AMBER: Error in running Replica Exchange MD with amber9
(Sat Feb 24 2007 - 00:49:49 PST)
AMBER: Error in running Replica Exchange MD with amber9
(Fri Feb 23 2007 - 06:15:48 PST)
AMBER: Errors in amber9 parallel installation
(Thu Feb 22 2007 - 05:34:23 PST)
AMBER: Error in running replica exchange MD
(Tue Feb 20 2007 - 03:45:38 PST)
Seth Hayik
Re: AMBER: Strange behavior on g95 compile.
(Wed Feb 07 2007 - 08:31:50 PST)
Seth Lilavivat
AMBER: Best way to apply WC basepair restraints during MD
(Sun Feb 25 2007 - 12:24:40 PST)
AMBER: applying restraints
(Thu Feb 22 2007 - 08:40:59 PST)
AMBER: Torsion Restraint on Glycosidic Bond
(Fri Feb 16 2007 - 13:13:52 PST)
AMBER: How to parameterize frcmod for NA
(Tue Feb 13 2007 - 11:27:59 PST)
RE: AMBER: Modified nucleotides
(Mon Feb 12 2007 - 20:59:37 PST)
AMBER: How to place torsion restraint
(Mon Feb 12 2007 - 17:24:40 PST)
Re: AMBER: problem with sander
(Fri Feb 09 2007 - 11:35:34 PST)
AMBER: problem with sander
(Fri Feb 09 2007 - 09:43:14 PST)
AMBER: Compiling AMBER 8 on RHEL4 AMD64
(Thu Feb 08 2007 - 11:53:44 PST)
Re: AMBER: Compiling Amber 8 on SuSE 10.2
(Wed Feb 07 2007 - 14:35:27 PST)
AMBER: Compiling Amber 8 on SuSE 10.2
(Wed Feb 07 2007 - 11:50:12 PST)
AMBER: Link to Modified NA bases files
(Mon Feb 05 2007 - 14:22:50 PST)
snoze pa
AMBER: ab initio modeling using Amber
(Thu Feb 01 2007 - 18:59:17 PST)
Sontum, Steve
AMBER: Sander slower on 16 processors than 8
(Thu Feb 22 2007 - 12:32:42 PST)
Sophie Barbe
AMBER: Solvate box
(Tue Feb 13 2007 - 05:21:28 PST)
Steve Seibold
RE: AMBER: Box dimensions
(Fri Feb 16 2007 - 09:12:41 PST)
AMBER: Box dimensions
(Fri Feb 16 2007 - 07:13:45 PST)
Steven Winfield
Re: AMBER: SCF convergence issues
(Fri Feb 23 2007 - 11:13:33 PST)
AMBER: SCF convergence issues
(Fri Feb 23 2007 - 03:27:38 PST)
Re: AMBER: Problem with dacdif when using cygwin
(Fri Feb 16 2007 - 12:15:00 PST)
AMBER: Problem with dacdif when using cygwin
(Fri Feb 16 2007 - 10:33:38 PST)
Re: AMBER: Deriving constraint forces on water molecules based on SETTLE moves
(Thu Feb 15 2007 - 05:28:00 PST)
Re: AMBER: hi
(Wed Feb 14 2007 - 14:21:01 PST)
Re: AMBER: hi
(Tue Feb 13 2007 - 02:42:16 PST)
Re: AMBER: problem in xleap
(Mon Feb 05 2007 - 08:06:12 PST)
Stéphane Téletchéa
AMBER: subscribe amber
(Thu Feb 01 2007 - 07:11:25 PST)
subhasish chatterjee
AMBER: Nanopore simulation
(Tue Feb 20 2007 - 20:02:56 PST)
AMBER: problem with AMBER8 installation
(Wed Feb 07 2007 - 09:50:48 PST)
Swarup Gupta
AMBER: AMBER ff in CHARMM format!!
(Tue Feb 20 2007 - 19:26:38 PST)
Syed Tarique Moin
RE: AMBER: Installing AMBER v9 in Linux
(Mon Feb 19 2007 - 02:13:35 PST)
RE: AMBER: Installing AMBER v9 in Linux
(Mon Feb 19 2007 - 00:25:13 PST)
RE: AMBER: Installing AMBER v9 in Linux
(Sun Feb 18 2007 - 23:26:33 PST)
RE: AMBER: Installing AMBER v9 in Linux
(Sun Feb 18 2007 - 21:51:55 PST)
AMBER: Installing AMBER v9 in Linux
(Sat Feb 17 2007 - 08:15:31 PST)
AMBER: Installing AMBER v9 in Linux
(Sat Feb 17 2007 - 08:12:28 PST)
Re: AMBER: mm_pbsa Array reference error
(Sat Feb 03 2007 - 21:51:27 PST)
Re: AMBER: mm_pbsa Array reference error
(Thu Feb 01 2007 - 20:43:50 PST)
Thomas Cheatham
Re: AMBER: How to modify the velocity of a water molecule?
(Thu Feb 15 2007 - 19:47:24 PST)
Re: AMBER: Modified nucleotides
(Mon Feb 12 2007 - 21:03:38 PST)
Thomas Cheatham III
Re: AMBER: Torsion Restraint on Glycosidic Bond
(Fri Feb 16 2007 - 13:32:30 PST)
Re: AMBER: Simulating a section of a molecule
(Thu Feb 15 2007 - 13:33:40 PST)
Re: AMBER: Ptraj: watershell and distance
(Thu Feb 01 2007 - 10:46:04 PST)
vanessa wai
Re: AMBER: MM-PBSA questions/clarifications
(Tue Feb 13 2007 - 02:36:27 PST)
WANG,YING
Re: AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain?
(Fri Feb 16 2007 - 21:55:53 PST)
AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain?
(Fri Feb 16 2007 - 12:57:40 PST)
Re: AMBER: Help!! I cannot perform the ambpdb
(Wed Feb 07 2007 - 13:23:16 PST)
RE: AMBER: Help!! I cannot perform the ambpdb
(Wed Feb 07 2007 - 12:19:29 PST)
Re: AMBER: Help!! I cannot perform the ambpdb
(Wed Feb 07 2007 - 11:49:46 PST)
AMBER: Help!! I cannot perform the ambpdb
(Wed Feb 07 2007 - 06:03:07 PST)
Re: AMBER: problem in xleap
(Tue Feb 06 2007 - 17:12:54 PST)
Re: AMBER: problem in xleap
(Tue Feb 06 2007 - 15:36:29 PST)
AMBER: problem in xleap
(Mon Feb 05 2007 - 07:45:14 PST)
Wei Chen
AMBER: momentum and periodic boundary condition
(Wed Feb 28 2007 - 17:59:49 PST)
Yong Duan
RE: AMBER: Sander slower on 16 processors than 8
(Thu Feb 22 2007 - 14:25:13 PST)
RE: AMBER: Sander slower on 16 processors than 8
(Thu Feb 22 2007 - 14:20:34 PST)
RE: AMBER: Sander slower on 16 processors than 8
(Thu Feb 22 2007 - 14:10:45 PST)
RE: AMBER: How precise is a MD simulation?
(Tue Feb 13 2007 - 11:45:48 PST)
RE: AMBER: force fields
(Tue Feb 06 2007 - 08:11:20 PST)
RE: AMBER: force fields
(Tue Feb 06 2007 - 08:13:58 PST)
RE: AMBER: force fields
(Mon Feb 05 2007 - 22:24:01 PST)
RE: AMBER: force fields
(Mon Feb 05 2007 - 09:15:10 PST)
RE: AMBER: equilibration in explicit solvent
(Sun Feb 04 2007 - 11:07:30 PST)
Z. Nevin Gerek
Re: AMBER: question about ADDLES module
(Fri Feb 16 2007 - 17:33:58 PST)
Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel)
(Wed Feb 07 2007 - 09:57:54 PST)
Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel)
(Wed Feb 07 2007 - 09:20:12 PST)
Last message date
:
Sun Mar 04 2007 - 06:07:28 PST
Archived on
: Fri Dec 20 2024 - 05:53:36 PST
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