Amber Archive Jan 2004: by date

Thursday, 1 January 2004
- Re: AMBER: Antechamber & Ptraj/Rdparm L Jin
- Re: AMBER: Antechamber & Ptraj/Rdparm zhaoxc.puccini.che.pitt.edu
- Re: AMBER: Antechamber & Ptraj/Rdparm Bill Ross
- AMBER: Molecular Frame Byungchan Kim
Friday, 2 January 2004
- AMBER: algorithm used in AMBER A. Hungie
- RE: AMBER: force field Ross Walker
- RE: AMBER: algorithm used in AMBER Ross Walker
- Re: AMBER: Molecular Frame David A. Case
- Re: AMBER: Molecular Frame Byungchan Kim
- Re: AMBER: Molecular Frame Bill Ross
Saturday, 3 January 2004
- Re: AMBER: Molecular Frame David A. Case
- Re: AMBER: Molecular Frame Byungchan Kim
Friday, 2 January 2004
- AMBER: force field A. Hungie
Monday, 5 January 2004
- AMBER: rms in ptraj L Jin
- Re: AMBER: rms in ptraj Thomas E. Cheatham, III
- AMBER: File format generated by respgen Lishan Yao
- AMBER: prep file Youyi Peng
- Re: AMBER: prep file Bill Ross
- Re: AMBER: prep file James W. Caldwell
- AMBER: Radius of gyration Bimo Ario Tejo
Tuesday, 6 January 2004
- AMBER: Parameters for deuterium Charlie Laughton
- Re: AMBER: Parameters for deuterium David A. Case
- Re: AMBER: Radius of gyration Alexey Onufriev
- AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning Robert Duke
Wednesday, 7 January 2004
- AMBER: Atom type L Jin
- Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning Andreas Svrcek-Seiler
- Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning Viktor Hornak
- Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning Robert Duke
- Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning Robert Duke
- Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning David E. Konerding
- AMBER: strange output of MD L Jin
- Re: AMBER: strange output of MD Rhonda Torres
- Re: AMBER: strange output of MD Bill Ross
- Re: AMBER: Atom type Rhonda Torres
- Re: AMBER: strange output of MD L Jin
- AMBER: .crg file for Delphi a b
- Re: AMBER: strange output of MD Bill Ross
- Re: AMBER: Atom type Rhonda Torres
Thursday, 8 January 2004
- AMBER: modeling GPCR in lipid environment Giulio Rastelli
- AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd Anna Schrey
- AMBER: Vlimit problem Yuqin Cai
- Re: AMBER: modeling GPCR in lipid environment Alexey Onufriev
- AMBER: running on Itanium machines northrop.chem.ucla.edu
- Re: AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd David A. Case
- Re: AMBER: Vlimit problem David A. Case
Friday, 9 January 2004
- Re: AMBER: running on Itanium machines David A. Case
- Re: AMBER: running on Itanium machines northrop.chem.ucla.edu
- Re: AMBER: Vlimit problem Thomas E. Cheatham, III
Saturday, 10 January 2004
- AMBER: Amber compilation in IBM-SP4 Jiten
- Re: AMBER: Amber compilation in IBM-SP4 David A. Case
Sunday, 11 January 2004
- AMBER: references? a b
Monday, 12 January 2004
- AMBER: Improper dihedral Herbert Georg
- Re: AMBER: Improper dihedral Bill Ross
- Re: AMBER: Improper dihedral Herbert Georg
- Re: AMBER: Improper dihedral Bill Ross
- Re: AMBER: Improper dihedral Herbert Georg
- Re: AMBER: Improper dihedral Bill Ross
- Re: AMBER: Improper dihedral David A. Case
- Re: AMBER: Improper dihedral Herbert Georg
- AMBER: disulfide bonds Wen Li
- Re: AMBER: disulfide bonds David A. Case
Tuesday, 13 January 2004
- Re: AMBER: disulfide bonds/ Engineered bishop
- AMBER: error in minimization Itziar Maestre Asenjo
- Re: AMBER: Improper dihedral Herbert Georg
- Re: AMBER: error in minimization David A. Case
- Re: AMBER: disulfide bonds Wen Li
- Re: AMBER: disulfide bonds David A. Case
- Re: AMBER: charris5
- Re: AMBER: Michael George Lerner
Wednesday, 14 January 2004
- AMBER: LEAP - Error loading units Miguel de Federico
- AMBER: DMF box Stefano.Pieraccini.unimi.it
- Re: AMBER: LEAP - Error loading units Bill Ross
- AMBER: "ATTN, need revision" klamothe.uiuc.edu
- Re: AMBER: "ATTN, need revision" Junmei Wang
- AMBER: free energy profile calculation Martina Roeselova
- Re: AMBER: error in minimization Itziar Maestre Asenjo
Thursday, 15 January 2004
- Re: AMBER: free energy profile calculation David Smith
- Re: AMBER: free energy profile calculation David A. Case
Friday, 16 January 2004
- AMBER: NTF L Jin
- Re: AMBER: NTF David A. Case
- AMBER: atom type CM Kristina Furse
- Re: AMBER: atom type CM Bill Ross
- Re: AMBER: atom type CM Junmei Wang
- RE: AMBER: atom type CM Kristina Furse
Tuesday, 20 January 2004
- AMBER: GB and Atom Type Steve Seibold
- AMBER: Question for PMEMD users Robert Duke
- AMBER: restraint tang kwa
- AMBER: Parm98 Vs 02 A.Madhumalar
- RE: AMBER: atom type CM Junmei Wang
- AMBER: PDB files Beale, John
- Re: AMBER: GB and Atom Type David A. Case
- Re: AMBER: restraint David A. Case
- Re: AMBER: Parm98 Vs 02 David A. Case
- Re: AMBER: PDB files David A. Case
- AMBER: Do I need to repeat MD simulation? aini.UMDNJ.EDU
- AMBER: segmentation fault in Leap Ioana Cozmuta
Wednesday, 21 January 2004
- Re: AMBER: segmentation fault in Leap Bill Ross
- Re: AMBER: Do I need to repeat MD simulation? Andreas Svrcek-Seiler
- AMBER: Errors in MM-PBSA??? ML
- AMBER: NMODE via MM-PBSA ML
- Re: AMBER: Errors in MM-PBSA??? Holger Gohlke
- Re: AMBER: NMODE via MM-PBSA Holger Gohlke
- Re: AMBER: Do I need to repeat MD simulation? Robert Duke
- Re: AMBER: NMODE via MM-PBSA ML
- Re: AMBER: Do I need to repeat MD simulation? bishop
- AMBER: antechamber and mopac5010mn S. Frank Yan
- Re: AMBER: Do I need to repeat MD simulation? Bill Ross
- Re: AMBER: antechamber and mopac5010mn David A. Case
- AMBER: crystal lattice determination Scott Brozell
- Re: AMBER: Parm98 Vs 02 A.Madhumalar
- Re: AMBER: Do I need to repeat MD simulation? aini.UMDNJ.EDU
- AMBER: oxs g5 machine file Knut Langsetmo
- AMBER: crosslink a residue with a small molecule Eric Hu
- AMBER: prep file for zinc finger Wen Li
- Re: AMBER: segmentation fault in Leap Ioana Cozmuta
- AMBER: remove rotational motion Itziar Maestre Asenjo
Thursday, 22 January 2004
- AMBER: How does LEaP place Na+ ions? tang kwa
- AMBER: restrt L Jin
- Re: AMBER: restrt Dr. Yong Duan
- Re: AMBER: How does LEaP place Na+ ions? Jose Ramon Blas
- Re: AMBER: restrt L Jin
- Re: AMBER: segmentation fault in Leap David E. Konerding
- Re: AMBER: How does LEaP place Na+ ions? Bill Ross
- Re: AMBER: How does LEaP place Na+ ions? Bill Ross
- Re: AMBER: restrt Bill Ross
- Re: AMBER: segmentation fault in Leap Bill Ross
- AMBER: Segmentation fault (core dumped) error of antechamber program S. Frank Yan
- Re: AMBER: restrt Dr. Yong Duan
- Re: AMBER: crystal lattice determination David A. Case
- Re: AMBER: remove rotational motion David A. Case
- Re: AMBER: Segmentation fault (core dumped) error of antechamber program David A. Case
- AMBER: oxygen positions around a DNA Ioana Cozmuta
- Re: AMBER: segmentation fault in Leap Ioana Cozmuta
Friday, 23 January 2004
- Re: AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd Anna Schrey
- AMBER: Problem using GLYCAM with sander Itziar Maestre Asenjo
- AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7 Ilyas Yildirim
- Re: AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7 Joey Harriman
- Re: AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7 Bill Ross
- Re: AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7 FyD
- Re: AMBER: Problem using GLYCAM with sander David A. Case
- AMBER: phosphothreonine Youyi Peng
- AMBER: Fwd: NVE & polarizable force field] Martina Roeselova
- Re: AMBER: Fwd: NVE & polarizable force field] Byungchan Kim
Saturday, 24 January 2004
- AMBER: Memory for AMBER 6 simulation Sergey
- Re: AMBER: Problem using GLYCAM with sander Bimo Ario Tejo
- Re: AMBER: Fwd: NVE & polarizable force field] darden
- Re: AMBER: Fwd: NVE & polarizable force field] David A. Case
- AMBER: NTR force constant for restraint !! Jiten
Sunday, 25 January 2004
- AMBER: Cartitian Restraint Error Jiten
- Re: AMBER: Cartitian Restraint Error Jiten
- Re: AMBER: Cartitian Restraint Error Bill Ross
- Re: AMBER: how to correctly change frcmod? David A. Case
- Re: AMBER: Cartitian Restraint Error Jiten
- Re: AMBER: How does LEaP place Na+ ions? Jiten
Monday, 26 January 2004
- Re: AMBER: Memory for AMBER 6 simulation Bimo Ario Tejo
- AMBER: mopac.sh Beale, John
- Re: AMBER: mopac.sh Joey Harriman
- AMBER: B factors from simulation and from cryst Vlad Cojocaru
- AMBER: B factors --- one more explanation Vlad Cojocaru
- Re: AMBER: B factors from simulation and from cryst Joseph Nachman
- Re: AMBER: ambpdb in AMBER7 Bill Ross
- RE: AMBER: ambpdb in AMBER7 Yong Duan
- AMBER: Lattice structures in xleap Brandon Tefft
- Re: AMBER: Lattice structures in xleap Bill Ross
Tuesday, 27 January 2004
- AMBER: trajectory file corruption John
- Re: AMBER: Which program to use to visualize the RESP Outputs FyD
- Re: AMBER: ambpdb in AMBER7 xhu1.memphis.edu
- AMBER: compilation under fedora core 1 Carsten Detering
- Re: AMBER: trajectory file corruption Peter Oelschlaeger
- Re: AMBER: trajectory file corruption James W. Caldwell
- Re: AMBER: compilation under fedora core 1 James W. Caldwell
- AMBER: Error message in antechamber Ilyas Yildirim
- Re: AMBER: Which program to use to visualize the RESP Outputs Ilyas Yildirim
- Re: AMBER: trajectory file corruption Bill Ross
- AMBER: A few questions in the protein unfolding simulations using GB model Jiayun Pang
- Re: AMBER: A few questions in the protein unfolding simulations using GB model Bill Ross
Wednesday, 28 January 2004
- AMBER: SANDER - Abnormal high velocities Miguel de Federico
- Re: AMBER: A few questions in the protein unfolding simulations using GB model Jiayun Pang
- RE: AMBER: A few questions in the protein unfolding simulations using GB model florent.barbault
- AMBER: Normal modes of protein-ligand Martin Lepsik
- AMBER: dielectric constant John
- Re: AMBER: dielectric constant Martin Lepsik
- Re: AMBER: Normal modes of protein-ligand bishop
- Re: AMBER: SANDER - Abnormal high velocities David A. Case
- Re: AMBER: SANDER - Abnormal high velocities Carlos Simmerling
- Re: AMBER: A few questions in the protein unfolding simulations using GB model Bill Ross
- RE: AMBER: A few questions in the protein unfolding simulations using GB model Bill Ross
- Re: AMBER: A few questions in the protein unfolding simulations using GB model Carlos Simmerling
- AMBER: LES question Lishan Yao
- Re: AMBER: LES question Carlos Simmerling
- Re: AMBER: Normal modes of protein-ligand Holger Gohlke
- Re: AMBER: Normal modes of protein-ligand Holger Gohlke
- Re: AMBER: Ibelly and Ewald error message when ewald should be off Scott Brozell
Thursday, 29 January 2004
- AMBER: sander and mpich Thomas Exner
- Re: AMBER: Normal modes of protein-ligand Martin Lepsik
- AMBER: CYS, CYX and CYM Nikolai Smolin
- Re: AMBER: A few questions in the protein unfolding simulations using GB model Jiayun Pang
- AMBER: conversion of amber trajectories to gromos /(xtc) Karin Schleinkofer
- Re: AMBER: A few questions in the protein unfolding simulations using GB model Andy Purkiss
- Re: AMBER: references? Martin Lepsik
- AMBER: XLEAP L Jin
- Re: AMBER: XLEAP Martin Lepsik
- Re: AMBER: LES question Lishan Yao
- Re: AMBER: XLEAP A.B.S.M Osman gani
- Re: AMBER: LES question Carlos Simmerling
- AMBER: Moil View on Linux Vlad Cojocaru
- AMBER: LES Simulations Vlad Cojocaru
- AMBER: question about LES simulation Vlad Cojocaru
- Re: AMBER: LES Simulations Carlos Simmerling
- Re: AMBER: Moil View on Linux Carlos Simmerling
- Re: AMBER: conversion of amber trajectories to gromos /(xtc) Luis Gracia
- Re: AMBER: conversion of amber trajectories to gromos /(xtc) Bill Ross
- AMBER: LES error Vlad Cojocaru
- Re: AMBER: LES error Carlos Simmerling
- AMBER: (No subject) opitz.che.udel.edu
- Re: AMBER: A few questions in the protein unfolding simulations using GB model David A. Case
- Re: AMBER: (No subject) David A. Case
Friday, 30 January 2004
- AMBER: test Vlad Cojocaru
- Re: AMBER: (No subject) Junmei Wang
- Re: AMBER: (No subject) opitz.che.udel.edu
- Re: AMBER: (No subject) Vlad Cojocaru
- Re: AMBER: (No subject) opitz.che.udel.edu
- Re: AMBER: (No subject) Junmei Wang
- Re: AMBER: sander and mpich (which compilers/mpich work) Jerry Grooms
- Re: AMBER: sander and mpich (which compilers/mpich work) Carlos Simmerling
- Re: AMBER: sander and mpich (which compilers/mpich work) Viktor Hornak
- AMBER: Nose Hoover chain thermostat Byungchan Kim
Saturday, 31 January 2004
- AMBER: sander.LES on IBM SP cluster Vlad Cojocaru
- Re: AMBER: sander.LES on IBM SP cluster Carlos Simmerling
- Re: AMBER: sander.LES on IBM SP cluster Vlad Cojocaru
- AMBER: Installing Amber on IBM AIX cluster Vlad Cojocaru
- Re: AMBER: sander.LES on IBM SP cluster David A. Case
- AMBER: AMBER on IBM SP cluster Vlad Cojocaru
- Re: AMBER: sander.LES on IBM SP cluster Carlos Simmerling
- Re: AMBER: sander.LES on IBM SP cluster Vlad Cojocaru
- Re: AMBER: sander.LES on IBM SP cluster Carlos Simmerling
- Re: AMBER: sander and mpich (which compilers/mpich work) Jerry Grooms
- AMBER: Unknown Amber Nomeclature Andrew M K Law
- Re: AMBER: sander and mpich (which compilers/mpich work) Jerry Grooms

Last message date: Sat Jan 31 2004 - 23:53:00 PST
Archived on: Fri Dec 20 2024 - 05:53:22 PST

Amber Archive Jan 2004 by date