Amber Archive Jan 2003 by thread
230 messages
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Starting
Thu Jan 02 2003 - 19:41:49 PST,
Ending
Fri Jan 31 2003 - 15:49:52 PST
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Sander box error and thanks on previous mdin error
kxg2248_at_njit.edu
(Thu Jan 02 2003 - 19:41:49 PST)
Re: Sander box error and thanks on previous mdin error
David A. Case
(Fri Jan 03 2003 - 07:40:07 PST)
Re: Sander box error and thanks on previous mdin error
kxg2248_at_njit.edu
(Fri Jan 03 2003 - 09:37:05 PST)
JACS 125th and PAK
Carlos Simmerling
(Fri Jan 03 2003 - 09:02:12 PST)
Re: JACS 125th and PAK
David A. Case
(Fri Jan 03 2003 - 10:36:47 PST)
Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap
Chris Switzer
(Fri Jan 03 2003 - 19:18:11 PST)
Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap
David Case
(Fri Jan 03 2003 - 21:46:00 PST)
Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap
Florian Barth
(Fri Jan 03 2003 - 22:36:27 PST)
looking for 'pdb_to_mass'
yuann
(Mon Jan 06 2003 - 22:54:32 PST)
Re: looking for 'pdb_to_mass'
CUI, Guanglei
(Tue Jan 07 2003 - 06:06:05 PST)
Small organic molecules
Dvira Segal
(Tue Jan 07 2003 - 07:55:31 PST)
Re: Small organic molecules
David A. Case
(Tue Jan 07 2003 - 08:16:48 PST)
water reordering in sander
Michael Trieb
(Tue Jan 07 2003 - 05:43:38 PST)
Re: water reordering in sander
David A. Case
(Tue Jan 07 2003 - 08:03:58 PST)
reducing restrains
Luis Gracia
(Tue Jan 07 2003 - 08:14:43 PST)
Re: reducing restrains
David A. Case
(Tue Jan 07 2003 - 09:08:24 PST)
Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap
Jim Newhouse
(Tue Jan 07 2003 - 11:07:32 PST)
virtual box
eric hu
(Tue Jan 07 2003 - 15:26:15 PST)
Re: virtual box
David A. Case
(Tue Jan 07 2003 - 15:56:29 PST)
Re: virtual box
eric hu
(Tue Jan 07 2003 - 23:35:09 PST)
Re: virtual box
eric hu
(Tue Jan 07 2003 - 23:35:21 PST)
building molecules by script files for leap
Dvira Segal
(Wed Jan 08 2003 - 08:07:57 PST)
Re: building molecules by script files for leap
David A. Case
(Wed Jan 08 2003 - 09:27:13 PST)
mm_gbsa error message
Mahadevan Seetharaman
(Wed Jan 08 2003 - 10:17:23 PST)
Re: mm_gbsa error message
Holger Gohlke
(Wed Jan 08 2003 - 13:52:31 PST)
Predefined Water_cap with xleap
Jose Ramon Blas
(Wed Jan 08 2003 - 10:42:16 PST)
mm_pbsa question
wentaofu
(Tue Jan 07 2003 - 16:17:08 PST)
Re: mm_pbsa question
Holger Gohlke
(Tue Jan 07 2003 - 16:41:30 PST)
the unit of velocity
Jian Zhang
(Tue Jan 07 2003 - 20:36:58 PST)
Re: the unit of velocity
David A. Case
(Wed Jan 08 2003 - 08:09:43 PST)
Re: the unit of velocity
Jian Zhang
(Wed Jan 08 2003 - 18:12:15 PST)
GIBBS - Routine TORCON failed. Required change is too large.
Miguel de Federico
(Thu Jan 09 2003 - 02:11:41 PST)
nmanal & quasih question
yuann
(Tue Jan 07 2003 - 23:16:56 PST)
Re: nmanal & quasih question
yuann
(Thu Jan 09 2003 - 08:13:30 PST)
Re: nmanal & quasih question
David A. Case
(Thu Jan 09 2003 - 09:16:11 PST)
MM_pbsa prmtop file
wentaofu
(Thu Jan 09 2003 - 15:29:38 PST)
Re: MM_pbsa prmtop file
David A. Case
(Thu Jan 09 2003 - 15:53:53 PST)
free energy perturbation (Gibbs/Amber 5)?
meiselba
(Thu Jan 09 2003 - 08:49:09 PST)
Re: free energy perturbation (Gibbs/Amber 5)?
Lepsa
(Fri Jan 10 2003 - 01:56:50 PST)
xleap crashes
Layi Adekoya
(Fri Jan 10 2003 - 04:16:26 PST)
Re: xleap crashes
David Case
(Fri Jan 10 2003 - 22:05:45 PST)
electrostatic potential calculations
Vlad Cojocaru
(Sat Jan 11 2003 - 08:05:07 PST)
Re: electrostatic potential calculations
Andreas Svrcek-Seiler
(Sat Jan 11 2003 - 08:43:33 PST)
Re: CCL:electrostatic potential calculations
Nathan A. Baker
(Mon Jan 13 2003 - 14:27:00 PST)
xleap crashes
Layi Adekoya
(Tue Jan 14 2003 - 00:46:49 PST)
Dummy atoms in free energy calculation
Lepsa
(Sat Jan 11 2003 - 10:18:44 PST)
Re: Dummy atoms in free energy calculation
David A. Case
(Sun Jan 12 2003 - 23:37:35 PST)
xleap crashes
Layi Adekoya
(Sun Jan 12 2003 - 23:54:20 PST)
Re: xleap crashes
David A. Case
(Mon Jan 13 2003 - 09:08:15 PST)
coordinates for quasih
Jake Isaacs
(Mon Jan 13 2003 - 06:43:54 PST)
Re: coordinates for quasih
Pratul Agarwal
(Mon Jan 13 2003 - 07:48:17 PST)
problem with antechamber
Craig A Bayse
(Sun Jan 12 2003 - 10:54:05 PST)
Re: problem with antechamber
David A. Case
(Sun Jan 12 2003 - 14:01:06 PST)
Re: electrostatic potential calculations
Peter Gannett
(Mon Jan 13 2003 - 09:32:19 PST)
IDSX0 in free energy calculations
Lepsa
(Fri Jan 10 2003 - 05:29:04 PST)
(no subject)
amkumar_at_post.its.mcw.edu
(Fri Jan 10 2003 - 09:35:12 PST)
errors in MD trajectories
Vlad Cojocaru
(Fri Jan 10 2003 - 10:13:03 PST)
pdb_to_mass
Jake Isaacs
(Fri Jan 10 2003 - 12:42:35 PST)
Re: pdb_to_mass
sychen
(Fri Jan 10 2003 - 17:53:37 PST)
Force Fields
Colin Connelly
(Fri Jan 10 2003 - 21:44:35 PST)
Amber parameters for Netropsin
Manuel Rueda
(Wed Jan 08 2003 - 15:48:12 PST)
Summary: mm_pbsa -- COMPT must be specified (correctly)
William Wei
(Tue Jan 14 2003 - 07:31:07 PST)
Re: how to stop mapping of N- and C-terminal residues in xleap (The RTFM solution)
Michael Ford
(Wed Jan 15 2003 - 10:02:52 PST)
octahedral volume
Peter Varnai
(Fri Jan 17 2003 - 02:26:58 PST)
Re: octahedral volume
David A. Case
(Tue Jan 21 2003 - 09:03:23 PST)
mm_pbsa Stop at statistics
William Wei
(Fri Jan 17 2003 - 10:52:48 PST)
UCSF Network changes to affect Amber Web site.
caldwell_at_heimdal.compchem.ucsf.edu
(Fri Jan 17 2003 - 11:41:19 PST)
RE: UCSF Network changes to affect Amber Web site.
Ross Walker
(Fri Jan 17 2003 - 12:07:29 PST)
Re: UCSF Network changes to affect Amber Web site.
David A. Case
(Fri Jan 17 2003 - 12:14:59 PST)
nucleic acid structures
Ioana Cozmuta
(Fri Jan 17 2003 - 17:12:35 PST)
Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold
John D. Chodera
(Sat Jan 18 2003 - 01:26:12 PST)
Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold
David A. Case
(Sat Jan 18 2003 - 10:53:54 PST)
High temperature MD
A.Madhumalar
(Sun Jan 19 2003 - 08:02:41 PST)
Re: High temperature MD
Lepsa
(Wed Jan 29 2003 - 23:27:19 PST)
Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold
David A. Case
(Sun Jan 19 2003 - 23:26:16 PST)
equilibrated solvent box
pu xuemei
(Mon Jan 20 2003 - 00:54:33 PST)
Re: equilibrated solvent box
David A. Case
(Wed Jan 22 2003 - 08:48:12 PST)
equilibrated solvent box
pu xuemei
(Mon Jan 20 2003 - 00:55:26 PST)
Has anyone ever used MEAD?
Vlad Cojocaru
(Mon Jan 20 2003 - 05:58:30 PST)
CARNAL
Lepsa
(Mon Jan 20 2003 - 07:22:22 PST)
Re: CARNAL
Lepsa
(Tue Jan 21 2003 - 01:33:37 PST)
Re: CARNAL
Lepsa
(Tue Jan 21 2003 - 10:07:18 PST)
Ewald error
Miguel de Federico
(Mon Jan 20 2003 - 07:32:21 PST)
Re: Ewald error
David A. Case
(Mon Jan 20 2003 - 09:31:49 PST)
scripts for compiling UHBD/MEAD with amber 7.0
eric hu
(Mon Jan 20 2003 - 09:54:37 PST)
morse potential
hagop demirdjian
(Mon Jan 20 2003 - 08:22:03 PST)
Re: morse potential
David A. Case
(Mon Jan 20 2003 - 09:29:59 PST)
script for Potential/kinectic energy
Layi Adekoya
(Mon Jan 20 2003 - 08:30:09 PST)
Re: script for Potential/kinectic energy
Holger Gohlke
(Mon Jan 20 2003 - 08:44:13 PST)
Re: script for Potential/kinectic energy
Luis Gracia
(Mon Jan 20 2003 - 10:16:52 PST)
SASA and H-bond over trajectories
Bimo Ario Tejo
(Mon Jan 20 2003 - 20:59:12 PST)
Amber tutorial crown-ether
Dvira Segal
(Tue Jan 21 2003 - 06:06:55 PST)
Re: Amber tutorial crown-ether
David A. Case
(Tue Jan 21 2003 - 08:48:47 PST)
(no subject)
Anke Eisenmann
(Tue Jan 21 2003 - 06:07:25 PST)
Re: your mail
David A. Case
(Tue Jan 21 2003 - 08:35:52 PST)
'hot-solvent' and 'cold solute' problem
Stefan Jungblut
(Tue Jan 21 2003 - 07:36:37 PST)
Re: 'hot-solvent' and 'cold solute' problem
David A. Case
(Tue Jan 21 2003 - 08:38:14 PST)
reduce the disk space
eric hu
(Tue Jan 21 2003 - 10:48:14 PST)
average structure generated by carnal
eric hu
(Tue Jan 21 2003 - 10:53:49 PST)
Re: average structure generated by carnal
Peter Gannett
(Tue Jan 21 2003 - 12:14:38 PST)
Re: average structure generated by carnal
Andreas Svrcek-Seiler
(Wed Jan 22 2003 - 07:16:53 PST)
Re: average structure generated by carnal
eric hu
(Tue Jan 21 2003 - 13:02:34 PST)
RE: average structure generated by carnal
Kristina Furse
(Tue Jan 21 2003 - 17:55:46 PST)
How to control box size
pu xuemei
(Wed Jan 22 2003 - 04:58:53 PST)
Re: How to control box size
David A. Case
(Wed Jan 22 2003 - 08:53:02 PST)
shake and belly
GUILLERMINA L ESTIU
(Tue Jan 21 2003 - 13:38:59 PST)
Re: shake and belly
David A. Case
(Wed Jan 22 2003 - 10:17:22 PST)
Re: shake and belly
GUILLERMINA L ESTIU
(Wed Jan 22 2003 - 10:47:30 PST)
SCSL
Joffre Heredia
(Wed Jan 22 2003 - 12:23:12 PST)
Re: SCSL
David A. Case
(Wed Jan 22 2003 - 08:37:33 PST)
Re: SCSL
Roberto Gomperts
(Thu Jan 23 2003 - 07:52:06 PST)
Proper torsion parameters missing?
Heike Meiselbach
(Thu Jan 23 2003 - 11:05:05 PST)
Re: Proper torsion parameters missing?
Miguel de Federico
(Fri Jan 24 2003 - 01:27:21 PST)
Shake problem in organic solvent
yuan bo
(Fri Jan 24 2003 - 04:03:48 PST)
Re: Shake problem in organic solvent
David A. Case
(Fri Jan 24 2003 - 13:43:20 PST)
RESP-group constraint
Artur Galstyan
(Fri Jan 24 2003 - 06:38:53 PST)
Nmode query
kinsellg
(Fri Jan 24 2003 - 07:00:40 PST)
Amber Web page.
caldwell_at_heimdal.compchem.ucsf.edu
(Fri Jan 24 2003 - 08:45:00 PST)
Zn2+ parameters
Xiang, Tian-Xiang
(Fri Jan 24 2003 - 13:42:07 PST)
Re: Zn2+ parameters
Robert G. Endres
(Sat Jan 25 2003 - 12:25:36 PST)
posphinic acid parameters
Alfonso Garcia Sosa
(Sun Jan 26 2003 - 08:28:11 PST)
polarization + ewald
GUILBAUD Philippe 153683
(Mon Jan 27 2003 - 03:21:44 PST)
Re: polarization + ewald
darden
(Mon Jan 27 2003 - 16:58:10 PST)
structure image
Xiang, Tian-Xiang
(Mon Jan 27 2003 - 07:31:46 PST)
RE: structure image
Xiang, Tian-Xiang
(Mon Jan 27 2003 - 08:25:34 PST)
gibbs run
Xiang, Tian-Xiang
(Mon Jan 27 2003 - 09:05:06 PST)
Re: gibbs run
David A. Case
(Mon Jan 27 2003 - 10:38:13 PST)
crystal structure of DNA/RNA homopolymers
Ioana Cozmuta
(Mon Jan 27 2003 - 11:34:13 PST)
Re: crystal structure of DNA/RNA homopolymers
David A. Case
(Mon Jan 27 2003 - 11:48:35 PST)
Re: crystal structure of DNA/RNA homopolymers
Ioana Cozmuta
(Mon Jan 27 2003 - 11:54:18 PST)
compiling amber on myrinet
Scott E. Boesch
(Mon Jan 27 2003 - 12:12:31 PST)
freeware to visualize RMSD matrices creatde with Carnal
Vlad Cojocaru
(Mon Jan 27 2003 - 14:41:00 PST)
xleap in Amber7
arubin_at_unmc.edu
(Mon Jan 27 2003 - 16:54:46 PST)
xleap in Amber7
arubin_at_unmc.edu
(Mon Jan 27 2003 - 16:56:16 PST)
lastrst
Steve Seibold
(Mon Jan 27 2003 - 09:46:57 PST)
Re: lastrst
David A. Case
(Mon Jan 27 2003 - 10:33:12 PST)
Re: structure image
A.Madhumalar
(Mon Jan 27 2003 - 17:51:35 PST)
Question: about restarting Energy
vannajan_at_chiangmai.ac.th
(Mon Jan 27 2003 - 17:53:30 PST)
Re: Question: about restarting Energy
David A. Case
(Mon Jan 27 2003 - 18:33:14 PST)
single point mutations to investigate the conformational change
Sichun Yang
(Mon Jan 27 2003 - 19:43:29 PST)
Intramolecular H-bonds in charge fitting
Lepsa
(Tue Jan 28 2003 - 01:05:58 PST)
RE: Intramolecular H-bonds in charge fitting
Bayly, Christopher
(Tue Jan 28 2003 - 07:35:14 PST)
one question
Fan Gao
(Tue Jan 28 2003 - 08:14:56 PST)
Re: one question
Lepsa
(Tue Jan 28 2003 - 08:16:05 PST)
Re: one question
Holger Gohlke
(Tue Jan 28 2003 - 08:17:02 PST)
script for H-bonds extracting
Bimo Ario Tejo
(Tue Jan 28 2003 - 02:00:52 PST)
RE: script for H-bonds extracting
Bayly, Christopher
(Tue Jan 28 2003 - 10:40:53 PST)
gibbs calculation
Xiang, Tian-Xiang
(Tue Jan 28 2003 - 11:03:44 PST)
Re: gibbs calculation
David A. Case
(Tue Jan 28 2003 - 12:03:37 PST)
MM_PBSA
Lepsa
(Wed Jan 29 2003 - 05:12:34 PST)
Re: MM_PBSA
Holger Gohlke
(Wed Jan 29 2003 - 07:24:58 PST)
antechamber and gamess
David A. Case
(Wed Jan 29 2003 - 08:16:03 PST)
mm_pbsa and ALA scan
Ahammadunny Pathiaseril
(Wed Jan 29 2003 - 08:24:06 PST)
Re: mm_pbsa and ALA scan
Lepsa
(Wed Jan 29 2003 - 08:31:41 PST)
Polymers
Ndubuisi Emmanuel Okoro
(Wed Jan 29 2003 - 13:40:53 PST)
Request
johneluwa_at_eircom.net
(Wed Jan 29 2003 - 18:42:28 PST)
naphthalene, anthracene force field
yuann
(Wed Jan 29 2003 - 06:58:47 PST)
antechamber and gamess
Arvid Soederhaell
(Wed Jan 29 2003 - 07:08:00 PST)
2drms command in ptraj
Vlad Cojocaru
(Tue Jan 28 2003 - 04:52:17 PST)
mm-pbsa error message
Thomas Steinbrecher
(Tue Jan 28 2003 - 07:02:04 PST)
Gibbs tutorial question
Patricia Burgess
(Wed Jan 22 2003 - 12:27:34 PST)
Re: Gibbs tutorial question
David A. Case
(Wed Jan 22 2003 - 13:54:10 PST)
MM_PBSA for Linux
Ramón Garduño-Juárez
(Wed Jan 22 2003 - 16:53:55 PST)
LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi
Dr Chris L. Brown
(Wed Jan 22 2003 - 19:10:34 PST)
Re: LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi
Chuck Schneider
(Thu Jan 23 2003 - 04:52:41 PST)
conformational sampling
Robert G. Endres
(Thu Jan 23 2003 - 06:17:57 PST)
Re: conformational sampling
Carlos Simmerling
(Thu Jan 23 2003 - 15:45:58 PST)
Polymers
Ndubuisi Emmanuel Okoro
(Thu Jan 23 2003 - 19:12:10 PST)
Chloroform Parameters
N. Jiten Singh
(Thu Jan 23 2003 - 21:27:24 PST)
How much is minimum distance
pu xuemei
(Thu Jan 23 2003 - 23:11:29 PST)
Dummy-parameters in Amber?
meiselba
(Thu Jan 23 2003 - 02:39:17 PST)
Re: Dummy-parameters in Amber?
Miguel de Federico
(Thu Jan 23 2003 - 03:07:14 PST)
question on ptraj
Ioana Cozmuta
(Wed Jan 22 2003 - 13:01:26 PST)
problems in equilibrating NaCl solution
Seongeun Yang
(Tue Jan 21 2003 - 14:48:04 PST)
Re: problems in equilibrating NaCl solution
David A. Case
(Fri Jan 24 2003 - 14:20:12 PST)
Re: problems in equilibrating NaCl solution
Seongeun Yang
(Fri Jan 24 2003 - 16:13:41 PST)
terminal phosphate group in RNA
David A. Case
(Fri Jan 24 2003 - 16:03:06 PST)
new amino acid residues
Nick Polfer
(Thu Jan 30 2003 - 04:58:41 PST)
Re: new amino acid residues
David A. Case
(Thu Jan 30 2003 - 09:46:35 PST)
Quasi-harmonic analysis
Pratul Agarwal
(Thu Jan 30 2003 - 15:48:22 PST)
Re: Quasi-harmonic analysis
David A. Case
(Thu Jan 30 2003 - 17:58:32 PST)
ptraj distanse question
Sichun Yang
(Thu Jan 30 2003 - 20:16:06 PST)
Re: ptraj distanse question
Lepsa
(Fri Jan 31 2003 - 04:16:25 PST)
AMBER7 & mpich
FyD
(Fri Jan 31 2003 - 06:05:41 PST)
ptraj on Methane in water box
Dvira Segal
(Fri Jan 31 2003 - 02:45:03 PST)
Re: Quasi-harmonic analysis
Miyashita, Osamu
(Fri Jan 31 2003 - 10:25:23 PST)
mm-pbsa problem & possible solution
Thomas Steinbrecher
(Thu Jan 30 2003 - 07:51:57 PST)
Re: mm-pbsa problem & possible solution
Holger Gohlke
(Thu Jan 30 2003 - 09:22:39 PST)
roar-cp : input for QM part ; output for CM2 charges
hagop demirdjian
(Fri Jan 31 2003 - 07:38:29 PST)
Domain/Helix movement/MD
Jianhui Wu
(Fri Jan 31 2003 - 08:35:18 PST)
Re: Domain/Helix movement/MD
Lepsa
(Fri Jan 31 2003 - 08:52:59 PST)
Re: Domain/Helix movement/MD
Pratul Agarwal
(Fri Jan 31 2003 - 13:00:54 PST)
Last message date
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Fri Jan 31 2003 - 15:49:52 PST
Archived on
: Wed Oct 30 2024 - 05:53:18 PDT
230 messages
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