Amber Archive Feb 2005: by date

Monday, 31 January 2005
- AMBER: amber8 in IBM-SP4 Jiten
- AMBER: N Metyl amino acids Andrew Box
Tuesday, 1 February 2005
- AMBER: vacuum bubbles in system equilibration Marie-Pierre Durrieu
- Re: AMBER: Problem in ptraj anshul.imtech.res.in
- Re: AMBER: N Metyl amino acids Carlos Simmerling
- AMBER: Carnal in Amber8 Vlad Cojocaru
- Re: AMBER: Carnal in Amber8 David A. Case
- AMBER: Multiple dihedral restraints Joseph Fernandez
- AMBER: Redhat Enterprise Linux Beale, John
- RE: AMBER: Redhat Enterprise Linux S. Frank Yan
- Re: AMBER: Problem in ptraj Furse, Kristina Elisabet
- Re: AMBER: Carnal in Amber8 Bill Ross
- Re: AMBER: Carnal in Amber8 Bill Ross
- AMBER: doubts with a new aminoacid Gustavo Pierdominici Sottile
- AMBER: External Electric Field Brandon Tefft
- AMBER: sander segmentation fault Xin Wang
- Re: AMBER: Multiple dihedral restraints David A. Case
- RE: AMBER: gaussian output file Junmei Wang
- Re: AMBER: doubts with a new aminoacid David A. Case
- RE: AMBER: Redhat Enterprise Linux Andrew Box
- Re: AMBER: doubts with a new aminoacid Bill Ross
- AMBER: xleap: different distance results from "check" command in xleap Woojin Lee
Wednesday, 2 February 2005
- Re: AMBER: Problem in ptraj anshul.imtech.res.in
- AMBER: Compilation problem at dual processor linux ! Pradipta Bandyopadhyay
- AMBER: change of prmtop file Gustavo Pierdominici Sottile
- AMBER: xleap MOVE and .lib file Stern, Julie
- RE: AMBER: Compilation problem at dual processor linux ! Ross Walker
- RE: AMBER: Redhat Enterprise Linux Beale, John
- Re: AMBER: change of prmtop file Guanglei Cui
- Re: AMBER: External Electric Field David A. Case
- AMBER: Multiple dihedral restraints (follow up) Joseph Fernandez
- Re: AMBER: Problem in ptraj Furse, Kristina Elisabet
- Re: AMBER: change of prmtop file David A. Case
- AMBER: amber 8 system requirements dkohen.carleton.edu
- Re: AMBER: Problem in ptraj Thomas E. Cheatham, III
- RE: AMBER: amber 8 system requirements Ross Walker
- Re: AMBER: Multiple dihedral restraints (follow up) David A. Case
- Re: AMBER: sander segmentation fault David A. Case
- Re: AMBER: sander segmentation fault Xin Wang
- Re: AMBER: sander segmentation fault David A. Case
- Re: AMBER: sander segmentation fault Furse, Kristina Elisabet
- AMBER: gaff frcmod file for TI calculation Eric Hu
- Re: AMBER: sander segmentation fault Thomas E. Cheatham, III
- Re: AMBER: gaff frcmod file for TI calculation David A. Case
- Re: AMBER: gaff frcmod file for TI calculation Eric Hu
- RE: AMBER: sander segmentation fault Ross Walker
- AMBER: question about tleap load pdb file xiaowen
Thursday, 3 February 2005
- AMBER: non-periodic condition gsciaini
- AMBER: protonate and input conversion error Stern, Julie
- Re: AMBER: protonate and input conversion error David A. Case
- RE: AMBER: non-periodic condition Ross Walker
- Re: AMBER: Multiple dihedral restraints (follow up) M. L. Dodson
- RE: AMBER: non-periodic condition Germán Sciaini
- AMBER: DNA melting free energy calculation lei jia
- AMBER: unnatural ligand Eric Hu
Friday, 4 February 2005
- AMBER: clusters Germán Sciaini
- AMBER: tleap load pdb file xiaowen
- Re: AMBER: tleap load pdb file David A. Case
- AMBER: dppsv returns error code: 29 Xiaowei (David) Li
- AMBER: tleap load pdb file xiaowen
- Re: AMBER: tleap load pdb file David A. Case
- Re: AMBER: dppsv returns error code: 29 David A. Case
- Re: AMBER: unnatural ligand David A. Case
- AMBER: Antechamber/formatting question Kara Di Giorgio
- AMBER: huge bond distances in new residue Stern, Julie
- AMBER: trajectory of minimization Stern, Julie
- AMBER: Is droplet boundary condition option possible ? Soo
Saturday, 5 February 2005
- Re: AMBER: tleap load pdb file xiaowen
- Re: AMBER: Is droplet boundary condition option possible ? David A. Case
- Re: AMBER: trajectory of minimization David A. Case
- Re: AMBER: huge bond distances in new residue David A. Case
- Re: AMBER: Antechamber/formatting question David A. Case
- AMBER: loading pdb in leap to create parmeter files mrbroad.ilstu.edu
- Re: AMBER: loading pdb in leap to create parmeter files David A. Case
Sunday, 6 February 2005
- AMBER: Tutorial Request Kara Di Giorgio
- Re: AMBER: Tutorial Request David A. Case
- RE: AMBER: trajectory of minimization Ross Walker
- RE: AMBER: tleap load pdb file Ross Walker
- AMBER: inconsistent ordering in an improper dihedral of TRP Sanghyun Park
Monday, 7 February 2005
- AMBER: correlation along PCA modes Vlad Cojocaru
- Re: AMBER: unnatural ligand Eric Hu
- AMBER: Creating an input file for GRASP using AMBER 8 Ilyas Yildirim
- Re: AMBER: Creating an input file for GRASP using AMBER 8 Bill Ross
- Re: AMBER: Creating an input file for GRASP using AMBER 8 FyD
- AMBER: problem in writing Gustavo Pierdominici Sottile
- RE: AMBER: tleap load pdb file xiaowen
- Re: AMBER: Creating an input file for GRASP using AMBER 8 Ilyas Yildirim
- Re: AMBER: Creating an input file for GRASP using AMBER 8 FyD
- Re: AMBER: problem in writing David A. Case
- RE: AMBER: tleap load pdb file xiaowen
- AMBER: How to calculate RESTRAINT value Mayumi Haga
Tuesday, 8 February 2005
- AMBER: dynamics error S.Sundar Raman
- AMBER: Dynamics error S.Sundar Raman
- Re: AMBER: Dynamics error Carlos Simmerling
- Re: AMBER: How to calculate RESTRAINT value Carlos Simmerling
- Re: AMBER: Dynamics error S.Sundar Raman
- AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel Fabien Cailliez
- AMBER: problem in minimization Gustavo Pierdominici Sottile
- Re: AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel David A. Case
- AMBER: Minimization Beale, John
- AMBER: Linux Enterprise Beale, John
- RE: AMBER: Linux Enterprise S. Frank Yan
- Re: AMBER: tleap load pdb file David A. Case
- Re: AMBER: problem in minimization David A. Case
- AMBER: Amber8 installation test possible failures Joe Nolan
- Re: AMBER: problem in minimization Natasja Brooijmans
- Re: AMBER: Linux Enterprise David A. Case
- RE: AMBER: Linux Enterprise Ross Walker
- Re: AMBER: Amber8 installation test possible failures David A. Case
- Re: AMBER: problem in minimization Bill Ross
- RE: AMBER: Amber8 installation test possible failures Ross Walker
- Re: AMBER: problem in minimization Carlos Simmerling
- Re: AMBER: problem in minimization Bill Ross
- Re: AMBER: problem in minimization David A. Case
- AMBER: leap bond angle building Stern, Julie
- Re: AMBER: leap bond angle building Bill Ross
- AMBER: minimize a ptraj average pdb structure Eric Hu
Wednesday, 9 February 2005
- RE: AMBER: minimize a ptraj average pdb structure Vineet Pande
- AMBER: energy plot in minimization Gustavo Pierdominici Sottile
- AMBER: stereo Filip Lankas
- RE: AMBER: energy plot in minimization Ross Walker
- AMBER: question about mm_gbsa output file michael chen
- RE: AMBER: stereo Vineet Pande
- Re: AMBER: tleap load pdb file xiaowen
- AMBER: Convert to Pdb Beale, John
- Re: AMBER: Convert to Pdb Peter Gannett
- RE: AMBER: tleap load pdb file Ross Walker
- RE: AMBER: Convert to Pdb Ross Walker
- Re: AMBER: Convert to Pdb M. L. Dodson
- AMBER: minimization.out Gustavo Pierdominici Sottile
- RE: AMBER: minimize a ptraj average pdb structure Bill Ross
- AMBER: DIVCON optimization Kara Di Giorgio
- Re: AMBER: minimization.out David A. Case
- Re: AMBER: stereo Chris Moth
- Re: AMBER: DIVCON optimization David A. Case
- AMBER: Can REM be used as multiple normal sander jobs on parallel machine qlu.notes.cc.sunysb.edu
- Re: AMBER: DIVCON optimization Kara Wald
- Re: AMBER: Can REM be used as multiple normal sander jobs on parallel machine Carlos Simmerling
- AMBER: desc NEWRES and blank unit type Stern, Julie
- Re: AMBER: DIVCON optimization David A. Case
- AMBER: question about surface area to GBsurf calculation michael chen
- AMBER: Another question about surface area calculation michael chen
Thursday, 10 February 2005
- Re: AMBER: question about surface area to GBsurf calculation David A. Case
- AMBER: Poisson Boltzmann dynamics error Rachel Burdge
- Re: AMBER: Poisson Boltzmann dynamics error David A. Case
- RE: AMBER: Poisson Boltzmann dynamics error Ross Walker
Tuesday, 8 February 2005
- Re: AMBER: Poisson Boltzmann dynamics error Ray Luo
Thursday, 10 February 2005
- Re: AMBER: Poisson Boltzmann dynamics error Rachel Burdge
- AMBER: Protonate state of ARG and LYS. Liu, Jingyuan
- AMBER: How to converts a binary mdcrd file thanyarat Udom
Friday, 11 February 2005
- AMBER: How to converts a binary mdcrd file thanyarat Udom
- AMBER: Cu++ and RED Cenk Andac
- AMBER: too much vacuum in the box created by Leap Marie-Pierre Durrieu
- Re: AMBER: too much vacuum in the box created by Leap Carlos Simmerling
- AMBER: ptraj error and min problems Gustavo Pierdominici Sottile
- AMBER: archive Gustavo Pierdominici Sottile
- Re: AMBER: too much vacuum in the box created by Leap David A. Case
- Re: AMBER: ptraj error and min problems David A. Case
- Re: AMBER: Cu++ and RED FyD
- Re: AMBER: inconsistent ordering in an improper dihedral of TRP David A. Case
- Re: AMBER: desc NEWRES and blank unit type David A. Case
- Re: AMBER: inconsistent ordering in an improper dihedral of TRP Carlos Simmerling
- AMBER: nucgen problem Ilyas Yildirim
- Re: AMBER: nucgen problem David A. Case
- Re: AMBER: inconsistent ordering in an improper dihedral of TRP Bill Ross
- AMBER: reverse TI charge perturbation Eric Hu
Saturday, 12 February 2005
- Re: AMBER: reverse TI charge perturbation David A. Case
Monday, 14 February 2005
- AMBER: S.Sundar Raman
- AMBER:how to analyse trajectory files S.Sundar Raman
- RE: AMBER:how to analyse trajectory files Vineet Pande
- AMBER: vlimit Gustavo Pierdominici Sottile
- AMBER: AMBER 8 : Water cap problem Guillaume Bollot
- AMBER: constrains Gustavo Pierdominici Sottile
- RE: AMBER: constrains Vineet Pande
- RE: AMBER: Ross Walker
- RE: AMBER: AMBER 8 : Water cap problem Ross Walker
- RE: AMBER: constrains Ross Walker
- RE: AMBER: vlimit Ross Walker
- AMBER: Restart Problem opitz.che.udel.edu
- RE: AMBER: Restart Problem Ross Walker
- AMBER: Mainchain example needed Kara Wald
- AMBER: running shell scripts in tleap? Cenk Andac
- Re: AMBER: running shell scripts in tleap? Lihua Wang
- RE: AMBER: running shell scripts in tleap? Ross Walker
- Re: AMBER: running shell scripts in tleap? John Bushnell
- Re: AMBER: reverse TI charge perturbation Eric Hu
- AMBER: Dummy Atom Types on both states Ilyas Yildirim
- Re: AMBER:how to analyse trajectory files S.Sundar Raman
- RE: AMBER: running shell scripts in tleap? Cenk Andac
- Re: AMBER: Cu++ and RED Cenk Andac
Tuesday, 15 February 2005
- Re: AMBER: Dummy Atom Types on both states Thomas Steinbrecher
- AMBER: Topology Format Amber 8 Stuart Murdock
- Re: AMBER: Topology Format Amber 8 Carlos Simmerling
- Re: AMBER: Topology Format Amber 8 Ian Withers
- Re: AMBER: Dummy Atom Types on both states yipinl.umich.edu
- Re: AMBER: Dummy Atom Types on both states Julien Michel
- Re: AMBER: Dummy Atom Types on both states david.evans.ulsop.ac.uk
- Re: AMBER: Dummy Atom Types on both states david.evans.ulsop.ac.uk
- Re: AMBER: Cu++ and RED FyD
- AMBER: problems with running sander in parallel on linux Piotr Cieplak
- RE: AMBER: problems with running sander in parallel on linux Ross Walker
- RE: AMBER: problems with running sander in parallel on linux Piotr Cieplak
- AMBER: blows up Gustavo Pierdominici Sottile
- AMBER: check in leap Gustavo Pierdominici Sottile
- Re: AMBER: problems with running sander in parallel on linux Scott Brozell
- Re: AMBER: problems with running sander in parallel on linux Robert Duke
- Re: AMBER: problems with running sander in parallel on linux David E. Konerding DSD staff
- Re: AMBER: problems with running sander in parallel on linux Piotr Cieplak
- Re: AMBER: problems with running sander in parallel on linux Scott Brozell
- AMBER: Cyclic peptide arubin.unmc.edu
- Re: AMBER: check in leap David A. Case
- Re: AMBER: problems with running sander in parallel on linux Robert Duke
- Re: AMBER: problems with running sander in parallel on linux Piotr Cieplak
- Re: AMBER: problems with running sander in parallel on linux Scott Brozell
- Re: AMBER: Dummy Atom Types on both states David A. Case
- AMBER: soft-cores and Amber David A. Case
- Re: AMBER: soft-cores and Amber Carlos Simmerling
- AMBER: PDB conversion to gzmat using antechamber Scott Pendley
- AMBER: EWALD and belly not strictly correct Stern, Julie
Wednesday, 16 February 2005
- AMBER: Why I couldnt used carnal for analyzed RMSD ? thanyarat Udom
- Re: AMBER: Cyclic peptide Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
- AMBER: Gustavo Pierdominici Sottile
- Re: AMBER: Carlos Simmerling
- Re: AMBER: Cyclic peptide Carlos Simmerling
- AMBER: rms Gustavo Pierdominici Sottile
- Re: AMBER: rms Carlos Simmerling
- AMBER: Beale, John
- AMBER: Phi-Psi-Energy plot L Jin
- Re: AMBER: EWALD and belly not strictly correct darden
- Re: AMBER: David A. Case
- Re: AMBER: EWALD and belly not strictly correct David A. Case
- AMBER: generate charmm paramater file from amber parm file HL Eastwood
- Re: AMBER: generate charmm paramater file from amber parm file david.evans.ulsop.ac.uk
- Re: AMBER: generate charmm paramater file from amber parm file David E. Konerding DSD staff
- Re: AMBER: Why I couldnt used carnal for analyzed RMSD ? Bill Ross
- AMBER: Amber7 nmropt Markus W. Germann
- RE: AMBER: Amber7 nmropt Ross Walker
- Re: AMBER: Amber7 nmropt Markus W. Germann
- Re: AMBER: Amber7 nmropt David A. Case
- RE: AMBER: Amber7 nmropt Ross Walker
- Re: AMBER: Amber7 nmropt Robert Duke
Thursday, 17 February 2005
- AMBER: installation of amber 8 on windows anshul.imtech.res.in
- AMBER: Re: pmemd problems Robert Duke
- AMBER: rotameric populations? Cenk Andac
- AMBER: moil-view Beale, John
- Re: AMBER: moil-view Carlos Simmerling
- Re: AMBER: installation of amber 8 on windows David Mathews
- AMBER: Antechamber help needed Kara Di Giorgio
- AMBER: Moil view trajectory clusters Austin B. Yongye
- AMBER: problem with ptraj and randomizeions Fabien Cailliez
- Re: AMBER: Moil view trajectory clusters Carlos Simmerling
- Re: AMBER: problem with ptraj and randomizeions Thomas E. Cheatham, III
- AMBER: PSC Summer Workshop: Modeling Proteins and Nucleic Acids with AMBER, VMD and the MMTSB Toolkit Troy Wymore
- AMBER: amber8 and moil-view Lihua Wang
- Re: AMBER: amber8 and moil-view Carlos Simmerling
- Re: AMBER: amber8 and moil-view Lihua Wang
- Re: AMBER: amber8 and moil-view Carlos Simmerling
- Re: AMBER: amber8 and moil-view Lihua Wang
- AMBER: Amber8 Solaris installation failure Joe Nolan
- Re: AMBER: Moil view trajectory clusters Austin B. Yongye
- AMBER: sander errors with atom restraints on ia64 Rachel Burdge
- Re: AMBER: sander errors with atom restraints on ia64 Viktor Hornak
- AMBER: leap saveamberparm chain types response Stern, Julie
- AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) Greg Recine
- Re: AMBER: leap saveamberparm chain types response Bill Ross
- Re: AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) M. L. Dodson
- Re: AMBER: Amber8 Solaris installation failure David A. Case
Friday, 18 February 2005
- Re: AMBER: installation of amber 8 on windows anshul.imtech.res.in
Thursday, 17 February 2005
- AMBER: GB solvation and "boxed" environment simulation Soo
- AMBER: molecule blowing apart during equilibration Stern, Julie
- Re: AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) David A. Case
- Re: AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) David A. Case
Friday, 18 February 2005
- Re: AMBER: problem with ptraj and randomizeions Fabien Cailliez
- Re: AMBER: problem with ptraj and randomizeions Marie-Pierre Durrieu
- Re: AMBER: problem with ptraj and randomizeions Marie-Pierre Durrieu
- Re: AMBER: problem with ptraj and randomizeions Filip Lankas
- AMBER: ptraj Gustavo Pierdominici Sottile
- Re: AMBER: sander errors with atom restraints on ia64 Rachel Burdge
- RE: AMBER: molecule blowing apart during equilibration Ross Walker
- AMBER: XMGR Beale, John
- Re: AMBER: Antechamber/formatting question Kara Di Giorgio
- Re: AMBER: molecule blowing apart during equilibration Carlos Simmerling
- Re: AMBER: amber8 and moil-view Carlos Simmerling
- Re: AMBER: XMGR Andreas Svrcek-Seiler
- AMBER: DNA Tutorial Dwayne Hoobler
- RE: AMBER: DNA Tutorial Ross Walker
- AMBER: Amber: sander error segmentation fault. S.Sundar Raman
- RE: AMBER: Amber: sander error segmentation fault. Ross Walker
Saturday, 19 February 2005
- Re: AMBER: installation of amber 8 on windows David Mathews
- AMBER: ptraj for RDF calculations Javier Perez Miron
- AMBER: simulation with explicit water molecules Ye MEI
Sunday, 20 February 2005
- AMBER: (no subject) yen li
- AMBER: AIX problem Mayumi Haga
Monday, 21 February 2005
- AMBER: ptraj for RDF calculations Javier Perez Miron
- AMBER: Amber 8 with lam compilation problem m m
- AMBER: problem with protein minimization yen li
- Re: AMBER: ptraj for RDF calculations Carlos Jaime
- RE: AMBER: Amber 8 with lam compilation problem Ross Walker
- AMBER: separate solvent-solvent and solvent-solute interaction Ye MEI
- Re: AMBER: Antechamber/formatting question YoungJin Cho
- Re: AMBER: separate solvent-solvent and solvent-solute interaction David A. Case
- AMBER: Formatting Questions Kara Di Giorgio
- RE: AMBER: DNA Tutorial Dwayne Hoobler
- AMBER: Free energy extimate for the same structure but different conformers claudio
- Re: AMBER: DNA Tutorial David A. Case
- Re: AMBER: Free energy extimate for the same structure but different conformers David A. Case
- Re: AMBER: AIX problem David A. Case
- Re: AMBER: problem with protein minimization David A. Case
- RE: AMBER: AIX problem Mayumi Haga
- Re: AMBER: Formatting Questions David A. Case
- Re: AMBER: Formatting Questions Kara Di Giorgio
- Re: Re: AMBER: separate solvent-solvent and solvent-solute interaction Ye MEI
Tuesday, 22 February 2005
- Re: AMBER: problem with protein minimization yen li
- AMBER: ptraj problem Mayumi Haga
- Re: AMBER: ptraj problem scopio
- AMBER: restraint only for Z cartegian coordinate? Jaroslav Hanus
- Re: AMBER: restraint only for Z cartegian coordinate? Carlos Simmerling
- AMBER: Restraint of atoms during minimization L Jin
- AMBER: dihedral driver? Beale, John
- Re: AMBER: Restraint of atoms during minimization Carlos Simmerling
- AMBER: vlimit exceeded and temperature blow up Stern, Julie
- Re: AMBER: vlimit exceeded and temperature blow up Carlos Simmerling
- RE: AMBER: problem with protein minimization Ross Walker
- AMBER: MPI for sander8 S. Frank Yan
- Re: AMBER: problem with protein minimization Robert Duke
- Re: AMBER: Restraint of atoms during minimization L Jin
- Re: AMBER: MPI for sander8 Viktor Hornak
- Re: AMBER: MPI for sander8 Thomas E. Cheatham, III
- Re: AMBER: Restraint of atoms during minimization David A. Case
- Re: AMBER: Restraint of atoms during minimization Carlos Simmerling
- Re: AMBER: Restraint of atoms during minimization Thomas E. Cheatham, III
- RE: AMBER: MPI for sander8 Ross Walker
- AMBER: ptraj8: trajectory windows Anselm Horn
- RE: AMBER: MPI for sander8 James W. Caldwell
- Re: AMBER: Amber8 Solaris installation failure Joe Nolan
- Re: AMBER: Amber8 Solaris installation failure Atro Tossavainen
- Re: AMBER: Formatting Questions Kara Di Giorgio
- AMBER: lastrst Stern, Julie
- Re: AMBER: Amber8 Solaris installation failure Joe Nolan
- RE: AMBER: Amber8 Solaris installation failure Ross Walker
- Re: AMBER: Formatting Questions Bill Ross
- RE: AMBER: Amber8 Solaris installation failure Bill Ross
- Re: AMBER: Amber8 Solaris installation failure David A. Case
- AMBER: lastrst Stern, Julie
- AMBER: minimizing structures before MM-PBSA? scopio
- AMBER: convert one functional group to another with TI Eric Hu
- Re: AMBER: minimizing structures before MM-PBSA? Carlos Simmerling
- Re: AMBER: lastrst Carlos Simmerling
- Re: AMBER: Amber8 Solaris installation failure M. L. Dodson
- Re: AMBER: lastrst Ilyas Yildirim
- AMBER: total energy of solvation Holly Freedman
- AMBER: size of solventbox mathew k varghese
- AMBER: parallel AMBER/pmemd installation problem on Opteron Jyh-Shyong Ho
- RE: AMBER: size of solventbox Ross Walker
- Re: AMBER: total energy of solvation David A. Case
- Re: AMBER: convert one functional group to another with TI David A. Case
- Re: AMBER: lastrst David A. Case
- Re: AMBER: convert one functional group to another with TI Eric Hu
- AMBER: RE:Amber 8 with lam compilation problem Maciej KA
- AMBER: mpirun sander8 problem S. Frank Yan
- RE: AMBER: RE:Amber 8 with lam compilation problem Ross Walker
Wednesday, 23 February 2005
- AMBER: RE:Amber 8 with lam compilation problem Maciej KA
- Re: AMBER: size of solventbox Germán Sciaini
- Re: AMBER: size of solventbox Fabien Cailliez
- Re: AMBER: mpirun sander8 problem Carlos Simmerling
- Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Robert Duke
- Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Lars Packschies
- RE: AMBER: mpirun sander8 problem S. Frank Yan
- Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Robert Duke
- RE: AMBER: RE:Amber 8 with lam compilation problem Ross Walker
- Re: AMBER: RE:Amber 8 with lam compilation problem Amber admin
- Re: AMBER: size of solventbox Brent Krueger
- Re: AMBER: lastrst Stern, Julie
- AMBER: classes Gustavo Pierdominici Sottile
- Re: AMBER: lastrst Furse, Kristina Elisabet
- Re: AMBER: convert one functional group to another with TI David A. Case
- Re: AMBER: convert one functional group to another with TI David A. Case
- Re: AMBER: convert one functional group to another with TI Eric Hu
- AMBER: solvateOct method Cameron Mura
- AMBER: RE:Amber 8 with lam compilation problem Maciej
Thursday, 24 February 2005
- FW: AMBER: mpirun sander8 problem S. Frank Yan
- Re: AMBER: Use of ibelly with nmode analysis marti
- AMBER: How to build dynamics input for guanine with tleap ? Maciej
- Re: AMBER: RE:Amber 8 with lam compilation problem Robert Duke
- RE: AMBER: classes Vineet Pande
- RE: AMBER: How to build dynamics input for guanine with tleap ? Vineet Pande
- AMBER: Joining residues/units Bogos Agianian
- Re: FW: AMBER: mpirun sander8 problem Guanglei Cui
- Re: AMBER: mpirun sander8 problem S. Frank Yan
- Re: AMBER: Use of ibelly with nmode analysis David A. Case
- AMBER: cross-correlation Xin Hu
- AMBER: ambpdb radii Harianto
- AMBER: units describing projection onto modes Vlad Cojocaru
- AMBER: correlation Gustavo Pierdominici Sottile
- Re: AMBER: Joining residues/units David A. Case
- Re: AMBER: Joining residues/units Bogos Agianian
- AMBER: pmemd + pgi 5.1 + ntr = 1 Peter Varnai
- Re: AMBER: pmemd + pgi 5.1 + ntr = 1 Robert Duke
- Re: AMBER: pmemd + pgi 5.1 + ntr = 1 Peter Varnai
- Re: AMBER: pmemd + pgi 5.1 + ntr = 1 Robert Duke
- Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Lars Packschies
- Re: AMBER: ambpdb radii David A. Case
- AMBER: Does delta.charge mean "final charge" for a dummy atom? Eric Hu
- Re: AMBER: Does delta.charge mean "final charge" for a dummy atom? David A. Case
- Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Robert Duke
- AMBER: My last posting Robert Duke
- AMBER: compile amber8 on RHEL4 HuiZhe Li
Friday, 25 February 2005
- AMBER: nmode entropy calculations in MMPBSA Fabien Cailliez
- Re: AMBER: restraint only for Z cartegian coordinate? Jaroslav Hanus
- Re: AMBER: compile amber8 on RHEL4 Ye MEI
- AMBER: vlimit Gustavo Pierdominici Sottile
- Re: AMBER: compile amber8 on RHEL4 Tru Huynh
- Re: AMBER: nmode entropy calculations in MMPBSA david.evans.ulsop.ac.uk
- Re: AMBER: ambpdb radii Harianto
- Re: AMBER: ambpdb radii David A. Case
- Re: AMBER: solvateOct method David A. Case
- Re: AMBER: Joining residues/units FyD
- AMBER: make test.lmod error yuann
- Re: AMBER: make test.lmod error David A. Case
- Re: AMBER: ambpdb radii Harianto
- Re: AMBER: ambpdb radii David A. Case
- AMBER: setBox buffer in leap Stern, Julie
- AMBER: problem with solvateBox ReichertD.mir.wustl.edu
- AMBER: Austin B. Yongye
- Re: AMBER: problem with solvateBox David A. Case
- Re: AMBER: Does delta.charge mean "final charge" for a dummy atom? Eric Hu
- Re: AMBER: Antechamber/formatting question Kara Di Giorgio
- Re: AMBER: Antechamber/formatting question Ilyas Yildirim
- AMBER: vlimit problem Ilyas Yildirim
- Re: AMBER: Antechamber/formatting question Kara Di Giorgio
- AMBER: ico(i)=-1? Xiao He
- AMBER: Pyranose pucker parameters Austin B. Yongye
Saturday, 26 February 2005
- Re: AMBER: ico(i)=-1? Guanglei Cui
Sunday, 27 February 2005
- RE: AMBER: Antechamber/formatting question Ross Walker
- RE: AMBER: Pyranose pucker parameters Ross Walker
- Re: AMBER: Antechamber/formatting question Kara Di Giorgio
- RE: AMBER: Pyranose pucker parameters Austin B. Yongye
- Re: AMBER: Antechamber/formatting question FyD
- Re: AMBER: Antechamber/formatting question FyD
- AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem praveena moldy
Monday, 28 February 2005
- AMBER: GBSA calculation Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
- AMBER: creating a new residue Amber admin
- Re: AMBER: correlation David A. Case
- Re: AMBER: vlimit problem David A. Case
- Re: AMBER: GBSA calculation David A. Case
- Re: AMBER: PDB conversion to gzmat using antechamber David A. Case
- Re: AMBER: Amber8 Solaris installation failure Joe Nolan
- Re: AMBER: Amber8 Solaris installation failure M. L. Dodson
- Re: AMBER: Amber8 Solaris installation failure David A. Case
- AMBER: Controlling number of water residues... Pavan G

Last message date: Tue Mar 01 2005 - 07:53:00 PST
Archived on: Wed Nov 13 2024 - 05:53:25 PST

Amber Archive Feb 2005 by date