Amber Archive Aug 2002: by date

Wednesday, 31 July 2002
- Re: Error decoding variable Rukman Hertadi
Thursday, 1 August 2002
- problem with amber7 mpi Bimo Ario Tejo
- Re: problem with amber7 mpi Carlos Simmerling
- Re: problem with amber7 mpi Shixiang Yan
- Potential Energy and RMS-Deviation Issues mdk7p_at_cms.mail.virginia.edu
- distance restraint stuff Layi Adekoya
- Re: Potential Energy and RMS-Deviation Issues CUI, Guanglei
- Re: distance restraint stuff CUI, Guanglei
- Re: Potential Energy and RMS-Deviation Issues Thomas Cheatham
- Re: Potential Energy and RMS-Deviation Issues David A. Case
- file Cozmuta
- proton_info/PS Cozmuta
- Using the new2oldparm command dianah_at_unm.edu
- Re: file David A. Case
- Re: Using the new2oldparm command Holger Gohlke
- RE: Using the new2oldparm command Karen Haskell
- MD on cytochrome Mahadevan Seetharaman
- Solvated DNA using Amber 7 Nicholson, James D Mr ARO
Friday, 2 August 2002
- Re: Using the new2oldparm command Pascal Bonnet
- reorder water with nmropt Peter Varnai
- Re: reorder water with nmropt David A. Case
- look for benchmark with myrinet vs. 100-BT Jianhui Wu
- Re: look for benchmark with myrinet vs. 100-BT Margaret Cheung
- FWD: RE: Including explicit waters in GB dynamics Kristina Furse
- igb=2 in amber7 Randy M. Wadkins
- water box-nonperiodic Cozmuta
- PROTON_INFO Cozmuta
- Re: water box-nonperiodic David Case
- Benchmarks Sanjeev B.S.
- Please give me a hand on understanding AMBER/MPI and locmem. Margaret Cheung
Saturday, 3 August 2002
- Generalized Born and OPLS potential Soonmin Jang
- Re: Please give me a hand on understanding AMBER/MPI and locmem. David Case
- Re: Please give me a hand on understanding AMBER/MPI and locmem. Margaret Cheung
- Re: PROTON_INFO Qing Zhang
Sunday, 4 August 2002
- Re: look for benchmark with myrinet vs. 100-BT C. Klein
- problems with parallel sander on linux clusters? David Case
- (no subject) sepideh ameli
- Import of CHARMM force field and GB potential parameters into Amber7 Soonmin Jang
- MD in alcohol Marc DOBLER
- Re: Import of CHARMM force field and GB potential parameters into Amber7 David Case
- Re: MD in alcohol David Case
Monday, 5 August 2002
- Re: MD in alcohol Marc DOBLER
- Information request - where to buy software Claire Edmonds
- Re: Generalized Born and OPLS potential David A. Case
Tuesday, 6 August 2002
- Amber trajectory movies in Powerpoint mdk7p_at_cms.mail.virginia.edu
- Re: "number of processors must be a power of two" Sanjeev B.S.
- Re: "number of processors must be a power of two" David A. Case
- creating a solvent box Bimo Ario Tejo
- Re: "number of processors must be a power of two" Michael Crowley
- Re: Amber trajectory movies in Powerpoint Cozmuta
- am1-bcc charges Sophia Kondratova
- Re: creating a solvent box David A. Case
- check-up question Cozmuta
- Re: am1-bcc charges David A. Case
- Leap error: PDB file with more than 10000 residues Pratul Agarwal
- Re: Leap error: PDB file with more than 10000 residues David A. Case
- Re: check-up question David A. Case
- Re: Leap error: PDB file with more than 10000 residues Pratul Agarwal
- Re: Leap error: PDB file with more than 10000 residues jim caldwell
- charges Cozmuta
- Re: Amber trajectory movies in Powerpoint Elsa de Sousa Henriques
Wednesday, 7 August 2002
- (no subject) Giulio Rastelli
- Re: your mail darden
- SHAKE problem Rosalia Pascual
- Amber+Mosix Jianhui Wu
- Re: charges David A. Case
- using belly with GB David A. Case
- Re: charges-again Cozmuta
- mpich, I/O, Master node, filesystem Jianhui Wu
- Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system. jeff dyason
- Re: Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system. Sanjeev B.S.
- Re: mpich, I/O, Master node, filesystem David Case
Thursday, 8 August 2002
- nmode segmentation fault zhongh_at_umich.edu
- Re: nmode segmentation fault Holger Gohlke
- Re: nmode segmentation fault jim caldwell
- Gentoo vs. Redhat Linux, shared/distributed filesystem Jianhui Wu
- protonation pH dependent Cozmuta
- Re: protonation pH dependent David A. Case
Friday, 9 August 2002
- LINMIN failure during minimization Giulio Rastelli
- namelist error with sander Andreas Kerzmann
- Re: nmode segmentation fault Haizhen Zhong
- problems runing gibbs on a IBM SP2 machine ramon kleber da rocha
- Re: namelist error with sander David A. Case
- Re: LINMIN failure during minimization David A. Case
- FW: Compiling on HP-UX 11.00 Hagedorn, Dan N
- Amber/Gentoo linux Jianhui Wu
Sunday, 11 August 2002
- RE: Amber/Gentoo linux Ross Walker
- RE: Amber+Mosix Ross Walker
- RE: Amber/Gentoo linux Margaret Cheung
- Nanotubes with AMBER Stefan Andreev Andreev
- Re: Nanotubes with AMBER David Case
Monday, 12 August 2002
- literature for NVE Khatcharin Siriwong
- Re: namelist error with sander Andreas Kerzmann
- Constant pressure MD problems (sander) Pratul Agarwal
- Memory and swap in sander William Wei
- Re: literature for NVE David A. Case
- Re: Constant pressure MD problems (sander) David A. Case
- Re: Memory and swap in sander David A. Case
- Re: literature for NVE Khatcharin Siriwong
- chesey.panther.gsu.edu Michael G Cooney
- misdirected message Michael G Cooney
Tuesday, 13 August 2002
- Format of prep input files dianah_at_unm.edu
- Re: Format of prep input files David A. Case
- sander minimizations failing John Bushnell
- minimization in amber7 for nonperiodic systems David Case
Wednesday, 14 August 2002
- dihedral parameter for conjugated double bonds in GAFF Giulio Rastelli
- GB in Amber7 Jithesh
- problem reading rstrnt file with pgf77 compiled sander Michael Petersen
- Carnal stream problem Vlad Cojocaru
- Re: minimization in amber7 for nonperiodic systems Giulio Rastelli
- Re: minimization in amber7 for nonperiodic systems David A. Case
- Re: GB in Amber7 David A. Case
- Running amber7 on Param10000 Sanjeev B.S.
- Q: waters in NPT & periodic boundary condition Masaki Tomimoto
- a question about carnal Vlad Cojocaru
- Re: Q: waters in NPT & periodic boundary condition David A. Case
- E going up and down??? Jiyoung Heo
- Re: Can we get trajectories coordinates after FIT in Carnal? Holger Gohlke
- Can we get trajectories coordinates after FIT in Carnal? William Wei
- mpi version of sander in Amber 6.0 with constraints Stefan Andreev Andreev
- Re: E going up and down??? David A. Case
- PMF with sander module mer_at_gordon.chem.wayne.edu
- problem with amber7 compiling on SGI Chris Switzer
- Re: PMF with sander module Pratul Agarwal
Thursday, 15 August 2002
- Re: Running amber7 on Param10000 Jithesh
- force field name A. Hungie
- RE: force field name Yong Duan
- sander on NEC-SX5 C. Klein
- RE: sander on NEC-SX5 Karen Haskell
- trajectory file limit??? Vlad Cojocaru
- Re: Help needed about mm_pbsa Holger Gohlke
- Re: trajectory file limit??? David A. Case
- Re: trajectory file limit??? jim caldwell
- Order of a protein, bound waters and ligand in saveamberparm Masaki Tomimoto
- Extra points Sarah Tschampel
- Re: trajectory file limit??? Pratul Agarwal
- RE: trajectory file limit??? Ross Walker
- Re: Extra points jim caldwell
- RE: Order of a protein, bound waters and ligand in saveamberparm Masaki Tomimoto
- Re: Extra points David A. Case
- RE: force field name Peter Gannett
- GB in amber6 Prabal Maiti
- Re: GB in amber6 CUI, Guanglei
- Re: GB in amber6 David Case
Friday, 16 August 2002
- add DUMMY atom into coordinate file yuann
- Re: problem reading rstrnt file with pgf77 Michael Petersen
- Re: GB in amber6 CUI, Guanglei
- dihedral parameter for conjugated double bonds in GAFF Giulio Rastelli
- Etot drops after restarting MD in sander Pratul Agarwal
- antechamber's prepc option Matthew Lee
- Re: PMF with sander module David A. Case
- Re: add DUMMY atom into coordinate file Alan Leo
- Re: antechamber's prepc option David A. Case
- a couple missing gaff angle terms Matthew Lee
- mol2_to_off Matthew Randolph Lee, Ph.D.
Sunday, 18 August 2002
- average of LES copies mer_at_chem.wayne.edu
Monday, 19 August 2002
- Antibody residue numbering Mark Hsieh
- Re: Antibody residue numbering David A. Case
- mail host switchover jim caldwell
- RE: Antibody residue numbering Mark Hsieh
- Im lost Sankha Subhra Som
Tuesday, 20 August 2002
- PC (principal component) analysis Soonmin Jang
- Re: Im lost David A. Case
- RE: Antibody residue numbering Mark Hsieh
- follow-up post on missing gaff terms Matthew Randolph Lee, Ph.D.
- segmentation fault Vlad Cojocaru
Wednesday, 21 August 2002
- Nitro parameters Jerry Matthew Parks
Monday, 26 August 2002
- RMSD by residue (fwd) amber_at_heimdal.compchem.ucsf.edu
- Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd) amber_at_heimdal.compchem.ucsf.edu
- adding_hydrogens_to_pdb (fwd) amber_at_heimdal.compchem.ucsf.edu
- ewald bomb in md equilibration (fwd) amber_at_heimdal.compchem.ucsf.edu
- why is mm_pbsa broken ? (fwd) amber_at_heimdal.compchem.ucsf.edu
- ambpdb problem (fwd) amber_at_heimdal.compchem.ucsf.edu
- Gibbs (FEP) (fwd) amber_at_heimdal.compchem.ucsf.edu
- QUICK HELP! Parameters for neutral amino acids (fwd) amber_at_heimdal.compchem.ucsf.edu
- amber7, gaff and minimization (fwd) amber_at_heimdal.compchem.ucsf.edu
- regarding RESP run from gamess output (fwd) amber_at_heimdal.compchem.ucsf.edu
- why is mm_pbsa broken ? (fwd) amber_at_heimdal.compchem.ucsf.edu
- Re: Can we get trajectories coordinates after FIT in Carnal? (fwd) amber_at_heimdal.compchem.ucsf.edu
- How to make mpeg files from amber trajectories (fwd) amber_at_heimdal.compchem.ucsf.edu
- Carnal RMSDs (fwd) amber_at_heimdal.compchem.ucsf.edu
- Re: Etot drops after restarting MD in sander (fwd) amber_at_heimdal.compchem.ucsf.edu
- turning off ewald (fwd) amber_at_heimdal.compchem.ucsf.edu
- a more general question about ff (fwd) amber_at_heimdal.compchem.ucsf.edu
- leaprc file (fwd) amber_at_heimdal.compchem.ucsf.edu
- Torsion restraint between center of mass groups Pratul Agarwal
- a more general question (fwd) amber_at_heimdal.compchem.ucsf.edu
- leaprc file (fwd) amber_at_heimdal.compchem.ucsf.edu
- Re: Extra points (fwd) amber_at_heimdal.compchem.ucsf.edu
- Scaling of Sander on Linux Clusters (fwd) amber_at_heimdal.compchem.ucsf.edu
- Re: "number of processors must be a power of two" (fwd) amber_at_heimdal.compchem.ucsf.edu
- Using GBSA for a DNA-PROTEIN complex (fwd) amber_at_heimdal.compchem.ucsf.edu
- test James W. Caldwell
- mail reflector James W. Caldwell
- ewald bomb in md equilibration Sophia Kondratova
- Re: Can we get trajectories coordinates after FIT in Carnal? Bill Ross
- Re: Carnal RMSDs Bill Ross
- Re: Scaling of Sander on Linux Clusters (fwd) Pratul Agarwal
- Re: adding_hydrogens_to_pdb (fwd) David A. Case
- Re: Scaling of Sander on Linux Clusters (fwd) Peter Gannett
- Re: RMSD by residue (fwd) Holger Gohlke
- Re: leaprc file (fwd) David A. Case
- Re: RMSD by residue (fwd) Carlos Simmerling
- Re: turning off ewald (fwd) David A. Case
- Re: Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd) David A. Case
- Re: ewald bomb in md equilibration (fwd) David A. Case
- Re: ambpdb problem (fwd) David A. Case
- Re: Gibbs (FEP) (fwd) David A. Case
- Re: QUICK HELP! Parameters for neutral amino acids (fwd) David A. Case
- Re: amber7, gaff and minimization (fwd) David A. Case
- Interface and Amber 7.0 Nigel D Priestley
- question Sankha Subhra Som
Tuesday, 27 August 2002
- Re: Scaling of Sander on Linux Clusters (fwd) St�phane Teletch�a
- Re: Scaling of Sander on Linux Clusters (fwd) Sanjeev B.S.
- Re: Scaling of Sander on Linux Clusters (fwd) St�phane Teletch�a
- Re: Interface and Amber 7.0 David A. Case
- amber7: ES40s Sanjeev B.S.
- difference 94 99 force field Vlad Cojocaru
- Re: How to make mpeg files from amber trajectories (fwd) Jake Isaacs
- Re: difference 94 99 force field Carlos Simmerling
- Re: how to make mpeg files from amber trajectories Anke Eisenmann
- Re: Interface and Amber 7.0 David Pearlman
- Re: why is mm_pbsa broken ? (fwd) Holger Gohlke
- Re: Scaling of Sander on Linux Clusters (fwd) Sanjeev B.S.
- restraints in parm in amber7 Sarah Tschampel
- problem in MD Xiang Mao
- Re: restraints in parm in amber7 Carlos Simmerling
- Re: problem in MD Carlos Simmerling
Wednesday, 28 August 2002
- Re: How to make mpeg files from amber trajectories (fwd) Michal Otyepka
- What's this "interface" the tutorial talks about? Andreas Kerzmann
- iwrap and image Sophia Kondratova
- Re: iwrap and image James W. Caldwell
- Fw: amber problem Carlos Simmerling
- can carnal do the job as anal to break down the energy? Haizhen Zhong
- [Re: can carnal do the job as anal to break down the energy?] Holger Gohlke
- RE: What's this "interface" the tutorial talks about? priestle
- Re: What's this "interface" the tutorial talks about? David Pearlman
- gibbs sara nunez
- [Re: can carnal do the job as anal to break down the energy?] Bill Ross
- a missing variable Vlad Cojocaru
- Re: a missing variable Matthew Randolph Lee, Ph.D.
- sorry!!!!maybe another stupid question Vlad Cojocaru
- Tutorial Error Message Joel Konkle-Parker
- Re: sorry!!!!maybe another stupid question Pratul Agarwal
Thursday, 29 August 2002
- IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...) Michael Jakusch
- MDaemon Warning - Virus Found postmaster_at_96com.com
- Re: IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...) Carlos Simmerling
- Re: IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...) Michael Jakusch
- MDaemon Warning - Virus Found postmaster_at_96com.com
- pbc in amber Xiang Mao
- Re: Tutorial Error Message Holger Gohlke
- MDaemon Warning - Virus Found postmaster_at_96com.com
- image command Sophia Kondratova
- PyMOL + AMBER Trajectories DeLano, Warren
- ES40 hangs amber7 jobs. Sanjeev B.S.
Friday, 30 August 2002
- dump coordinate into mdcrd A. Hungie
- MDaemon Warning - Virus Found postmaster_at_96com.com
- example gibbs file for the methane tutorial Andreas Kerzmann
- NTX value giudice
- MDaemon Warning - Virus Found postmaster_at_96com.com
- sander7 on IBM 7040-681 under AIX 5.1 Peter Varnai
- ewald bomb Vlad Cojocaru
- Re: ES40 hangs amber7 jobs. James W. Caldwell
- Re: NTX value James W. Caldwell
- Vanderbilt Biomolecular Modeling Symposium Jarrod Smith
- Re: NTX value James W. Caldwell
- Re: NTX value David A. Case
- Re: ewald bomb David A. Case
- RE: Vanderbilt Biomolecular Modeling Symposium Douglas Kojetin
- Binding site volume/Sander MD Jianhui Wu
- GBSA with IGB=2, setting the PBradii bondi Sarangan Ravichandran
Saturday, 31 August 2002
- Re: GBSA with IGB=2, setting the PBradii bondi David Case

Last message date: Sat Aug 31 2002 - 10:58:35 PDT
Archived on: Wed Apr 17 2024 - 05:53:10 PDT

Amber Archive Aug 2002 by date