Amber Archive Feb 2003: by date

Saturday, 1 February 2003
- Gibbs stops after a finite number of window runs Seongeun Yang
- Re: Gibbs stops after a finite number of window runs David A. Case
- Re: Gibbs stops after a finite number of window runs Seongeun Yang
- Re: Gibbs stops after a finite number of window runs caldwell_at_heimdal.compchem.ucsf.edu
- Re: question about ligand Lishan Yao
Sunday, 2 February 2003
- gibbs input file Patricia Burgess
- questions about AMBER Guoxi Zhang
- How to calculate new force field? k.watanabe
Monday, 3 February 2003
- some questions in gibbs calculation Xiang, Tian-Xiang
- question about temperature Lishan Yao
- Neutral ARG Osmar Norberto de Souza
- Re: question about temperature Carlos Simmerling
- boron parameters Fabian Boes
- Re: How to calculate new force field? Jose Ramon Blas
- SASA calculation Luis Gracia
- Re: SASA calculation Michael Ford
- trajectory file in mm_pbsa eric hu
- desolvation energy in mm_pbsa eric hu
- Acetonitrile parameters N. Jiten Singh
- MM-PBSA error Bimo Ario Tejo
Tuesday, 4 February 2003
- Ptraj problem with small molecules Dvira Segal
- Re: desolvation energy in mm_pbsa Michael Ford
- Amber7 & mpich FyD
- Re: some questions in gibbs calculation David A. Case
- Re: Ptraj problem with small molecules David A. Case
- Re: Acetonitrile parameters Pascal Bonnet
- ifc, gibbs and ewald David Smith
- RESP charge derivation Lepsa
- [Fwd: Re: trajectory file in mm_pbsa] Holger Gohlke
- Re: Amber7 & mpich Michael Crowley
- Re: acetonitrile parameters Jose Ramon Blas
- Re: desolvation energy in mm_pbsa eric hu
- Re: desolvation energy in mm_pbsa Holger Gohlke
- Re: Amber7 & mpich Florian Barth
- How to do the image using ptraj? Yuhui Cheng
- Re: MM-PBSA error Bimo Ario Tejo
- bond command Craig A Bayse
- Re: bond command David A. Case
Wednesday, 5 February 2003
- Fw: RESP charge derivation Lepsa
- stacking energy thenmalar rathinavelan
- Re: Amber7 & mpich FyD
- about Mg++ Lishan Yao
- noninteger charge eric hu
- Re: noninteger charge David A. Case
- Re: bond command Craig A Bayse
- Re: bond command David A. Case
Thursday, 6 February 2003
- Gibbs: DynamicWin and NSTMEQ? Paula Petrone
- Carnal problem... Andrei Leit�o
Friday, 7 February 2003
- Misaligned Coords from Alanine Scanning Robert J. Woods
- Re: Misaligned Coords from Alanine Scanning Holger Gohlke
- essential dynamics Lishan Yao
- Re: essential dynamics Yongxing Liu
- Carnal DECLARE of TORSION problem William Wei
- Re: Carnal DECLARE of TORSION problem Holger Gohlke
- Re: essential dynamics David A. Case
- mpi/sander help Thu Zar Lwin
- Re: mpi/sander help Michael Crowley
- Backbone torsional angles' format? William Wei
- Re: Gibbs: DynamicWin and NSTMEQ? David A. Case
- [Fwd: Re: Backbone torsional angles' format?] Holger Gohlke
- Periodic Box John Finke
- Re: Backbone torsional angles' format? Bill Ross
Saturday, 8 February 2003
- RE: Periodic Box Xiang, Tian-Xiang
- energy calculation thenmalar rathinavelan
Sunday, 9 February 2003
- Re: energy calculation Carlos Simmerling
- RE: energy calculation Yong Duan
- Question about quasih Lishan Yao
- Re: Question about quasih CUI, Guanglei
Monday, 10 February 2003
- decrease a force const. for angle Michal Otyepka
- mm_pbsa energy unit eric hu
- Internal dielectric in MM-GBSA Robert J. Woods
- Re: mm_pbsa energy unit Holger Gohlke
- force field problem Bayly, Christopher
- Re: Internal dielectric in MM-GBSA David A. Case
- AMBER mail reflector archive Jarrod Smith
- Re: decrease a force const. for angle David A. Case
- UCSF moving day. caldwell_at_heimdal.compchem.ucsf.edu
- references Ioana Cozmuta
Tuesday, 11 February 2003
- Itanium II Jose Ramon Blas
- MM_PBSA Errors Ram�n Gardu�o-Ju�rez
Wednesday, 12 February 2003
- Re: MM_PBSA Errors Pascal Bonnet
- NTC=3 for organic solvent and NTC=2 for soluter? yuan bo
- NTC=3 for organic solvent and NTC=2 for solute? yuan bo
- hexane parameters pu xuemei
- Error Massage in Sander amber7 in Linux N. Jiten Singh
- Re: Error Massage in Sander amber7 in Linux David A. Case
- Re: Re: Error Massage in Sander amber7 in Linux N. Jiten Singh
- How to put the outside atoms back to the truncated octahedron box? Ling Zhang
- Re: How to put the outside atoms back to the truncated octahedron box? Natasja Brooijmans
- question about antechamber Lishan Yao
- amber web site Steve Seibold
- The image command of ptraj of Amber 6 is not working. Ling Zhang
- delphi and charge file Sue Heavner
- Re: amber web site Mengjuei Hsieh
- RE: amber web site Ross Walker
- Re: bond command Craig A Bayse
- Re: The image command of ptraj of Amber 6 is not working. Thomas Cheatham
- Re: Error Massage in Sander amber7 in Linux John Bushnell
- Re: delphi and charge file Holger Gohlke
- RE: Itanium II Ross Walker
- RE: Itanium II Scott Brozell
- Including the Peroidiic Box info ?? N. Jiten Singh
- About antechamber k.watanabe
Thursday, 13 February 2003
- Isotropic Solvent Box N. Jiten Singh
- compatibility of amber with NAMD Ioana Cozmuta
- xleap crash under Irix FyD
- Re: xleap crash under Irix David A. Case
- Re: compatibility of amber with NAMD Peter Gannett
- inter & intra-molecular interaction energies Tian-Xiang Xiang
- question about antechamber Lishan Yao
- Re: inter & intra-molecular interaction energies David A. Case
- web page update caldwell_at_heimdal.compchem.ucsf.edu
- RE: inter & intra-molecular interaction energies Xiang, Tian-Xiang
- Re: bond command David A. Case
Friday, 14 February 2003
- Postdoctoral position available in Molecular Modeling Nicolas Le Novere
- Re: compatibility of amber with NAMD Andreas Svrcek-Seiler
- Re: compatibility of amber with NAMD Luis Gracia
- charge determination for polariable ff02 force fields Xiang, Tian-Xiang
- MAXINT problem yuan bo
Saturday, 15 February 2003
- charges, opt and iops Lepsa
- Fw: charge determination for polariable ff02 force fields Lepsa
Sunday, 16 February 2003
- TAUP and density problem yuan bo
- (no subject) Majid moghaddam
- RE: charge determination for polariable ff02 force fields Xiang, Tian-Xiang
- question on EWALD Sichun Yang
- RE: TAUP and density problem case
Monday, 17 February 2003
- Re: charge determination for polariable ff02 force fields Lepsa
- RE:RE: TAUP and density problem yuan bo
- Velocity A. Hungie
- Re: Velocity caldwell_at_heimdal.compchem.ucsf.edu
- Number of water too large kalyan_at_mbu.iisc.ernet.in
- Re: Velocity Carlos Simmerling
- Re: RE: TAUP and density problem David A. Case
- Re: question on EWALD David A. Case
- Re: question on EWALD Sichun Yang
- Re: question on EWALD Sichun Yang
- Amber Documents Nicole A Rutkowski
- RE: Velocity Yong Duan
- URGENT UPDATE . frankikpendu_at_hknetmail.com
- RE: question on EWALD Yong Duan
- RE: question on EWALD Sichun Yang
- RE: question on EWALD Yong Duan
- RE: question on EWALD Sichun Yang
- one time evaluation Ioana Cozmuta
- question about partial charge yuann
- Re: question about partial charge Lepsa
Tuesday, 18 February 2003
- metallic ions Marc Dobler
- interaction between ligand & protein Lishan Yao
- Re: interaction between ligand & protein Lepsa
- Gibbs: Electrostatic Decoupling Paula Petrone
- adding hydrogens CUI, Guanglei
- charge neutralization in DNA Mahadevan Seetharaman
- Final energy minimization step Andrei Leit�o
- restrained atoms NTR Sichun Yang
- Re: (no subject) David A. Case
- Re: File in the tutorial David A. Case
- Re: Final energy minimization step David A. Case
- Re: charge neutralization in DNA David A. Case
- mm_pbsa Yongmei Wang
- File in the tutorial Alexei Valiaev
- Re: mm_pbsa Holger Gohlke
- Re: question about partial charge sychen
- Re: restrained atoms NTR David A. Case
Wednesday, 19 February 2003
- Re: adding hydrogens Oliver Hucke
- Re: adding hydrogens Lepsa
- How do NTC=2 recognize hydrogen atom? yuan bo
- hexane parameters pu xuemei
- RE: adding hydrogens CUI, Guanglei
- Fw: adding hydrogens Lepsa
- Re: restrained atoms NTR Sichun Yang
- no statistics.out in mm_pbsa binding energy calculations eric hu
- Re: no statistics.out in mm_pbsa binding energy calculations Holger Gohlke
- antechamber and its prepin files Steve Seibold
- Re: antechamber and its prepin files David A. Case
- Web site problems. caldwell.heimdal.compchem.ucsf.edu
- Energy calculation Sichun Yang
- Re: Energy calculation Holger Gohlke
- Minimization after dynamic? Andrei Leitão
- Re: Energy calculation Sichun Yang
- Nmode thenmalar rathinavelan
Thursday, 20 February 2003
- Re: How do NTC=2 recognize hydrogen atom? David A. Case
- Re: Nmode Holger Gohlke
- probelms with antechamber Yongmei Wang
- Re: probelms with antechamber David A. Case
Friday, 21 February 2003
- AMBER6 problem in Solaris 8 S.Swaminathan
Thursday, 20 February 2003
- Re: AMBER6 problem in Solaris 8 David A. Case
Friday, 21 February 2003
- about urea and glycerol Nikolai Smolin
- minimization with fixed UC dimensions Ioana Cozmuta
- Re: minimization with fixed UC dimensions David A. Case
- failure of minimization Ioana Cozmuta
- Re: minimization with fixed UC dimensions Ioana Cozmuta
- RE: failure of minimization Yong Duan
Sunday, 23 February 2003
- new-style prmtop file chernhoe
- Binary output switch (IOUTFM=1) broken in sander? (AMBER7) John D. Chodera
- Re: new-style prmtop file David A. Case
- Re: new-style prmtop file chernhoe
Monday, 24 February 2003
- GB/SA Franck Chevalier
- Force field ? Subba.Raju
- RE: failure of minimization Ioana Cozmuta
- RE: failure of minimization Ioana Cozmuta
- RE: failure of minimization Yong Duan
Tuesday, 25 February 2003
- adjust virial Ioana Cozmuta
- problem patch files chernhoe
- ptraj residue number out of range Giulio Rastelli
- Compilation error of Amber 7 using pgi and mpich on Linux Cluster Fabrice Yerly
- Info request: Amber on 64-bit CPUs Daniel Svozil
- Re: Compilation error of Amber 7 using pgi and mpich on Linux Cluster Tormod Skauge
- Re: Info request: Amber on 64-bit CPUs Chuck Schneider
- Re: ptraj residue number out of range Holger Gohlke
- Re: ptraj residue number out of range Giulio Rastelli
- Re: ptraj residue number out of range Holger Gohlke
- Re: Info request: Amber on 64-bit CPUs Carlos P. Sosa
- (no subject) Robert Cave
- Re: Amber under Linux Scott Brozell
- EXTRA_PTS: frtype 2 Should not be here Artem Mamonov
- Re: EXTRA_PTS: frtype 2 Should not be here Artem Mamonov
Wednesday, 26 February 2003
- Re: AMBER6 problem in Solaris 8 S.Swaminathan
Tuesday, 25 February 2003
- Re: AMBER6 problem in Solaris 8 Sanjeev B.S.
Wednesday, 26 February 2003
- mm_pbsa Layi Adekoya
- Analysis of close waters Markus Drumm
- Re: mm_pbsa Lepsa
- Namelist READ error Thomas Steinbrecher
- Re: Namelist READ error - solved Thomas Steinbrecher
Thursday, 27 February 2003
- nmode on Linux : another memory question E.S.
- Beyond 1,000,000 atoms... Vlad
- seperate one trajectory file into two eric hu
- Re: seperate one trajectory file into two Holger Gohlke
- protein dna simulation chernhoe
- how to validate ff parameters obtained from antechamber Jiyoung Heo
Friday, 28 February 2003
- Re: GB/SA David A. Case

Last message date: Sat Mar 01 2003 - 02:53:02 PST
Archived on: Sun Nov 17 2024 - 05:53:16 PST

Amber Archive Feb 2003 by date