Amber Archive Aug 2007: by date

Wednesday, 1 August 2007
- AMBER: how to calculate the ps/day of md simulation using using my cluster system in amber7 Syed Tarique Moin
- AMBER: problem compiling Amber9 on 64-machine fatima.chami.durham.ac.uk
- Fwd: RE: AMBER: Average potential energies and conformer ratios Francesco Pietra
- Re: AMBER: problem compiling Amber9 on 64-machine David A. Case
- Re: AMBER: problem compiling Amber9 on 64-machine S.Sundar Raman
- Re: AMBER: problem compiling Amber9 on 64-machine fatima.chami.durham.ac.uk
- Re: AMBER: problem compiling Amber9 on 64-machine fatima.chami.durham.ac.uk
- RE: AMBER: problem compiling Amber9 on 64-machine Ross Walker
- Re: AMBER: problem compiling Amber9 on 64-machine David A. Case
- Re: AMBER: problem compiling Amber9 on 64-machine David A. Case
- AMBER: Problem with Antechamber and point charges anna duraj
- Re: AMBER: Problem with Antechamber and point charges Carlos Simmerling
- AMBER: neutral terminals Jena M
- Re: AMBER: bugfix for impropers in parmchk Jiten
- Re: AMBER: problem compiling Amber9 on 64-machine S.Sundar Raman
- Re: AMBER: bugfix for impropers in parmchk David A. Case
- Re: AMBER: Problem while saving .top and .crd files. Anju Sharma
- Re: AMBER: bugfix for impropers in parmchk Jiten
- AMBER: Problem with antechamber Anju Sharma
- AMBER: (no subject) Syed Tarique Moin
Thursday, 2 August 2007
- Re: AMBER: Problem with antechamber gurpreet singh
- Re: AMBER: (no subject) gurpreet singh
- Re: AMBER: Problem with antechamber Anju Sharma
- Re: AMBER: neutral terminals Carlos Simmerling
- Re: AMBER: (no subject) Syed Tarique Moin
- Re: AMBER: (no subject) Carlos Simmerling
- AMBER: planarity restraints for NA Seth Lilavivat
- Re: AMBER: planarity restraints for NA Carlos Simmerling
- Re: AMBER: planarity restraints for NA Seth Lilavivat
- AMBER: restrained md and mm pbsa Christopher Gaughan
- Re: AMBER: planarity restraints for NA Carlos Simmerling
- RE: AMBER: Problem while saving .top and .crd files. Ross Walker
- Re: AMBER: Problem with antechamber David A. Case
- RE: AMBER: Problem with antechamber Ross Walker
- AMBER: vector corrplane Servaas Michielssens
- AMBER: Force Field Parameters Beale, John
- AMBER: Calculating cumulative average Francesco Pietra
- Re: AMBER: planarity restraints for NA Seth Lilavivat
- Re: AMBER: Force Field Parameters Prashanth Athri
- AMBER: edit.out amber version 9 Greg Gannon
- Re: AMBER: edit.out amber version 9 David A. Case
- RE: AMBER: planarity restraints for NA Hu, Shaowen (JSC-SK)[USRA]
- AMBER: Problem generating .prepin file in Antechamber Lili Peng
- Re: AMBER: Problem generating .prepin file in Antechamber Lili Peng
- Re: AMBER: planarity restraints for NA Seth Lilavivat
- Re: AMBER: Force Field Parameters Raviprasad Aduri
- Re: AMBER: Problem with antechamber Bill Ross
- RE: AMBER: (no subject) Gustavo Seabra
- Re: AMBER: edit.out amber version 9 WANG,YING
- Re: AMBER: Problem generating .prepin file in Antechamber David A. Case
- AMBER: Any experience on Dell two quad core system? Ilyas Yildirim
- Re: AMBER: Antechamber formal charges with Gasteiger method Scott Brozell
- Re: AMBER: Any experience on Dell two quad core system? Ye Mei
- Re: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler
- Re: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim
- AMBER: Information about Amber 9 Lycourgos Chiniadis
- AMBER: force field for hydrogels Prem Prakash Pathak
Friday, 3 August 2007
- AMBER: unable to save prmtop/inpcrd for chcl3box Francesco Pietra
- AMBER: Fwd: unable to save prmtop/inpcrd for chcl3box Francesco Pietra
- AMBER: Successful compile on Mac OSX + Intel compilers Viv Kendon
- Re: AMBER: Information about Amber 9 David A. Case
- Re: AMBER: unable to save prmtop/inpcrd for chcl3box David A. Case
- Re: AMBER: bug in nonbond_list.f (nee ew_setup.f) David A. Case
- Re: AMBER: Successful compile on Mac OSX + Intel compilers Viv Kendon
- RE: AMBER: Any experience on Dell two quad core system? Ross Walker
- Re: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim
- Re: AMBER: Problem with Antechamber and point charges anna duraj
- Re: AMBER: Problem with Antechamber and point charges Carlos Simmerling
- Re: AMBER: Antechamber formal charges with Gasteiger method David A. Case
- AMBER: Binary file curiosities David LeBard
- Re: AMBER: Binary file curiosities David A. Case
- Re: AMBER: Binary file curiosities Thomas Cheatham III
- RE: AMBER: (no subject) Syed Tarique Moin
Saturday, 4 August 2007
- AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra
- Re: AMBER: (no subject) Carlos Simmerling
- AMBER: nucleic acid electrostatic energy Tiago Sobreira
- Re: AMBER: (no subject) Syed Tarique Moin
- Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson
- AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra
- Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson
- Re: AMBER: nucleic acid electrostatic energy David A. Case
- RE: AMBER: (no subject) Ross Walker
- RE: AMBER: Fwd: QM region + cutoff larger that box Gustavo Seabra
- AMBER: GAFF atom typing for flavin Hans Martin Senn
- Re: AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra
- AMBER: force field for irregulate DNA ends Hu, Shaowen (JSC-SK)[USRA]
- Re: AMBER: Antechamber formal charges with Gasteiger method Scott Brozell
- AMBER: setting dimensions of truncated octahedron Lillian chong
- Re: AMBER: Binary file curiosities David LeBard
- Re: AMBER: setting dimensions of truncated octahedron Thomas Cheatham
Sunday, 5 August 2007
- Re: AMBER: setting dimensions of truncated octahedron Lillian chong
- AMBER: RE: tutorial file polyAT_vac.prmtop Ross Walker
- AMBER: Problem while carrying out minimisation of drug molecule using sander Anju Sharma
- RE: AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra
Monday, 6 August 2007
- Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson
- AMBER: Specific heat graph is a straight line priya priya
- Re: AMBER: Problem while carrying out minimisation of drug molecule using sander David A. Case
- Re: AMBER: Binary file curiosities David A. Case
- Re: AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra
- Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson
- RE: AMBER: Fwd: QM region + cutoff larger that box Gustavo Seabra
- AMBER: Integrating the alpha-helix bias correction into ff94 Andrew Borgert
- Re: AMBER: Integrating the alpha-helix bias correction into ff94 Carlos Simmerling
- AMBER: hybridization in Amber, pertaining to resonant structures, ions Karen Callahan
- Re: AMBER: Problem while carrying out minimisation of drug molecule using sander Anju Sharma
Tuesday, 7 August 2007
- AMBER: heical content in simulations priya priya
- Re: AMBER: heical content in simulations Chng Choon-Peng
- Re: AMBER: heical content in simulations priya priya
- Re: AMBER: Problem while carrying out minimisation of drug molecule using sander Carlos Simmerling
- AMBER: Problem with minimization Syed Tarique Moin
- AMBER: compile amber8 with mpich2 Kailee
- RE: AMBER: Problem with minimization Ross Walker
- AMBER: Positive EPtot in QM-MM Francesco Pietra
- AMBER: about shake linfu
Wednesday, 8 August 2007
- AMBER: msubhamoy.ibab.ac.in
- AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA msubhamoy.ibab.ac.in
- RE: AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA Ross Walker
- AMBER: RE: TUTORIAL B1 file polyAT_vac.prmtop Ross Walker
- Re: AMBER: about shake Steven Winfield
- AMBER: RE: Problem loading pdf into tleap Ross Walker
- Re: AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA linfu
- Re: AMBER: bug in nonbond_list.f (nee ew_setup.f) neville forlemu
- AMBER: Cygwin error Lili Peng
- Re: AMBER: Cygwin error Bill Ross
- Re: AMBER: Cygwin error Lili Peng
- Re: AMBER: Cygwin error Mark Williamson
- Re: AMBER: Cygwin error Lili Peng
- Re: AMBER: Cygwin error Gustavo Seabra
- Re: AMBER: Cygwin error Bill Ross
- Re: AMBER: Cygwin error Lili Peng
- Re: AMBER: Cygwin error Gustavo Seabra
- Re: Re: AMBER: about shake linfu
- Re: AMBER: program bug? M. Maeda
- Re: AMBER: compile amber8 with mpich2 Scott Brozell
- AMBER: how to combine two molecules Wenyong Tong
Thursday, 9 August 2007
- Re: AMBER: Cygwin error Lili Peng
- RE: AMBER: Cygwin error Ross Walker
- Re: AMBER: Cygwin error Lili Peng
- Re: AMBER: Cygwin error Gustavo Seabra
- Re: AMBER: Cygwin error Lili Peng
- AMBER: NVE energy and temperature drift Nikola Trbovic
- Re: AMBER: Cygwin error Gustavo Seabra
- Re: AMBER: Cygwin error Bill Ross
- Re: AMBER: Cygwin error Gustavo Seabra
- Re: AMBER: NVE energy and temperature drift Robert Duke
- Re: AMBER: NVE energy and temperature drift Thomas Cheatham III
- Re: AMBER: NVE energy and temperature drift Nikola Trbovic
- Re: AMBER: NVE energy and temperature drift Robert Duke
- RE: AMBER: NVE energy and temperature drift Nikola Trbovic
- Re: AMBER: NVE energy and temperature drift Robert Duke
Friday, 10 August 2007
- Re: AMBER: NVE energy and temperature drift Vlad Cojocaru
- Re: AMBER: NVE energy and temperature drift Vlad Cojocaru
- Re: AMBER: how to combine two molecules Benjamin Juhl
- AMBER: Implicit solvent simulation is too slow. SeungPyo Hong
- Re: AMBER: Implicit solvent simulation is too slow. Carlos Simmerling
- Re: AMBER: Implicit solvent simulation is too slow. SeungPyo Hong
- AMBER: How to couple only one residue to the temperature bath? Michael Lerner
- Re: AMBER: How to couple only one residue to the temperature bath? Carlos Simmerling
- RE: AMBER: Implicit solvent simulation is too slow. Ross Walker
- AMBER: short 2'OH-OP contacts in RNA Jose Gallego
- AMBER: vlimit exceeded for the step Sudha Mani Karra
- RE: AMBER: vlimit exceeded for the step Ross Walker
- AMBER: Steve Seibold
- Re: AMBER: Thomas Pochapsky
- Re: AMBER: How to couple only one residue to the temperature bath? Michael Lerner
- Re: AMBER: How to couple only one residue to the temperature bath? Carlos Simmerling
Saturday, 11 August 2007
- AMBER: Citation for Langevin thermostat? Marc Baaden
- AMBER: Using charmm force field in amber Seongeun Yang
- AMBER: Failure to SCF convergence Francesco Pietra
- Re: AMBER: Citation for Langevin thermostat? David A. Case
- AMBER: imin=5 and inptraj Nikola Trbovic
- Re: AMBER: NVE energy and temperature drift David A. Case
- Re: AMBER: hybridization in Amber, pertaining to resonant structures, ions David A. Case
- Re: AMBER: imin=5 and inptraj Carlos Simmerling
- Re: AMBER: imin=5 and inptraj Nikola Trbovic
- Re: AMBER: NVE energy and temperature drift Nikola Trbovic
- Re: AMBER: imin=5 and inptraj Chris Moth
- AMBER: Neutralize charges for simulated annealing? Francesco Pietra
- RE: AMBER: Failure to SCF convergence Ross Walker
- Re: AMBER: how to combine two molecules Wenyong Tong
Sunday, 12 August 2007
- RE: AMBER: Failure to SCF convergence & parallelization and memory Francesco Pietra
Monday, 13 August 2007
- AMBER: MM_PBSA No radius found for Br!! Urszula Uciechowska
- Re: AMBER: MM_PBSA No radius found for Br!! Antonio Morreale
- RE: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler
- Re: AMBER: Any experience on Dell two quad core system? M. L. Dodson
- AMBER: setbox command error priya priya
- Re: AMBER: how to combine two molecules David A. Case
- RE: AMBER: Failure to SCF convergence & parallelization and memory Ross Walker
- Re: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler
- AMBER: unsubscribe Pan, Yongmei
- Re: AMBER: Any experience on Dell two quad core system? M. L. Dodson
- RE: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim
- Re: AMBER: setbox command error David A. Case
- RE: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler
- Re: AMBER: Any experience on Dell two quad core system? David Cerutti
- AMBER: Using TLEAP to set up MD in the crystal lattice space? David Cerutti
- Re: AMBER: how to combine two molecules Wenyong Tong
- Re: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim
- Re: AMBER: Using TLEAP to set up MD in the crystal lattice space? David A. Case
- Re: AMBER: Using TLEAP to set up MD in the crystal lattice space? Thomas Cheatham
- AMBER: Normal Mode Analysis Kresimir Sikic
- AMBER: Machine environment to install AMBER 8 M. Maeda
- AMBER: regarding implicit simulation gurpreet singh
- Re: AMBER: setbox command error priya priya
Tuesday, 14 August 2007
- Re: AMBER: setbox command error Steven Winfield
- AMBER: MMPBSA NOT Getting results msubhamoy.ibab.ac.in
- Re: AMBER: Machine environment to install AMBER 8 Benjamin Juhl
- RE: AMBER: MMPBSA NOT Getting results Rafi Ahmad
- AMBER: How to carry out drug-dna complex simulations Anju Sharma
- Re: AMBER: Machine environment to install AMBER 8 M. Maeda
- Re: AMBER: setbox command error priya priya
- Re: AMBER: setbox command error Steven Winfield
- Re: AMBER: Machine environment to install AMBER 8 Benjamin Juhl
- Re: AMBER: Machine environment to install AMBER 8 M. Maeda
- Re: AMBER: Machine environment to install AMBER 8 Bertrand Russell
- Re: AMBER: Machine environment to install AMBER 8 M. Maeda
- Re: AMBER: Machine environment to install AMBER 8 Bertrand Russell
- AMBER: Tutorial about SMD? Qiang Zhong
- Re: AMBER: Machine environment to install AMBER 8 Benjamin Juhl
- Re: AMBER: regarding implicit simulation Carlos Simmerling
- AMBER: Parallelizin antechamber? Francesco Pietra
- Re: AMBER: MM_PBSA No radius found for Br!! Urszula Uciechowska
- Re: AMBER: Parallelizin antechamber? M. L. Dodson
- Re: AMBER: Any experience on Dell two quad core system? David Cerutti
- Re: AMBER: How to carry out drug-dna complex simulations David A. Case
- Re: AMBER: David A. Case
- AMBER: MM_PBSA No radius found for Br!! Urszula Uciechowska
- Re: AMBER: Any experience on Dell two quad core system? Robert Duke
- AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky
- Re: AMBER: torsional restraints in a solvated MD simulation. Carlos Simmerling
- Re: AMBER: torsional restraints in a solvated MD simulation. David A. Case
- Re: AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky
- Re: AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky
- Re: AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky
- Re: AMBER: Machine environment to install AMBER 8 M. Maeda
- Re: AMBER: Machine environment to install AMBER 8 Bertrand Russell
Wednesday, 15 August 2007
- AMBER: antechamber, how does it work Francesco Pietra
- AMBER: Building parallel Amber 9.0 Beale, John
- Re: AMBER: Parallelizin antechamber? Junmei Wang
- Re: AMBER: antechamber, how does it work Junmei Wang
- Re: AMBER: Building parallel Amber 9.0 Gustavo Seabra
- Re: AMBER: antechamber, how does it work Gustavo Seabra
- Re: AMBER: antechamber, how does it work Francesco Pietra
- RE: AMBER: Building parallel Amber 9.0 Ross Walker
- AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra
- Re: AMBER: Distance restraints between center of mass of two molecules Carlos Simmerling
- Re: AMBER: antechamber, how does it work Francesco Pietra
- Re: AMBER: antechamber, how does it work Seth Hayik
- RE: AMBER: Building parallel Amber 9.0 Rajendra P. OJHA
- Re: AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra
- RE: AMBER: Building parallel Amber 9.0 Rajendra P. OJHA
- Re: AMBER: Distance restraints between center of mass of two molecules Carlos Simmerling
- Re: AMBER: antechamber, how does it work Francesco Pietra
- AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade
- Re: AMBER: antechamber, how does it work David A. Case
- Re: AMBER: EXTRA_PTS: frtype 2 Should not be here David A. Case
- AMBER: docking ability anna duraj
- RE: AMBER: Building parallel Amber 9.0 Ross Walker
- AMBER: Bug in ptraj mask processing? Steve Spronk
- Re: AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra
- Re: AMBER: Distance restraints between center of mass of two molecules Carlos Simmerling
- Re: AMBER: antechamber, how does it work Francesco Pietra
- Re: AMBER: Normal Mode Analysis David A. Case
- Re: AMBER: antechamber, how does it work Thomas Cheatham III
- RE: AMBER: Building parallel Amber 9.0 Balvinder Singh
- RE: AMBER: Building parallel Amber 9.0 Balvinder Singh
- Re: AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade
- Re: AMBER: antechamber, how does it work Francesco Pietra
Thursday, 16 August 2007
- Re: AMBER: antechamber, how does it work David A. Case
- Re: AMBER: EXTRA_PTS: frtype 2 Should not be here David A. Case
- Re: AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade
- Re: AMBER: antechamber, how does it work Francesco Pietra
- AMBER: Missplaced TERs Steve Seibold
- Re: AMBER: Missplaced TERs David A. Case
- RE: AMBER: Missplaced TERs Steve Seibold
- AMBER: What is the best computer for running AMBER simulations? Lili Peng
- Re: AMBER: What is the best computer for running AMBER simulations? David LeBard
- Re: AMBER: What is the best computer for running AMBER simulations? Andreas Svrcek-Seiler
- Re: AMBER: MPI Quiescence problem in REMD In Hee Park
- Re: AMBER: What is the best computer for running AMBER simulations? David A. Case
- Re: AMBER: What is the best computer for running AMBER simulations? Yu Chen
- Re: AMBER: What is the best computer for running AMBER simulations? Lili Peng
- AMBER: NAN and vlimit exceeded errors in restrained MD.. using IBELLY Sandeep Kaushik
- Re: AMBER: about parallelization in QM-MM Francesco Pietra
Friday, 17 August 2007
- AMBER: Thermodynamic Integration for a CHARGED molecule ming hui
- AMBER: MPI Beale, John
- Re: AMBER: MPI Mark Williamson
- Re: AMBER: Thermodynamic Integration for a CHARGED molecule David Mobley
- Re: AMBER: Thermodynamic Integration for a CHARGED molecule David A. Case
- RE: AMBER: about parallelization in QM-MM Ross Walker
- AMBER: Molsurf error Pankaj R. Daga
- RE: AMBER: about parallelization in QM-MM Ross Walker
- AMBER: ptraj hydrogen bonding defaults Michael Lerner
- Re: AMBER: ptraj hydrogen bonding defaults Thomas Cheatham
Saturday, 18 August 2007
- AMBER: DFTB email address Francesco Pietra
- Re: AMBER: What is the best computer for running AMBER simulations? Prem Prakash Pathak
- AMBER: question about a 20 kDa protein David A. Case
- AMBER: charges in PBSA calculation Neha Gandhi
Sunday, 19 August 2007
- Re: AMBER: charges in PBSA calculation Ray Luo
- Re: AMBER: MM_PBSA No radius found for Br!! Scott Brozell
- Re: AMBER: How to carry out drug-dna complex simulations Scott Brozell
- Re: AMBER: docking ability Scott Brozell
- Re: AMBER: DFTB email address tomas.kubar.marge.uochb.cas.cz
- Re: AMBER: charges in PBSA calculation Neha Gandhi
- Re: AMBER: charges in PBSA calculation David A. Case
Monday, 20 August 2007
- AMBER: CRESP charges in antechamber prepin Francesco Pietra
- AMBER: mmpbsa calculation msubhamoy.ibab.ac.in
- AMBER: TEST_FAILURES Qiang Zhong
- Re: AMBER: TEST_FAILURES Martin Stennett
- AMBER: Entropy in MM_PBSA Sergey Samsonov
- AMBER: Beale, John
- Re: AMBER: TEST_FAILURES Qiang Zhong
- Re: AMBER: David A. Case
- AMBER: $tleap is not normal Qiang Zhong
- RE: AMBER: $tleap is not normal Ross Walker
- AMBER: Regarding free energy calculation and covalent bond nag raj
- AMBER: Error in MMPBSA Calculation msubhamoy.ibab.ac.in
Tuesday, 21 August 2007
- Re: AMBER: Error in MMPBSA Calculation jitrayut jitonnom
- AMBER: command tleap is not normal Qiang Zhong
- Re: AMBER: command tleap is not normal Ilyas Yildirim
- AMBER: how to include mpirun in this script Syed Tarique Moin
- AMBER: How to use AMBER Parameter Database ? Qiang Zhong
- AMBER: Thermodynamic Integration for conformational changes? Francesco Pietra
- RE: AMBER: how to include mpirun in this script Ross Walker
- AMBER: xLeap "Could not find type" error Lili Peng
- AMBER: Octahedral box orientation David Cerutti
- AMBER: Force field for RNA with U-turn motif Cenk Andac
- AMBER: Tutorial of document about QM/MM in reaction pathways? Qiang Zhong
- Re: AMBER: Octahedral box orientation David Cerutti
- Re: AMBER: xLeap "Could not find type" error David A. Case
- Re: AMBER: xLeap "Could not find type" error Lili Peng
- Re: AMBER: Thermodynamic Integration for conformational changes? Gustavo Seabra
- Re: AMBER: Thermodynamic Integration for conformational changes? Gustavo Seabra
- AMBER: a question about xleap WANG,YING
- Re: AMBER: Thermodynamic Integration for conformational changes? Francesco Pietra
Wednesday, 22 August 2007
- Re: AMBER: Force field for RNA with U-turn motif Vlad Cojocaru
- AMBER: How to use AMBER Parameter Database ? Qiang Zhong
- AMBER: How to delete particular frame from mdcrd file (not with ptraj). saurabh agrawal
- Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj). Steven Winfield
- Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj). saurabh agrawal
- AMBER: MM-PBSA calculations of entropy within the sphere Sergey Samsonov
- AMBER: xLeap "Could not find type" error WANG,YING
- Re: AMBER: xLeap "Could not find type" error David A. Case
- Re: AMBER: xLeap "Could not find type" error Wei Zhang
- Re: AMBER: xLeap "Could not find type" error WANG,YING
- Re: AMBER: xLeap "Could not find type" error David A. Case
- Re: AMBER: Force field for RNA with U-turn motif Cenk Andac
- Re: AMBER: Force field for RNA with U-turn motif Jiri Sponer
- Re: AMBER: Force field for RNA with U-turn motif Cenk Andac
- AMBER: Running Gaussian to get .out files Lili Peng
- AMBER: Performance of polarizable model simulations Jones de Andrade
- AMBER: Parse charges for small molecules Neha Gandhi
Thursday, 23 August 2007
- AMBER: Ca(2+) parameter Qiang Zhong
- RE: AMBER: Running Gaussian to get .out files Steve Spronk
- RE: AMBER: How to delete particular frame from mdcrd file (not with ptraj). Steve Spronk
- [Fwd: Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj).] Steven Winfield
- Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj). Adrian Roitberg
- Re: AMBER: Ca(2+) parameter David A. Case
- AMBER: Unable to open MDCRD file using vmd priya priya
- AMBER: How to perform MD simulation in NVT ensemble? WANG,YING
- Re: AMBER: Regarding free energy calculation and covalent bond David A. Case
- Re: AMBER: How to use AMBER Parameter Database ? David A. Case
- Re: AMBER: How to perform MD simulation in NVT ensemble? Chris Moth
- RE: AMBER: Unable to open MDCRD file using vmd Ross Walker
- AMBER: Prepin error (?) in xleap Lili Peng
- Re: AMBER: How to perform MD simulation in NVT ensemble? WANG,YING
- Re: AMBER: Prepin error (?) in xleap David A. Case
- AMBER: protonation of His residue! Qiang Zhong
- Re: AMBER: protonation of His residue! jitrayut jitonnom
Friday, 24 August 2007
- AMBER: ow to split MDCRD file using ptraj priya priya
- AMBER: QM/MM in reaction pathways? Qiang Zhong
- AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra
- AMBER: SMD simulation Qiang Zhong
- AMBER: NETCDF Geoff Wood
- Re: AMBER: SMD simulation Adrian Roitberg
- Re: AMBER: NETCDF Chris Moth
- AMBER: articles Beale, John
- AMBER: NETCDF Chris Moth
- RE: AMBER: solvateCap minin and mdin for qm-mm dftb Ross Walker
- Re: AMBER: solvateCap minin and mdin for qm-mm dftb M. L. Dodson
- RE: AMBER: SMD simulation Ross Walker
- AMBER: PM6? Thomas Patko (CSULB)
- AMBER: Running Gaussian to get .out files Steve Spronk
- Re: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra
- Re: AMBER: solvateCap minin and mdin for qm-mm dftb M. L. Dodson
- Re: AMBER: Entropy in MM_PBSA David Mobley
- RE: AMBER: PM6? Ross Walker
- RE: AMBER: solvateCap minin and mdin for qm-mm dftb Ross Walker
- RE: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra
- Re: AMBER: PM6? Thomas Patko
- Re: AMBER: articles Lili Peng
- Re: AMBER: Prepin error (?) in xleap Lili Peng
- Re: AMBER: Prepin error (?) in xleap Lili Peng
- RE: AMBER: PM6? Ross Walker
- Re: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra
- Re: AMBER: solvateCap minin and mdin for qm-mm dftb M. L. Dodson
- RE: AMBER: solvateCap minin and mdin for qm-mm dftb Ross Walker
- RE: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra
- Re: AMBER: ow to split MDCRD file using ptraj Gustavo Seabra
- Re: AMBER: How to perform MD simulation in NVT ensemble? Gustavo Seabra
Saturday, 25 August 2007
- Re: AMBER: SMD simulation Qiang Zhong
- AMBER: SCC convergence failure in QM-MM DFTB Francesco Pietra
- Re: AMBER: SCC convergence failure in QM-MM DFTB Adrian Roitberg
Sunday, 26 August 2007
- AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra
- AMBER: personal computer configuration for parallel computing emine cebe
- AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra
- Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB M. L. Dodson
- Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra
- Fwd: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra
Monday, 27 August 2007
- Re: AMBER: NETCDF Geoff Wood
- Re: AMBER: Prepin error (?) in xleap David A. Case
- Re: AMBER: SCC convergence failure in QM-MM DFTB Gustavo Seabra
- AMBER: metalloprotein dynamics Sally Pias
- AMBER: generating a .rst file from an .mdcrd file Thomas Pochapsky
- AMBER: Add hydrogen and charge calculation snoze pa
- Re: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Gustavo Seabra
- Re: AMBER: generating a .rst file from an .mdcrd file Gustavo Seabra
- Re: AMBER: Add hydrogen and charge calculation Chris Moth
- Re: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Gustavo Seabra
- Re: AMBER: Prepin error (?) in xleap Lili Peng
- Re: AMBER: Prepin error (?) in xleap Junmei Wang
- Re: AMBER: Prepin error (?) in xleap David A. Case
- Re: AMBER: Add hydrogen and charge calculation snoze pa
Tuesday, 28 August 2007
- AMBER: QM/MM in reaction pathways? Qiang Zhong
- Re: AMBER: QM/MM in reaction pathways? Gustavo Seabra
- RE: AMBER: QM/MM in reaction pathways? Ross Walker
- AMBER: protocols for high pressure simulation brmeher.iitg.ernet.in
- Re: AMBER: protocols for high pressure simulation David A. Case
- AMBER: heating up system Francesco Pietra
- Re: AMBER: heating up system Adrian Roitberg
- RE: AMBER: QM/MM in reaction pathways? Qiang Zhong
Wednesday, 29 August 2007
- AMBER: energy minimization parameter Qiang Zhong
- Re: AMBER: energy minimization parameter Lorenzo Gontrani
- AMBER: refinement of NMR struture using AMBER Prem Prakash Pathak
- Re: AMBER: How to perform MD simulation in NVT ensemble? WANG,YING
- Re: AMBER: How to perform MD simulation in NVT ensemble? Gustavo Seabra
- AMBER: Criteria for classical md being OK to move to QM-MM Francesco Pietra
- Re: AMBER: Criteria for classical md being OK to move to QM-MM M. L. Dodson
- Re: AMBER: Criteria for classical md being OK to move to QM-MM Francesco Pietra
- Re: AMBER: Criteria for classical md being OK to move to QM-MM Gustavo Seabra
- Re: AMBER: Criteria for classical md being OK to move to QM-MM M. L. Dodson
- RE: AMBER: Criteria for classical md being OK to move to QM-MM Ross Walker
- AMBER: Schedule for QM-MM with Amber9/Amber10 Francesco Pietra
Thursday, 30 August 2007
- AMBER: RDF unit cell volume BJÖRN KARLSSON
- AMBER: Dihedrals in Sander Martin Stennett
- AMBER: AMBER at WESTGRID Eduardo Mendez-Villuendas
- Re: AMBER: AMBER at WESTGRID Gustavo Seabra
- AMBER: bad atom type:F Emilia Wu
- AMBER: Beale, John
- AMBER: Fwd: Schedule for QM-MM with Amber9/Amber10 Francesco Pietra
- Re: AMBER: bad atom type:F David A. Case
- AMBER: Squished dimer during transition from NVT to NPT Katrina Lexa
- AMBER: Connecting two ethanes in LEaP Kliman, Michal
- AMBER: Scaling for octahedral versus rectilinear boxes David Cerutti
Friday, 31 August 2007
- Re: AMBER: Scaling for octahedral versus rectilinear boxes Robert Duke
- Re: AMBER: Scaling for octahedral versus rectilinear boxes David Cerutti
- Re: AMBER: Confusion about Langevin dymamics Carlos Simmerling
- AMBER: Confusion about Langevin dymamics Hayden Eastwood
- AMBER: antechamber question Beale, John
- Re: AMBER: Scaling for octahedral versus rectilinear boxes Robert Duke
- Re: AMBER: Confusion about Langevin dymamics David A. Case
- Re: AMBER: Confusion about Langevin dymamics David Mobley
- Re: AMBER: Connecting two ethanes in LEaP David A. Case
- Re: AMBER: Melinda Layten
Thursday, 30 August 2007
- Re: AMBER: Prepin error (?) in xleap Lili Peng
Friday, 31 August 2007
- Re: AMBER: Schedule for QM-MM with Amber9/Amber10 Gustavo Seabra
- AMBER: Converting AMBER-format force fields for tinker Aaron Virshup
- AMBER: Measuring Bond Angle over simulation Seth Lilavivat
- Re: AMBER: Measuring Bond Angle over simulation Carlos Simmerling
- Re: AMBER: antechamber question Junmei Wang
- AMBER: modified leaprc for glycoproteins Irene Newhouse
- Re: AMBER: Prepin error (?) in xleap Junmei Wang
- AMBER: Using ntr=1 in xleap Lili Peng
- Re: AMBER: Using ntr=1 in xleap David A. Case
- Re: AMBER: modified leaprc for glycoproteins David A. Case
- Re: AMBER: Using ntr=1 in xleap Carlos Simmerling
- RE: AMBER: modified leaprc for glycoproteins Irene Newhouse

Last message date: Sun Sep 02 2007 - 06:07:39 PDT
Archived on: Wed Nov 20 2024 - 05:53:28 PST

Amber Archive Aug 2007 by date