Amber Archive Sep 2002: by date

Sunday, 1 September 2002
- mpirun Ioana Cozmuta
- additional info Ioana Cozmuta
- RE: mpirun Ross Walker
Monday, 2 September 2002
- Re: NTX value giudice
- mm_pbsa positive binding energies Mathy Froeyen
- MDaemon Warning - Virus Found postmaster_at_96com.com
- MDaemon Warning - Virus Found postmaster_at_96com.com
- carnal averaging Vlad Cojocaru
- Re: mm_pbsa positive binding energies David A. Case
- Re: carnal averaging Holger Gohlke
- atoms coming too close during MD (with SHAKE on) Pratul Agarwal
- Re: ES40 hangs amber7 jobs. Sanjeev B.S.
- Re: protein minimization Lepsa
Tuesday, 3 September 2002
- MDaemon Warning - Virus Found postmaster_at_96com.com
- Re: protein minimization CUI, Guanglei
- compile Moil-View, GL header files Jianhui Wu
- protein minimization m.elizabeth sophia
- Re: compile Moil-View, GL header files Renee olano
- question Ioana Cozmuta
- RE: PyMOL + AMBER Trajectories DeLano, Warren
Wednesday, 4 September 2002
- MDaemon Warning - Virus Found postmaster_at_96com.com
- Escaping Atoms ch cureton
- old prmtop Thomas Steinbrecher
- Re: old prmtop C. Klein
- Re: old prmtop Holger Gohlke
- Re: old prmtop Peter Gannett
- how to detect bad contact? X. Tan
- cut-off question Ioana Cozmuta
- DNA Tutorial Script Joel Konkle-Parker
- Re: DNA Tutorial Script Holger Gohlke
Thursday, 5 September 2002
- RE: Escaping Atoms case
- bondbydistance eric hu
Friday, 6 September 2002
- MDaemon Warning - Virus Found postmaster_at_96com.com
- group selection for all heavy atoms ? Raik Grunberg
- compiling amber on a linux box using DMEM-ALLOC ramon kleber da rocha
- Re: compiling amber on a linux box using DMEM-ALLOC Scott Brozell
- Re: compiling amber on a linux box using DMEM-ALLOC Florian Barth
- cut-off question Cozmuta
- Re: compiling amber on a linux box using DMEM-ALLOC ramon kleber da rocha
- Re: compiling amber on a linux box using DMEM-ALLOC John Bushnell
- RE: cut-off question case
- RE: bondbydistance case
- Re: compiling amber on a linux box using DMEM-ALLOC Scott Brozell
- Re: compiling amber on a linux box using DMEM-ALLOC James W. Caldwell
Saturday, 7 September 2002
- RE: bondbydistance Nicholson, James D Mr ARO
Sunday, 8 September 2002
- about amber and charmm, thanks Zhang Jian
- who to address this to?... Jessica Swanson
Monday, 9 September 2002
- Distace dependent dielectric constant Lorenzo Gontrani
- parameterization of a new class of compounds (nucleic acid base analogues) Vlad Cojocaru
- MDaemon Warning - Virus Found postmaster_at_96com.com
- Re: who to address this to?... Holger Gohlke
- Re: who to address this to?... Michael Crowley
- amber7 compilation on irix6.4 mp K.Seshadri
- How to check whether the trajectory file matches the coordinates file or not? Ling Zhang
- Re: How to check whether the trajectory file matches the coordinates file or not? Shixiang Yan
- RE: How to check whether the trajectory file matches the coordinates file or not? Kristina Furse
Tuesday, 10 September 2002
- why are the results so large difference calculating by mm_pbsa and mm_gbsa? Yongjun Jiang
- Strange MD simulation results with GB solvation at high temp. Soonmin Jang
- Re: Strange MD simulation results with GB solvation at high temp. Carlos Simmerling
- nmode compile question? Yongjun Jiang
- GBSA and surface crystal waters Raik Grunberg
- Re: Strange MD simulation results with GB solvation at high temp. Soonmin Jang
- MDaemon Warning - Virus Found postmaster_at_96com.com
- Re: nmode compile question? Holger Gohlke
- Re: why are the results so large difference calculating by mm_pbsa and mm_gbsa? Holger Gohlke
- Re: nmode compile question? James W. Caldwell
- rdparm Joffre Heredia
- loadpdb error messages Joel Konkle-Parker
- Re: loadpdb error messages James W. Caldwell
Wednesday, 11 September 2002
- Polarizability, a general question Michal Otyepka
- memory allocation in mm_pbsa Giulio Rastelli
- just a test Vlad Cojocaru
- Re: memory allocation in mm_pbsa James W. Caldwell
- Re: memory allocation in mm_pbsa Holger Gohlke
- Problems during equilibration Pratul Agarwal
- Re: Problems during equilibration Pratul Agarwal
- Dual Processor AMD vs. Single Processor DeLano, Warren
- Re: Strange MD simulation results with GB solvation at high temp. David A. Case
- Re: Strange MD simulation results with GB solvation at high temp. Carlos Simmerling
- Re: Problems during equilibration Pratul Agarwal
Thursday, 12 September 2002
- why are the results so large difference calculating by mm_pbsaandmm_gbsa? Yongjun Jiang
- Re: Dual Processor AMD vs. Single Processor St�phane Teletch�a
- Qustion about calculation of pressure Nikolai Smolin
- sorry this is just a test Vlad Cojocaru
- leap and topology file Marcela Madrid
- sander.LES questions Peter Varnai
- Re: Qustion about calculation of pressure James W. Caldwell
- Re: sander.LES questions Carlos Simmerling
- large energy fluctration eric hu
- the amino group of 2amino purine has strange behaviour Vlad Cojocaru
- Re: large energy fluctration Carlos Simmerling
- Re: Distace dependent dielectric constant David A. Case
- Changing MAXINT Joel Konkle-Parker
- binding site volume Shixiang Yan
- problems on IBM AIX Giovanni Fossati
- Re: Strange MD simulation results with GB solvation at high temp. Soonmin Jang
Friday, 13 September 2002
- Re: binding site volume Michal Otyepka
- MDaemon Warning - Virus Found postmaster_at_96com.com
- MDaemon Warning - Virus Found postmaster_at_96com.com
- Re: leap and topology file Lepsa
- Re: problems on IBM AIX David A. Case
- Re: problems on IBM AIX Carlos P. Sosa
- Beowulf killing jobs Peter Gannett
- Help using moilview to make animations of trajectories Nicholson, James D Mr ARO
- Re: Changing MAXINT John Bushnell
Saturday, 14 September 2002
- D-tryptophan Perdita Barran
- Re: D-tryptophan James W. Caldwell
Sunday, 15 September 2002
- amber K.Veluraja
Monday, 16 September 2002
- amber question yao yong
- RE: Changing MAXINT Ross Walker
- RE: Beowulf killing jobs Ross Walker
- example 1 problems Alicia Hopkins
- assistance required amit kumar
- Re: example 1 problems David A. Case
- Re: example 1 problems Natasja Brooijmans
- Re: amber question David A. Case
- Re: amber question James W. Caldwell
- SETVEL, incorrect number of arguments? Giovanni Fossati
- non-bonded metal ion in complex yuann
Tuesday, 17 September 2002
- question about nmode again. Yongjun Jiang
- Re: example 1 problems Alicia Hopkins
- Re: non-bonded metal ion in complex Pratul Agarwal
- Re: example 1 problems James W. Caldwell
- Re: question about nmode again. David A. Case
- Re: example 1 problems David A. Case
- mm_pbsa question. wentaofu
- Density during equilibration (sander) Pratul Agarwal
- Re: SETVEL, incorrect number of arguments? David A. Case
- Re: Density during equilibration (sander) David A. Case
- Z DNA Sue Heavner
- Re: Density during equilibration (sander) Pratul Agarwal
- Re: Density during equilibration (sander) Marc Dobler
- Re: Density during equilibration (sander) Carlos Simmerling
Wednesday, 18 September 2002
- Re: Density during equilibration (sander) Marc Dobler
- Carnal+HBond confusion Sanjeev B.S.
Thursday, 19 September 2002
- bug in New2oldparm Pascal Bonnet
- new2oldparm format (2) Pascal Bonnet
- a freeware to display RMSD matrices Vlad Cojocaru
- Re: a freeware to display RMSD matrices CUI, Guanglei
- Re: bug in New2oldparm David A. Case
- offset of temperature when running MD with CAP and no periodic conditions Therese Malliavin
- Re: offset of temperature when running MD with CAP and no periodic conditions Andreas Svrcek-Seiler
- image X. Tan
- Question about Counterions Markus Drumm
- Re: image David A. Case
- RE: compiling without ISTAR2 Ross Walker
- BLOWUP after 100 ns??? Randy M. Wadkins
- Re: BLOWUP after 100 ns??? Randy M. Wadkins
- Re: BLOWUP after 100 ns??? David A. Case
- Re: BLOWUP after 100 ns??? Randy M. Wadkins
Friday, 20 September 2002
- Dynamic Movement of Molecule Yuuki Komata
- Re: Parameters for AMBER David A. Case
- mol2 file format in the future of amber M. L. Dodson
- Re: large energy fluctration eric hu
- Re: Dynamic Movement of Molecule Thomas Cheatham
- Re: vlimit and vmax Thomas Cheatham
- Re: vlimit and vmax darden
- mm_pbsa Sue Heavner
- ptraj rdf output Prabal Maiti
- Periodicity Question DeLano, Warren
Sunday, 22 September 2002
- Re: mol2 file format in the future of amber David A. Case
- Re: mol2 file format in the future of amber M. L. Dodson
- Re: Do I have to rerun 1ns MD?? Holger Gohlke
- Re: betaP,SURFOFF inconsistency Holger Gohlke
- Re: mm_pbsa Holger Gohlke
- Re: mm_pbsa Mahadevan Seetharaman
Monday, 23 September 2002
- ptraj-6.4/LES Peter Varnai
- Re: mm_pbsa David A. Case
- Fw: Do I have to rerun 1ns MD?? Lepsa
- mm_pbsa output error Michael Murray
- antechamber best practices/charge equivalence w/ AM1-BCC Tom Bishop
- Re: mm_pbsa output error Holger Gohlke
Tuesday, 24 September 2002
- watershell in ptraj Michael Trieb
- Re: Carnal+HBond confusion Sanjeev B.S.
- expression of V(lambda) in GIBBS hagop demirdjian
- Re: expression of V(lambda) in GIBBS David A. Case
- RE: antechamber best practices/charge equivalence w/ AM1-BCC Bayly, Christopher
- Mopac509mn/linux James W. Caldwell
- Re: watershell in ptraj Thomas Cheatham
Wednesday, 25 September 2002
- ambpdb? Arvid Soederhaell
- Re: ambpdb? Lepsa
- ptraj - BONDS_WITHOUT_HYDROGEN Sophia Kondratova
- (no subject) Apostoluk, Wlodzimierz K
- compiling amber 7 with Intel Fortran Compiler 6.0 ramon kleber da rocha
- sander_classic: Recompile without ISTAR2 Mahadevan Seetharaman
- ISTAR2 - oops, just found the answer... Mahadevan Seetharaman
- Re: compiling amber 7 with Intel Fortran Compiler 6.0 Scott Brozell
- compiling amber 7 with Intel Fortran Compiler 6.0 (fwd) John Bushnell
- Re: compiling amber 7 with Intel Fortran Compiler 6.0 James W. Caldwell
- RMSD for heavy atoms only Pratul Agarwal
- Re: compiling amber 7 with Intel Fortran Compiler 6.0 James W. Caldwell
- Question about Antechamber Masaki Tomimoto
Thursday, 26 September 2002
- mm_pbsa and statistic program Pascal Bonnet
- different counterions for special type of DNA Vlad Cojocaru
- Re: Density during equilibration (sander) Pratul Agarwal
- Re: Question about Antechamber David A. Case
- Re: GB tutorial David A. Case
- Re: mm_pbsa and statistic program David A. Case
- Torsion driving ch cureton
- Question on Antechamber paper Nicholson, James D Mr ARO
- Amber Reflector James W. Caldwell
- Constant pressure equilibration in a system with a solvent cap dianah_at_unm.edu
Friday, 27 September 2002
- Re: Constant pressure equilibration in a system with a solvent cap James W. Caldwell
- nmanal help request Peter Fojan
- Re: Constant pressure equilibration in a system with a solvent cap David A. Case
- Re: nmanal help request David A. Case
- Re: Constant pressure equilibration in a system with a solvent cap David Smith
- MM-PBSA basics Michael Ford
- MD Primers Joel Konkle-Parker
- Is H-bonding really there? suvendu lomash
- Re: Is H-bonding really there? Thomas Cheatham
- Re: Is H-bonding really there? Pratul Agarwal
- Re: Is H-bonding really there? Ioana Cozmuta
- Anal Error : Group Lifeng Tian
- Re: MD Primers Peter Gannett
- Request for help with Antechamber Nicholson, James D Mr ARO
- Re: Request for help with Antechamber David A. Case
- RE: Request for help with Antechamber Nicholson, James D Mr ARO
- Re: Request for help with Antechamber James W. Caldwell
Saturday, 28 September 2002
- question about using 10-12 in amber7/sander. Margaret Cheung
- Re: question about using 10-12 in amber7/sander. Margaret Cheung
Sunday, 29 September 2002
- parameters for sugars A.Madhumalar
- Re: MM-PBSA basics Holger Gohlke
Monday, 30 September 2002
- Re: MM-PBSA basics Lepsa
- groups in targeted md Christoph Brockmann
- Re: groups in targeted md Carlos Simmerling
- Re: groups in targeted md Christoph Brockmann
- Amber 7 and 6 topology files. Miguel de Federico
- Re: Amber 7 and 6 topology files. James W. Caldwell
- BondEn shoots in solvent minimization suvendu lomash
- write problem on IBM-AIX Giovanni Fossati
- Image charges with the solvate cap command dkeller_at_unm.edu
- Re: your mail David A. Case
- Re: parameters for sugars Elsa de Sousa Henriques
- Problems with poly(A)-poly(T) tutorial... Andrei Leit�o
- Partial charge generation RESP/antechamber James W. Caldwell
- divalent cations parameters Apostoluk, Wlodzimierz K
- Re: Image charges with the solvate cap command David A. Case

Last message date: Mon Sep 30 2002 - 17:34:28 PDT
Archived on: Mon Nov 25 2024 - 05:53:12 PST

Amber Archive Sep 2002 by date