Amber Archive Sep 2004: by date

Tuesday, 31 August 2004
- RE: AMBER: Increase lastrst in the &cntrl namelist Osman Gani
Wednesday, 1 September 2004
- AMBER: question on mm-pbsa cailliez
- AMBER: [0] MPI Abort by user Aborting program ! tang kwa
- AMBER: Setting up thermodynamic integration david.evans.ulsop.ac.uk
- Re: AMBER: [0] MPI Abort by user Aborting program ! Melinda Layten
- AMBER: Re. HSG Convention jwcraft.uh.edu
- Re: AMBER: Re. HSG Convention David A. Case
- Re: AMBER: Pulling versus Distance Restraints Furse, Kristina Elisabet
- RE: AMBER: Increase lastrst in the &cntrl namelist Sichun Yang
- Re: AMBER: Setting up thermodynamic integration david.evans.ulsop.ac.uk
- Re: AMBER: About tree structure of TRP residue David A. Case
- Re: AMBER: Increase lastrst in the &cntrl namelist Carlos Simmerling
- Re: AMBER: Increase lastrst in the &cntrl namelist David A. Case
- Re: AMBER: question on mm-pbsa Holger Gohlke
- AMBER: parameters-DGnp John
Thursday, 2 September 2004
- AMBER: error in installing amber8 anshul.imtech.res.in
- Re: AMBER: error in installing amber8 David A. Case
- Re: AMBER: error in installing amber8 Scott Brozell
- AMBER: loading frcmod.mod_phipsi.1 bybaker.itsa.ucsf.edu
- AMBER: Water Box & MD bybaker.itsa.ucsf.edu
- Re: AMBER: loading frcmod.mod_phipsi.1 Bill Ross
- Re: AMBER: loading frcmod.mod_phipsi.1 bybaker.itsa.ucsf.edu
Saturday, 4 September 2004
- Re: AMBER: Differences in RESP charges for G in RG and DG residues FyD
- AMBER: Amber7 tleap problem Ed Pate
- Re: AMBER: Amber7 tleap problem David A. Case
Monday, 6 September 2004
- AMBER: general questions Marsita M
Tuesday, 7 September 2004
- AMBER: Electrostatic potential from the trajectory ! Pradipta Bandyopadhyay
- Re: AMBER: general questions Stefano.Pieraccini.unimi.it
- AMBER: is it a bug in mmpbsa Shan, Jufang
Wednesday, 8 September 2004
- AMBER: xLeap menus not working properly Hannes Barsch
- Re: AMBER: xLeap menus not working properly Heike.Meiselbach.chemie.uni-erlangen.de
- Re: AMBER: error in installing amber8 anshul.imtech.res.in
- RE: AMBER: Electrostatic potential from the trajectory ! Ross Walker
- AMBER: Amber: BOMB Helios
- AMBER: Spike in energy and RMS Balvinder Singh
- RE: AMBER: Spike in energy and RMS Ross Walker
- RE: AMBER: Amber: BOMB Ross Walker
- Re: AMBER: error in installing amber8 Bill Ross
- Re: AMBER: Amber: BOMB David A. Case
- Re: AMBER: error in installing amber8 David A. Case
- AMBER: REST Yanze Zhang
- Re: AMBER: REST Melinda Layten
- AMBER: Nucgen and PNA? opitz.che.udel.edu
- Re: AMBER: Nucgen and PNA? Rhonda Torres
- AMBER: Antechamber Failure Johnson Agbo
- Re: AMBER: Antechamber Failure David A. Case
- AMBER: Amber:how to increase the memory allocation? Helios
Thursday, 9 September 2004
- Re: AMBER: Spike in energy and RMS Andreas Svrcek-Seiler
- Re: AMBER: Nucgen and PNA? opitz.che.udel.edu
- Re: AMBER: Amber:how to increase the memory allocation? David A. Case
- AMBER: REM make test Sergio E. Wong
- AMBER: MAC Based Beowulf Cluster Peter Gannett
- Re: AMBER: REM make test David A. Case
- Re: AMBER: REM make test Sergio E. Wong
- AMBER: GB and langevin dynamics Sergio E. Wong
Friday, 10 September 2004
- AMBER: How many ions? Volodymyr Zloy
- AMBER: make install error Abd Ghani Bin Abd Aziz
- AMBER: Monte Carlo simulation tang kwa
- AMBER: MPICH problem Abd Ghani Bin Abd Aziz
- Re: AMBER: REM make test Carlos Simmerling
- AMBER: Test Calculation of atomic charges (RESP) for RNA bases Vlad Cojocaru
- AMBER: re:your message to amber... hj zou
- AMBER: Amber7 - mm_pbsa/molsurf Nadine Homeyer
- Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases Piotr Cieplak
- Re: AMBER: Amber7 - mm_pbsa/molsurf Oliver Hucke
- Re: AMBER: Monte Carlo simulation David A. Case
- RE: AMBER: make install error Ross Walker
- Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases FyD
- AMBER: An question about PTRAJ b86203054.ntu.edu.tw
Saturday, 11 September 2004
- Re: AMBER: An question about PTRAJ Stef
- AMBER: make install error Abd Ghani Bin Abd Aziz
- Re: AMBER: An question about PTRAJ Thomas E. Cheatham, III
Sunday, 12 September 2004
- RE: AMBER: make install error Ross Walker
- RE: AMBER: MPICH problem Ross Walker
- RE: AMBER: make install error Abd Ghani Bin Abd Aziz
- Re: AMBER: make install error Robert Duke
- Re: AMBER: make install error Abd Ghani Bin Abd Aziz
- Re: AMBER: make install error Robert Duke
- Re: AMBER: make install error Abd Ghani Bin Abd Aziz
Monday, 13 September 2004
- Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases Vlad Cojocaru
- AMBER: mmpbsa: can not generate coordinates/snapshots Magne Olufsen
- AMBER: AMBER7 : update gaff and parm99 force field Guillaume Bollot
- AMBER: Compilation Problem in Amber 7 Stephen P. Molnar, Ph.D.
- AMBER: AMBER7 : Hybrid macromolecule Guillaume Bollot
- Re: AMBER: AMBER7 : Hybrid macromolecule david.evans.ulsop.ac.uk
- Re: AMBER: An question about PTRAJ b86203054.ntu.edu.tw
- Re: AMBER: An question about PTRAJ b86203054.ntu.edu.tw
- Re: AMBER: AMBER7 : update gaff and parm99 force field David A. Case
- Re: AMBER: GB and langevin dynamics David A. Case
- AMBER: target rmsd William Andrew McLaughlin
- Re: AMBER: target rmsd Carlos Simmerling
- Re: AMBER: target rmsd Viktor Hornak
- Re: AMBER: target rmsd William Andrew McLaughlin
- Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases FyD
- Re: AMBER: target rmsd Viktor Hornak
- RE: AMBER: Compilation Problem in Amber 7 Ross Walker
Tuesday, 14 September 2004
- AMBER: bond between two polypeptides Jagdish Rai
- AMBER: mm_pbsa for Delphi Helios Chen
- AMBER: Re: to Francois Vlad Cojocaru
- AMBER: MM binding energy with ANAL Ben Cossins
- AMBER: amber 8 Abd Ghani Bin Abd Aziz
- RE: AMBER: amber 8 Ross Walker
- Re: AMBER: make install error Abd Ghani Bin Abd Aziz
- RE: AMBER: amber 8 Abd Ghani Bin Abd Aziz
- RE: AMBER: amber 8 Ross Walker
- Re: AMBER: bond between two polypeptides David A. Case
- AMBER: want to generate ammonium ion..where to start? Grace Li
- AMBER: TI with sander Oliver Hucke
- Re: AMBER: TI with sander David A. Case
- AMBER: Restraints in sander.QMMM Joseph Fernandez
- AMBER: restrain on the distance between two molecules. Qiang Lu
- Re: AMBER: restrain on the distance between two molecules. Nhat-hang Duong
- Re: AMBER: Restraints in sander.QMMM David A. Case
- AMBER: nmode Carsten Detering
- Re: AMBER: MM binding energy with ANAL David A. Case
- Re: AMBER: nmode David A. Case
Wednesday, 15 September 2004
- AMBER: Intel Fortran Compiler Problem Stephen P. Molnar, Ph.D.
- Re: AMBER: Intel Fortran Compiler Problem Viktor Hornak
- AMBER: F90 compiler for linux ppc64 Guanglei Cui
- Re: AMBER: Intel Fortran Compiler Problem Stephen P. Molnar, Ph.D.
- AMBER: principal axis Alberto Perez
- Re: AMBER: Intel Fortran Compiler Problem Robert Duke
- Re: AMBER: Intel Fortran Compiler Problem Viktor Hornak
- Re: AMBER: Intel Fortran Compiler Problem Stephen P. Molnar, Ph.D.
- AMBER: bond constraints in nmode richard dimelow
- Re: AMBER: Intel Fortran Compiler Problem Viktor Hornak
- Re: AMBER: F90 compiler for linux ppc64 Guanglei Cui
- Re: AMBER: F90 compiler for linux ppc64 Carlos P. Sosa
- Re: AMBER: Intel Fortran Compiler Problem Robert Duke
- Re: AMBER: Intel Fortran Compiler Problem Robert Duke
- Re: AMBER: principal axis Thomas E. Cheatham, III
- Re: AMBER: Intel Fortran Compiler Problem Stephen P. Molnar, Ph.D.
- Re: AMBER: bond constraints in nmode David A. Case
- AMBER: md problem Volodymyr Zloy
- Re: AMBER: Intel Fortran Compiler Problem David A. Case
- Re: AMBER: Intel Fortran Compiler Problem Robert Duke
- Re: AMBER: R.E.D. II to Vlad FyD
- AMBER: A tool for building coordinates of huge macromolecules Hwankyu Lee
- Re: AMBER: A tool for building coordinates of huge macromolecules Joachim Reichelt
- Re: AMBER: GB and langevin dynamics Sergio E. Wong
- Re: AMBER: md problem Furse, Kristina Elisabet
- Re: AMBER: GB and langevin dynamics David A. Case
- AMBER: back interpret Joshua Hicks
- Re: AMBER: back interpret Carlos Simmerling
- Re: AMBER: back interpret David A. Case
- AMBER: Sander TI with NTR = 1. Chunhu Tan
Thursday, 16 September 2004
- RE: AMBER: md problem Ross Walker
- AMBER: VDWAALS error during minimisation anita pachaimuthu
- Re: AMBER: Sander TI with NTR = 1. David A. Case
- RE: AMBER: VDWAALS error during minimisation Ross Walker
- AMBER: extra points richard dimelow
- AMBER: restraining internal coordinates Taner E. Dirama
- Re: AMBER: restraining internal coordinates Carlos Simmerling
- Re: AMBER: extra points David A. Case
- AMBER: Force Compiling AMBER8 for an SGI O2 Justin Sanders
- RE: AMBER: Intel Fortran Compiler Problem Ross Walker
- AMBER: amber8 performance problem on Itanium II's Sergio E. Wong
Friday, 17 September 2004
- Re: AMBER: amber8 performance problem on Itanium II's Andreas Svrcek-Seiler
- AMBER: Amber 7 Compiling Problem Stephen P. Molnar, Ph.D.
- AMBER: Problem with MacroMolecule to AMBER7 Guillaume Bollot
- Re: AMBER: Problem with MacroMolecule to AMBER7 Sébastien Osborne
- Re: AMBER: Amber 7 Compiling Problem David A. Case
- AMBER: PMEMD Greg Kellogg
- Re: AMBER: PMEMD Robert Duke
- Re: AMBER: Amber 7 Compiling Problem Stephen P. Molnar, Ph.D.
- Re: AMBER: Amber 7 Compiling Problem David A. Case
- Re: AMBER: Amber 7 Compiling Problem Stephen P. Molnar, Ph.D.
- Re: AMBER: Amber 7 Compiling Problem Stephen P. Molnar, Ph.D.
- Re: AMBER: amber8 performance problem on Itanium II's Sergio E. Wong
- AMBER: Moil-view & Amber trajectory opitz.che.udel.edu
- Re: AMBER: Moil-view & Amber trajectory Carlos Simmerling
- Re: AMBER: Moil-view & Amber trajectory Thomas E. Cheatham, III
- AMBER: mm_pbsa nmode problem Fang, Jianwen
- AMBER: Re: Delphi PATH question hj zou
- AMBER: about PARALLEL run on SGI. Ji Changge
Saturday, 18 September 2004
- Re: AMBER: About binding energy Oliver Hucke
Sunday, 19 September 2004
- AMBER: More details about free energy Xiao He
- AMBER: ifort installation mathew k varghese
- Re: AMBER: ifort installation Nhat-hang Duong
- Re: AMBER: about PARALLEL run on SGI. David A. Case
- AMBER: Questions on simulating dendrimer in AMBER. Hwankyu Lee
Monday, 20 September 2004
- AMBER: The question about SAS calculation in MM_PBSA Jack Lei
- RE: AMBER: Trajectory file conversion between Amber & Charmm CK Sim
- Re: AMBER: Trajectory file conversion between Amber & Charmm Carlos Simmerling
- RE: AMBER: md problem Volodymyr Zloy
- RE: AMBER: Trajectory file conversion between Amber & Charmm Thomas E. Cheatham, III
- AMBER: RESP problem... FyD
- AMBER: sander8 compile: myrinet and mpigm Guanglei Cui
- Re: AMBER: Moil-view & Amber trajectory opitz.che.udel.edu
- AMBER: about MM-PBSA Xiao He
- RE: AMBER: about MM-PBSA S. Frank Yan
Tuesday, 21 September 2004
- Re: RE: AMBER: about MM-PBSA Xiao He
Monday, 20 September 2004
- Re: AMBER: about MM-PBSA Ray Luo
Tuesday, 21 September 2004
- Re: AMBER: Moil-view & Amber trajectory Carlos Simmerling
- AMBER: Ptraj data Steve Seibold
- Re: AMBER: Ptraj data Viktor Hornak
- Re: AMBER: Ptraj data Thomas E. Cheatham, III
- AMBER: MAXRING Antechamber problem Karl N. Kirschner
- RE: AMBER: MAXRING Antechamber problem Ross Walker
- Re: AMBER: Ptraj data Elijah Gregory
- AMBER: Question about Parallel Compilation David LeBard
- Re: Re: AMBER: about MM-PBSA Xiao He
Wednesday, 22 September 2004
- AMBER: amber8 installation mathew k varghese
- AMBER: all_nucleic02 and all_nucleic94 Vlad Cojocaru
- Re: AMBER: amber8 installation Andreas Svrcek-Seiler
- AMBER: Re: Re: Delphi PATH question hj zou
- AMBER: amber8 tests mathew k varghese
- AMBER: all_nucleic94 versus all_nucleic02 Vlad Cojocaru
- Re: AMBER: all_nucleic94 versus all_nucleic02 Jiten
- Re: AMBER: Re: Re: Delphi PATH question Xiao He
- RE: AMBER: all_nucleic94 versus all_nucleic02 Ross Walker
- AMBER: building parameters with Amber Amber admin
- Re: AMBER: Question about Parallel Compilation David A. Case
- AMBER: compressed files Jessica Koplin
- Re: AMBER: all_nucleic02 and all_nucleic94 David A. Case
- RE: AMBER: all_nucleic94 versus all_nucleic02 Ross Walker
- RE: AMBER: compressed files Ross Walker
- Re: AMBER: The question about SAS calculation in MM_PBSA David A. Case
- Re: AMBER: amber8 tests David A. Case
- Re: AMBER: building parameters with Amber Furse, Kristina Elisabet
- AMBER: mm_pbsa.pl nmode entropy estimating problem jwfang
- RE: AMBER: MAXRING Antechamber problem Karl N. Kirschner
- Re: AMBER: mm_pbsa.pl nmode entropy estimating problem David A. Case
- Re: AMBER: Question about Parallel Compilation David LeBard
Thursday, 23 September 2004
- AMBER: RESTARTED DUE TO LINMIN FAILURE ... ying xiong
- AMBER: Jiten
- Re: AMBER: RESTARTED DUE TO LINMIN FAILURE ... cailliez
- AMBER: replica exchange with thermodynamic integration david.evans.ulsop.ac.uk
- AMBER: trajectory Wen Li
- AMBER: question about J. Am. Chem. Soc. 2001, 123, 5221 paper jwfang
- AMBER: Amber job submission using PBS Jiten
- Re: AMBER: Amber job submission using PBS Guanglei Cui
- Re: AMBER: Amber job submission using PBS Jiten
- Re: AMBER: Amber job submission using PBS Guanglei Cui
- Re: AMBER: Amber job submission using PBS Jiten
- Re: AMBER: Amber job submission using PBS Jiten
- RE: AMBER: Ross Walker
- RE: AMBER: Amber job submission using PBS Ross Walker
- Re: AMBER: Amber job submission using PBS Guanglei Cui
- Re: AMBER: Amber job submission using PBS Thomas E. Cheatham, III
- RE: AMBER: Amber job submission using PBS Bill Ross
- AMBER: Amber 8 installation error on Xeon 2-CPU Kei ODAI
- RE: AMBER: Amber 8 installation error on Xeon 2-CPU Ross Walker
- AMBER: ptraj problem Marsita M
- Re: AMBER: Amber 8 installation error on Xeon 2-CPU Bill Ross
- AMBER: about mm_pbsa parameter Xiao He
- Re: AMBER: Amber job submission using PBS Jiten
- Re: AMBER: Amber job submission using PBS Jiten
- Re: AMBER: Amber job submission using PBS Jiten
- AMBER: nbflag cailliez
Friday, 24 September 2004
- AMBER: phosphoserine library component jwcraft.uh.edu
- Re: AMBER: phosphoserine library component Jiten
- Re: AMBER: nbflag David A. Case
- Re: AMBER: phosphoserine library component David A. Case
- Re: AMBER: nbflag cailliez
- Re: AMBER: replica exchange with thermodynamic integration David A. Case
- Re: AMBER: about mm_pbsa parameter Oliver Hucke
- AMBER: regular ewald sum in Amber8 Jianwen Jiang
- Re: AMBER: phosphoserine library component FyD
- AMBER: Parameters for Inosine yuqin cai
- Re: AMBER: regular ewald sum in Amber8 David A. Case
- AMBER: Question Amber8 install errer with Windows Amber admin
- Re: AMBER: Parameters for Inosine Jiri Sponer
- Re: AMBER: Question Amber8 install errer with Windows David A. Case
- AMBER: nmode error Xiao He
- AMBER: Analysis mm_pbsa result Xiao He
Saturday, 25 September 2004
- AMBER: output of mm_pbsa.log Xiao He
- AMBER: minimization problem hj zou
- AMBER: Abd Ghani Bin Abd Aziz
- Re: AMBER: minimization problem David A. Case
- Re: AMBER: nmode error David A. Case
- AMBER: radius of gyration Marsita M
- Re: AMBER: radius of gyration Sanjeev B.S.
- Re: AMBER: radius of gyration Marsita M
Sunday, 26 September 2004
- Re: AMBER: radius of gyration Sanjeev B.S.
- AMBER: amber 8 error on installation Abd Ghani Bin Abd Aziz
- Re: AMBER: amber 8 error on installation Carlos Simmerling
- Re: AMBER: amber 8 error on installation Abd Ghani Bin Abd Aziz
- AMBER: dihedral hj zou
- Re: AMBER: dihedral Thomas E. Cheatham, III
- Re: AMBER: radius of gyration Bill Ross
- Re: AMBER: radius of gyration Bill Ross
- AMBER: Atom distance bybaker.itsa.ucsf.edu
Monday, 27 September 2004
- Re: AMBER: Atom distance Tomas Linhart
- AMBER: Principal Component Analysis Vlad Cojocaru
- AMBER: unformatted md problem richard dimelow
- AMBER: Great help:Analysis mm_pbsa result Xiao He
- Re: AMBER: unformatted md problem David A. Case
- AMBER: how to visualize modes from PCA Vlad Cojocaru
- Re: AMBER: how to visualize modes from PCA Carlos Simmerling
- AMBER: Amber-7:Bugfix.47 sachin patil
- Re: AMBER: Amber-7:Bugfix.47 David A. Case
- RE: AMBER: Amber-7:Bugfix.47 Ross Walker
- Re: AMBER: Atom distance bybaker.itsa.ucsf.edu
- Re: AMBER: Atom distance Thomas E. Cheatham, III
- AMBER: intramolecular energies Guanglei Cui
- Re: AMBER: intramolecular energies David A. Case
- AMBER: Re: Atom distance bybaker.itsa.ucsf.edu
- Re: AMBER: intramolecular energies Guanglei Cui
Tuesday, 28 September 2004
- Re: AMBER: intramolecular energies David A. Case
- Re: AMBER: intramolecular energies Guanglei Cui
- AMBER: question about delphi and UHBD xhu1.memphis.edu
- Re: AMBER: intramolecular energies David A. Case
- Re: AMBER: intramolecular energies Guanglei Cui
- AMBER: Ahammadunny Pathiaseril
- Re: AMBER: question about delphi and UHBD Ray Luo
- Re: AMBER: Ray Luo
- AMBER: The convergence of energy minimisation Binbin Liu
- AMBER: Amber bybaker.itsa.ucsf.edu
- Re: AMBER: question about delphi and UHBD Thomas E. Cheatham, III
- Re: AMBER: Amber Thomas E. Cheatham, III
- Re: AMBER: Amber Tomas Linhart
- Re: AMBER: question about delphi and UHBD xhu1.memphis.edu
- AMBER: Phosphoserine parameters Venkata S Koppuravuri
- Re: AMBER: question about delphi and UHBD Carlos Simmerling
- AMBER: Re: Amber bybaker.itsa.ucsf.edu
- Re: AMBER: question about delphi and UHBD xhu1.memphis.edu
- Re: AMBER: question about delphi and UHBD Ray Luo
- Re: AMBER: Phosphoserine parameters Oliver Hucke
Wednesday, 29 September 2004
- AMBER: scaling 1-4 NB interaction for rings j-shimada.az.jp.nec.com
- AMBER: (no subject) Rasha Radwan
- Re: AMBER: scaling 1-4 NB interaction for rings David A. Case
- Re: AMBER: (no subject) Jiten
- Re: AMBER: (no subject) M. L. Dodson
- Re: AMBER: (no subject) David A. Case
- Re: AMBER: Phosphoserine parameters Joseph Nachman
- AMBER: impose: Illegal angle internal definition Madalin Giambasu
- AMBER: resp error message Andre Farias de Moura
- Re: AMBER: question about delphi and UHBD xhu1.memphis.edu
- Re: AMBER: impose: Illegal angle internal definition David A. Case
- Re: AMBER: resp error message FyD
- Re: AMBER: resp error message Andre Farias de Moura
- Re: AMBER: resp error message FyD
- Re: AMBER: (no subject) Anselm Horn
Thursday, 30 September 2004
- AMBER: Compiling AMBER8 Justin Sanders
- Re: AMBER: Compiling AMBER8 David A. Case
- Re: AMBER: resp error message Andre Farias de Moura
- Re: AMBER: question about delphi and UHBD xhu1.memphis.edu
- Re: AMBER: resp error message FyD
- AMBER: Testing Delphi for mm_pbsa Scott Pendley
- AMBER: anal error Guanglei Cui

Last message date: Thu Sep 30 2004 - 21:53:00 PDT
Archived on: Fri Dec 20 2024 - 05:53:24 PST

Amber Archive Sep 2004 by date