Amber Archive Feb 2007 By Thread
- AMBER: format of .xyz files and pdb Gobind Singh Bisht (Wed Jan 31 2007 - 14:05:24 PST)
- AMBER: Still puzzled about this virial computation David Cerutti (Thu Feb 01 2007 - 00:00:10 PST)
- AMBER: xleap deepti nayar (Thu Feb 01 2007 - 00:04:09 PST)
- AMBER: subscribe amber Stéphane Téletchéa (Thu Feb 01 2007 - 07:11:25 PST)
- Re: AMBER: mm_pbsa Array reference error Scott Pendley (Thu Feb 01 2007 - 09:05:27 PST)
- Re: AMBER: Ptraj: watershell and distance Thomas Cheatham III (Thu Feb 01 2007 - 10:46:04 PST)
- AMBER: Example needed for addAtomType command Kara Di Giorgio (Thu Feb 01 2007 - 13:26:12 PST)
- AMBER: ab initio modeling using Amber snoze pa (Thu Feb 01 2007 - 18:59:17 PST)
- Re: AMBER: some questions about minimization and MD of DNA duplex with sander Chengwen Chen (Thu Feb 01 2007 - 21:40:11 PST)
- AMBER: Problem with paralell installation Martin Stennett (Fri Feb 02 2007 - 00:22:25 PST)
- AMBER: RESP Charges for Charged Carboxylate in Organic Ligand Akshay Patny (Fri Feb 02 2007 - 08:05:35 PST)
- AMBER: iRED and corrired Francois Theillet (Fri Feb 02 2007 - 09:07:47 PST)
- AMBER: calculating distance between two atoms bertrand russell (Fri Feb 02 2007 - 09:49:07 PST)
- AMBER: How do I make and enter new ff parameters into AMBER MARY O'CONNOR (Fri Feb 02 2007 - 11:35:20 PST)
- AMBER: How do I make and enter new ff parameters into AMBER HL Eastwood (Fri Feb 02 2007 - 13:26:46 PST)
- AMBER: angle command in Ptraj Esther Brugger (Fri Feb 02 2007 - 16:20:34 PST)
- AMBER: addions Amit Kumar (Sat Feb 03 2007 - 05:17:57 PST)
- AMBER: ptraj hbond jacopo.sgrignani.unifi.it (Sat Feb 03 2007 - 08:28:20 PST)
- AMBER: equilibration in explicit solvent Amarda Shehu (Sun Feb 04 2007 - 09:40:12 PST)
- AMBER: Calculate force constants Markus Weingarth (Sun Feb 04 2007 - 14:13:28 PST)
- AMBER: force fields deepti nayar (Sun Feb 04 2007 - 23:05:09 PST)
- AMBER: replacement of mutated atoms in protein structure bertrand russell (Mon Feb 05 2007 - 02:42:37 PST)
- AMBER: MAXGRP error message Alexander Steudle (Mon Feb 05 2007 - 06:03:45 PST)
- AMBER: problem in xleap WANG,YING (Mon Feb 05 2007 - 07:45:14 PST)
- AMBER: Force fields for iron MARY O'CONNOR (Mon Feb 05 2007 - 08:19:52 PST)
- AMBER: Tutorial for chemical shift calculation? Mike Summers (Mon Feb 05 2007 - 17:04:48 PST)
- AMBER: Link to Modified NA bases files Seth Lilavivat (Mon Feb 05 2007 - 14:22:50 PST)
- AMBER: Glycam Beale, John (Tue Feb 06 2007 - 05:07:22 PST)
- AMBER: MM-PBSA questions/clarifications Rima Chaudhuri (Tue Feb 06 2007 - 10:51:08 PST)
- AMBER: Compile Amber9 for MVAPICH Mike Hanby (Tue Feb 06 2007 - 11:51:18 PST)
- AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Nevin Gerek (Tue Feb 06 2007 - 15:08:08 PST)
- AMBER: Missing Value for MM ELE Rima Chaudhuri (Tue Feb 06 2007 - 15:26:08 PST)
- AMBER: side chain orientation Esther Brugger (Tue Feb 06 2007 - 15:36:48 PST)
- AMBER: trajectory problem Miguel Ferreira (Tue Feb 06 2007 - 20:52:25 PST)
- AMBER: antechamber for topology file deepti nayar (Wed Feb 07 2007 - 02:42:51 PST)
- AMBER: Help!! I cannot perform the ambpdb WANG,YING (Wed Feb 07 2007 - 06:03:07 PST)
- AMBER: Strange behavior on g95 compile. Martin Stennett (Wed Feb 07 2007 - 08:00:23 PST)
- AMBER: problem with AMBER8 installation Subhasish Chatterjee (Wed Feb 07 2007 - 09:50:48 PST)
- AMBER: Compiling Amber 8 on SuSE 10.2 Seth Lilavivat (Wed Feb 07 2007 - 11:50:12 PST)
- AMBER: Membrane Simulation: NPT issues Akshay Patny (Wed Feb 07 2007 - 10:29:36 PST)
- AMBER: Binding free energy calculation - MM-pbsa Rima Chaudhuri (Wed Feb 07 2007 - 12:55:26 PST)
- AMBER: Membrane Simulation: NPT Issues Akshay Patny (Wed Feb 07 2007 - 09:28:05 PST)
- AMBER: Missing values for MM ELE (MM-PBSA)..help!! Rima Chaudhuri (Wed Feb 07 2007 - 08:21:38 PST)
- AMBER: Compiling Amber 7 David J. Powers (Thu Feb 08 2007 - 07:13:00 PST)
- AMBER: H-Bond Esther Brugger (Thu Feb 08 2007 - 09:06:57 PST)
- AMBER: Protonation of Aspartate sai vikram (Thu Feb 08 2007 - 09:12:03 PST)
- AMBER: Calcium and peptides Beale, John (Thu Feb 08 2007 - 10:20:30 PST)
- AMBER: Compiling AMBER 8 on RHEL4 AMD64 Seth Lilavivat (Thu Feb 08 2007 - 11:53:44 PST)
- AMBER: Energy calculation by Anal Alexander Rubinstein (Thu Feb 08 2007 - 12:11:16 PST)
- AMBER: phe-phe prep file deepti nayar (Thu Feb 08 2007 - 22:09:15 PST)
- AMBER: assigning charges to a prepi file deepti nayar (Thu Feb 08 2007 - 22:38:27 PST)
- AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9) Chengwen Chen (Fri Feb 09 2007 - 00:25:00 PST)
- AMBER: Umbrella sampling Franck Vendeix (Fri Feb 09 2007 - 06:37:35 PST)
- AMBER: amber9 possible failure tgtmd jlalonde (Fri Feb 09 2007 - 08:19:19 PST)
- AMBER: problem with sander Seth Lilavivat (Fri Feb 09 2007 - 09:43:14 PST)
- AMBER: ptraj dipole calculation in QMMM simulation Evan Kelly (Fri Feb 09 2007 - 10:36:30 PST)
- AMBER: Heating the system prior to production run Ilyas Yildirim (Fri Feb 09 2007 - 13:28:08 PST)
- AMBER: Umbrella sampling - Tutorial bertrand russell (Fri Feb 09 2007 - 23:35:31 PST)
- AMBER: extracting coordinates from crd file gurpreet singh (Sat Feb 10 2007 - 00:40:44 PST)
- AMBER: extracting coordinate from crd file gurpreet singh (Sat Feb 10 2007 - 02:05:20 PST)
- AMBER: simulating part of a molecule with homology modeling Dave, Sonya (Sat Feb 10 2007 - 16:00:11 PST)
- Re: AMBER: simulating part of a molecule with homology modeling Fenghui Fan (Sat Feb 10 2007 - 20:26:41 PST)
- RE: AMBER: simulating part of a molecule with homology modeling Dave, Sonya (Mon Feb 12 2007 - 08:50:36 PST)
- AMBER: How precise is a MD simulation? Dave, Sonya (Mon Feb 12 2007 - 16:00:07 PST)
- Re: AMBER: How precise is a MD simulation? Fenghui Fan (Mon Feb 12 2007 - 17:47:09 PST)
- Re: AMBER: How precise is a MD simulation? David Mobley (Tue Feb 13 2007 - 11:36:17 PST)
- RE: AMBER: How precise is a MD simulation? Yong Duan (Tue Feb 13 2007 - 11:45:48 PST)
- Re: AMBER: How precise is a MD simulation? David Mobley (Tue Feb 13 2007 - 12:11:17 PST)
- RE: AMBER: How precise is a MD simulation? Dave, Sonya (Tue Feb 13 2007 - 12:01:23 PST)
- Re: AMBER: How precise is a MD simulation? David Mobley (Tue Feb 13 2007 - 12:19:13 PST)
- AMBER: Best Force field for protein, DNA, and organic compounds? Catein Catherine (Tue Feb 13 2007 - 20:13:31 PST)
- Re: AMBER: Best Force field for protein, DNA, and organic compounds? Carlos Simmerling (Wed Feb 14 2007 - 04:28:05 PST)
- RE: AMBER: Best Force field for protein, DNA, and organic compounds? Rafi Ahmad (Wed Feb 14 2007 - 05:35:28 PST)
- Re: AMBER: Best Force field for protein, DNA, and organic compounds? Carlos Simmerling (Wed Feb 14 2007 - 06:08:17 PST)
- Re: AMBER: How precise is a MD simulation? Which strcutures should be reported? Catein Catherine (Tue Feb 13 2007 - 20:28:09 PST)
- Re: AMBER: How precise is a MD simulation? Which strcutures should be reported? Carlos Simmerling (Wed Feb 14 2007 - 04:25:02 PST)
- RE: AMBER: How precise is a MD simulation? Dave, Sonya (Wed Feb 14 2007 - 10:35:16 PST)
- AMBER: quasiharnomic analysis Hans Lee (Sun Feb 11 2007 - 13:12:52 PST)
- Re: AMBER: extracting coordinate from crd file Bill Ross (Sun Feb 11 2007 - 21:13:38 PST)
- AMBER: connect atom deepti nayar (Mon Feb 12 2007 - 03:01:57 PST)
- AMBER: help me out... Anju Sharma (Mon Feb 12 2007 - 04:21:00 PST)
- AMBER: reporting EPtot and EKtot separately for two molecules Gabbar S. Daaku (Mon Feb 12 2007 - 08:15:09 PST)
- AMBER: Lone Pairs Beale, John (Mon Feb 12 2007 - 10:52:48 PST)
- AMBER: How to place torsion restraint Seth Lilavivat (Mon Feb 12 2007 - 17:24:40 PST)
- AMBER: Modified nucleotides mathew k varghese (Mon Feb 12 2007 - 20:44:31 PST)
- AMBER: hi Anju Sharma (Tue Feb 13 2007 - 02:08:01 PST)
- AMBER: Constraint virial David Cerutti (Tue Feb 13 2007 - 02:22:20 PST)
- AMBER: Box problems in vacuum minimization with sander.serial 8 j j (Tue Feb 13 2007 - 11:05:16 PST)
- AMBER: How to parameterize frcmod for NA Seth Lilavivat (Tue Feb 13 2007 - 11:27:59 PST)
- AMBER: Replica Exchange Christopher Gaughan (Tue Feb 13 2007 - 13:20:08 PST)
- AMBER: Positive binding free energy! Rima Chaudhuri (Tue Feb 13 2007 - 14:53:05 PST)
- AMBER: SANDER bug Ichinkhorloo Erdenebaatar (Tue Feb 13 2007 - 17:19:21 PST)
- AMBER: LeaP: Mol2 files A Box (Tue Feb 13 2007 - 17:44:08 PST)
- AMBER: Comparison of normal modes with ptraj? Harald Lanig (Wed Feb 14 2007 - 02:10:19 PST)
- AMBER: NMR violations increase in explicite water Michel Becker (Wed Feb 14 2007 - 12:15:14 PST)
- AMBER: Deriving constraint forces on water molecules based on SETTLE moves David Cerutti (Wed Feb 14 2007 - 16:08:45 PST)
- AMBER: Prepgen A Box (Wed Feb 14 2007 - 20:15:21 PST)
- AMBER: units in hessian matrix Marie Brut (Thu Feb 15 2007 - 08:52:01 PST)
- AMBER: Simulating a section of a molecule Dave, Sonya (Thu Feb 15 2007 - 08:59:53 PST)
- AMBER: implicit solvent free energy calcs David Mobley (Thu Feb 15 2007 - 10:07:37 PST)
- AMBER: read the data Esther Brugger (Thu Feb 15 2007 - 11:53:45 PST)
- AMBER: Density of a system in MD Akshay Patny (Thu Feb 15 2007 - 12:45:27 PST)
- AMBER: How to modify the velocity of a water molecule? Ji-Lai Li (Thu Feb 15 2007 - 18:15:45 PST)
- AMBER: Box dimensions Steve Seibold (Fri Feb 16 2007 - 07:13:45 PST)
- AMBER: H-bond ptraj dilemma Lorenzo Gontrani (Fri Feb 16 2007 - 07:46:54 PST)
- AMBER: Problem with dacdif when using cygwin Steven Winfield (Fri Feb 16 2007 - 10:33:38 PST)
- AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain? WANG,YING (Fri Feb 16 2007 - 12:57:40 PST)
- AMBER: Torsion Restraint on Glycosidic Bond Seth Lilavivat (Fri Feb 16 2007 - 13:13:52 PST)
- AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa Rima Chaudhuri (Fri Feb 16 2007 - 14:17:49 PST)
- AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Sat Feb 17 2007 - 08:12:28 PST)
- AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Sat Feb 17 2007 - 08:15:31 PST)
- AMBER: REMD error on first exchange Daniel Oehme (Sun Feb 18 2007 - 18:31:57 PST)
- AMBER: Water density calculation mathew k varghese (Sun Feb 18 2007 - 22:51:57 PST)
- AMBER: Residence time of WATER gurpreet singh (Mon Feb 19 2007 - 00:33:59 PST)
- AMBER: MDGRAPE and AMBER Craig Gough (Mon Feb 19 2007 - 00:34:43 PST)
- AMBER: crd to pdb conversion AYTUG TUNCEL (Mon Feb 19 2007 - 05:27:34 PST)
- AMBER: carbohydrate-peptide Beale, John (Mon Feb 19 2007 - 08:09:54 PST)
- AMBER: DNA and RNA computations Jiri Sponer (Mon Feb 19 2007 - 10:16:53 PST)
- AMBER: problems with bonding disulfide linkages Beale, John (Mon Feb 19 2007 - 12:39:10 PST)
- AMBER: Error in running replica exchange MD Seongeun Yang (Tue Feb 20 2007 - 03:45:38 PST)
- AMBER: Beale, John (Tue Feb 20 2007 - 05:02:24 PST)
- AMBER: oops Beale, John (Tue Feb 20 2007 - 05:35:19 PST)
- AMBER: RE: about ANTECHAMBER Ross Walker (Tue Feb 20 2007 - 08:22:21 PST)
- AMBER: AMBER ff in CHARMM format!! Swarup Gupta (Tue Feb 20 2007 - 19:26:38 PST)
- AMBER: Nanopore simulation subhasish chatterjee (Tue Feb 20 2007 - 20:02:56 PST)
- AMBER: Is this system too large? Hu, Shaowen \(JSC-SK\)[USRA] (Tue Feb 20 2007 - 20:17:41 PST)
- AMBER: LEaP Problem Beale, John (Wed Feb 21 2007 - 05:11:13 PST)
- AMBER: Amber/ANAL and psf files rebeca.mmb.pcb.ub.es (Wed Feb 21 2007 - 08:24:33 PST)
- AMBER: native contact analysis! r. a. (Wed Feb 21 2007 - 18:52:37 PST)
- AMBER: atom types deepti nayar (Wed Feb 21 2007 - 21:43:38 PST)
- AMBER: Errors in amber9 parallel installation Seongeun Yang (Thu Feb 22 2007 - 05:34:23 PST)
- AMBER: applying restraints Seth Lilavivat (Thu Feb 22 2007 - 08:40:59 PST)
- AMBER: Sander slower on 16 processors than 8 Sontum, Steve (Thu Feb 22 2007 - 12:32:42 PST)
- AMBER: ptraj bug? -- doesn't like restart files from REMD Nicolas Lux Fawzi (Thu Feb 22 2007 - 13:33:58 PST)
- AMBER: Problems with QMMM tests on Altix Jarrod Smith (Thu Feb 22 2007 - 14:03:14 PST)
- AMBER: units of mwcovar matrix befor conversion Chris Moth (Thu Feb 22 2007 - 15:01:57 PST)
- AMBER: [rsachdeva@imtech.res.in: Pls help - REMD with torsional restraints] David A. Case (Thu Feb 22 2007 - 18:03:47 PST)
- AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 Craig Gough (Fri Feb 23 2007 - 00:47:36 PST)
- AMBER: SCF convergence issues Steven Winfield (Fri Feb 23 2007 - 03:27:38 PST)
- AMBER: Error in running Replica Exchange MD with amber9 Seongeun Yang (Fri Feb 23 2007 - 06:15:48 PST)
- AMBER: MD temperature and MM_pbsa temperature Rima Chaudhuri (Fri Feb 23 2007 - 13:22:30 PST)
- AMBER: RESP calculation of modified nucleotides mathew k varghese (Fri Feb 23 2007 - 22:50:23 PST)
- AMBER: Best way to apply WC basepair restraints during MD Seth Lilavivat (Sun Feb 25 2007 - 12:24:40 PST)
- AMBER: problem with atom restraints Ed Pate (Sun Feb 25 2007 - 20:53:31 PST)
- AMBER: getting same box dimension bertrand russell (Sun Feb 25 2007 - 21:27:40 PST)
- AMBER: phe-phe molecule deepti nayar (Sun Feb 25 2007 - 22:01:26 PST)
- AMBER: Modified nucleotides-ATOM TYPES mathew k varghese (Mon Feb 26 2007 - 01:13:59 PST)
- AMBER: PTRAJ problem Beale, John (Mon Feb 26 2007 - 10:26:21 PST)
- AMBER: Re: REMD with torsional restraints- Temperature swapping not occuring David A. Case (Mon Feb 26 2007 - 15:01:41 PST)
- AMBER: IFVARI parameter Ed Pate (Tue Feb 27 2007 - 13:22:43 PST)
- AMBER: abnormal high temperature during NPT ensembles MD ebright HMS (Tue Feb 27 2007 - 15:13:29 PST)
- AMBER: AM1-bcc Evan Kelly (Tue Feb 27 2007 - 16:26:22 PST)
- AMBER: Disulfide Bonds Beale, John (Wed Feb 28 2007 - 04:56:55 PST)
- AMBER: LEaP crashes Beale, John (Wed Feb 28 2007 - 08:29:16 PST)
- AMBER: solvent accessible surface area (SASA) Esther Brugger (Wed Feb 28 2007 - 10:38:55 PST)
- AMBER: Difference in Equilibration & Production MD in Amber Akshay Patny (Wed Feb 28 2007 - 12:33:56 PST)
- AMBER: momentum and periodic boundary condition Wei Chen (Wed Feb 28 2007 - 17:59:49 PST)
- Last message date: Sun Mar 04 2007 - 06:07:28 PST
- Archived on: Sun Mar 14 2010 - 06:00:09 PDT
