Amber Archive Feb 2007: by date

Wednesday, 31 January 2007
- AMBER: format of .xyz files and pdb Gobind Singh Bisht
Thursday, 1 February 2007
- AMBER: Still puzzled about this virial computation David Cerutti
- AMBER: xleap deepti nayar
- AMBER: subscribe amber Stéphane Téletchéa
- Re: AMBER: Still puzzled about this virial computation Robert Duke
- RE: AMBER: xleap Ross Walker
- Re: AMBER: Still puzzled about this virial computation Robert Duke
- Re: AMBER: xleap David A. Case
- Re: AMBER: mm_pbsa Array reference error Scott Pendley
- AMBER: workaround for ibm xlf90 powerpc FORTRAN compiler: -q64 and -O3 yield Run.dhfr.min failure Chris Moth
- Re: AMBER: Ptraj: watershell and distance Thomas Cheatham III
- AMBER: Example needed for addAtomType command Kara Di Giorgio
- Re: AMBER: Example needed for addAtomType command David A. Case
- Re: AMBER: Example needed for addAtomType command Kara Di Giorgio
- AMBER: ab initio modeling using Amber snoze pa
- Re: AMBER: ab initio modeling using Amber Gustavo Seabra
- Re: AMBER: mm_pbsa Array reference error Syed Tarique Moin
- Re: AMBER: some questions about minimization and MD of DNA duplex with sander Chengwen Chen
Friday, 2 February 2007
- AMBER: Problem with paralell installation Martin Stennett
- RE: AMBER: Problem with paralell installation Ross Walker
- AMBER: RESP Charges for Charged Carboxylate in Organic Ligand Akshay Patny
- AMBER: iRED and corrired Francois Theillet
- Re: AMBER: mm_pbsa Array reference error Scott Pendley
- RE: AMBER: some questions about minimization and MD of DNA duplex with sander Ross Walker
- Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand HL Eastwood
- Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand HL Eastwood
- AMBER: calculating distance between two atoms bertrand russell
- Re: AMBER: iRED and corrired David A. Case
- AMBER: How do I make and enter new ff parameters into AMBER MARY O'CONNOR
- Re: AMBER: iRED and corrired Francois Theillet
- AMBER: How do I make and enter new ff parameters into AMBER HL Eastwood
- Re: AMBER: calculating distance between two atoms Carlos Simmerling
- AMBER: angle command in Ptraj Esther Brugger
- Re: AMBER: angle command in Ptraj Esther Brugger
Saturday, 3 February 2007
- Re: AMBER: angle command in Ptraj Carlos Simmerling
- AMBER: addions Amit Kumar
- AMBER: ptraj hbond jacopo.sgrignani.unifi.it
- Re: AMBER: mm_pbsa Array reference error Syed Tarique Moin
Sunday, 4 February 2007
- Re: AMBER: iRED and corrired Gohlke.bioinformatik.uni-frankfurt.de
- Re: AMBER: addions David A. Case
- AMBER: equilibration in explicit solvent Amarda Shehu
- Re: AMBER: equilibration in explicit solvent David A. Case
- Re: AMBER: equilibration in explicit solvent Amarda Shehu
- RE: AMBER: equilibration in explicit solvent Yong Duan
- AMBER: Calculate force constants Markus Weingarth
- Re: AMBER: equilibration in explicit solvent Ilyas Yildirim
- Re: AMBER: equilibration in explicit solvent David A. Case
- AMBER: force fields deepti nayar
Monday, 5 February 2007
- AMBER: replacement of mutated atoms in protein structure bertrand russell
- Re: AMBER: calculating distance between two atoms bertrand russell
- Re: AMBER: force fields Carlos Simmerling
- Re: AMBER: calculating distance between two atoms Carlos Simmerling
- AMBER: MAXGRP error message Alexander Steudle
- AMBER: problem in xleap WANG,YING
- Re: AMBER: problem in xleap Steven Winfield
- Re: AMBER: iRED and corrired Holger Gohlke
- AMBER: Force fields for iron MARY O'CONNOR
- RE: AMBER: force fields Yong Duan
- AMBER: positive binding energy saurabh agrawal
- Re: AMBER: equilibration in explicit solvent Carlos Simmerling
- AMBER: Tutorial for chemical shift calculation? Mike Summers
- AMBER: Link to Modified NA bases files Seth Lilavivat
- Re: AMBER: Link to Modified NA bases files Ilyas Yildirim
- Re: AMBER: force fields deepti nayar
- Re: AMBER: some questions about minimization and MD of DNA duplex with sander Chengwen Chen
- RE: AMBER: force fields Yong Duan
Tuesday, 6 February 2007
- Re: AMBER: force fields deepti nayar
- Re: AMBER: force fields deepti nayar
- Re: AMBER: force fields Carlos Simmerling
- AMBER: Glycam Beale, John
- Re: AMBER: Glycam David A. Case
- Re: AMBER: Tutorial for chemical shift calculation? David A. Case
- RE: AMBER: force fields Yong Duan
- Re: AMBER: Tutorial for chemical shift calculation? Mike Summers
- AMBER: MM-PBSA questions/clarifications Rima Chaudhuri
- Re: AMBER: Glycam kkirschn.hamilton.edu
- AMBER: Compile Amber9 for MVAPICH Mike Hanby
- Re: AMBER: Compile Amber9 for MVAPICH David A. Case
- AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Nevin Gerek
- AMBER: Missing Value for MM ELE Rima Chaudhuri
- AMBER: side chain orientation Esther Brugger
- Re: AMBER: problem in xleap WANG,YING
- Re: AMBER: problem in xleap Carlos Simmerling
- Re: AMBER: side chain orientation Fenghui Fan
- Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) David A. Case
- Re: AMBER: problem in xleap WANG,YING
- Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Mike Summers
- RE: AMBER: force fields Yong Duan
- AMBER: trajectory problem Miguel Ferreira
Wednesday, 7 February 2007
- AMBER: antechamber for topology file deepti nayar
- Re: AMBER: antechamber for topology file Carlos Simmerling
- Re: AMBER: antechamber for topology file FyD
- AMBER: Help!! I cannot perform the ambpdb WANG,YING
- Re: AMBER: side chain orientation Esther Brugger
- AMBER: Strange behavior on g95 compile. Martin Stennett
- Re: AMBER: Help!! I cannot perform the ambpdb Mark Williamson
- Re: AMBER: Strange behavior on g95 compile. Mark Williamson
- RE: AMBER: Strange behavior on g95 compile. Ross Walker
- Re: AMBER: Strange behavior on g95 compile. Seth Hayik
- Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Z. Nevin Gerek
- Re: AMBER: MAXGRP error message David A. Case
- Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Mark Williamson
- AMBER: problem with AMBER8 installation Subhasish Chatterjee
- Re: AMBER: trajectory problem David A. Case
- Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Z. Nevin Gerek
- Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Scott Brozell
- Re: AMBER: side chain orientation Ilyas Yildirim
- RE: AMBER: problem with AMBER8 installation Ross Walker
- Re: AMBER: problem with AMBER8 installation David A. Case
- RE: AMBER: Help!! I cannot perform the ambpdb Ross Walker
- Re: AMBER: Help!! I cannot perform the ambpdb WANG,YING
- AMBER: Compiling Amber 8 on SuSE 10.2 Seth Lilavivat
- Re: AMBER: Compiling Amber 8 on SuSE 10.2 Cenk Andac
- RE: AMBER: Help!! I cannot perform the ambpdb WANG,YING
- Re: AMBER: Help!! I cannot perform the ambpdb Mark Williamson
- AMBER: Membrane Simulation: NPT issues Akshay Patny
- AMBER: Binding free energy calculation - MM-pbsa Rima Chaudhuri
- AMBER: Membrane Simulation: NPT Issues Akshay Patny
- Re: AMBER: Help!! I cannot perform the ambpdb WANG,YING
- Re: AMBER: Compiling Amber 8 on SuSE 10.2 Seth Lilavivat
- AMBER: Missing values for MM ELE (MM-PBSA)..help!! Rima Chaudhuri
- Re: AMBER: antechamber for topology file deepti nayar
- RE: AMBER: antechamber for topology file Akshay Patny
- Re: AMBER: antechamber for topology file deepti nayar
- Re: AMBER: antechamber for topology file David A. Case
Thursday, 8 February 2007
- Re: AMBER: antechamber for topology file FyD
- AMBER: Compiling Amber 7 David J. Powers
- RE: AMBER: Compiling Amber 7 Ross Walker
- AMBER: H-Bond Esther Brugger
- AMBER: Protonation of Aspartate sai vikram
- Re: AMBER: Protonation of Aspartate Adrian Roitberg
- Re: AMBER: equilibration in explicit solvent Amarda Shehu
- AMBER: Calcium and peptides Beale, John
- RE: AMBER: Compiling Amber 7 David J. Powers
- Re: AMBER: equilibration in explicit solvent Amarda Shehu
- AMBER: Compiling AMBER 8 on RHEL4 AMD64 Seth Lilavivat
- Re: AMBER: equilibration in explicit solvent Ilyas Yildirim
- AMBER: Energy calculation by Anal Alexander Rubinstein
- AMBER: phe-phe prep file deepti nayar
- Re: AMBER: Compiling AMBER 8 on RHEL4 AMD64 David A. Case
- AMBER: assigning charges to a prepi file deepti nayar
- Re: AMBER: assigning charges to a prepi file David A. Case
Friday, 9 February 2007
- AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9) Chengwen Chen
- AMBER: Umbrella sampling Franck Vendeix
- AMBER: amber9 possible failure tgtmd jlalonde
- AMBER: problem with sander Seth Lilavivat
Saturday, 10 February 2007
- Re: AMBER: problem with sander David A. Case
Friday, 9 February 2007
- AMBER: ptraj dipole calculation in QMMM simulation Evan Kelly
- RE: AMBER: ptraj dipole calculation in QMMM simulation Ross Walker
- Re: AMBER: ptraj dipole calculation in QMMM simulation Gustavo Seabra
- Re: AMBER: problem with sander Seth Lilavivat
- AMBER: Heating the system prior to production run Ilyas Yildirim
- AMBER: Umbrella sampling - Tutorial bertrand russell
Saturday, 10 February 2007
- AMBER: extracting coordinates from crd file gurpreet singh
- Re: AMBER: extracting coordinates from crd file Ilyas Yildirim
- AMBER: extracting coordinate from crd file gurpreet singh
- Re: AMBER: extracting coordinate from crd file Amit Kumar
- RE: AMBER: Compiling Amber 7 David J. Powers
- Re: AMBER: extracting coordinate from crd file David A. Case
- RE: AMBER: Compiling Amber 7 Ross Walker
- AMBER: simulating part of a molecule with homology modeling Dave, Sonya
- Re: AMBER: simulating part of a molecule with homology modeling Fenghui Fan
- Re: AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9) David A. Case
Sunday, 11 February 2007
- AMBER: quasiharnomic analysis Hans Lee
- Re: AMBER: extracting coordinate from crd file Bill Ross
- AMBER: atomicfluct Catein Catherine
Monday, 12 February 2007
- RE: AMBER: atomicfluct Rafi Ahmad
- AMBER: connect atom deepti nayar
- AMBER: help me out... Anju Sharma
- AMBER: Fwd: help me out... Anju Sharma
- Re: AMBER: Fwd: help me out... Chris Moth
- RE: AMBER: help me out... Ross Walker
- AMBER: reporting EPtot and EKtot separately for two molecules Gabbar S. Daaku
- AMBER: Re: reporting EPtot and EKtot separately for two molecules Gabbar S. Daaku
- Re: AMBER: reporting EPtot and EKtot separately for two molecules David A. Case
- Re: AMBER: connect atom David A. Case
- Re: AMBER: quasiharnomic analysis David A. Case
- RE: AMBER: simulating part of a molecule with homology modeling Dave, Sonya
- AMBER: Lone Pairs Beale, John
- Re: AMBER: Lone Pairs David A. Case
- AMBER: How precise is a MD simulation? Dave, Sonya
- AMBER: How to place torsion restraint Seth Lilavivat
- Re: AMBER: How precise is a MD simulation? Fenghui Fan
- AMBER: Modified nucleotides mathew k varghese
- Re: AMBER: Modified nucleotides Ilyas Yildirim
- RE: AMBER: Modified nucleotides Seth Lilavivat
- Re: AMBER: Modified nucleotides Thomas Cheatham
- Re: AMBER: amber9 possible failure tgtmd David A. Case
- Re: AMBER: Modified nucleotides Sean Rathlef
Tuesday, 13 February 2007
- AMBER: hi Anju Sharma
- Re: AMBER: MM-PBSA questions/clarifications vanessa wai
- Re: AMBER: hi Steven Winfield
- AMBER: Constraint virial David Cerutti
- AMBER: Solvate box Sophie Barbe
- RE: AMBER: Lone Pairs Beale, John
- Re: AMBER: Lone Pairs David A. Case
- RE: AMBER: hi Ross Walker
- RE: AMBER: Solvate box Ross Walker
- Re: AMBER: How to place torsion restraint Gustavo Seabra
- Re: AMBER: Modified nucleotides Raviprasad Aduri
- AMBER: Box problems in vacuum minimization with sander.serial 8 j j
- AMBER: How to parameterize frcmod for NA Seth Lilavivat
- Re: AMBER: Box problems in vacuum minimization with sander.serial 8 David A. Case
- Re: AMBER: How precise is a MD simulation? David Mobley
- Re: AMBER: Box problems in vacuum minimization with sander.serial 8 j j
- RE: AMBER: How precise is a MD simulation? Yong Duan
- RE: AMBER: How precise is a MD simulation? Dave, Sonya
- Re: AMBER: How precise is a MD simulation? David Mobley
- Re: AMBER: How precise is a MD simulation? David Mobley
- AMBER: Replica Exchange Christopher Gaughan
- AMBER: Positive binding free energy! Rima Chaudhuri
- Re: AMBER: Positive binding free energy! David Cerutti
- AMBER: SANDER bug Ichinkhorloo Erdenebaatar
- AMBER: LeaP: Mol2 files A Box
- RE: AMBER: atomicfluct Catein Catherine
- Re: AMBER: Solvate box M. L. Dodson
- Re: AMBER: Modified nucleotides mathew k varghese
- Re: AMBER: Modified nucleotides Ilyas Yildirim
- AMBER: Best Force field for protein, DNA, and organic compounds? Catein Catherine
- AMBER: Help: 1 ns for implicit solvent (GB) calculations, enough? Catein Catherine
- Re: AMBER: How precise is a MD simulation? Which strcutures should be reported? Catein Catherine
- Re: AMBER: hi Anju Sharma
- Re: AMBER: hi Anju Sharma
Wednesday, 14 February 2007
- AMBER: Comparison of normal modes with ptraj? Harald Lanig
- Re: AMBER: How precise is a MD simulation? Which strcutures should be reported? Carlos Simmerling
- Re: AMBER: Help: 1 ns for implicit solvent (GB) calculations, enough? Carlos Simmerling
- Re: AMBER: Modified nucleotides FyD
- Re: AMBER: Best Force field for protein, DNA, and organic compounds? Carlos Simmerling
- Re: AMBER: Comparison of normal modes with ptraj? Gohlke.bioinformatik.uni-frankfurt.de
- RE: AMBER: Best Force field for protein, DNA, and organic compounds? Rafi Ahmad
- Re: AMBER: Best Force field for protein, DNA, and organic compounds? Carlos Simmerling
- RE: AMBER: hi Ross Walker
- Re: AMBER: LeaP: Mol2 files FyD
- Re: AMBER: SANDER bug David A. Case
- RE: AMBER: How precise is a MD simulation? Dave, Sonya
- AMBER: NMR violations increase in explicite water Michel Becker
Tuesday, 13 February 2007
- Re: AMBER: hi Anju Sharma
Monday, 12 February 2007
- RE: AMBER: Membrane Simulation: NPT Issues Akshay Patny
- Re: AMBER: Umbrella sampling Jerome.GOLEBIOWSKI.unice.fr
Wednesday, 14 February 2007
- Re: AMBER: hi Ilyas Yildirim
- Re: AMBER: hi Steven Winfield
- Re: AMBER: Membrane Simulation: NPT Issues David A. Case
- AMBER: Deriving constraint forces on water molecules based on SETTLE moves David Cerutti
- Re: AMBER: Modified nucleotides Raviprasad Aduri
- Re: AMBER: Umbrella sampling Franck Vendeix
- AMBER: Prepgen A Box
- Re: AMBER: Modified nucleotides mathew k varghese
Thursday, 15 February 2007
- Re: AMBER: Deriving constraint forces on water molecules based on SETTLE moves Steven Winfield
- Re: AMBER: NMR violations increase in explicite water David A. Case
- AMBER: units in hessian matrix Marie Brut
- RE: AMBER: Membrane Simulation: NPT Issues Akshay Patny
- AMBER: Simulating a section of a molecule Dave, Sonya
- Re: AMBER: units in hessian matrix David A. Case
- Re: AMBER: units in hessian matrix Adrian Roitberg
- Re: AMBER: units in hessian matrix David A. Case
- Re: AMBER: Simulating a section of a molecule Carlos Simmerling
- AMBER: implicit solvent free energy calcs David Mobley
- Re: AMBER: read the data Florian Haberl
- Re: AMBER: implicit solvent free energy calcs David A. Case
- AMBER: read the data Esther Brugger
- AMBER: Density of a system in MD Akshay Patny
- Re: AMBER: Simulating a section of a molecule Thomas Cheatham III
- Re: AMBER: read the data David LeBard
- RE: AMBER: Simulating a section of a molecule Dave, Sonya
- AMBER: How to modify the velocity of a water molecule? Ji-Lai Li
- Re: AMBER: How to modify the velocity of a water molecule? Carlos Simmerling
- Re: AMBER: How to modify the velocity of a water molecule? Thomas Cheatham
Friday, 16 February 2007
- AMBER: Box dimensions Steve Seibold
- AMBER: H-bond ptraj dilemma Lorenzo Gontrani
- Re: AMBER: Box dimensions Gustavo Seabra
- RE: AMBER: Box dimensions Akshay Patny
- Re: AMBER: Box dimensions David A. Case
- RE: AMBER: Box dimensions Steve Seibold
- Re: AMBER: read the data Esther Brugger
- AMBER: Problem with dacdif when using cygwin Steven Winfield
- Re: AMBER: read the data David LeBard
Thursday, 15 February 2007
- Re: AMBER: read the data Esther Brugger
Friday, 16 February 2007
- Re: AMBER: read the data Esther Brugger
- Re: AMBER: read the data Esther Brugger
- Re: AMBER: read the data David LeBard
- Re: AMBER: read the data Esther Brugger
- Re: AMBER: read the data David LeBard
- Re: AMBER: Problem with dacdif when using cygwin Scott Brozell
- Re: AMBER: Problem with dacdif when using cygwin David A. Case
- Re: AMBER: Problem with dacdif when using cygwin Steven Winfield
- Re: AMBER: Problem with dacdif when using cygwin Scott Brozell
- AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain? WANG,YING
- AMBER: Torsion Restraint on Glycosidic Bond Seth Lilavivat
- Re: AMBER: Torsion Restraint on Glycosidic Bond Thomas Cheatham III
- Re: AMBER: Torsion Restraint on Glycosidic Bond Carlos Simmerling
- Re: AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain? Franck Vendeix
- AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa Rima Chaudhuri
- Re: AMBER: read the data Ilyas Yildirim
- Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa David A. Case
- Re: AMBER: question about ADDLES module Z. Nevin Gerek
- Re: AMBER: question about ADDLES module Carlos Simmerling
- Re: AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain? WANG,YING
Saturday, 17 February 2007
- AMBER: Installing AMBER v9 in Linux Syed Tarique Moin
- AMBER: Installing AMBER v9 in Linux Syed Tarique Moin
- RE: AMBER: Installing AMBER v9 in Linux Ross Walker
- Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa Rima Chaudhuri
- Re: AMBER: read the data Esther Brugger
- Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa David A. Case
- Re: AMBER: Installing AMBER v9 in Linux Ilyas Yildirim
Sunday, 18 February 2007
- AMBER: REMD error on first exchange Daniel Oehme
- RE: AMBER: Installing AMBER v9 in Linux Syed Tarique Moin
- AMBER: Water density calculation mathew k varghese
- RE: AMBER: Installing AMBER v9 in Linux Ross Walker
- RE: AMBER: Installing AMBER v9 in Linux Syed Tarique Moin
- RE: AMBER: Installing AMBER v9 in Linux Ross Walker
Monday, 19 February 2007
- RE: AMBER: Installing AMBER v9 in Linux Syed Tarique Moin
- AMBER: Residence time of WATER gurpreet singh
- AMBER: MDGRAPE and AMBER Craig Gough
- RE: AMBER: Installing AMBER v9 in Linux Ross Walker
- RE: AMBER: Installing AMBER v9 in Linux Syed Tarique Moin
- RE: AMBER: Installing AMBER v9 in Linux Peter Gannett
- AMBER: crd to pdb conversion AYTUG TUNCEL
- Re: AMBER: crd to pdb conversion Ilyas Yildirim
- Re: AMBER: REMD error on first exchange Carlos Simmerling
- Re: AMBER: MDGRAPE and AMBER Carlos Simmerling
- AMBER: Pseudo-CSA in Amber? Mike Summers
- Re: Re: AMBER: crd to pdb conversion AYTUG TUNCEL
- AMBER: carbohydrate-peptide Beale, John
- Re: Re: AMBER: crd to pdb conversion Ilyas Yildirim
- RE: AMBER: Installing AMBER v9 in Linux Ross Walker
- AMBER: DNA and RNA computations Jiri Sponer
- AMBER: problems with bonding disulfide linkages Beale, John
- Re: AMBER: problems with bonding disulfide linkages Carlos Simmerling
- Re: AMBER: problems with bonding disulfide linkages Pankaj R. Daga
Tuesday, 20 February 2007
- AMBER: Error in running replica exchange MD Seongeun Yang
- AMBER: Beale, John
- AMBER: oops Beale, John
- Re: AMBER: Error in running replica exchange MD Carlos Simmerling
- Re: AMBER: Error in running replica exchange MD Carlos Simmerling
- AMBER: RE: about ANTECHAMBER Ross Walker
- AMBER: interior dielectric constant Miguel Ferreira
- AMBER: AMBER ff in CHARMM format!! Swarup Gupta
- AMBER: Nanopore simulation subhasish chatterjee
- AMBER: Is this system too large? Hu, Shaowen \(JSC-SK\)[USRA]
- Re: AMBER: Is this system too large? Fenghui Fan
Wednesday, 21 February 2007
- AMBER: LEaP Problem Beale, John
- AMBER: Amber/ANAL and psf files rebeca.mmb.pcb.ub.es
- RE: AMBER: Is this system too large? Hu, Shaowen \(JSC-SK\)[USRA]
- AMBER: contacts in ptraj (Amber 9) rebeca.mmb.pcb.ub.es
- RE: AMBER: Is this system too large? Fenghui Fan
- Re: AMBER: Pseudo-CSA in Amber? David A. Case
- Re: AMBER: carbohydrate-peptide David A. Case
- Re: AMBER: Is this system too large? David A. Case
- AMBER: native contact analysis! r. a.
- Re: AMBER: Amber/ANAL and psf files David A. Case
- AMBER: atom types deepti nayar
Thursday, 22 February 2007
- AMBER: Errors in amber9 parallel installation Seongeun Yang
- RE: AMBER: Errors in amber9 parallel installation Ross Walker
- RE: AMBER: Is this system too large? Hu, Shaowen \(JSC-SK\)[USRA]
- AMBER: applying restraints Seth Lilavivat
- AMBER: Sander slower on 16 processors than 8 Sontum, Steve
- Re: AMBER: Sander slower on 16 processors than 8 Martin Stennett
- Re: AMBER: Sander slower on 16 processors than 8 Carlos Simmerling
- Re: AMBER: Sander slower on 16 processors than 8 Adrian Roitberg
- AMBER: ptraj bug? -- doesn't like restart files from REMD Nicolas Lux Fawzi
- Re: AMBER: Sander slower on 16 processors than 8 Martin Stennett
- AMBER: Problems with QMMM tests on Altix Jarrod Smith
- RE: AMBER: Sander slower on 16 processors than 8 Ross Walker
- RE: AMBER: Sander slower on 16 processors than 8 Yong Duan
- RE: AMBER: Sander slower on 16 processors than 8 Yong Duan
- RE: AMBER: Sander slower on 16 processors than 8 Ross Walker
- RE: AMBER: Sander slower on 16 processors than 8 Yong Duan
- Re: AMBER: Problems with QMMM tests on Altix Luis Gracia
- RE: AMBER: Sander slower on 16 processors than 8 Ross Walker
- AMBER: units of mwcovar matrix befor conversion Chris Moth
- RE: AMBER: Problems with QMMM tests on Altix Ross Walker
- Re: AMBER: Is this system too large? David A. Case
- AMBER: [rsachdeva.imtech.res.in: Pls help - REMD with torsional restraints] David A. Case
- Re: AMBER: LEaP Problem David A. Case
- Re: AMBER: Sander slower on 16 processors than 8 Robert Duke
Friday, 23 February 2007
- AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 Craig Gough
- AMBER: AMBER question: Combining Gaff and ff99 forcefields for a single molecule Chris-Kriton Skylaris
- Re: AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 Andreas Svrcek-Seiler
- AMBER: SCF convergence issues Steven Winfield
- AMBER: Error in running Replica Exchange MD with amber9 Seongeun Yang
- Re: AMBER: Error in running Replica Exchange MD with amber9 Carlos Simmerling
- RE: AMBER: Is this system too large? Hu, Shaowen \(JSC-SK\)[USRA]
- RE: AMBER: SCF convergence issues Ross Walker
- Re: AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 David A. Case
- Re: AMBER: SCF convergence issues Steven Winfield
- RE: AMBER: Problems with QMMM tests on Altix Jarrod Smith
- RE: AMBER: SCF convergence issues Ross Walker
- AMBER: MD temperature and MM_pbsa temperature Rima Chaudhuri
- AMBER: RESP calculation of modified nucleotides mathew k varghese
Saturday, 24 February 2007
- RE: AMBER: Problems with QMMM tests on Altix Ross Walker
- Re: AMBER: Error in running Replica Exchange MD with amber9 Seongeun Yang
- Re: AMBER: Error in running Replica Exchange MD with amber9 Carlos Simmerling
- Re: AMBER: RESP calculation of modified nucleotides rpaduri.chem.wayne.edu
Sunday, 25 February 2007
- Re: AMBER: RESP calculation of modified nucleotides FyD
- AMBER: Best way to apply WC basepair restraints during MD Seth Lilavivat
- Re: AMBER: RESP calculation of modified nucleotides mathew k varghese
- AMBER: problem with atom restraints Ed Pate
- AMBER: getting same box dimension bertrand russell
- AMBER: phe-phe molecule deepti nayar
- Re: AMBER: phe-phe molecule bertrand russell
- Re: AMBER: phe-phe molecule deepti nayar
Monday, 26 February 2007
- Re: AMBER: phe-phe molecule bertrand russell
- AMBER: Modified nucleotides-ATOM TYPES mathew k varghese
- Re: AMBER: Modified nucleotides-ATOM TYPES David A. Case
- Re: AMBER: RESP calculation of modified nucleotides Raviprasad Aduri
- AMBER: PTRAJ problem Beale, John
- AMBER: Re: REMD with torsional restraints- Temperature swapping not occuring David A. Case
- Re: AMBER: getting same box dimension David A. Case
- Re: AMBER: phe-phe molecule deepti nayar
Tuesday, 27 February 2007
- AMBER: IFVARI parameter Ed Pate
- Re: AMBER: IFVARI parameter Kristina Furse
- AMBER: abnormal high temperature during NPT ensembles MD ebright HMS
- AMBER: AM1-bcc Evan Kelly
- Re: AMBER: abnormal high temperature during NPT ensembles MD Carlos Simmerling
- RE: AMBER: AM1-bcc Junmei Wang
Wednesday, 28 February 2007
- Re: AMBER: RESP calculation of modified nucleotides mathew k varghese
- AMBER: Disulfide Bonds Beale, John
- Re: AMBER: Disulfide Bonds Jerome.GOLEBIOWSKI.unice.fr
- RE: AMBER: Disulfide Bonds Beale, John
- AMBER: LEaP crashes Beale, John
- Re: AMBER: abnormal high temperature during NPT ensembles MD ebright HMS
- Re: AMBER: LEaP crashes David A. Case
- Re: AMBER: phe-phe molecule David A. Case
- AMBER: solvent accessible surface area (SASA) Esther Brugger
- Re: AMBER: problem with atom restraints David A. Case
- AMBER: Difference in Equilibration & Production MD in Amber Akshay Patny
- Re: AMBER: Difference in Equilibration & Production MD in Amber Gustavo Seabra
- Re: AMBER: RESP calculation of modified nucleotides Raviprasad Aduri
- Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa Rima Chaudhuri
- Re: AMBER: solvent accessible surface area (SASA) Carlos Simmerling
- Re: AMBER: solvent accessible surface area (SASA) Esther Brugger
- AMBER: momentum and periodic boundary condition Wei Chen

Last message date: Sun Mar 04 2007 - 06:07:28 PST
Archived on: Wed Apr 24 2024 - 05:53:33 PDT

Amber Archive Feb 2007 by date