Amber Archive Mar 2007: by date

Thursday, 1 March 2007
- Re: AMBER: solvent accessible surface area (SASA) Carlos Simmerling
- AMBER: Disulfide Problem Beale, John
- Re: AMBER: Disulfide Problem Carlos Simmerling
- Re: AMBER: RESP calculation of modified nucleotides mathew k varghese
- RE: AMBER: Disulfide Problem Beale, John
- Re: AMBER: solvent accessible surface area (SASA) Esther Brugger
- Re: AMBER: solvent accessible surface area (SASA) Carlos Simmerling
- AMBER: Restart from restart file obtained from ptraj with added velocities j j
- RE: AMBER: Disulfide Problem Kristina Furse
- Re: AMBER: solvent accessible surface area (SASA) Esther Brugger
- Re: AMBER: solvent accessible surface area (SASA) David A. Case
- Re: AMBER: Restart from restart file obtained from ptraj with added velocities Thomas Cheatham III
- Re: AMBER: momentum and periodic boundary condition David A. Case
- Re: AMBER: Disulfide Problem David A. Case
- AMBER: [rsachdeva.imtech.res.in: A query] David A. Case
- Re: AMBER: solvent accessible surface area (SASA) Esther Brugger
- Re: AMBER: Restart from restart file obtained from ptraj with added velocities j j
- Re: AMBER: RESP calculation of modified nucleotides Raviprasad Aduri
- Re: AMBER: solvent accessible surface area (SASA) David A. Case
- Re: AMBER: [rsachdeva.imtech.res.in: A query] Viktor Hornak
- Re: AMBER: solvent accessible surface area (SASA) Esther Brugger
- Re: AMBER: solvent accessible surface area (SASA) Carlos Simmerling
- Re: AMBER: solvent accessible surface area (SASA) Esther Brugger
- Re: AMBER: RESP calculation of modified nucleotides mathew k varghese
Friday, 2 March 2007
- Re: AMBER: RESP calculation of modified nucleotides mathew k varghese
- Re: AMBER: solvent accessible surface area (SASA) Carlos Simmerling
- Re: AMBER: SCF convergence issues Steven Winfield
- AMBER: qm/mm ti Ben Sattelle
- Re: AMBER: qm/mm ti Adrian Roitberg
- Re: AMBER: Disulfide Problem xiaoqin huang
- Re: AMBER: Disulfide Problem Carlos Simmerling
- AMBER: Restart Files Steve Seibold
- Re: AMBER: Restart Files Carlos Simmerling
- AMBER: restraints during MD Seth Lilavivat
- Re: AMBER: restraints during MD Carlos Simmerling
- AMBER: reproducibility between software Stern, Julie
- Re: AMBER: reproducibility between software Carlos Simmerling
- AMBER: OpenMPI on MacBook Pro -- problems Mike Summers
- RE: AMBER: Restart Files Steve Seibold
- Re: AMBER: RESP calculation of modified nucleotides Raviprasad Aduri
- Re: AMBER: reproducibility between software Thomas Cheatham III
- Re: AMBER: OpenMPI on MacBook Pro -- problems David A. Case
- AMBER: Amber 9 make parallel fails with mpich Rene Salmon
- Re: AMBER: reproducibility between software Robert Duke
- Re: AMBER: Amber 9 make parallel fails with mpich David A. Case
- Re: AMBER: Restart Files Gustavo Seabra
- AMBER: ptraj average structure strip water Youyi Peng
- RE: AMBER: Restart Files Steve Seibold
- AMBER: Calcium parameters Lei Jia
- Re: AMBER: OpenMPI on MacBook Pro -- problems Mike Summers
- Re: AMBER: OpenMPI on MacBook Pro -- problems Mike Summers
- Re: AMBER: Restart Files Gustavo Seabra
- AMBER: Restraints on modified NA's Seth Lilavivat
- Re: AMBER: Calcium parameters Qing Zhang
- AMBER: calculate RMSD of only chain C 赵亚雪
Saturday, 3 March 2007
- Re: AMBER: calculate RMSD of only chain C Carlos Simmerling
- Re: AMBER: OpenMPI on MacBook Pro -- problems Mike Summers
- AMBER: TI calculation: charge is not zero in the perturbed state brmeher.iitg.ernet.in
- Re: AMBER: TI calculation: charge is not zero in the perturbed state David A. Case
- AMBER: denaturing salt conditions Sean Rathlef
- Re: AMBER: coordinate changes using ptraj Mike Summers
- Re: AMBER: coordinate changes using ptraj Carlos Simmerling
- Re: AMBER: denaturing salt conditions Jiri Sponer
- AMBER: coordinate changes using ptraj Mike Summers
Sunday, 4 March 2007
- AMBER: Question about translational and rotational degree of freedom in MM-PBSA v9 computations Cenk Andac
- Re: AMBER: coordinate changes using ptraj Carlos Simmerling
- AMBER: prep file limit exceeding gurpreet singh
Monday, 5 March 2007
- AMBER: distance calculation! r. a.
- AMBER: psi , phi angles deepti nayar
- Re: AMBER: psi , phi angles Carlos Simmerling
- AMBER: pbsa installation problem bala
- Re: AMBER: coordinate changes using ptraj David A. Case
- Re: AMBER: Restraints on modified NA's David A. Case
- Re: AMBER: psi , phi angles Piotr Cieplak
- Re: AMBER: psi , phi angles Carlos Simmerling
- Re: AMBER: psi , phi angles M. L. Dodson
- Re: AMBER: pbsa installation problem David A. Case
- AMBER: Beale, John
- AMBER: Beale, John
- Re: AMBER: psi , phi angles Piotr Cieplak
- Re: AMBER: psi , phi angles Carlos Simmerling
- Re: AMBER: psi , phi angles Piotr Cieplak
- AMBER: constraint pdb file Stern, Julie
- AMBER: mm_pbsa individual contributions of residues AYTUG TUNCEL
- AMBER: how to incorporate ismem =1 into mm_pbsa AYTUG TUNCEL
- AMBER: any general approach to create SiO2 wall Sisir Das
- Re: AMBER: prep file limit exceeding David A. Case
Tuesday, 6 March 2007
- Re: AMBER: psi , phi angles Ilyas Yildirim
- AMBER: Trimannoside Problem Sandeep Kaushik
- AMBER: how is the standard deviations calculated in mm-pbsa? Magne Olufsen
- AMBER: DHAS_10_12 compilation aborted for egb.f Jesus Angulo
- Re: AMBER: DHAS_10_12 compilation aborted for egb.f David A. Case
- RE: AMBER: DHAS_10_12 compilation aborted for egb.f Jesus Angulo
- Re: AMBER: Trimannoside Problem kkirschn.hamilton.edu
- AMBER: how to modify map.DG-AMBER file? Seth Lilavivat
- Re: AMBER: how to modify map.DG-AMBER file? David A. Case
- Re: AMBER: how is the standard deviations calculated in mm-pbsa? David A. Case
- AMBER: addles segmentation fault deepti nayar
Wednesday, 7 March 2007
- AMBER: Topology file problem in TI ! Pradipta Bandyopadhyay
- Re: AMBER: Topology file problem in TI ! Thomas Steinbrecher
- Re: AMBER: addles segmentation fault David A. Case
- Re: AMBER: Amber 9, sander imin = 5, -y flag S.Sundar Raman
- Re: AMBER: Topology file problem in TI ! Ilyas Yildirim
- Re: AMBER: DHAS_10_12 compilation aborted for egb.f David A. Case
- Re: AMBER: Amber 9, sander imin = 5, -y flag Carlos Simmerling
- Re: AMBER: Topology file problem in TI ! Thomas Steinbrecher
- AMBER: simulation of the phosphorylated protein Fenghui Fan
- Re: AMBER: Topology file problem in TI ! Pradipta Bandyopadhyay
- Re: AMBER: Trimannoside Problem Sandeep Kaushik
Thursday, 8 March 2007
- Re: AMBER: addles segmentation fault deepti nayar
- Re: AMBER: Trimannoside Problem kkirschn.hamilton.edu
- Re: AMBER: Trimannoside Problem Austin B. Yongye
- Re: AMBER: Topology file problem in TI ! David A. Case
- Re: AMBER: Topology file problem in TI ! Pradipta Bandyopadhyay
- Re: AMBER: Problems with QMMM tests on Altix Roberto Gomperts
Friday, 9 March 2007
- AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? Chengwen Chen
- Re: AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? Carlos Simmerling
- AMBER: problem with ptraj with calculating auto time correlation functions Terry Lang
- AMBER: abnormal termination of tleap Pankaj R. Daga
- Re: AMBER: problem with ptraj with calculating auto time correlation functions David A. Case
- Re: AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? Chengwen Chen
Saturday, 10 March 2007
- AMBER: rmsd calculation in ptraj gurpreet singh
- AMBER: rmsd calculation in ptraj gurpreet singh
- Re: AMBER: rmsd calculation in ptraj Carlos Simmerling
- Re: AMBER: problem with ptraj with calculating auto time correlation functions Terry Lang
- Re: AMBER: problem with ptraj with calculating auto time correlation functions David A. Case
- AMBER: rmsd calculation in ptraj II gurpreet singh
- Re: AMBER: rmsd calculation in ptraj II David A. Case
Sunday, 11 March 2007
- AMBER: unable to run test Anju Sharma
- AMBER: addles deepti nayar
- Re: AMBER: unable to run test David A. Case
Monday, 12 March 2007
- AMBER: Essential ions and water molecules in MMPBSA computations Cenk Andac
- AMBER: NEB tutorial deepti nayar
- Re: AMBER: addles Carlos Simmerling
- Re: AMBER: addles deepti nayar
- AMBER: The parallel test fails while sander.MPI seems to be installed correctly Mostafa Sadighi
- Re: AMBER: The parallel test fails while sander.MPI seems to be installed correctly Carlos Simmerling
- AMBER: DNA Helicoïdal Plots over time Stéphane Téletchéa
- Re: AMBER: DNA Helicoïdal Plots over time Vitor Felix
- Re: AMBER: Essential ions and water molecules in MMPBSA computations Jiri Sponer
- Re: AMBER: The parallel test fails while sander.MPI seems to be installed correctly Gustavo Seabra
- Re: AMBER: Essential ions and water molecules in MMPBSA computations Cenk Andac
- Re: AMBER: Essential ions and water molecules in MMPBSA computations Jiri Sponer
- AMBER: Can I measure improper torsion by ptarj? Chengwen Chen
- Re: AMBER: Can I measure improper torsion by ptarj? David A. Case
- Re: AMBER: Can I measure improper torsion by ptarj? Chengwen Chen
Tuesday, 13 March 2007
- AMBER: hi.. Anju Sharma
- Re: AMBER: hi.. Carlos Simmerling
- Re: AMBER: hi.. Anju Sharma
- Re: AMBER: hi.. Carlos Simmerling
- RE: AMBER: hi.. Rafi Ahmad
- Re: AMBER: hi.. Anju Sharma
- Re: AMBER: hi.. Anju Sharma
- RE: AMBER: hi.. Rafi Ahmad
- AMBER: problem with mm_pbsa Yves Boulard
- Re: AMBER: Can I measure improper torsion by ptarj? David A. Case
- Re: AMBER: Can I measure improper torsion by ptarj? Bill Ross
- AMBER: poor performance of sander on a quad-core linux machine Lillian chong
- Re: AMBER: poor performance of sander on a quad-core linux machine David A. Case
- AMBER: problem while running minimisation Anju Sharma
- Re: AMBER: problem while running minimisation Anju Sharma
- AMBER: Problem Solved Anju Sharma
- AMBER: NEB tutorial and addles deepti nayar
- AMBER: problem while analysing result Anju Sharma
- Re: AMBER: problem while analysing result puneet kacker
- Re: AMBER: problem while analysing result Anju Sharma
- Re: AMBER: problem while analysing result Syed Tarique Moin
- Re: AMBER: problem while analysing result puneet kacker
Wednesday, 14 March 2007
- AMBER: dna forcefield: PARMBSC0 Alberto Perez
- AMBER: Need help in Analysis Anju Sharma
- Re: AMBER: Need help in Analysis Heike.Meiselbach.chemie.uni-erlangen.de
- Re: AMBER: Need help in Analysis Gustavo Seabra
- AMBER: AMBER hydrophobic Box : script Sophie Barbe
- AMBER: torsion angle deepti nayar
- Re: AMBER: torsion angle Carlos Simmerling
- Re: AMBER: AMBER hydrophobic Box : script David A. Case
- Re: AMBER: AMBER hydrophobic Box : script Sophie Barbe
- Re: AMBER: AMBER hydrophobic Box : script David A. Case
- AMBER: Question about Boron Kara Di Giorgio
- AMBER: mmpbsa free energy pairwise decomposition Gianluca Degliesposti
- AMBER: Regarding counter ions Rafi Ahmad
- AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) Eric Shamay
- Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) Carlos Simmerling
- Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) Eric Shamay
- AMBER: Lipid bilayer nag raj
- AMBER: How to build organic compound in Amber Anju Sharma
- Re: AMBER: torsion angle deepti nayar
Thursday, 15 March 2007
- AMBER: hii Anju Sharma
- AMBER: problem decomposing energies (MMPBSA) Cyril Bauvais
- Re: AMBER: hii Benjamin Juhl
- AMBER: Problem related simulation of dimer priya priya
- Re: AMBER: Problem related simulation of dimer Carlos Simmerling
- AMBER: Dipolar and Inertia Moments kepa koldo burusco
- Re: AMBER: Problem related simulation of dimer Abhilash
- RE: AMBER: NEB tutorial and addles Ross Walker
- Re: AMBER: solvate shell Carlos Simmerling
- AMBER: solvate shell janavi raghavan
- Re: AMBER: Problem related simulation of dimer David A. Case
- Re: AMBER: Problem related simulation of dimer janavi raghavan
- Re: AMBER: solvate shell janavi raghavan
- Re: AMBER: Problem related simulation of dimer janavi raghavan
- AMBER: van der waals parameters. Stefano Tonzani
- Re: AMBER: van der waals parameters. David A. Case
- Re: AMBER: solvate shell David A. Case
- AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap Laura McDriscoll
Friday, 16 March 2007
- Re: AMBER: Problem related simulation of dimer Sandeep Kaushik
- AMBER: hi Anju Sharma
- Re: AMBER: hi Carlos Simmerling
- AMBER: Problem with anisotropic pressure scaling Linda Prengaman
- Re: AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap David A. Case
- RE: AMBER: Problem with anisotropic pressure scaling Akshay Patny
- Re: AMBER: Problem with anisotropic pressure scaling Robert Duke
- Re: AMBER: Problem with anisotropic pressure scaling Andy Purkiss-Trew
- Re: AMBER: Problem with anisotropic pressure scaling David A. Case
- Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) David A. Case
- AMBER: vlimit error Amit Kumar
- AMBER: antechamber error Ilyas Yildirim
Saturday, 17 March 2007
- AMBER: targeted MD problem gurpreet singh
- Re: AMBER: targeted MD problem Carlos Simmerling
Sunday, 18 March 2007
- AMBER: targetedMD problem gurpreet singh
- AMBER: MMPBSA with water molecule in active site saurabh agrawal
- Re: AMBER: MMPBSA with water molecule in active site Carlos Simmerling
- AMBER: antechamber Ilyas Yildirim
- Re: AMBER: MMPBSA with water molecule in active site saurabh agrawal
- Re: AMBER: MMPBSA with water molecule in active site Carlos Simmerling
- Re: AMBER: MMPBSA with water molecule in active site Jiri Sponer
- Re: AMBER: MMPBSA with water molecule in active site saurabh agrawal
- Re: AMBER: antechamber David A. Case
- AMBER: hi Anju Sharma
- AMBER: Problem while creating structure in xLeap Anju Sharma
- RE: AMBER: hi Ross Walker
- Re: AMBER: Problem related simulation of dimer priya priya
- AMBER: Problem!! Anju Sharma
Monday, 19 March 2007
- Re: AMBER: Trimannoside Problem Sandeep Kaushik
- Re: AMBER: Problem related simulation of dimer Sandeep Kaushik
- Re: AMBER: Problem related simulation of dimer priya priya
- Re: AMBER: Problem related simulation of dimer Sandeep Kaushik
- Re: AMBER: Essential ions and water molecules in MMPBSA computations Cenk Andac
- Re: AMBER: Essential ions and water molecules in MMPBSA computations Cenk Andac
- Re: AMBER: Essential ions and water molecules in MMPBSA computations David A. Case
- RE: AMBER: Problem!! Ross Walker
- Re: AMBER: vlimit error David A. Case
Tuesday, 20 March 2007
- AMBER: problem decomposing energies (MMPBSA) Cyril Bauvais
- AMBER: MM-GBSA residues decomposition comparison Sergey Samsonov
- AMBER: basis set for RESP calculation Michel Becker
- AMBER: Problem while loading Pdb in xleap Anju Sharma
- Re: AMBER: Problem while loading Pdb in xleap David A. Case
Wednesday, 21 March 2007
- Re: AMBER: basis set for RESP calculation FyD
- AMBER: Problem while running Antechamber Anju Sharma
- Re:AMBER: Problem while running Antechamber Kateryna Miroshnychenko
- AMBER: Modified Nucleic Acid Problem SHARAD gupta
- AMBER: How to reimage the trajectories of LES calculations? Kailee
- Re: AMBER: Modified Nucleic Acid Problem FyD
- Re: AMBER: Modified Nucleic Acid Problem FyD
- Re: AMBER: How to reimage the trajectories of LES calculations? Carlos Simmerling
- Re: AMBER: basis set for RESP calculation FyD
- AMBER: ntt=1 or ntt= 3? Therese Malliavin
- Re: AMBER: How to reimage the trajectories of LES calculations? Kailee
- Re: AMBER: basis set for RESP calculation Mark Williamson
- Re: AMBER: ntt=1 or ntt= 3? Carlos Simmerling
- RE: AMBER: ntt=1 or ntt= 3? Yong Duan
- AMBER: xLeAP: TI calculation: the perturbed charge is not integral Ignacio Faustino
- AMBER: TI calculation: the perturbed charge is not integral Ignacio Faustino
- Re: AMBER: ntt=1 or ntt= 3? David A. Case
- Re: AMBER: xLeAP: TI calculation: the perturbed charge is not integral David A. Case
Thursday, 22 March 2007
- AMBER: restraint in minimization deepti nayar
- Re: AMBER: Problem while loading Pdb in xleap Sandeep Kaushik
- RE: AMBER: ntt=1 or ntt= 3? Yong Duan
- Re: AMBER: restraint in minimization Carlos Simmerling
- AMBER: Holding NA Base syn during annealing Seth Lilavivat
- Re: AMBER: Holding NA Base syn during annealing David A. Case
- RE: AMBER: ntt=1 or ntt= 3? Hu, Shaowen \(JSC-SK\)[USRA]
- Re: AMBER: ntt=1 or ntt= 3? Carlos Simmerling
- AMBER: Generating structure of polyethylene glycol in AMBER Lili Peng
- RE: AMBER: ntt=1 or ntt= 3? Hu, Shaowen \(JSC-SK\)[USRA]
- Re: AMBER: ntt=1 or ntt= 3? Carlos Simmerling
- Re: AMBER: Generating structure of polyethylene glycol in AMBER FyD
- Re: AMBER: Generating structure of polyethylene glycol in AMBER Lili Peng
- Re: AMBER: Generating structure of polyethylene glycol in AMBER luckyang.gmail.com
- Re: AMBER: Generating structure of polyethylene glycol in AMBER FyD
Friday, 23 March 2007
- Re: AMBER: sander/topology problem Jin-Soo Kim
- Re: AMBER: sander/topology problem Gustavo Seabra
- AMBER: anneal algorthm Seth Lilavivat
- AMBER: Error - must define AMBERHOME environment variable bertrand russell
- AMBER: Combining RESP with AM1-BCC Ilyas Yildirim
- AMBER: water density Esther Brugger
- AMBER: amber 9 - output of forces Eric Shamay
- Re: AMBER: water density Cenk Andac
- Re: AMBER: Combining RESP with AM1-BCC David Mobley
- Re: AMBER: Combining RESP with AM1-BCC Ilyas Yildirim
- AMBER: sander.MPI vs MPICH2 problem!!! Swarup Gupta
- Re: AMBER: amber 9 - output of forces David A. Case
- Re: AMBER: amber 9 - output of forces Eric Shamay
Saturday, 24 March 2007
- Re: AMBER: Combining RESP with AM1-BCC FyD
- Re: AMBER: sander/topology problem Jin-Soo Kim
- AMBER: Does Sander.MPI support coupling effect between different molecules at the same area at the same temperature in the mixture? Jin-Soo Kim
- Re: AMBER: Problem while creating structure in xLeap Jin-Soo Kim
Friday, 23 March 2007
- Re: AMBER: Error - must define AMBERHOME environment variable Eric Shamay
Saturday, 24 March 2007
- Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell
- Re: AMBER: Error - must define AMBERHOME environment variable Eric Shamay
- RE: AMBER: Error - must define AMBERHOME environment variable Ross Walker
Sunday, 25 March 2007
- AMBER: Please check the total charge and your -nc flag snoze pa
Monday, 26 March 2007
- AMBER: phe-phe simulation deepti nayar
- Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell
- Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell
- AMBER: pmemd segmentation fault Vlad Cojocaru
- Re: AMBER: restraint in minimization Sandeep Kaushik
- Re: AMBER: restraint in minimization Carlos Simmerling
- Re: AMBER: phe-phe simulation Carlos Simmerling
- Re: AMBER: pmemd segmentation fault Robert Duke
- Re: AMBER: pmemd segmentation fault Vlad Cojocaru
- Re: AMBER: pmemd segmentation fault Robert Duke
- AMBER: pdb file produced by vmd Rita Cassia
- AMBER: DNA Flat Angle Restraints Kyle L. Brown
- RE: AMBER: Error - must define AMBERHOME environment variable Ross Walker
- Re: AMBER: pmemd segmentation fault Vlad Cojocaru
- Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell
- Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell
- Re: AMBER: pmemd segmentation fault Robert Duke
- RE: AMBER: pmemd segmentation fault Ross Walker
- RE: AMBER: Error - must define AMBERHOME environment variable Ross Walker
- Re: AMBER: amber 9 - output of forces Eric Shamay
- AMBER: distcovar in ptraj Zhenyu Lu
- Re: AMBER: restraint in minimization deepti nayar
- Re: AMBER: phe-phe simulation deepti nayar
- AMBER: Parameter file for Dipeptide Neelanjana Sengupta
- Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell
Tuesday, 27 March 2007
- Re: AMBER: pmemd segmentation fault Vlad Cojocaru
- Re: AMBER: phe-phe simulation deepti nayar
- AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit j j
- Re: AMBER: Parameter file for Dipeptide Carlos Simmerling
- Re: AMBER: phe-phe simulation Carlos Simmerling
- RE: AMBER: Error - must define AMBERHOME environment variable Ross Walker
- AMBER: Question about loadMol2 David LeBard
- Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell
- Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell
- Re: AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit j j
- Re: AMBER: Question about loadMol2 Scott Brozell
- AMBER: amber 9 install: patch reject Stern, Julie
- AMBER: amber 9: fortran/test failures Stern, Julie
- AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable) Ross Walker
- Re: AMBER: Question about loadMol2 David Mobley
- AMBER: residue types for GLY/high pH Stern, Julie
- Re: AMBER: Question about loadMol2 Thomas Steinbrecher
- Re: AMBER: amber 9 - output of forces Eric Shamay
- Re: AMBER: Question about loadMol2 David LeBard
- AMBER: Amber 9 TI Details Lachele Foley (Lists)
- Re: AMBER: Question about loadMol2 Scott Brozell
- Re: AMBER: Amber 9 TI Details Thomas Steinbrecher
- Re: AMBER: amber 9: fortran/test failures David A. Case
- Re: AMBER: Amber 9 TI Details David A. Case
- Re: AMBER: Please check the total charge and your -nc flag David A. Case
- Re: AMBER: Question about loadMol2 David LeBard
- Re: AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable) bertrand russell
Wednesday, 28 March 2007
- AMBER: Minimization Sophie Barbe
- Re: AMBER: Minimization Jerome.GOLEBIOWSKI.unice.fr
- Re: AMBER: Minimization Sophie Barbe
- Re: AMBER: phe-phe simulation deepti nayar
- AMBER: specifying psi and phi for a dipeptide deepti nayar
- AMBER: DISAVE value1 Kyle L. Brown
- AMBER: rms and rmsf in ptraj Mingfeng Yang
- Re: AMBER: rms and rmsf in ptraj Thomas Cheatham
- AMBER: problem in implcit simulation gurpreet singh
- RE: AMBER: problem in implcit simulation Ross Walker
Thursday, 29 March 2007
- Re: AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable) bertrand russell
- AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Vlad Cojocaru
- AMBER: minimization not running deepti nayar
- Re: AMBER: minimization not running Vlad Cojocaru
- Re: AMBER: minimization not running deepti nayar
- AMBER: minimization energy query deepti nayar
- Re: AMBER: minimization energy query Vlad Cojocaru
- Re: AMBER: minimization energy query deepti nayar
- Re: AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Robert Duke
- Re: AMBER: rms and rmsf in ptraj Scott Brozell
- Re: AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Vlad Cojocaru
- Re: AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Robert Duke
- AMBER: is possible to compile pmemd using scali MPI? Andrea Bortolato
- Re: AMBER: is possible to compile pmemd using scali MPI? Robert Duke
- RE: AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable) Ross Walker
- AMBER: Amber9 Sander Error A Box
- AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished Pankaj R. Daga
- RE: AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished Ross Walker
Friday, 30 March 2007
- Re: AMBER: minimization energy query deepti nayar
- AMBER: minimization + simulation deepti nayar
- Re: AMBER: minimization + simulation Vlad Cojocaru
- Re: AMBER: minimization energy query Vlad Cojocaru
- Re: AMBER: minimization energy query deepti nayar
- AMBER: RST can not be opened deepti nayar
- AMBER: problem regarding water handling in explicit simu gurpreet singh
- AMBER: Fwd: problem regarding water handling in explicit simu gurpreet singh
- Re: AMBER: RST can not be opened Vlad Cojocaru
- AMBER: Problem with PCSHIFT module Edoardo Saccenti
- Re: AMBER: Amber9 Sander Error David A. Case
- AMBER: PDB file with charge and size in mm_pbsa calculations Wang, Xuelin
- Re: AMBER: DISAVE value1 David A. Case
- RE: AMBER: RST can not be opened Ross Walker
- AMBER: mm_pbsa error Wang, Xuelin
- AMBER: Some problems during the testing of Amber. Liang, Lei
- Re: AMBER: is possible to compile pmemd using scali MPI? Andrea Bortolato
- Re: AMBER: problem regarding water handling in explicit simu Mingfeng Yang
- Re: AMBER: is possible to compile pmemd using scali MPI? Gustavo Seabra
- AMBER: A question about biomineral simulation, help!! WANG,YING
- AMBER: Distance restraint to centre of mass Evan Kelly
Saturday, 31 March 2007
- Re: AMBER: Some problems during the testing of Amber. David A. Case
- Re: AMBER: Problem with PCSHIFT module David A. Case
- Re: AMBER: Distance restraint to centre of mass David A. Case

Last message date: Sun Apr 01 2007 - 06:08:06 PDT
Archived on: Mon Dec 23 2024 - 05:53:30 PST

Amber Archive Mar 2007 by date