Amber Archive Jul 2003: by date

Tuesday, 1 July 2003
- Nmode recompilation Thomas Steinbrecher
- g77 on 32 bits cpu (was Re: Nmode recompilation) Tru Huynh
- Re: AMBER Cutoff Darren Davies
- parallel version amber installation problem Raja Swaminathan
- parallel version amber installation problem Raja Swaminathan
- (no subject) Lifang Xu
- Re: AMBER Cutoff David A. Case
- Re: your mail (IBM runtime problem) Thomas Cheatham
- Re: protonate David A. Case
- Re: Questions about output archive and micromolecules David A. Case
- Re: parallel version amber installation problem David A. Case
- input problem Herbert Georg
- Re: input problem David A. Case
- Nmode doesn't work ? Gus Carri
- about the read error Zhi Qiang ZHOU
Wednesday, 2 July 2003
- PMF X. Tan
- Nmanal Gus Carri
Thursday, 3 July 2003
- Antechamber Shweta Sikri
- Re: Antechamber David A. Case
- Re: Antechamber Shweta Sikri
- Re: Antechamber David A. Case
Friday, 4 July 2003
- sander,ntt=5 Monika Fuxreiter
- How to do a rigid solvent model? Marco Aurelio Correia Preto
- Machine file available for ICC compiler ? Teletchéa Stéphane
- Re: sander,ntt=5 David A. Case
- Re: How to do a rigid solvent model? David A. Case
- Re: How to do a rigid solvent model? Carlos Simmerling
- Re: Machine file available for ICC compiler ? David A. Case
Saturday, 5 July 2003
- vlimit exceeded Peter Anderson
- RE: How to do a rigid solvent model? Yong Duan
- Re: How to do a rigid solvent model? Carlos Simmerling
Sunday, 6 July 2003
- RE: How to do a rigid solvent model? Yong Duan
Monday, 7 July 2003
- RE: How to do a rigid solvent model? Marco Aurelio Correia Preto
- parallelisation gold gunaseelan
- Re: parallelisation Carlos Simmerling
- ALAscan of Proline Martin Lepsik
- Valdiation of Latest Amber parameters Sia Meshkat
- ptraj Ioana Cozmuta
- New program available: PMEMD (Particle Mesh Ewald Molecular Dynamics) David A. Case
- correction to location of the PMEMD program David A. Case
- Re: Valdiation of Latest Amber parameters David A. Case
- RE: Valdiation of Latest Amber parameters Sia Meshkat
- RE: Valdiation of Latest Amber parameters caldwell.heimdal.compchem.ucsf.edu
- diffusion in ptraj Ioana Cozmuta
- Re: Valdiation of Latest Amber parameters David A. Case
- RE: Valdiation of Latest Amber parameters Sia Meshkat
- RE: Valdiation of Latest Amber parameters Yong Duan
- Re: Valdiation of Latest Amber parameters Carlos Simmerling
- RE: Valdiation of Latest Amber parameters Sia Meshkat
Tuesday, 8 July 2003
- constraint + restraint tang kwa
- Distribution Min with truncated octahedron box Ling Zhang
- Re: constraint + restraint David A. Case
- Re: Distribution Min with truncated octahedron box Bill Ross
- Re: Distribution Min with truncated octahedron box Ling Zhang
- carnal in big systems GUILLERMINA L ESTIU
- Re: carnal in big systems Bill Ross
- Lennard-Jones A and B coefficients Gus Carri
- memory shortage with mm_pbsa Peter Anderson
- Re: memory shortage with mm_pbsa David A. Case
- RE: Valdiation of Latest Amber parameters Yong Duan
Wednesday, 9 July 2003
- Ar as a solvent ENikitina
- May I get your help? Wu Yingliang
- memory problem zhaoxc.puccini.che.pitt.edu
- Refining a docked protein complex Wu Yingliang
- Re: Valdiation of Latest Amber parameters Jiri Sponer
- (no subject) Richard Dayton Smith
- Adding missing parameters Peter Anderson
- npscal Shuang Ding
- Temperature control Andrei Leitão
- Re: Temperature control Carlos Simmerling
- Re: Temperature control David A. Case
- Re: npscal David A. Case
- Re: Temperature control Carlos Simmerling
- RE: Valdiation of Latest Amber parameters Yong Duan
- van der Waals term David
- AMBER question David
Thursday, 10 July 2003
- RE: AMBER question Marco Aurelio Correia Preto
- Amber7 on Opteron Florian Barth
- 3 simultaneous simulations in one computer ptolonen.cc.joensuu.fi
- RE: Amber7 on Opteron Ross Walker
- nab compilation Vlad Cojocaru
- RE: 3 simultaneous simulations in one computer Ross Walker
- Opteron Experience ian r gould
- effect of forcing neutrality zhaoxc.puccini.che.pitt.edu
- resp for charged molecule? quch quch
- Re: Adding missing parameters David A. Case
- Re: your mail David A. Case
- Re: memory problem David A. Case
- Re: May I get your help? David A. Case
Saturday, 12 July 2003
- Re: memory shortage with mm_pbsa - some more thoughts Joffre Heredia
Friday, 11 July 2003
- Comparative MD FyD
- AMBER question David
- RE: AMBER question Marco Aurelio Correia Preto
- parallelisation gold gunaseelan
- Re: AMBER question Carlos Simmerling
- RE: May I get your help? Zhijun Li
- delphi with amber 7 Noriaki Okimoto
- Re: Comparative MD Thomas Cheatham
- Re: delphi with amber 7 Guanglei Cui
- Re: delphi with amber 7 Nori
Saturday, 12 July 2003
- ntx in sander dvira
Sunday, 13 July 2003
- Strange F.E.P. behavior Peter Anderson
Monday, 14 July 2003
- methylphosphonate A. Hungie
- Bad atom type: f Sukjoon Yoon
- Re: effect of forcing neutrality David A. Case
- parallelisation gold gunaseelan
- Sander_classic output: NAN pantelo.okstate.edu
- Re: parallelisation Carlos P. Sosa
- Re: effect of forcing neutrality zhaoxc.puccini.che.pitt.edu
- big changes coming caldwell.heimdal.compchem.ucsf.edu
- mail reflector address is changing David A. Case
- Welcome to amber Majordomo.scripps.edu
- Re: parallelisation David A. Case
- Re: Sander_classic output: NAN David A. Case
- AMBER: Re: memory shortage with mm_pbsa - some more thoughts Qing Zhang
- AMBER: Re: methylphosphonate David A. Case
- AMBER: question on LJ parameters for molecules Ioana Cozmuta
- Re: AMBER: Re: methylphosphonate Piotr Cieplak
- AMBER: Re: methylphosphonate Thomas E. Cheatham, III
- RE: AMBER: question on LJ parameters for molecules Yong Duan
- Re: AMBER: Re: methylphosphonate Piotr Cieplak
Tuesday, 15 July 2003
- AMBER: Re: methylphosphonate A. Hungie
- AMBER: PMF X. Tan
- AMBER: Questions about mm_pbsa and alanine scanning Haizhen Zhong
- Re: AMBER: Questions about mm_pbsa and alanine scanning Natasja Brooijmans
- Re: AMBER: Questions about mm_pbsa and alanine scanning Haizhen Zhong
- AMBER: Coordinate resetting (SHAKE) cannot be accomplished Anton B. Guliaev
- Re: AMBER: Coordinate resetting (SHAKE) cannot be accomplished David A. Case
Wednesday, 16 July 2003
- Re: AMBER: PMF David Smith
- Re: AMBER: Questions about mm_pbsa and alanine scanning Haizhen Zhong
- AMBER: neutral N- and C- termini ! Xavier Periole
- AMBER: curves nomenclature Sue Heavner
- Re: AMBER: Coordinate resetting (SHAKE) cannot be accomplished Bill Ross
- AMBER: N/C termini Xavier Periole
- Re: AMBER: curves nomenclature David A. Case
- AMBER: PMEMD and sander from AMBER6 performances Teletchéa Stéphane
- Re: AMBER: PMEMD and sander from AMBER6 performances Robert Duke
Thursday, 17 July 2003
- AMBER: RADII in DELPHI Obdulia Rabal
Wednesday, 16 July 2003
- AMBER: Big system in Gibbs ENikitina
Thursday, 17 July 2003
- Re: AMBER: Big system in Gibbs David A. Case
- Re: AMBER: RADII in DELPHI David A. Case
- Re: AMBER: neutral N- and C- termini ! David A. Case
Friday, 18 July 2003
- AMBER: question about quasih? Lishan Yao
- AMBER: Fwd: Minimizing after solvation Angela Pantelogianis
- Re: AMBER: question about quasih? Thomas E. Cheatham, III
Saturday, 19 July 2003
- Re: AMBER: Fwd: Minimizing after solvation David A. Case
Sunday, 20 July 2003
- Returned mail: see transcript for details Mail Delivery Subsystem
Monday, 21 July 2003
- Returned mail: see transcript for details Mail Delivery Subsystem
- AMBER: variable not in namelist for Sander input Haizhen Zhong
- RE: AMBER: variable not in namelist for Sander input Yong Duan
- Re: AMBER: variable not in namelist for Sander input Angela Pantelogianis
- Re: AMBER: variable not in namelist for Sander input Vlad Cojocaru
- AMBER: dielectric in sander Michele Lunelli
- Re: AMBER: Fwd: Minimizing after solvation Dr. Yong Duan
- Re: AMBER: Fwd: Minimizing after solvation David A. Case
- Re: AMBER: Fwd: Minimizing after solvation Angela Pantelogianis
- Re: AMBER: dielectric in sander David A. Case
- RE: AMBER: variable not in namelist for Sander input Haizhen Zhong
- Re: AMBER: variable not in namelist for Sander input Teletchéa Stéphane
- Re: AMBER: variable not in namelist for Sander input Thomas E. Cheatham, III
- Re: AMBER: variable not in namelist for Sander input Haizhen Zhong
- Re: AMBER: variable not in namelist for Sander input Thomas E. Cheatham, III
- RE: AMBER: variable not in namelist for Sander input Yong Duan
- AMBER: Odd Problem with PMEMD Chen, Ya
- Re: AMBER: Odd Problem with PMEMD Johannes Zuegg
Tuesday, 22 July 2003
- Re: AMBER: Odd Problem with PMEMD Robert Duke
- Re: AMBER: Big system in Gibbs ENikitina
- AMBER: (no subject) ENikitina
- Re: AMBER: (no subject) David A. Case
- AMBER: FILE UNITIO.C Obdulia Rabal
- Re: AMBER: FILE UNITIO.C David A. Case
- AMBER: Non-standard Residue Ran Ye
- Re: AMBER: Non-standard Residue David A. Case
- AMBER: HB dynamics in water and Ion solvation free energies Ioana Cozmuta
- Re: AMBER: HB dynamics in water and Ion solvation free energies David A. Case
Wednesday, 23 July 2003
- RE: AMBER: FILE UNITIO.C Obdulia Rabal
- Re: AMBER: FILE UNITIO.C David A. Case
- Re: AMBER: Non-standard Residue Ran Ye
- AMBER: strange problem with a small system GUILLERMINA L ESTIU
- Re: AMBER: Non-standard Residue David A. Case
- AMBER: addition to: problem with a small system GUILLERMINA L ESTIU
- Re: AMBER: strange problem with a small system David A. Case
- Re: AMBER: strange problem with a small system GUILLERMINA L ESTIU
Thursday, 24 July 2003
- AMBER: /exe/teLeap does not exist Mizuguchi Mineyuki
- AMBER: water box problem Omar Wahab
- Re: AMBER: water box problem Carlos Simmerling
- AMBER: (no subject) Narang Manpreet Kaur
- Re: AMBER: (no subject) Holger Gohlke
- AMBER: question about ptraj? Lishan Yao
- Re: AMBER: (no subject) Thomas E. Cheatham, III
- Re: AMBER: question about ptraj? Thomas E. Cheatham, III
- Re: AMBER: question about ptraj? rluo.uci.edu
- Re: AMBER: TEMP is not reaching 300K Carlos Simmerling
- Re: AMBER: TEMP is not reaching 300K Vlad Cojocaru
- AMBER: running AMBER on an IBM P690 cluster Vlad Cojocaru
- AMBER: TEMP is not reaching 300K sd233.georgetown.edu
- AMBER: PMF calculation Lishan Yao
- AMBER: MOPAC509mn test jobs on linux takanori.kanazawa.pharma.novartis.com
- Re: AMBER: /exe/teLeap does not exist David A. Case
- Re: AMBER: (no subject) Narang Manpreet Kaur
- Re: AMBER: strange problem with a small system David A. Case
Friday, 25 July 2003
- Re: AMBER: TEMP is not reaching 300K Michele Lunelli
- AMBER: Dynamics and Simulated Annealing Narang Manpreet Kaur
- Re: AMBER: Dynamics and Simulated Annealing Carlos Simmerling
- Re: AMBER: Dynamics and Simulated Annealing Teletchéa Stéphane
- AMBER: Taisung Lee/San Diego/Accelrys is out of the office. Taisung Lee
- AMBER: monitor vdw along time Ling Zhang
- AMBER: DYNAMICS RUN sd233.georgetown.edu
- Re: AMBER: monitor vdw along time Holger Gohlke
- Re: AMBER: monitor vdw along time Suse Broyde
Saturday, 26 July 2003
- AMBER: a note on problems with MPI and sander David A. Case
Sunday, 27 July 2003
- AMBER: AMBER and NAMD Vlad Cojocaru
- Re: AMBER: AMBER and NAMD Andreas Svrcek-Seiler
- Re: AMBER: AMBER and NAMD Vlad Cojocaru
- AMBER: Impropers from Amber parm files to NAMD Vlad Cojocaru
Monday, 28 July 2003
- AMBER: please let me know if this is correct Vlad Cojocaru
- AMBER: Question about quasih analysis Lishan Yao
- Re: AMBER: PMF calculation Carlos Simmerling
- Re: AMBER: strange problem with a small system GUILLERMINA L ESTIU
- Re: AMBER: please let me know if this is correct Andreas Svrcek-Seiler
- Re: AMBER: Question about quasih analysis David A. Case
- Re: AMBER: please let me know if this is correct David A. Case
- Re: AMBER: strange problem with a small system David A. Case
- Re: AMBER: Question about quasih analysis Lishan Yao
- Re: AMBER: Question about quasih analysis David A. Case
- AMBER: ambpdb and residue number Vlad Cojocaru
- Re: AMBER: Question about quasih analysis Lishan Yao
- Re: AMBER: Question about quasih analysis David A. Case
- AMBER: H-O-H angle in TIP3P water model during minimization Vlad Cojocaru
- RE: AMBER: H-O-H angle in TIP3P water model during minimization Yong Duan
- AMBER: chemical potential Petrodler.aol.com
Tuesday, 29 July 2003
- Re: AMBER: chemical potential David A. Case
- AMBER: dynamics of isolated system Herbert Georg
- Re: AMBER: dynamics of isolated system Vlad Cojocaru
- Re: AMBER: dynamics of isolated system Dr. Yong Duan
- Re: AMBER: dynamics of isolated system Herbert Georg
- Re: AMBER: dynamics of isolated system Herbert Georg
- Re: AMBER: dynamics of isolated system Dr. Yong Duan
- AMBER: combine prep files Mi-Kyung Seo
- Re: AMBER: combine prep files David A. Case
- Re: AMBER: dynamics of isolated system David A. Case
Wednesday, 30 July 2003
- Re: AMBER: chemical potential Petrodler.aol.com
- AMBER: Ewald_Bomb Susanna Monti
- AMBER: Ewald problem Shuang Ding
- Re: AMBER: Ewald_Bomb David A. Case
- Re: AMBER: chemical potential David A. Case
- Re: AMBER: Ewald problem David A. Case
- Re: AMBER: Ewald problem Shuang Ding
- Re: AMBER: (no subject) Junmei Wang
- AMBER: (no subject) Mi-Kyung Seo
- AMBER: compile problem Shuang Ding
- AMBER: Aki Hoji
- AMBER: frequency analysis Lishan Yao
- Re: AMBER: frequency analysis Piotr Cieplak
- Re: AMBER: compile problem David A. Case
- Re: AMBER: compile problem Scott Brozell
- AMBER: question about ptraj Ioana Cozmuta
- Re: AMBER: question about ptraj Thomas E. Cheatham, III
- RE: AMBER: frequency analysis Yong Duan
Thursday, 31 July 2003
- AMBER: parallelisation gold gunaseelan
- AMBER: parallelisation gold gunaseelan
- AMBER: Running Amber on MacOSX(XDarwin) Aki Hoji
- AMBER: add Ran Ye
- AMBER: chage WATBOX216 Ioana Cozmuta
- Re: AMBER: add Scott Brozell
- Re: AMBER: add Ran Ye
- Re: AMBER: add Scott Brozell

Last message date: Fri Aug 01 2003 - 00:53:01 PDT
Archived on: Mon Nov 03 2025 - 05:53:21 PST

Amber Archive Jul 2003 by date