AMBER Archive (2007) - Feb 2007 By ThreadMost recent messages
435 messages sorted by:
[ author ]
[ date ]
[ subject ]
About this archive
Starting: Thu Feb 01 2007 - 02:00:10 CST
Ending: Wed Feb 28 2007 - 19:59:49 CST
- AMBER: Still puzzled about this virial computation David Cerutti (Thu Feb 01 2007 - 02:00:10 CST)
- AMBER: xleap deepti nayar (Thu Feb 01 2007 - 02:04:09 CST)
- AMBER: subscribe amber Stéphane Téletchéa (Thu Feb 01 2007 - 09:11:25 CST)
- AMBER: Example needed for addAtomType command Kara Di Giorgio (Thu Feb 01 2007 - 15:26:12 CST)
- AMBER: ab initio modeling using Amber snoze pa (Thu Feb 01 2007 - 20:59:17 CST)
- AMBER: Problem with paralell installation Martin Stennett (Fri Feb 02 2007 - 02:22:25 CST)
- AMBER: RESP Charges for Charged Carboxylate in Organic Ligand Akshay Patny (Fri Feb 02 2007 - 10:05:35 CST)
- AMBER: iRED and corrired Francois Theillet (Fri Feb 02 2007 - 11:07:47 CST)
- AMBER: calculating distance between two atoms bertrand russell (Fri Feb 02 2007 - 11:49:07 CST)
- AMBER: How do I make and enter new ff parameters into AMBER MARY O'CONNOR (Fri Feb 02 2007 - 13:35:20 CST)
- AMBER: How do I make and enter new ff parameters into AMBER HL Eastwood (Fri Feb 02 2007 - 15:26:46 CST)
- AMBER: angle command in Ptraj Esther Brugger (Fri Feb 02 2007 - 18:20:34 CST)
- AMBER: addions Amit Kumar (Sat Feb 03 2007 - 07:17:57 CST)
- AMBER: ptraj hbond jacopo.sgrignani_at_unifi.it (Sat Feb 03 2007 - 10:28:20 CST)
- AMBER: equilibration in explicit solvent Amarda Shehu (Sun Feb 04 2007 - 11:40:12 CST)
- AMBER: Calculate force constants Markus Weingarth (Sun Feb 04 2007 - 16:13:28 CST)
- AMBER: force fields deepti nayar (Mon Feb 05 2007 - 01:05:09 CST)
- AMBER: replacement of mutated atoms in protein structure bertrand russell (Mon Feb 05 2007 - 04:42:37 CST)
- AMBER: MAXGRP error message Alexander Steudle (Mon Feb 05 2007 - 08:03:45 CST)
- AMBER: problem in xleap WANG,YING (Mon Feb 05 2007 - 09:45:14 CST)
- AMBER: Force fields for iron MARY O'CONNOR (Mon Feb 05 2007 - 10:19:52 CST)
- AMBER: Tutorial for chemical shift calculation? Mike Summers (Mon Feb 05 2007 - 19:04:48 CST)
- AMBER: Link to Modified NA bases files Seth Lilavivat (Mon Feb 05 2007 - 16:22:50 CST)
- AMBER: Glycam Beale, John (Tue Feb 06 2007 - 07:07:22 CST)
- AMBER: MM-PBSA questions/clarifications Rima Chaudhuri (Tue Feb 06 2007 - 12:51:08 CST)
- AMBER: Compile Amber9 for MVAPICH Mike Hanby (Tue Feb 06 2007 - 13:51:18 CST)
- AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Nevin Gerek (Tue Feb 06 2007 - 17:08:08 CST)
- AMBER: Missing Value for MM ELE Rima Chaudhuri (Tue Feb 06 2007 - 17:26:08 CST)
- AMBER: side chain orientation Esther Brugger (Tue Feb 06 2007 - 17:36:48 CST)
- AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Nevin Gerek (Tue Feb 06 2007 - 17:08:08 CST)
- AMBER: trajectory problem Miguel Ferreira (Tue Feb 06 2007 - 22:52:25 CST)
- AMBER: antechamber for topology file deepti nayar (Wed Feb 07 2007 - 04:42:51 CST)
- AMBER: Help!! I cannot perform the ambpdb WANG,YING (Wed Feb 07 2007 - 08:03:07 CST)
- AMBER: Strange behavior on g95 compile. Martin Stennett (Wed Feb 07 2007 - 10:00:23 CST)
- AMBER: problem with AMBER8 installation Subhasish Chatterjee (Wed Feb 07 2007 - 11:50:48 CST)
- AMBER: Compiling Amber 8 on SuSE 10.2 Seth Lilavivat (Wed Feb 07 2007 - 13:50:12 CST)
- AMBER: Membrane Simulation: NPT issues Akshay Patny (Wed Feb 07 2007 - 12:29:36 CST)
- AMBER: Binding free energy calculation - MM-pbsa Rima Chaudhuri (Wed Feb 07 2007 - 14:55:26 CST)
- AMBER: Membrane Simulation: NPT Issues Akshay Patny (Wed Feb 07 2007 - 11:28:05 CST)
- AMBER: Compiling Amber 8 on SuSE 10.2 Seth Lilavivat (Wed Feb 07 2007 - 13:50:12 CST)
- AMBER: Missing values for MM ELE (MM-PBSA)..help!! Rima Chaudhuri (Wed Feb 07 2007 - 10:21:38 CST)
- AMBER: Compiling Amber 7 David J. Powers (Thu Feb 08 2007 - 09:13:00 CST)
- AMBER: H-Bond Esther Brugger (Thu Feb 08 2007 - 11:06:57 CST)
- AMBER: Protonation of Aspartate sai vikram (Thu Feb 08 2007 - 11:12:03 CST)
- AMBER: Calcium and peptides Beale, John (Thu Feb 08 2007 - 12:20:30 CST)
- AMBER: Compiling AMBER 8 on RHEL4 AMD64 Seth Lilavivat (Thu Feb 08 2007 - 13:53:44 CST)
- AMBER: Energy calculation by Anal Alexander Rubinstein (Thu Feb 08 2007 - 14:11:16 CST)
- AMBER: Energy calculation by Anal Alexander Rubinstein (Thu Feb 08 2007 - 14:11:16 CST)
- AMBER: phe-phe prep file deepti nayar (Fri Feb 09 2007 - 00:09:15 CST)
- AMBER: assigning charges to a prepi file deepti nayar (Fri Feb 09 2007 - 00:38:27 CST)
- AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9) Chengwen Chen (Fri Feb 09 2007 - 02:25:00 CST)
- AMBER: Umbrella sampling Franck Vendeix (Fri Feb 09 2007 - 08:37:35 CST)
- AMBER: amber9 possible failure tgtmd jlalonde (Fri Feb 09 2007 - 10:19:19 CST)
- AMBER: problem with sander Seth Lilavivat (Fri Feb 09 2007 - 11:43:14 CST)
- AMBER: ptraj dipole calculation in QMMM simulation Evan Kelly (Fri Feb 09 2007 - 12:36:30 CST)
- AMBER: Heating the system prior to production run Ilyas Yildirim (Fri Feb 09 2007 - 15:28:08 CST)
- AMBER: Umbrella sampling - Tutorial bertrand russell (Sat Feb 10 2007 - 01:35:31 CST)
- AMBER: extracting coordinates from crd file gurpreet singh (Sat Feb 10 2007 - 02:40:44 CST)
- AMBER: extracting coordinate from crd file gurpreet singh (Sat Feb 10 2007 - 04:05:20 CST)
- AMBER: simulating part of a molecule with homology modeling Dave, Sonya (Sat Feb 10 2007 - 18:00:11 CST)
- Re: AMBER: simulating part of a molecule with homology modeling Fenghui Fan (Sat Feb 10 2007 - 22:26:41 CST)
- RE: AMBER: simulating part of a molecule with homology modeling Dave, Sonya (Mon Feb 12 2007 - 10:50:36 CST)
- AMBER: How precise is a MD simulation? Dave, Sonya (Mon Feb 12 2007 - 18:00:07 CST)
- Re: AMBER: How precise is a MD simulation? Fenghui Fan (Mon Feb 12 2007 - 19:47:09 CST)
- Re: AMBER: How precise is a MD simulation? David Mobley (Tue Feb 13 2007 - 13:36:17 CST)
- RE: AMBER: How precise is a MD simulation? Yong Duan (Tue Feb 13 2007 - 13:45:48 CST)
- Re: AMBER: How precise is a MD simulation? David Mobley (Tue Feb 13 2007 - 14:11:17 CST)
- RE: AMBER: How precise is a MD simulation? Dave, Sonya (Tue Feb 13 2007 - 14:01:23 CST)
- Re: AMBER: How precise is a MD simulation? David Mobley (Tue Feb 13 2007 - 14:19:13 CST)
- AMBER: Best Force field for protein, DNA, and organic compounds? Catein Catherine (Tue Feb 13 2007 - 22:13:31 CST)
- Re: AMBER: Best Force field for protein, DNA, and organic compounds? Carlos Simmerling (Wed Feb 14 2007 - 06:28:05 CST)
- RE: AMBER: Best Force field for protein, DNA, and organic compounds? Rafi Ahmad (Wed Feb 14 2007 - 07:35:28 CST)
- Re: AMBER: Best Force field for protein, DNA, and organic compounds? Carlos Simmerling (Wed Feb 14 2007 - 08:08:17 CST)
- Re: AMBER: How precise is a MD simulation? Which strcutures should be reported? Catein Catherine (Tue Feb 13 2007 - 22:28:09 CST)
- Re: AMBER: How precise is a MD simulation? Which strcutures should be reported? Carlos Simmerling (Wed Feb 14 2007 - 06:25:02 CST)
- RE: AMBER: How precise is a MD simulation? Dave, Sonya (Wed Feb 14 2007 - 12:35:16 CST)
- AMBER: quasiharnomic analysis Hans Lee (Sun Feb 11 2007 - 15:12:52 CST)
- Re: AMBER: extracting coordinate from crd file Bill Ross (Sun Feb 11 2007 - 23:13:38 CST)
- AMBER: connect atom deepti nayar (Mon Feb 12 2007 - 05:01:57 CST)
- AMBER: help me out... Anju Sharma (Mon Feb 12 2007 - 06:21:00 CST)
- AMBER: reporting EPtot and EKtot separately for two molecules Gabbar S. Daaku (Mon Feb 12 2007 - 10:15:09 CST)
- AMBER: Lone Pairs Beale, John (Mon Feb 12 2007 - 12:52:48 CST)
- AMBER: How to place torsion restraint Seth Lilavivat (Mon Feb 12 2007 - 19:24:40 CST)
- AMBER: Modified nucleotides mathew k varghese (Mon Feb 12 2007 - 22:44:31 CST)
- AMBER: hi Anju Sharma (Tue Feb 13 2007 - 04:08:01 CST)
- AMBER: Constraint virial David Cerutti (Tue Feb 13 2007 - 04:22:20 CST)
- AMBER: Box problems in vacuum minimization with sander.serial 8 j j (Tue Feb 13 2007 - 13:05:16 CST)
- AMBER: How to parameterize frcmod for NA Seth Lilavivat (Tue Feb 13 2007 - 13:27:59 CST)
- AMBER: Replica Exchange Christopher Gaughan (Tue Feb 13 2007 - 15:20:08 CST)
- AMBER: Positive binding free energy! Rima Chaudhuri (Tue Feb 13 2007 - 16:53:05 CST)
- AMBER: SANDER bug Ichinkhorloo Erdenebaatar (Tue Feb 13 2007 - 19:19:21 CST)
- AMBER: LeaP: Mol2 files A Box (Tue Feb 13 2007 - 19:44:08 CST)
- AMBER: Comparison of normal modes with ptraj? Harald Lanig (Wed Feb 14 2007 - 04:10:19 CST)
- AMBER: NMR violations increase in explicite water Michel Becker (Wed Feb 14 2007 - 14:15:14 CST)
- AMBER: Deriving constraint forces on water molecules based on SETTLE moves David Cerutti (Wed Feb 14 2007 - 18:08:45 CST)
- AMBER: Prepgen A Box (Wed Feb 14 2007 - 22:15:21 CST)
- AMBER: units in hessian matrix Marie Brut (Thu Feb 15 2007 - 10:52:01 CST)
- AMBER: Simulating a section of a molecule Dave, Sonya (Thu Feb 15 2007 - 10:59:53 CST)
- AMBER: implicit solvent free energy calcs David Mobley (Thu Feb 15 2007 - 12:07:37 CST)
- AMBER: read the data Esther Brugger (Thu Feb 15 2007 - 13:53:45 CST)
- AMBER: Density of a system in MD Akshay Patny (Thu Feb 15 2007 - 14:45:27 CST)
- AMBER: How to modify the velocity of a water molecule? Ji-Lai Li (Thu Feb 15 2007 - 20:15:45 CST)
- AMBER: Box dimensions Steve Seibold (Fri Feb 16 2007 - 09:13:45 CST)
- AMBER: H-bond ptraj dilemma Lorenzo Gontrani (Fri Feb 16 2007 - 09:46:54 CST)
- AMBER: Problem with dacdif when using cygwin Steven Winfield (Fri Feb 16 2007 - 12:33:38 CST)
- AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain? WANG,YING (Fri Feb 16 2007 - 14:57:40 CST)
- AMBER: Torsion Restraint on Glycosidic Bond Seth Lilavivat (Fri Feb 16 2007 - 15:13:52 CST)
- AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa Rima Chaudhuri (Fri Feb 16 2007 - 16:17:49 CST)
- AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Sat Feb 17 2007 - 10:12:28 CST)
- AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Sat Feb 17 2007 - 10:15:31 CST)
- AMBER: REMD error on first exchange Daniel Oehme (Sun Feb 18 2007 - 20:31:57 CST)
- AMBER: Water density calculation mathew k varghese (Mon Feb 19 2007 - 00:51:57 CST)
- AMBER: Residence time of WATER gurpreet singh (Mon Feb 19 2007 - 02:33:59 CST)
- AMBER: MDGRAPE and AMBER Craig Gough (Mon Feb 19 2007 - 02:34:43 CST)
- AMBER: crd to pdb conversion AYTUG TUNCEL (Mon Feb 19 2007 - 07:27:34 CST)
- AMBER: carbohydrate-peptide Beale, John (Mon Feb 19 2007 - 10:09:54 CST)
- AMBER: DNA and RNA computations Jiri Sponer (Mon Feb 19 2007 - 12:16:53 CST)
- AMBER: problems with bonding disulfide linkages Beale, John (Mon Feb 19 2007 - 14:39:10 CST)
- AMBER: Error in running replica exchange MD Seongeun Yang (Tue Feb 20 2007 - 05:45:38 CST)
- AMBER: Beale, John (Tue Feb 20 2007 - 07:02:24 CST)
- AMBER: oops Beale, John (Tue Feb 20 2007 - 07:35:19 CST)
- AMBER: RE: about ANTECHAMBER Ross Walker (Tue Feb 20 2007 - 10:22:21 CST)
- AMBER: AMBER ff in CHARMM format!! Swarup Gupta (Tue Feb 20 2007 - 21:26:38 CST)
- AMBER: Nanopore simulation subhasish chatterjee (Tue Feb 20 2007 - 22:02:56 CST)
- AMBER: Is this system too large? Hu, Shaowen \(JSC-SK\)[USRA] (Tue Feb 20 2007 - 22:17:41 CST)
- AMBER: LEaP Problem Beale, John (Wed Feb 21 2007 - 07:11:13 CST)
- AMBER: native contact analysis! r. a. (Wed Feb 21 2007 - 20:52:37 CST)
- AMBER: atom types deepti nayar (Wed Feb 21 2007 - 23:43:38 CST)
- AMBER: Errors in amber9 parallel installation Seongeun Yang (Thu Feb 22 2007 - 07:34:23 CST)
- AMBER: applying restraints Seth Lilavivat (Thu Feb 22 2007 - 10:40:59 CST)
- AMBER: Sander slower on 16 processors than 8 Sontum, Steve (Thu Feb 22 2007 - 14:32:42 CST)
- AMBER: ptraj bug? -- doesn't like restart files from REMD Nicolas Lux Fawzi (Thu Feb 22 2007 - 15:33:58 CST)
- AMBER: Problems with QMMM tests on Altix Jarrod Smith (Thu Feb 22 2007 - 16:03:14 CST)
- AMBER: units of mwcovar matrix befor conversion Chris Moth (Thu Feb 22 2007 - 17:01:57 CST)
- AMBER: [rsachdeva@imtech.res.in: Pls help - REMD with torsional restraints] David A. Case (Thu Feb 22 2007 - 20:03:47 CST)
- AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 Craig Gough (Fri Feb 23 2007 - 02:47:36 CST)
- AMBER: SCF convergence issues Steven Winfield (Fri Feb 23 2007 - 05:27:38 CST)
- AMBER: Error in running Replica Exchange MD with amber9 Seongeun Yang (Fri Feb 23 2007 - 08:15:48 CST)
- AMBER: MD temperature and MM_pbsa temperature Rima Chaudhuri (Fri Feb 23 2007 - 15:22:30 CST)
- AMBER: RESP calculation of modified nucleotides mathew k varghese (Sat Feb 24 2007 - 00:50:23 CST)
- AMBER: Best way to apply WC basepair restraints during MD Seth Lilavivat (Sun Feb 25 2007 - 14:24:40 CST)
- AMBER: problem with atom restraints Ed Pate (Sun Feb 25 2007 - 22:53:31 CST)
- AMBER: getting same box dimension bertrand russell (Sun Feb 25 2007 - 23:27:40 CST)
- AMBER: phe-phe molecule deepti nayar (Mon Feb 26 2007 - 00:01:26 CST)
- AMBER: Modified nucleotides-ATOM TYPES mathew k varghese (Mon Feb 26 2007 - 03:13:59 CST)
- AMBER: PTRAJ problem Beale, John (Mon Feb 26 2007 - 12:26:21 CST)
- AMBER: Re: REMD with torsional restraints- Temperature swapping not occuring David A. Case (Mon Feb 26 2007 - 17:01:41 CST)
- AMBER: IFVARI parameter Ed Pate (Tue Feb 27 2007 - 15:22:43 CST)
- AMBER: abnormal high temperature during NPT ensembles MD ebright HMS (Tue Feb 27 2007 - 17:13:29 CST)
- AMBER: AM1-bcc Evan Kelly (Tue Feb 27 2007 - 18:26:22 CST)
- AMBER: Disulfide Bonds Beale, John (Wed Feb 28 2007 - 06:56:55 CST)
- AMBER: LEaP crashes Beale, John (Wed Feb 28 2007 - 10:29:16 CST)
- AMBER: solvent accessible surface area (SASA) Esther Brugger (Wed Feb 28 2007 - 12:38:55 CST)
- AMBER: Difference in Equilibration & Production MD in Amber Akshay Patny (Wed Feb 28 2007 - 14:33:56 CST)
- AMBER: momentum and periodic boundary condition Wei Chen (Wed Feb 28 2007 - 19:59:49 CST)
Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:08 CST
435 messages sorted by:
[ author ]
[ date ]
[ subject ]
About this archive
|