Amber Archive Feb 2007: by subject

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

Amber Archive Feb 2007 by subject