Amber Archive Sep 2008: by date

Monday, 1 September 2008
- AMBER: tleap and Zn parameter Aust, Susanne
- AMBER: ptraj and netcdf with AmberTools1.2 ? Lars Skjærven
- Re: AMBER: RE: Personal favor fatima.chami.durham.ac.uk
- Re: AMBER: tleap and Zn parameter David A. Case
- Re: AMBER: solvent interaction in active site S.Sundar Raman
- Re: AMBER: solvent interaction in active site Carlos Simmerling
- AW: AMBER: tleap and Zn parameter Aust, Susanne
Tuesday, 2 September 2008
- Re: AMBER: compilation problem john smith
- Re: AMBER: compilation problem Vlad Cojocaru
- AMBER: mmpbsa Henrik Öberg
- AMBER: AMBER9 installation problen with open mpi saurabh agrawal
- Re: AMBER: AMBER9 installation problen with open mpi Vlad Cojocaru
- Re: AMBER: mmpbsa Neha Gandhi
- RE: AMBER: mmpbsa Henrik Öberg
- Re: AMBER: mmpbsa Matthew Peterson
- Re: AMBER: compilation problem David A. Case
- AMBER: ptraj & imaging of velocities FyD
- Re: AMBER: ptraj & imaging of velocities Lars Skjærven
- Re: AMBER: mmpbsa Hannes Kopitz
- Re: AMBER: tleap and Zn parameter David A. Case
- AMBER: a question about matrix command? TaoPaul
- AMBER: MM_PBSA - SASA - Question Deepangi Pandit
Wednesday, 3 September 2008
- AW: AMBER: tleap and Zn parameter Aust, Susanne
- RE: AMBER: mmpbsa Henrik Öberg
- Re: RE: AMBER: mmpbsa Hannes Kopitz
- AMBER: Need help... High energies for complex... Waqas Nasir
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling
- Re: AMBER: Need help... High energies for complex... Waqas Nasir
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling
- Re: AMBER: Need help... High energies for complex... Neha Gandhi
- Re: AMBER: AMBER9 installation problen with open mpi saurabh agrawal
- RE: AMBER: tleap and Zn parameter Ross Walker
- RE: AMBER: AMBER9 installation problen with open mpi Ross Walker
- AMBER: help...ptraj does not output bounding box info Jose Borreguero
- Re: AMBER: help...ptraj does not output bounding box info Carlos Simmerling
- Re: AMBER: help...ptraj does not output bounding box info Jose Borreguero
- Re: AMBER: help...ptraj does not output bounding box info Bill Ross
- Re: AMBER: help...ptraj does not output bounding box info Carlos Simmerling
- Re: AMBER: help...ptraj does not output bounding box info Jose Borreguero
- Re: AMBER: help...ptraj does not output bounding box info Carlos Simmerling
- Re: AMBER: help...ptraj does not output bounding box info Jose Borreguero
- AMBER: Marisa Frechero
- AMBER: matrix correl Steve Seibold
- RE: AMBER: Ross Walker
- AMBER: nmode units Arturas Ziemys
- Re: AMBER: nmode units Chris Moth
- AMBER: mmpbsa molsurf.c error Ilyas Yildirim
Thursday, 4 September 2008
- AMBER: No bond and angle parameters for - -????? Waqas Nasir
- Re: AMBER: Need help... High energies for complex... Waqas Nasir
- AMBER: Need help... High energies for complex... Waqas Nasir
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling
- AMBER: antechamber cannot generate prep files moitrayee.mbu.iisc.ernet.in
- Re: AMBER: No bond and angle parameters for - -????? Lachele Foley (Lists)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir
- Re: AMBER: nmode units Arturas Ziemys
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling
- Re: AMBER: Need help... High energies for complex... David A. Case
- Re: AMBER: nmode units David A. Case
- Re: AMBER: nmode units Arturas Ziemys
- Re: AMBER: Need help... High energies for complex... Waqas Nasir
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling
- Re: AMBER: Need help... High energies for complex... Waqas Nasir
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling
- AMBER: help... structure factors from amber trajectories? Jose Borreguero
- Re: AMBER: xleap fails to savemol2 FyD
- Re: AMBER: mmpbsa molsurf.c error Ilyas Yildirim
- AMBER: resp and 99999 Markus Kaukonen
Friday, 5 September 2008
- Re: AMBER: Need help... High energies for complex... Waqas Nasir
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling
- AMBER: help...sander "segmentation fault" after 2hours of minimization Jose Borreguero
- Re: AMBER: help...sander "segmentation fault" after 2hours of minimization David A. Case
- RE: AMBER: help...sander "segmentation fault" after 2hours of minimization Ross Walker
- Re: AMBER: help...sander "segmentation fault" after 2hours of minimization Jose Borreguero
- AMBER: error when using tleap with leaprc.ff02EP Yongmei Pan
- RE: AMBER: error when using tleap with leaprc.ff02EP Ross Walker
- RE: AMBER: help...sander "segmentation fault" after 2hours of minimization Ross Walker
- Re: AMBER: help...sander "segmentation fault" after 2hours of minimization Jose Borreguero
- AMBER: RE: reference paper - pls help Ross Walker
- RE: AMBER: help...sander "segmentation fault" after 2hours of minimization Ross Walker
- AMBER: mm_pbsa error : Scale paremeter for PBSA CHAMI F.
- RE: AMBER: mm_pbsa error : Scale paremeter for PBSA Ray Luo
- AMBER: ESURF - SASA - isolate residues Deepangi Pandit
- RE: AMBER: resp and 99999 Ross Walker
- AMBER: Problem in EVB and Trajectory analysis sai kumar ramadugu
- AMBER: Question: GAFF Chih-Ying Lin
- AMBER: QM/MM Chih-Ying Lin
Saturday, 6 September 2008
- AMBER: Explanation of the energy unit ? Marek Malý
Sunday, 7 September 2008
- AMBER: Test error in installing amber 10 using four threads on a single-cpu machine haixiao jin
- Re: AMBER: Test error in installing amber 10 using four threads on a single-cpu machine David A. Case
- Re: AMBER: Test error in installing amber 10 using four threads on a single-cpu machine haixiao jin
- Re: AMBER: Test error in installing amber 10 using four threads on a single-cpu machine David A. Case
- Re: AMBER: Explanation of the energy unit ? David A. Case
- AMBER: PMEMD installation problem. Cenk \(Jenk\) Andac
Monday, 8 September 2008
- RE: AMBER: PMEMD installation problem. Ross Walker
- RE: AMBER: PMEMD installation problem. Cenk \(Jenk\) Andac
- Re: AMBER: PMEMD installation problem. Robert Duke
- AMBER: amber minimisation Majeed Shaik
- Re: AMBER: amber minimisation Carlos Simmerling
- Re: AMBER: PMEMD installation problem. Cenk \(Jenk\) Andac
- Re: AMBER: amber minimisation David A. Case
- AMBER: Changes in the Amber web site David A. Case
- Re: AMBER: Explanation of the energy unit ? Marek Malý
- Re: AMBER: Explanation of the energy unit ? Carlos Simmerling
- RE: AMBER: Changes in the Amber web site Majeed Shaik
- Re: AMBER: Changes in the Amber web site Carlos Simmerling
- AMBER: problem when running energy minimization with polarizable potential Yongmei Pan
- AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors Ben Roberts
- AMBER: Another problem when trying to compile Sander in debug mode Ben Roberts
- Re: AMBER: Need help... High energies for complex... Waqas Nasir
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling
- RE: AMBER: Install problems Marisa Frechero
- Re: AMBER: Explanation of the energy unit ? Marek Malý
- Re: AMBER: Install problems Gustavo Seabra
- Re: AMBER: Explanation of the energy unit ? Carlos Simmerling
- Re: AMBER: Explanation of the energy unit ? Gustavo Seabra
- Re: AMBER: Explanation of the energy unit ? Marek Malý
- Re: AMBER: Explanation of the energy unit ? Marek Malý
- Re: AMBER: Explanation of the energy unit ? Carlos Simmerling
- Re: AMBER: Is there a way to cluster frames of a trajectory? Sasha Buzko
- AMBER: who can give a sample input file regarding the energy decomposition with sander? Yongmei Pan
- Re: AMBER: Is there a way to cluster frames of a trajectory? Carlos Simmerling
- Re: AMBER: Explanation of the energy unit ? David A. Case
- AMBER: NAB parameter: wcons ramu.vt.edu
- Re: AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors David A. Case
- Re: AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors Ben Roberts
- Re: AMBER: who can give a sample input file regarding the energy decomposition with sander? David A. Case
- AMBER: energy decomposition with sander? Yongmei Pan
- Re: AMBER: Is there a way to cluster frames of a trajectory? Sasha Buzko
- Re: AMBER: Install problems Mark Williamson
Tuesday, 9 September 2008
- Re: AMBER: Install problems David A. Case
- Re: AMBER: Need help... High energies for complex... Waqas Nasir
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling
- Re: AMBER: Using AMBER forces Germain Vallverdu
- AMBER: PMEMD and sander.MPI Germain Vallverdu
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling
- Re: AMBER: Need help... High energies for complex... Waqas Nasir
- Re: AMBER: Need help... High energies for complex... Lachele Foley (Lists)
- Re: AMBER: PMEMD and sander.MPI Robert Duke
- AMBER: Amber10 Compilation Anthony Cruz
- AMBER: D2O Chih-Ying Lin
- Re: AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors Ben Roberts
- Re: AMBER: D2O Carlos Simmerling
- Re: AMBER: Install problems Mark Williamson
- Re: AMBER: D2O David A. Case
- Re: AMBER: problem when running energy minimization with polarizable potential David A. Case
- Re: AMBER: Install problems M. L. Dodson
- AMBER: about NMR refinement in explicit solvent Rogelio Hernández
- Re: AMBER: Install problems David A. Case
- Re: AMBER: D2O Chih-Ying Lin
- Re: AMBER: problem when running energy minimization with polarizable potential Yongmei Pan
- AMBER: Emperical Valence Bond sai kumar ramadugu
- Re: AMBER: D2O Carlos Simmerling
- AMBER: Preparing peptides with D-amino acids David Watson
- Re: AMBER: Preparing peptides with D-amino acids Carlos Simmerling
- Re: AMBER: Preparing peptides with D-amino acids Carlos Simmerling
- Re: AMBER: Preparing peptides with D-amino acids David Watson
- Re: AMBER: Preparing peptides with D-amino acids Carlos Simmerling
Wednesday, 10 September 2008
- AMBER: RDF: Segmentation fault Sergey Samsonov
- Re: AMBER: Explanation of the energy unit ? Marek Malý
- AMBER: steered MD Germain Vallverdu
- Re: AMBER: steered MD Carlos Simmerling
- Re: AMBER: steered MD Germain Vallverdu
- Re: AMBER: steered MD Carlos Simmerling
- Re: AMBER: steered MD David A. Case
- Re: AMBER: steered MD Adrian Roitberg
- Re: AMBER: steered MD Germain Vallverdu
- Re: AMBER: NAB parameter: wcons David A. Case
- RE: AMBER: Amber10 Compilation Ross Walker
- AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik
- AMBER: binding energy: high ELE CHAMI F.
- RE: AMBER: Cutoff list exceeds largest sphere in unit cell Ross Walker
- RE: AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik
- RE: AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik
- RE: AMBER: Cutoff list exceeds largest sphere in unit cell Ross Walker
Thursday, 11 September 2008
- RE: AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik
- AMBER: Nonbonded FE parameter missing in frcmod. moitrayee.mbu.iisc.ernet.in
- Re: AMBER: D2O Chih-Ying Lin
- Re: AMBER: D2O Carlos Simmerling
- Re: AMBER: D2O Adrian Roitberg
- Re: AMBER: binding energy: high ELE David A. Case
- Re: AMBER: Nonbonded FE parameter missing in frcmod. David A. Case
- RE: AMBER: binding energy: high ELE CHAMI F.
- Re: AMBER: about NMR refinement in explicit solvent David A. Case
- Re: AMBER: Nonbonded FE parameter missing in frcmod. moitrayee.mbu.iisc.ernet.in
- AMBER: Help...which commands in ptraj does clustering by RMSD? Jose Borreguero
- Re: AMBER: Help...which commands in ptraj does clustering by RMSD? Sasha Buzko
- Re: AMBER: Help...which commands in ptraj does clustering by RMSD? Jose Borreguero
- Re: AMBER: Help...which commands in ptraj does clustering by RMSD? Sasha Buzko
- Re: AMBER: Help...which commands in ptraj does clustering by RMSD? Jose Borreguero
- Re: AMBER: D2O Chih-Ying Lin
- AMBER: xleap and Sirius on ubuntu 8.04 alsarraj
- Re: AMBER: xleap and Sirius on ubuntu 8.04 Gustavo Seabra
- Re: AMBER: xleap and Sirius on ubuntu 8.04 Sasha Buzko
- Re: AMBER: compilation problem john smith
Friday, 12 September 2008
- Re: AMBER: compilation problem David A. Case
- AMBER: EVB allocation problem sai kumar ramadugu
Sunday, 14 September 2008
- AMBER: Comment: constant pH, non-integer charge -> weird error Markus Kaukonen
- AMBER: mulliken charges in QM/MM calculation Barbault Florent
- RE: AMBER: mulliken charges in QM/MM calculation Ross Walker
- AMBER: Failure of antechamber in amber10 Francesco Pietra
- AMBER: problem in installing parallel version of amber10 with lam Shibasish Chowdhury
- AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in
Monday, 15 September 2008
- Re: AMBER: 3fe-4s cluster parameter file generation David A. Case
- Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in
- Re: AMBER: 3fe-4s cluster parameter file generation David A. Case
- Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in
- Re: AMBER: 3fe-4s cluster parameter file generation Hakkim Boy
- Re: AMBER: 3fe-4s cluster parameter file generation S.Sundar Raman
- Re: AMBER: 3fe-4s cluster parameter file generation David A. Case
- AMBER: question about dihedral angles Harry (Yicun) Ni
- AMBER: Hydrogen bond energies in explicit solvent. Waqas Nasir
- Re: AMBER: Hydrogen bond energies in explicit solvent. Carlos Simmerling
- Re: AMBER: question about dihedral angles Ilyas Yildirim
- Re: AMBER: Hydrogen bond energies in explicit solvent. Waqas Nasir
- Re: AMBER: Hydrogen bond energies in explicit solvent. Carlos Simmerling
- Re: AMBER: Hydrogen bond energies in explicit solvent. Waqas Nasir
- Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in
- Re: AMBER: Hydrogen bond energies in explicit solvent. Carlos Simmerling
- AMBER: Minimizaton stops after Ncyc steps only mon_sharma.research.iiit.ac.in
- AMBER: Announcement of ACS COMP Division CCG and HP award deadlines for Spring 2009 meeting Carlos Simmerling
- Re: AMBER: D2O Nicolas Lux Fawzi
- Re: AMBER: 3fe-4s cluster parameter file generation S.Sundar Raman
- Re: AMBER: Minimizaton stops after Ncyc steps only Carlos Simmerling
- AMBER: parallel amber 10 sander.MPI (low cpu utilization) meandme meandme
- AMBER: amber 10 parallel cpu utlization meandme meandme
- AMBER: AMBER10 Compilation (SGI Altix) Anthony Cruz
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross
- AMBER: MM-PBSA/NMODE in Amber 10 Peterson, Matthew W. (MPETERSON)
- AMBER: Temperature regulation julliane Yoneda
- Re: AMBER: Temperature regulation Carlos Simmerling
- Re: AMBER: MM-PBSA/NMODE in Amber 10 Daniel Oehme
- RE: AMBER: problem in installing parallel version of amber10 with lam Ross Walker
- RE: AMBER: amber 10 parallel cpu utlization Ross Walker
- RE: AMBER: AMBER10 Compilation (SGI Altix) Ross Walker
Tuesday, 16 September 2008
- AMBER: top and crd files without hydrogen Waqas Nasir
- Re: AMBER: top and crd files without hydrogen Carlos Simmerling
- Re: AMBER: top and crd files without hydrogen Waqas Nasir
- RE: AMBER: problem in installing parallel version of amber10 with lam Shibasish Chowdhury
- Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in
- AMBER: nmode/nab entropy calculations memory issues chaitanya koppisetty
- Re: AMBER: nmode/nab entropy calculations memory issues Andreas Svrcek-Seiler
- AMBER: problem with editing with xleap moitrayee.mbu.iisc.ernet.in
- Re: AMBER: AMBER10 Compilation (SGI Altix) Anthony Cruz
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross
- Re: AMBER: Temperature regulation julliane Yoneda
- Re: AMBER: Temperature regulation Carlos Simmerling
- Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in
- Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross
- Re: AMBER: Temperature regulation Myunggi Yi
- Re: AMBER: Temperature regulation julliane Yoneda
- Re: AMBER: Temperature regulation julliane Yoneda
- AMBER: AMBER9 Compilation chen bents
- AMBER: amber 9 install chen bents
- Re: AMBER: amber 9 install Ye Mei
- Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in
Wednesday, 17 September 2008
- Re: AMBER: amber 9 install chen bents
- AMBER: nmode/nab entropy calculations without hydrogens chaitanya koppisetty
- AMBER: acetone box parvesh singh
- AMBER: Question Beale, John
- Re: AMBER: Question Carlos Simmerling
- Re: AMBER: 3fe-4s cluster parameter file generation David A. Case
- Re: AMBER: problem with editing with xleap David A. Case
- Re: AMBER: mmpbsa molsurf.c error David A. Case
- AMBER: MD simulation crashed Aust, Susanne
- Re: AMBER: MD simulation crashed Carlos Simmerling
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross
- AMBER: adding new potential function Harianto Tjong
- AMBER: Some Problems With the Installation of Ambertools Manikandan Chandrasekaran
- AMBER: Dihedral: ptraj waqasuddin.khan.iccs.edu
Thursday, 18 September 2008
- Re: AMBER: Some Problems With the Installation of Ambertools Atro Tossavainen
- Re: AMBER: Dihedral: ptraj Carlos Simmerling
- Re: AMBER: Dihedral: ptraj waqasuddin.khan.iccs.edu
- Re: AMBER: Dihedral: ptraj Carlos Simmerling
- Re: AMBER: Some Problems With the Installation of Ambertools David A. Case
- AMBER: Single point energy calculations with explicit solvent. Waqas Nasir
- Re: AMBER: Single point energy calculations with explicit solvent. Carlos Simmerling
- AMBER: problem with traj and strip waters Steve Seibold
- Re: AMBER: problem with traj and strip waters Carlos Simmerling
- Re: AMBER: problem with traj and strip waters David A. Case
- AMBER: problem with traj and strip waters Steve Seibold
- Re: AMBER: problem with traj and strip waters Carlos Simmerling
- AMBER: Error: PB bomb in pb_reslist(): maxnbr too small Rajendra P. OJHA
- Re: AMBER: Some Problems With the Installation of Ambertools Manikandan Chandrasekaran
- Re: AMBER: Some Problems With the Installation of Ambertools David A. Case
- Re: AMBER: xleap fails to savemol2 alsarraj
- AMBER: RMSD restraint in umbrella sampling nurith.rice.edu
- AMBER: help can amber couple part of the system to different heat bath? Jose Borreguero
- AMBER: help can amber couple part of the system to different heat bath? Jose Borreguero
- AMBER: problems with ptraj and strip waters Steve Seibold
- Re: AMBER: RMSD restraint in umbrella sampling Carlos Simmerling
- Re: AMBER: problems with ptraj and strip waters Carlos Simmerling
- Re: AMBER: problems with ptraj and strip waters Gustavo Seabra
Friday, 19 September 2008
- AMBER: increasing temperature smoothly Germain Vallverdu
- Re: AMBER: increasing temperature smoothly David A. Case
- RE: AMBER: increasing temperature smoothly Ross Walker
- Re: AMBER: Some Problems With the Installation of Ambertools Manikandan Chandrasekaran
- Re: AMBER: xleap fails to savemol2 alsarraj
- AMBER: molecule drift out of water box? Qiuting Hong
- Re: AMBER: molecule drift out of water box? Ilyas Yildirim
Saturday, 20 September 2008
- AMBER: Dihedral Drive Hashem Taha
- Re: AMBER: Dihedral Drive Ilyas Yildirim
- Re: AMBER: Some Problems With the Installation of Ambertools David A. Case
- Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? cgji
- AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber? Zhao, Zhen (zhaozh)
- Re: AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber? Barbault Florent
Sunday, 21 September 2008
- AMBER: bis(trifluoromethylsulfonyl)imide (Tf2N) babak minoofar
- Re: AMBER: bis(trifluoromethylsulfonyl)imide (Tf2N) David Watson
- Re: AMBER: molecule drift out of water box? Qiuting Hong
- Re: AMBER: molecule drift out of water box? Ilyas Yildirim
- AMBER: multiple heat baths in a single simulation? Jose Borreguero
- Re: AMBER: molecule drift out of water box? Qiuting Hong
- Re: AMBER: molecule drift out of water box? Ilyas Yildirim
Monday, 22 September 2008
- Re: AMBER: MM-PBSA/NMODE in Amber 10 Daniel Oehme
- Re: AMBER: mmpbsa molsurf.c error parvesh singh
- AMBER: fix for POL3 heating problem? Grange Hermitage
- Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? David A. Case
- Re: AMBER: increasing temperature smoothly Germain Vallverdu
- Re: AMBER: increasing temperature smoothly David A. Case
- Re: AMBER: compilation problem john smith
- Re: AMBER: compilation problem David A. Case
- AMBER: Re: reaction coordinate in umbrella sampling Sudha Mani Karra
- AMBER: Position: Postdoctoral Fellow Willy Valdivia-Granda
- Re: AMBER: increasing temperature smoothly Germain Vallverdu
- AMBER: The forming of micelle Chih-Ying Lin
- Re: AMBER: The forming of micelle Adrian Roitberg
- Re: AMBER: xleap fails to savemol2 Mark Williamson
- AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. Zhao, Zhen (zhaozh)
- Re: AMBER: The forming of micelle Chih-Ying Lin
- AMBER: The size of the simulation box and the # of solute / water molecules? Chih-Ying Lin
- Re: AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. Tom Darden
Tuesday, 23 September 2008
- Re: AMBER: Re: reaction coordinate in umbrella sampling Jerome.GOLEBIOWSKI.unice.fr
- AMBER: MMPBSA error Cristina Sisu
- RE: AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. Zhao, Zhen (zhaozh)
- AMBER: replica exchange with amber9 greddy1.umd.edu
- Re: AMBER: replica exchange with amber9 Carlos Simmerling
- Re: AMBER: The forming of micelle Chih-Ying Lin
- AMBER: MD goes wrong baohua zhang
- Re: AMBER: MD goes wrong Adrian Roitberg
- RE: AMBER: MD goes wrong Ross Walker
Wednesday, 24 September 2008
- AMBER: to prepare pdb file fro unusual amino acid. priya priya
- Re: AMBER: to prepare pdb file fro unusual amino acid. Hakkim Boy
- AMBER: error while running REMD in amber9 priya priya
- Re: AMBER: The forming of micelle (CMC) Chih-Ying Lin
- Re: AMBER: error while running REMD in amber9 Carlos Simmerling
- Re: AMBER: to prepare pdb file fro unusual amino acid. FyD
- AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support Pablo Englebienne
- AMBER: solvate without translating Anuradha Mittal
- Re: AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support Robert Duke
- Re: AMBER: The forming of micelle (CMC) Gustavo Seabra
- AMBER: how to enlarge the TIP3PBOX size Qiuting Hong
- Re: AMBER: how to enlarge the TIP3PBOX size Carlos Simmerling
- Re: AMBER: to prepare pdb file fro unusual amino acid. waqasuddin.khan.iccs.edu
- Re: AMBER: how to enlarge the TIP3PBOX size waqasuddin.khan.iccs.edu
- RE: AMBER: to prepare pdb file fro unusual amino acid. Ross Walker
- RE: AMBER: solvate without translating Ross Walker
- RE: AMBER: how to enlarge the TIP3PBOX size Ross Walker
Thursday, 25 September 2008
- AMBER: Amber GB problems on PMEMD !! Sampath Koppole
- Re: AMBER: Amber GB problems on PMEMD !! Robert Duke
- Re: AMBER: Amber GB problems on PMEMD !! Sampath Koppole
- RE: AMBER: how to enlarge the TIP3PBOX size Ross Walker
- RE: AMBER: to prepare pdb file fro unusual amino acid. Ross Walker
- RE: AMBER: solvate without translating Ross Walker
- Re: AMBER: Amber GB problems on PMEMD !! Andreas Svrcek-Seiler
- RE: AMBER: Amber GB problems on PMEMD !! Ross Walker
- Re: AMBER: to prepare pdb file fro unusual amino acid. priya priya
- Re: AMBER: error while running REMD in amber9 priya priya
- Re: AMBER: error while running REMD in amber9 Carlos Simmerling
- Re: AMBER: error while running REMD in amber9 priya priya
- Re: AMBER: error while running REMD in amber9 Carlos Simmerling
- Re: AMBER: error while running REMD in amber9 priya priya
- Re: AMBER: error while running REMD in amber9 Carlos Simmerling
- Re: AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support Pablo Englebienne
- Re: AMBER: compilation problem Atro Tossavainen
- AMBER: Amber on Infiniband clusters: SDR vs DDR cables? Sasha Buzko
Friday, 26 September 2008
- Re: AMBER: how to enlarge the TIP3PBOX size Qiuting Hong
- AMBER: Problem In Paralklel Amber Ranga Swamy
- Re: AMBER: Problem In Paralklel Amber Carlos Simmerling
- Re: AMBER: compilation problem David A. Case
- Re: AMBER: how to enlarge the TIP3PBOX size David A. Case
- AMBER: MD at a given pH Beale, John
- AMBER: Harmonic restraint between two atoms greddy1.umd.edu
- Re: AMBER: Harmonic restraint between two atoms Adrian Roitberg
- Re: AMBER: compilation problem Manikandan Chandrasekaran
- Re: AMBER: MM_PBSA snapshot statistic calc problem haixiao jin
Saturday, 27 September 2008
- AMBER: mmpbsa errors in redoing the tutorial A3:MMPBSA haixiao jin
- AMBER: Constant pH simulation force field Soonmin Jang
- Re: AMBER: MD at a given pH David A. Case
- Re: AMBER: Constant pH simulation force field David A. Case
- Re: AMBER: compilation problem David A. Case
- AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra
- Re: AMBER: Leap atoms CL and OXT do not have a type Carlos Simmerling
- Re: AMBER: Leap atoms CL and OXT do not have a type David A. Case
- Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra
- Re: AMBER: Leap atoms CL and OXT do not have a type David A. Case
- Re: AMBER: Leap atoms CL and OXT do not have a type Carlos Simmerling
- Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra
- Re: AMBER: Leap atoms CL and OXT do not have a type Carlos Simmerling
- Re: AMBER: compilation problem Atro Tossavainen
- Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra
Sunday, 28 September 2008
- AMBER: a question Adrien Delmont
- RE: AMBER: a question Ross Walker
- Re: AMBER: Problem In Paralklel Amber Ranga Swamy
Monday, 29 September 2008
- AMBER: energy terms in hybrid REMD calculation Ye Mei
- RE: AMBER: a question oguz gurbulak
- RE: AMBER: a question oguz gurbulak
- Re: AMBER: a question Adrien Delmont
- AMBER: Location of vdw radii and partial charges for ff99SB Charles Letner, Ph.D.
- RE: AMBER: Problem In Paralklel Amber Ross Walker
- RE: AMBER: a question Ross Walker
- RE: AMBER: Location of vdw radii and partial charges for ff99SB Ross Walker
- AMBER: unsubscribe amber steinbrt.scripps.edu
- Re: AMBER: Location of vdw radii and partial charges for ff99SB Carlos Simmerling
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross
- Re: AMBER: MM_PBSA snapshot statistic calc problem Vasu Chandrasekaran
- Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra
- RE: AMBER: MM_PBSA snapshot statistic calc problem Peterson, Matthew W.
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross
- AMBER: coordinate file question Robert Hanson
- RE: AMBER: coordinate file question Ross Walker
Tuesday, 30 September 2008
- Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra
- AMBER: Ac-Co Parameters for Amber suhaib sh
- Re: AMBER: coordinate file question Robert Hanson
- RE: AMBER: coordinate file question Ross Walker
- AMBER: Ca ions not recognized Cristina Sisu
- RE: AMBER: Ca ions not recognized Peterson, Matthew W.
- AMBER: Buckingham potential Diddo Diddens
- Re: AMBER: Buckingham potential Andreas Svrcek-Seiler
- Re: AMBER: Buckingham potential Diddo Diddens
- AMBER: cluster for running amber10 Guillermo Mulliert Carlín
- Re: AMBER: Buckingham potential Adrian Roitberg
- RE: AMBER: cluster for running amber10 Ross Walker
- AMBER: MM-PBSA problem : Missing PBCAV for PB Carra, Claudio (JSC-SK)[USRA]
- AMBER: problem with parmchck aneesh cna
- Re: AMBER: coordinate file question Robert Hanson
- AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE liu junjun
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross
- RE: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE Ross Walker
- AMBER: FW: Amber 9 mhamed.birzeit.edu
- Re: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE Jed W Pitera
- Re: AMBER: FW: Amber 9 Gustavo Seabra
- Re: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE liu junjun
- Re: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE liu junjun
- AMBER: problem of use MPICHI2 to run RMED on amber10 xwu.purdue.edu
- Re: AMBER: problem of use MPICHI2 to run RMED on amber10 Carlos Simmerling
- Re: AMBER: problem of use MPICHI2 to run RMED on amber10 xwu.purdue.edu
- Re: AMBER: problem of use MPICHI2 to run RMED on amber10 Carlos Simmerling
- AMBER: How to set up a water slab in Amber? Zhao, Zhen (zhaozh)
- Re: AMBER: problem of use MPICHI2 to run RMED on amber10 xwu.purdue.edu
- Re: AMBER: problem of use MPICHI2 to run RMED on amber10 Carlos Simmerling
- Re: AMBER: Ac-Co Parameters for Amber suhaib sh

Last message date: Wed Oct 01 2008 - 05:12:12 PDT
Archived on: Fri Dec 20 2024 - 05:53:45 PST

Amber Archive Sep 2008 by date