Amber Archive Jan 2003: by date

Thursday, 2 January 2003
- Sander box error and thanks on previous mdin error kxg2248_at_njit.edu
Friday, 3 January 2003
- Re: Sander box error and thanks on previous mdin error David A. Case
- JACS 125th and PAK Carlos Simmerling
- Re: Sander box error and thanks on previous mdin error kxg2248_at_njit.edu
- Re: JACS 125th and PAK David A. Case
- Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap Chris Switzer
- Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap David Case
- Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap Florian Barth
Monday, 6 January 2003
- looking for 'pdb_to_mass' yuann
Tuesday, 7 January 2003
- water reordering in sander Michael Trieb
- Re: looking for 'pdb_to_mass' CUI, Guanglei
- Small organic molecules Dvira Segal
- Re: water reordering in sander David A. Case
- reducing restrains Luis Gracia
- Re: Small organic molecules David A. Case
- Re: reducing restrains David A. Case
- Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap Jim Newhouse
- virtual box eric hu
- Re: virtual box David A. Case
- mm_pbsa question wentaofu
- Re: mm_pbsa question Holger Gohlke
- the unit of velocity Jian Zhang
- nmanal & quasih question yuann
- Re: virtual box eric hu
- Re: virtual box eric hu
Wednesday, 8 January 2003
- building molecules by script files for leap Dvira Segal
- Re: the unit of velocity David A. Case
- Re: building molecules by script files for leap David A. Case
- mm_gbsa error message Mahadevan Seetharaman
- Predefined Water_cap with xleap Jose Ramon Blas
- Re: mm_gbsa error message Holger Gohlke
- Amber parameters for Netropsin Manuel Rueda
- Re: the unit of velocity Jian Zhang
Thursday, 9 January 2003
- GIBBS - Routine TORCON failed. Required change is too large. Miguel de Federico
- Re: nmanal & quasih question yuann
- free energy perturbation (Gibbs/Amber 5)? meiselba
- Re: nmanal & quasih question David A. Case
- MM_pbsa prmtop file wentaofu
- Re: MM_pbsa prmtop file David A. Case
Friday, 10 January 2003
- Re: free energy perturbation (Gibbs/Amber 5)? Lepsa
- xleap crashes Layi Adekoya
- IDSX0 in free energy calculations Lepsa
- (no subject) amkumar_at_post.its.mcw.edu
- errors in MD trajectories Vlad Cojocaru
- pdb_to_mass Jake Isaacs
- Re: pdb_to_mass sychen
- Force Fields Colin Connelly
- Re: xleap crashes David Case
Saturday, 11 January 2003
- electrostatic potential calculations Vlad Cojocaru
- Re: electrostatic potential calculations Andreas Svrcek-Seiler
- Dummy atoms in free energy calculation Lepsa
Sunday, 12 January 2003
- problem with antechamber Craig A Bayse
- Re: problem with antechamber David A. Case
- Re: Dummy atoms in free energy calculation David A. Case
- xleap crashes Layi Adekoya
Monday, 13 January 2003
- coordinates for quasih Jake Isaacs
- Re: coordinates for quasih Pratul Agarwal
- Re: mm_pbsa -- COMPT must be specified (correctly) Holger Gohlke
- Re: xleap crashes David A. Case
- Re: electrostatic potential calculations Peter Gannett
- RE: mm_pbsa -- COMPT must be specified (correctly) William Wei
- mm_pbsa -- COMPT must be specified (correctly) William Wei
- Re: CCL:electrostatic potential calculations Nathan A. Baker
Tuesday, 14 January 2003
- xleap crashes Layi Adekoya
- Re: mm_pbsa -- COMPT must be specified (correctly) Lepsa
- chloroform, dichlormethane f.f. Arvid Soederhaell
- MEAD on SuSE 8.1 Vlad Cojocaru
- Summary: mm_pbsa -- COMPT must be specified (correctly) William Wei
- Re: chloroform, dichlormethane f.f. David A. Case
- Re: CCL:MEAD on SuSE 8.1 Szilveszter Juhos
- mm_gbsa: Unit 5 Error on OPEN: sander_com.in William Wei
- Re: mm_gbsa: Unit 5 Error on OPEN: sander_com.in Michael Ford
- Moil-view Ling Zhang
- Re: Moil-view CUI, Guanglei
- how to stop mapping of N- and C-terminal residues in xleap Michael Ford
- Re: how to stop mapping of N- and C-terminal residues in xleap David A. Case
- solvatecap GUILLERMINA L ESTIU
- Re: solvatecap David A. Case
- Re: chloroform, dichlormethane f.f. Jose Ramon Blas
- nscm Kristina Furse
- Re: nscm David A. Case
- compiling amber: Machine file for new 64 bit HP-Itanium II CPU Ying-Chieh Sun
Wednesday, 15 January 2003
- solvatecap GUILLERMINA L ESTIU
- Re: mm_gbsa: Unit 5 Error on OPEN: sander_com.in Michael Ford
- Re: how to stop mapping of N- and C-terminal residues in xleap (The RTFM solution) Michael Ford
- RE: nscm Kristina Furse
Thursday, 16 January 2003
- mail reflector caldwell_at_heimdal.compchem.ucsf.edu
- solvent free energy, GB Robert G. Endres
- terminal phosphate group in RNA Mahadevan Seetharaman
- Re: solvent free energy, GB David A. Case
Friday, 17 January 2003
- Polarization charges -geometry Lepsa
- octahedral volume Peter Varnai
- mm_pbsa Stop at statistics William Wei
- UCSF Network changes to affect Amber Web site. caldwell_at_heimdal.compchem.ucsf.edu
- RE: UCSF Network changes to affect Amber Web site. Ross Walker
- Re: UCSF Network changes to affect Amber Web site. David A. Case
- nucleic acid structures Ioana Cozmuta
Saturday, 18 January 2003
- Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold John D. Chodera
- Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold David A. Case
Sunday, 19 January 2003
- High temperature MD A.Madhumalar
- Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold David A. Case
Monday, 20 January 2003
- equilibrated solvent box pu xuemei
- equilibrated solvent box pu xuemei
- Has anyone ever used MEAD? Vlad Cojocaru
- CARNAL Lepsa
- Ewald error Miguel de Federico
- morse potential hagop demirdjian
- script for Potential/kinectic energy Layi Adekoya
- Re: script for Potential/kinectic energy Holger Gohlke
- Re: morse potential David A. Case
- Re: Ewald error David A. Case
- scripts for compiling UHBD/MEAD with amber 7.0 eric hu
- Re: script for Potential/kinectic energy Luis Gracia
- SASA and H-bond over trajectories Bimo Ario Tejo
Tuesday, 21 January 2003
- Re: CARNAL Lepsa
- Amber tutorial crown-ether Dvira Segal
- (no subject) Anke Eisenmann
- 'hot-solvent' and 'cold solute' problem Stefan Jungblut
- Re: your mail David A. Case
- Re: 'hot-solvent' and 'cold solute' problem David A. Case
- Re: Amber tutorial crown-ether David A. Case
- Re: Polarization charges -geometry David A. Case
- shake and H-O-H angle Luis Gracia
- Re: octahedral volume David A. Case
- pi-pi in AMBER Lepsa
- Probelm with the generation of topology file Jash, Panchatapa
- Re: CARNAL Lepsa
- reduce the disk space eric hu
- average structure generated by carnal eric hu
- Re: shake and H-O-H angle Andreas Svrcek-Seiler
- Re: average structure generated by carnal Peter Gannett
- Re: average structure generated by carnal eric hu
- shake and belly GUILLERMINA L ESTIU
- problems in equilibrating NaCl solution Seongeun Yang
- RE: average structure generated by carnal Kristina Furse
Wednesday, 22 January 2003
- How to control box size pu xuemei
- Re: average structure generated by carnal Andreas Svrcek-Seiler
- Re: SCSL David A. Case
- Re: equilibrated solvent box David A. Case
- Re: How to control box size David A. Case
- Re: shake and belly David A. Case
- Re: shake and belly GUILLERMINA L ESTIU
- SCSL Joffre Heredia
- Gibbs tutorial question Patricia Burgess
- question on ptraj Ioana Cozmuta
- Re: Gibbs tutorial question David A. Case
- MM_PBSA for Linux Ram�n Gardu�o-Ju�rez
- LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi Dr Chris L. Brown
Thursday, 23 January 2003
- Dummy-parameters in Amber? meiselba
- Re: Dummy-parameters in Amber? Miguel de Federico
- Re: LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi Chuck Schneider
- conformational sampling Robert G. Endres
- Re: SCSL Roberto Gomperts
- Proper torsion parameters missing? Heike Meiselbach
- Re: conformational sampling Carlos Simmerling
- Polymers Ndubuisi Emmanuel Okoro
- Chloroform Parameters N. Jiten Singh
- How much is minimum distance pu xuemei
Friday, 24 January 2003
- Re: Proper torsion parameters missing? Miguel de Federico
- Shake problem in organic solvent yuan bo
- RESP-group constraint Artur Galstyan
- Nmode query kinsellg
- Amber Web page. caldwell_at_heimdal.compchem.ucsf.edu
- Zn2+ parameters Xiang, Tian-Xiang
- Re: Shake problem in organic solvent David A. Case
- Re: problems in equilibrating NaCl solution David A. Case
- terminal phosphate group in RNA David A. Case
- Re: problems in equilibrating NaCl solution Seongeun Yang
Saturday, 25 January 2003
- Re: Zn2+ parameters Robert G. Endres
Sunday, 26 January 2003
- posphinic acid parameters Alfonso Garcia Sosa
Monday, 27 January 2003
- polarization + ewald GUILBAUD Philippe 153683
- structure image Xiang, Tian-Xiang
- RE: structure image Xiang, Tian-Xiang
- gibbs run Xiang, Tian-Xiang
- lastrst Steve Seibold
- Re: lastrst David A. Case
- Re: gibbs run David A. Case
- crystal structure of DNA/RNA homopolymers Ioana Cozmuta
- Re: crystal structure of DNA/RNA homopolymers David A. Case
- Re: crystal structure of DNA/RNA homopolymers Ioana Cozmuta
- compiling amber on myrinet Scott E. Boesch
- freeware to visualize RMSD matrices creatde with Carnal Vlad Cojocaru
- xleap in Amber7 arubin_at_unmc.edu
- xleap in Amber7 arubin_at_unmc.edu
- Re: polarization + ewald darden
- Re: structure image A.Madhumalar
- Question: about restarting Energy vannajan_at_chiangmai.ac.th
- Re: Question: about restarting Energy David A. Case
- single point mutations to investigate the conformational change Sichun Yang
Tuesday, 28 January 2003
- Intramolecular H-bonds in charge fitting Lepsa
- script for H-bonds extracting Bimo Ario Tejo
- 2drms command in ptraj Vlad Cojocaru
- mm-pbsa error message Thomas Steinbrecher
- RE: Intramolecular H-bonds in charge fitting Bayly, Christopher
- one question Fan Gao
- Re: one question Lepsa
- Re: one question Holger Gohlke
- RE: script for H-bonds extracting Bayly, Christopher
- gibbs calculation Xiang, Tian-Xiang
- Re: gibbs calculation David A. Case
Wednesday, 29 January 2003
- MM_PBSA Lepsa
- naphthalene, anthracene force field yuann
- antechamber and gamess Arvid Soederhaell
- Re: MM_PBSA Holger Gohlke
- antechamber and gamess David A. Case
- mm_pbsa and ALA scan Ahammadunny Pathiaseril
- Re: mm_pbsa and ALA scan Lepsa
- Polymers Ndubuisi Emmanuel Okoro
- Request johneluwa_at_eircom.net
- Re: High temperature MD Lepsa
Thursday, 30 January 2003
- new amino acid residues Nick Polfer
- mm-pbsa problem & possible solution Thomas Steinbrecher
- Re: mm-pbsa problem & possible solution Holger Gohlke
- Re: new amino acid residues David A. Case
- Quasi-harmonic analysis Pratul Agarwal
- Re: Quasi-harmonic analysis David A. Case
- ptraj distanse question Sichun Yang
Friday, 31 January 2003
- ptraj on Methane in water box Dvira Segal
- Re: ptraj distanse question Lepsa
- AMBER7 & mpich FyD
- roar-cp : input for QM part ; output for CM2 charges hagop demirdjian
- Domain/Helix movement/MD Jianhui Wu
- Re: Domain/Helix movement/MD Lepsa
- Re: Quasi-harmonic analysis Miyashita, Osamu
- Re: Domain/Helix movement/MD Pratul Agarwal
- Re: Gibbs, ewald and ifc David A. Case
- Gibbs, ewald and ifc David Smith
- question about ligand Lishan Yao
- Re: question about ligand David A. Case
- Gibbs dummy atom Paula Petrone

Last message date: Fri Jan 31 2003 - 15:49:52 PST
Archived on: Fri Dec 20 2024 - 05:53:20 PST

Amber Archive Jan 2003 by date