Amber Archive May 2006: by date

Sunday, 30 April 2006
- AMBER: Amber 9, sander imin = 5, -y flag z3020110.student.unsw.edu.au
Monday, 1 May 2006
- Re: AMBER: Amber 9, sander imin = 5, -y flag Carlos Simmerling
- Re: AMBER: error propagation in MM-PBSA binding free energy calculation Jianyin Shao
- AMBER: sequential execution of number of parallel jobs In Hee Park
- Re: AMBER: internal coordinates David A. Case
- AMBER: distance restraints mkseo
- AMBER: some new tutorials David A. Case
- AMBER: How does amber calculate HB? Li Su
- Re: AMBER: How does amber calculate HB? David A. Case
Tuesday, 2 May 2006
- Re: AMBER: sequential execution of number of parallel jobs Petr Kulhanek
- AMBER: AMBER Workshops, London UK 26th - 30th June 2006 Ross Walker
- AMBER: Simulation of crystal - problem with excluded atom list Jennie Thomas
- Re: AMBER: internal coordinates Ioana Cozmuta
- AMBER: MPI parallel problem in AMBER 8.0 mkseo
- RE: AMBER: MPI parallel problem in AMBER 8.0 Ross Walker
- Re: AMBER: MPI parallel problem in AMBER 8.0 mkseo
- RE: AMBER: MPI parallel problem in AMBER 8.0 Ross Walker
- AMBER: Shared libraries error Andrew Box
- AMBER: proper restart procedure? John J. Love
Wednesday, 3 May 2006
- AMBER: Question bonds and angles in frcmod and lib files Jennie Thomas
- AMBER: Error while running test.serial in Amber9 Priti Hansia
- Re: AMBER: proper restart procedure? Carlos Simmerling
- Re: AMBER: Error while running test.serial in Amber9 Carlos Simmerling
- Re: AMBER: Error while running test.serial in Amber9 Priti Hansia
- AMBER: cluster architecture for the best amber performance Kateryna Miroshnychenko
- RE: AMBER: Shared libraries error Ross Walker
- Re: AMBER: proper restart procedure? David A. Case
- RE: AMBER: Error while running test.serial in Amber9 Ross Walker
- Re: AMBER: Question bonds and angles in frcmod and lib files David A. Case
- RE: AMBER: cluster architecture for the best amber performance Ross Walker
- Re: AMBER: Question bonds and angles in frcmod and lib files Jennie Thomas
- Re: AMBER: Question bonds and angles in frcmod and lib files Bill Ross
- AMBER: concatenating .mdcrd files Kenley Barrett
- RE: AMBER: concatenating .mdcrd files Ross Walker
- Re: AMBER: cluster architecture for the best amber performance Robert Duke
- Re: AMBER: Question bonds and angles in frcmod and lib files Jennie Thomas
- AMBER: question about group format Holly Freedman
- [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Jennie Thomas
- Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Bill Ross
- Re: AMBER: AMBER9: MacG5 parallel sander.MPI Mengjuei Hsieh
- AMBER: Amber install on RedHat Linux a a
- RE: AMBER: Amber install on RedHat Linux Ross Walker
- RE: AMBER: Error while running test.serial in Amber9 Priti Hansia
- Re: AMBER: Error while running test.serial in Amber9 David A. Case
Thursday, 4 May 2006
- RE: AMBER: Amber install on RedHat Linux a a
- AMBER: carnal prob bala
- Re: AMBER: carnal prob Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
- Re: AMBER: Amber install on RedHat Linux David A. Case
- RE: AMBER: Amber install on RedHat Linux Ross Walker
- AMBER: conflicting types for XawScrolledTableSetLocation K. Yarem
- Re: AMBER: Error while running test.serial in Amber9 Priti Hansia
- AMBER: molsurf.c error Miguel Ferreira
- RE: AMBER: molsurf.c error Ross Walker
- AMBER: amber9 serial compilation error Arvind Marathe
- Re: AMBER: conflicting types for XawScrolledTableSetLocation Wei Zhang
- AMBER: Trouble with ptraj closestwater in Amber8 Kerry P Donny-Clark
- Re: AMBER: carnal prob Bill Ross
- Re: AMBER: amber9 serial compilation error David A. Case
- AMBER: lipid bi-layer system Lwin, ThuZar
- AMBER: restraintmask Joseph Fernandez
- Re: AMBER: restraintmask Viktor Hornak
- Re: AMBER: question about group format Viktor Hornak
- Re: AMBER: Shared libraries error Viktor Hornak
- RE: AMBER: molsurf.c error Miguel Ferreira
- Re: AMBER: molsurf.c error David A. Case
- Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Jennie Thomas
- Re: AMBER: question about group format Holly Freedman
Friday, 5 May 2006
- Re: AMBER: molsurf.c error Miguel Ferreira
- Re: AMBER: molsurf.c error David A. Case
- AMBER: Problem with shared libraries: libimf.so Priti Hansia
- RE: AMBER: Problem with shared libraries: libimf.so Ross Walker
- AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson
- RE: AMBER: Problem with shared libraries: libimf.so Priti Hansia
- Re: AMBER: experiences with compiling amber9 for FreeBSD David A. Case
- Re: AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson
- Re: AMBER: experiences with compiling amber9 for FreeBSD David A. Case
- RE: AMBER: experiences with compiling amber9 for FreeBSD Ross Walker
- RE: AMBER: Problem with shared libraries: libimf.so Ross Walker
- Re: AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson
- Re: AMBER: experiences with compiling amber9 for FreeBSD Mengjuei Hsieh
- Re: AMBER: experiences with compiling amber9 for FreeBSD Mengjuei Hsieh
- Re: AMBER: experiences with compiling amber9 for FreeBSD David A. Case
- Re: AMBER: experiences with compiling amber9 for FreeBSD Mengjuei Hsieh
- Re: AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson
- AMBER: xleap on iMac G5 Evan Kelly
- Re: AMBER: xleap on iMac G5 Mengjuei Hsieh
- Re: AMBER: experiences with compiling amber9 for FreeBSD Xuebin Qiao
Saturday, 6 May 2006
- RE: AMBER: Problem with shared libraries: libimf.so Priti Hansia
- Re: AMBER: Problem with shared libraries: libimf.so David A. Case
- Re: AMBER: Problem with shared libraries: libimf.so Priti Hansia
Sunday, 7 May 2006
- AMBER: AMBER9 INSTALLATION problem on O2 sgi system S.Sundar Raman
- Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system David A. Case
- Re: AMBER: AMBER9: MacG5 parallel sander.MPI Mengjuei Hsieh
- RE: AMBER: Problem with shared libraries: libimf.so Ross Walker
- AMBER: xleap not recognizing residue Kenley Barrett
- Re: AMBER: xleap not recognizing residue David A. Case
Monday, 8 May 2006
- AMBER: question on distance calculation bala
- Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system S.Sundar Raman
- Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system Atro Tossavainen
- RE: AMBER: AMBER9 INSTALLATION problem on O2 sgi system Ross Walker
- Re: AMBER: xleap not recognizing residue Kenley Barrett
- AMBER: Amber9 test error on SGI Altix amit.mbu.iisc.ernet.in
- AMBER: Problem with impose in lep Osmar Norberto de Souza
- Re: AMBER: Amber9 test error on SGI Altix David A. Case
- AMBER: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 Ross Walker
- Re: AMBER: Amber9 test error on SGI Altix David A. Case
Tuesday, 9 May 2006
- Re: AMBER: Amber9 test error on SGI Altix Ray Luo
Monday, 8 May 2006
- AMBER: Intel compiler version 9.0.033 Ross Walker
- AMBER: PMEMD compilation error Joseph Fernandez
- Re: AMBER: Intel compiler version 9.0.033 Priti Hansia
- Re: AMBER: PMEMD compilation error Robert Duke
- AMBER: About the Amber trajectories converted to XPLOR ( = DCD) format wang
Tuesday, 9 May 2006
- AMBER: San Fransisco Amber users homeira amirkhani
- AMBER: Amber9 test error on SGI Altix Priti Hansia
- AMBER: RE: Intel Compiler. Ross Walker
- Re: AMBER: Amber9 test error on SGI Altix Robert Duke
- AMBER: Compiler with AMD 64 bit support alfredoq.fcq.unc.edu.ar
- AMBER: RE: Intel Compiler. Priti Hansia
- RE: AMBER: Compiler with AMD 64 bit support Ross Walker
- RE: AMBER: RE: Intel Compiler. Ross Walker
- AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 amit.mbu.iisc.ernet.in
- RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 Ross Walker
- Re: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 David A. Case
- Re: AMBER: xleap not recognizing residue David A. Case
Wednesday, 10 May 2006
- RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 amit.mbu.iisc.ernet.in
- AMBER: problem with prep file Simon Whitehead
- AMBER: bug in ambpdb (AMBER8) Petr Kulhanek
- AMBER: Hexahydrated Counterions Mahalakshmi Sahasranaman
- Re: AMBER: bug in ambpdb (AMBER8) David A. Case
- Re: AMBER: Hexahydrated Counterions David A. Case
- RE: AMBER: RE: Intel Compiler. Priti Hansia
- Re: AMBER: problem with prep file David A. Case
- [Fwd: AMBER: Problem with impose in lep] Osmar Norberto de Souza
- Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why Kenley Barrett
- AMBER: I'm very sorry, please disregard previous e-mail--problem seems to be fixed Kenley Barrett
- Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why David A. Case
- AMBER: which patch for ioutfm = 1 in Amber8? Hannes Loeffler
Thursday, 11 May 2006
- AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1? Pan, Yongmei
- Re: AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1? David A. Case
- AMBER: bond information in amber snoze pa
- Re: AMBER: bond information in amber Navnit Kumar Mishra
- Re: AMBER: bond information in amber snoze pa
- Re: AMBER: bond information in amber snoze pa
- AMBER: Opteron vs. Xeon performance Jim Paugh
- AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7 Pan, Yongmei
- Re: AMBER: bond information in amber snoze pa
- AMBER: Amber9/mpich2 performance Joseph Fernandez
- RE: AMBER: Amber9/mpich2 performance Ross Walker
- RE: AMBER: Opteron vs. Xeon performance Ross Walker
- Re: AMBER: Opteron vs. Xeon performance Robert Duke
- AMBER: question about REDII Raffaella D'Auria
- AMBER: About mm_pbsa calculation setting up alfredoq.fcq.unc.edu.ar
- AMBER: AMBER 8 - dihedral angles when clambda=1 Ilyas Yildirim
- Re: AMBER: bond information in amber Navnit Kumar Mishra
- Re: AMBER: question about REDII FyD
Friday, 12 May 2006
- Re: AMBER: Opteron vs. Xeon performance ian gould
- Re: AMBER: Opteron vs. Xeon performance Ye Mei
- AMBER: Xleap compilation problem Sergio Dall'Angelo
- AMBER: Xleap compilation problem Sergio Dall'Angelo
- AMBER: RMSD calculation between ligands Stefan Henrich
- Re: AMBER: Opteron vs. Xeon performance Robert Duke
- Re: AMBER: Opteron vs. Xeon performance Robert Duke
- Re: Re: AMBER: Opteron vs. Xeon performance Ye Mei
- RE: AMBER: Opteron vs. Xeon performance Ross Walker
- Re: AMBER: Xleap compilation problem Sergio Dall'Angelo
- AMBER: another question: is rms 2E-2 good for nmode ntrun=1? Pan, Yongmei
- Re: AMBER: Opteron vs. Xeon performance Robert Duke
- Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1? David A. Case
- Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1? nadiav.soton.ac.uk
- Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1? David A. Case
- Re: AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7 David Mobley
- Re: AMBER: question about REDII Raffaella D'Auria
- AMBER: binpos file Varsha Goyal
- RE: AMBER: Amber9/mpich2 performance Joseph Fernandez
Saturday, 13 May 2006
- AMBER: strange mm_pbsa output alfredoq.fcq.unc.edu.ar
Friday, 12 May 2006
- Re: AMBER: strange mm_pbsa output Ray Luo
Saturday, 13 May 2006
- Re: AMBER: strange mm_pbsa output alfredoq.fcq.unc.edu.ar
- Re: AMBER: strange mm_pbsa output David A. Case
Sunday, 14 May 2006
- AMBER: Compilers and libraries for AMBER in HPC! Pradipta Bandyopadhyay
- Re: AMBER: strange mm_pbsa output alfredoq.fcq.unc.edu.ar
- AMBER: PBS script for lemieux Stern, Julie
- RE: AMBER: Opteron vs. Xeon performance Yong Duan
- AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs Zhihong Yu
- RE: AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs Ross Walker
Monday, 15 May 2006
- RE: AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs Zhihong Yu
- AMBER: AMBER9 compilation error on IBM Cluster amit.mbu.iisc.ernet.in
- AMBER: Problem with "impose" in leap Osmar Norberto de Souza
- AMBER: fail to execute addles pang zhao
- Re: AMBER: fail to execute addles Carlos Simmerling
- AMBER: ff02 + POL3 problem ! Pradipta Bandyopadhyay
- Re: AMBER: fail to execute addles pang zhao
- RE: AMBER: ff02 + POL3 problem ! Yong Duan
- Re: AMBER: fail to execute addles David A. Case
- Re: AMBER: fail to execute addles Carlos Simmerling
- AMBER: installation problem Mahalakshmi Sahasranaman
- Re: AMBER: installation problem Robert Duke
- RE: AMBER: problem with prep file Junmei Wang
- RE: AMBER: AMBER9 compilation error on IBM Cluster Ross Walker
- AMBER: density mathew k varghese
- RE: AMBER: density Yong Duan
- Re: AMBER: fail to execute addles pang zhao
- Re: AMBER: fail to execute addles pang zhao
- Re: AMBER: fail to execute addles pang zhao
Tuesday, 16 May 2006
- AMBER: amber8 compiled erro on opteron with 64 bit renyanliang
- Re: AMBER: amber8 compiled erro on opteron with 64 bit Andreas Svrcek-Seiler
- Re: AMBER: fail to execute addles Carlos Simmerling
- RE: AMBER: ff02 + POL3 problem ! Pradipta Bandyopadhyay
- Re: AMBER: fail to execute addles pang zhao
- RE: AMBER: ff02 + POL3 problem ! Yong Duan
- AMBER: trouble stripping waters with ptraj Adam Pelzer
- Re: AMBER: trouble stripping waters with ptraj Asim Okur
- RE: AMBER: density mathew k varghese
- AMBER: amber compilation on Red Hat 8 with MPICH kawamura_hiro.riken.jp
- AMBER: "atom number exceeds the MAXATOM" BAUVAIS.itodys.jussieu.fr
- AMBER: Tutorial one : libsvml.so error a a
Wednesday, 17 May 2006
- Re: AMBER: Tutorial one : libsvml.so error Mark Williamson
- AMBER: Tutorial one : xaLeap command not found. a a
- AMBER: distance dependent dielectric constant Mahalakshmi Sahasranaman
- Re: AMBER: amber compilation on Red Hat 8 with MPICH David A. Case
- Re: AMBER: "atom number exceeds the MAXATOM" David A. Case
- Re: AMBER: distance dependent dielectric constant David A. Case
- RE: AMBER: density Ross Walker
- RE: AMBER: amber compilation on Red Hat 8 with MPICH Ross Walker
- RE: AMBER: Tutorial one : xaLeap command not found. Ross Walker
- RE: AMBER: density mathew k varghese
- RE: AMBER: density Ross Walker
- AMBER: "The system has extended beyond" error message Atsutoshi Okabe
Thursday, 18 May 2006
- AMBER: Correlation matrix used in quasih (Amber 7) Craig Gough
- AMBER: AMBER9 installation error on Compaq machine. Soonmin Jang
- AMBER: vlimit exceeded aixiaoli
- AMBER: problem with installation, or bug? Kenley Barrett
- Re: AMBER: "The system has extended beyond" error message german
- Re: AMBER: vlimit exceeded David A. Case
- Re: AMBER: Correlation matrix used in quasih (Amber 7) David A. Case
- Re: AMBER: "The system has extended beyond" error message David A. Case
- AMBER: force field parameters Douali, Latifa
- Re: AMBER: force field parameters Navnit Kumar Mishra
- RE: AMBER: force field parameters Douali, Latifa
- AMBER: RMSd calculations Claire Zerafa
- AMBER: OT: software to support AMBER? Steve Gwaltney
- RE: AMBER: AMBER9 installation error on Compaq machine. Ross Walker
- AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Hall, Spencer
- RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Ross Walker
Friday, 19 May 2006
- AMBER: process_mdout.perl error a a
- AMBER: Intel fortran compiler 7? Simon Whitehead
- AMBER: xmgr error a a
- Re: AMBER: xmgr error mathew k varghese
- Re: AMBER: force field parameters Navnit Kumar Mishra
- Re: AMBER: Intel fortran compiler 7? Robert Duke
- AMBER: Fw: RMSd calculations Claire Zerafa
- Re: AMBER: Fw: RMSd calculations Carlos Simmerling
- AMBER: problem loading forcefield leaprc.ff86 Mahalakshmi Sahasranaman
- RE: AMBER: process_mdout.perl error Ross Walker
- Re: AMBER: problem loading forcefield leaprc.ff86 David A. Case
- AMBER: RE: PMEMD compilation problems Simon Whitehead
- Re: AMBER: RE: PMEMD compilation problems Robert Duke
- RE: AMBER: xmgr error Douali, Latifa
- AMBER: amber .off file format question Ilyas Yildirim
Saturday, 20 May 2006
- AMBER: RE: trouble stripping waters with ptraj Adam Pelzer
- Re: AMBER: RE: trouble stripping waters with ptraj Carlos Simmerling
- AMBER: Problem with running xleap remotely heaton.chem.utah.edu
- RE: AMBER: Problem with running xleap remotely Ross Walker
- RE: AMBER: Problem with running xleap remotely heaton.chem.utah.edu
Sunday, 21 May 2006
- AMBER: trajin and rms a a
- RE: AMBER: trajin and rms Ross Walker
Monday, 22 May 2006
- AMBER: RMSd error Claire Zerafa
- RE: AMBER: trajin and rms a a
- Re: AMBER: amber .off file format question Ilyas Yildirim
- AMBER: Water density output Navnit Kumar Mishra
- AMBER: A dummy atom on the center of solute molecule Atsutoshi Okabe
- Re: AMBER: A dummy atom on the center of solute molecule Ilyas Yildirim
- Re: AMBER: trajin and rms Carlos Simmerling
- Re: AMBER: RMSd error Carlos Simmerling
- AMBER: Macromodel Amber* vs. Amber7 opitz.che.udel.edu
- AMBER: More Amber 9 Benchmarks available Robert Duke
- Re: AMBER: RE: trouble stripping waters with ptraj Asim Okur
- Re: AMBER: Problems compiling amber9 Don Harden
- Re: AMBER: amber .off file format question Wei Zhang
- Re: AMBER: amber .off file format question Bill Ross
- Re: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Michael Crowley
- Re: AMBER: Problems compiling amber9 David A. Case
- Re: AMBER: Problems compiling amber9 Andreas Svrcek-Seiler
- AMBER: Again SASA lucas luquitas
- AMBER: 3Dsig: Struct Bioinfo & Comp Biophysics Meeting, 4-5 Aug. Brazil 3Dsig06
- Re: AMBER: amber .off file format question Ilyas Yildirim
- Re: AMBER: amber .off file format question David A. Case
Tuesday, 23 May 2006
- Re: AMBER: Problems compiling amber9 Don Harden
- RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Hall, Spencer
- RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Hall, Spencer
- AMBER: error in AMBER 9.0 mkseo
- RE: AMBER: A dummy atom on the center of solute molecule Atsutoshi Okabe
- RE: AMBER: A dummy atom on the center of solute molecule Ilyas Yildirim
- Re: AMBER: error in AMBER 9.0 David A. Case
Wednesday, 24 May 2006
- AMBER: amber8 bugfix effects kawamura_hiro.riken.jp
- RE: AMBER: trajin and rms a a
- Re: AMBER: amber8 bugfix effects David A. Case
- AMBER: simulate proteins with non-standard residues Hui Lei
- AMBER: freeze interval vibrations Eric Hu
- Re: AMBER: freeze interval vibrations David A. Case
- AMBER: problem with prepfile Shafinaz
- Re: AMBER: problem with prepfile David A. Case
- AMBER: use_pme=0 problem luckyang.gmail.com
- AMBER: output of first stage RESP calculation JunJun Liu
- Re: AMBER: use_pme=0 problem David A. Case
- Re: AMBER: use_pme=0 problem luckyang.gmail.com
- Re: AMBER: use_pme=0 problem David A. Case
- Re: AMBER: use_pme=0 problem luckyang.gmail.com
- AMBER: How to built the deprotonated form of lysine and tyrosine jitrayut jitonnom
- AMBER: Fwd: RESP for deprotonated tyrosine and lysine jitrayut jitonnom
- AMBER: Qestion about input for RESP program JunJun Liu
- AMBER: How to build NH2 of amino acid in amber jitrayut jitonnom
- Re: AMBER: Qestion about input for RESP program Ilyas Yildirim
Thursday, 25 May 2006
- Re: AMBER: output of first stage RESP calculation FyD
- Re: AMBER: Qestion about input for RESP program FyD
- Re: AMBER: Fwd: RESP for deprotonated tyrosine and lysine FyD
- AMBER: question about QM/MM in amber9 aixiaoli
- AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) Soonmin Jang
- Re: AMBER: question about QM/MM in amber9 Adrian Roitberg
- AMBER: 1st 2 lines of restart files hayden
- Re: AMBER: 1st 2 lines of restart files Steven Winfield
- Re: AMBER: Qestion about input for RESP program JunJun Liu
- RE: AMBER: question about QM/MM in amber9 Ross Walker
- Re: AMBER: Qestion about input for RESP program FyD
- RE: AMBER: problem with prepfile Junmei Wang
- Re: AMBER: use_pme=0 problem luckyang.gmail.com
Wednesday, 24 May 2006
- Re: AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) Ray Luo
Thursday, 25 May 2006
- Re: AMBER: use_pme=0 problem David A. Case
- Re: AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) David A. Case
- AMBER: alpha helix preference problem harianto
- Re: AMBER: alpha helix preference problem Carlos Simmerling
- Re: AMBER: use_pme=0 problem luckyang.gmail.com
- AMBER: RMSd error Claire Zerafa
- AMBER: RE: trouble stripping waters with ptraj Adam Pelzer
Friday, 26 May 2006
- AMBER: ptraj: calculating distances between atoms in charges residues Magne Olufsen
- AMBER: Question about .off file Sergey Krishtal
- Re: AMBER: Question about .off file Ilyas Yildirim
- Re: AMBER: RE: trouble stripping waters with ptraj Carlos Simmerling
- Re: AMBER: RMSd error Carlos Simmerling
- Re: AMBER: RMSd error Claire Zerafa
- Re: AMBER: RMSd error Carlos Simmerling
- Re: AMBER: RMSd error Claire Zerafa
- AMBER: different TI calculations starting from the same state Andrea Bortolato
- Re: AMBER: alpha helix preference problem harianto
- AMBER: different TI calculations starting from the same state Andrea Bortolato
- AMBER: Saving RMSD values in VMD nag raj
- Re: AMBER: different TI calculations starting from the same state David A. Case
- RE: AMBER: alpha helix preference problem Ross Walker
- RE: AMBER: Saving RMSD values in VMD Ross Walker
- Re: AMBER: Saving RMSD values in VMD Carlos Simmerling
- Re: AMBER: RMSd error Thomas Cheatham
- Re: [UCE]AMBER: RE: trouble stripping waters with ptraj Thomas Cheatham
- Re: AMBER: ptraj: calculating distances between atoms in charges residues Thomas Cheatham
- AMBER: check as error: load prepin in tleap jitrayut jitonnom
- Re: AMBER: use_pme=0 problem David A. Case
- Re: AMBER: use_pme=0 problem luckyang.gmail.com
- AMBER: Please reply Shafinaz
- Re: AMBER: use_pme=0 problem David A. Case
- Re: AMBER: Please reply Ananda Rama Krishnan Selvaraj
- Re: AMBER: Please reply David A. Case
- Re: AMBER: use_pme=0 problem luckyang.gmail.com
- Re: AMBER: use_pme=0 problem Bill Ross
- AMBER: Installing / Compiling Question Seth Lilavivat
Saturday, 27 May 2006
- Re: AMBER: Installing / Compiling Question David A. Case
- RE: AMBER: Installing / Compiling Question Ross Walker
Sunday, 28 May 2006
- Re: AMBER: RMSd error Claire Zerafa
- AMBER: md error : sander jitrayut jitonnom
- Re: AMBER: md error : sander Carlos Simmerling
- AMBER: Pt containing complex: xleap a a
- AMBER: Pt containing complex: antechamber a a
- Re: AMBER: Pt containing complex: xleap Ilyas Yildirim
- RE: AMBER: A dummy atom on the center of solute molecule Ilyas Yildirim
- RE: AMBER: A dummy atom on the center of solute molecule Atsutoshi Okabe
Monday, 29 May 2006
- AMBER: which time should I use to calculate the number of "ps/Day" Zhihong Yu
- AMBER: antechamber help needed for FAD pkb bioinfo
- Re: AMBER: which time should I use to calculate the number of "ps/Day" Carlos Simmerling
- Re: AMBER: which time should I use to calculate the number of "ps/Day" Robert Duke
- AMBER: Thermodynamic integration using the amber 9 Vitor Manuel Sousa F?x
- AMBER: Difference in results for TI calculation brmeher.iitg.ernet.in
- AMBER: Difference in results for TI calculation brmeher.iitg.ernet.in
- Re: AMBER: Thermodynamic integration using the amber 9 Ilyas Yildirim
- AMBER: problems with antechamber JAVIER PEREZ
- AMBER: energy terms JAVIER PEREZ
- AMBER: SAVEPDB in Xleap could not save 4 character atom names Jiayun Pang
- Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names Bill Ross
- AMBER: RE: trouble stripping waters with ptraj Adam Pelzer
- Re: AMBER: which time should I use to calculate the number of "ps/Day" Zhihong Yu
Tuesday, 30 May 2006
- AMBER: Antechamber : +ve charge species a a
- AMBER: ESP calculations. a a
- Re: AMBER: ESP calculations. FyD
- Re: AMBER: ESP calculations. Ken Merz
- Re: AMBER: ESP calculations. Ken Merz
- Re: AMBER: problems with antechamber linfu
- RE: AMBER: problems with antechamber Junmei Wang
- RE: AMBER: Antechamber : +ve charge species Junmei Wang
- Re: [UCE]AMBER: RE: trouble stripping waters with ptraj Thomas Cheatham
- Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names David A. Case
- Re: AMBER: Pt containing complex: antechamber David A. Case
- Re: AMBER: Difference in results for TI calculation David A. Case
- Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names Andy Purkiss
- RE: AMBER: A dummy atom on the center of solute molecule Ilyas Yildirim
Wednesday, 31 May 2006
- AMBER: Different results for TI calculation Biswa Ranjan Meher
- AMBER: Replica exchage: about exchange interval Atsutoshi Okabe
- Re: AMBER: Replica exchage: about exchange interval Carlos Simmerling
- AMBER: Force units in forcedump.dat Steven Winfield
- AMBER: Namelists in input files Steven Winfield
- AMBER: SHAKE, TIP3P and 2fs Timesteps Mark Williamson
- Re: AMBER: Force units in forcedump.dat darden
- RE: AMBER: SHAKE, TIP3P and 2fs Timesteps Ross Walker
- AMBER: xleap problem and answer Thomas Pochapsky
- RE: AMBER: SHAKE, TIP3P and 2fs Timesteps Andreas Svrcek-Seiler
- AMBER: AMBER mdcrd file bigger than 2GB snoze pa
- AMBER: Installation of Amber8 on Fedora Core 5 DAVID P. RANGEL
- Re: AMBER: AMBER mdcrd file bigger than 2GB snoze pa
- Re: AMBER: AMBER mdcrd file bigger than 2GB Thomas Cheatham

Last message date: Sun Jun 04 2006 - 06:07:09 PDT
Archived on: Fri May 03 2024 - 05:53:21 PDT

Amber Archive May 2006 by date