AMBER Archive (2003) -
By Thread
Most recent messages
2933 messages sorted by:
[ author ]
[ date ]
[ subject ]
About this archive
Starting:
Thu Jan 02 2003 - 04:37:41 CST
Ending:
Fri Feb 06 2004 - 10:15:04 CST
TFE input
Raja Swaminathan
(Thu Jan 02 2003 - 04:37:41 CST)
Sander box error and thanks on previous mdin error
kxg2248_at_njit.edu
(Thu Jan 02 2003 - 21:41:49 CST)
Re: Sander box error and thanks on previous mdin error
David A. Case
(Fri Jan 03 2003 - 09:40:07 CST)
Re: Sander box error and thanks on previous mdin error
kxg2248_at_njit.edu
(Fri Jan 03 2003 - 11:37:05 CST)
JACS 125th and PAK
Carlos Simmerling
(Fri Jan 03 2003 - 11:02:12 CST)
Re: JACS 125th and PAK
David A. Case
(Fri Jan 03 2003 - 12:36:47 CST)
Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap
Chris Switzer
(Fri Jan 03 2003 - 21:18:11 CST)
Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap
David Case
(Fri Jan 03 2003 - 23:46:00 CST)
Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap
Florian Barth
(Sat Jan 04 2003 - 00:36:27 CST)
Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap
Jim Newhouse
(Tue Jan 07 2003 - 13:07:32 CST)
looking for 'pdb_to_mass'
yuann
(Tue Jan 07 2003 - 00:54:32 CST)
Re: looking for 'pdb_to_mass'
CUI, Guanglei
(Tue Jan 07 2003 - 08:06:05 CST)
water reordering in sander
Michael Trieb
(Tue Jan 07 2003 - 07:43:38 CST)
Re: water reordering in sander
David A. Case
(Tue Jan 07 2003 - 10:03:58 CST)
Small organic molecules
Dvira Segal
(Tue Jan 07 2003 - 09:55:31 CST)
Re: Small organic molecules
David A. Case
(Tue Jan 07 2003 - 10:16:48 CST)
reducing restrains
Luis Gracia
(Tue Jan 07 2003 - 10:14:43 CST)
Re: reducing restrains
David A. Case
(Tue Jan 07 2003 - 11:08:24 CST)
virtual box
eric hu
(Tue Jan 07 2003 - 17:26:15 CST)
Re: virtual box
David A. Case
(Tue Jan 07 2003 - 17:56:29 CST)
Re: virtual box
eric hu
(Wed Jan 08 2003 - 01:35:09 CST)
Re: virtual box
eric hu
(Wed Jan 08 2003 - 01:35:21 CST)
mm_pbsa question
wentaofu
(Tue Jan 07 2003 - 18:17:08 CST)
Re: mm_pbsa question
Holger Gohlke
(Tue Jan 07 2003 - 18:41:30 CST)
the unit of velocity
Jian Zhang
(Tue Jan 07 2003 - 22:36:58 CST)
Re: the unit of velocity
David A. Case
(Wed Jan 08 2003 - 10:09:43 CST)
Re: the unit of velocity
Jian Zhang
(Wed Jan 08 2003 - 20:12:15 CST)
nmanal & quasih question
yuann
(Wed Jan 08 2003 - 01:16:56 CST)
Re: nmanal & quasih question
yuann
(Thu Jan 09 2003 - 10:13:30 CST)
Re: nmanal & quasih question
David A. Case
(Thu Jan 09 2003 - 11:16:11 CST)
building molecules by script files for leap
Dvira Segal
(Wed Jan 08 2003 - 10:07:57 CST)
Re: building molecules by script files for leap
David A. Case
(Wed Jan 08 2003 - 11:27:13 CST)
mm_gbsa error message
Mahadevan Seetharaman
(Wed Jan 08 2003 - 12:17:23 CST)
Re: mm_gbsa error message
Holger Gohlke
(Wed Jan 08 2003 - 15:52:31 CST)
Predefined Water_cap with xleap
Jose Ramon Blas
(Wed Jan 08 2003 - 12:42:16 CST)
Amber parameters for Netropsin
Manuel Rueda
(Wed Jan 08 2003 - 17:48:12 CST)
GIBBS - Routine TORCON failed. Required change is too large.
Miguel de Federico
(Thu Jan 09 2003 - 04:11:41 CST)
free energy perturbation (Gibbs/Amber 5)?
meiselba
(Thu Jan 09 2003 - 10:49:09 CST)
Re: free energy perturbation (Gibbs/Amber 5)?
Lepsa
(Fri Jan 10 2003 - 03:56:50 CST)
MM_pbsa prmtop file
wentaofu
(Thu Jan 09 2003 - 17:29:38 CST)
Re: MM_pbsa prmtop file
David A. Case
(Thu Jan 09 2003 - 17:53:53 CST)
xleap crashes
Layi Adekoya
(Fri Jan 10 2003 - 06:16:26 CST)
Re: xleap crashes
David Case
(Sat Jan 11 2003 - 00:05:45 CST)
IDSX0 in free energy calculations
Lepsa
(Fri Jan 10 2003 - 07:29:04 CST)
(no subject)
amkumar_at_post.its.mcw.edu
(Fri Jan 10 2003 - 11:35:12 CST)
Re: (no subject)
David A. Case
(Tue Feb 18 2003 - 16:16:34 CST)
errors in MD trajectories
Vlad Cojocaru
(Fri Jan 10 2003 - 12:13:03 CST)
pdb_to_mass
Jake Isaacs
(Fri Jan 10 2003 - 14:42:35 CST)
Re: pdb_to_mass
sychen
(Fri Jan 10 2003 - 19:53:37 CST)
Force Fields
Colin Connelly
(Fri Jan 10 2003 - 23:44:35 CST)
electrostatic potential calculations
Vlad Cojocaru
(Sat Jan 11 2003 - 10:05:07 CST)
Re: electrostatic potential calculations
Andreas Svrcek-Seiler
(Sat Jan 11 2003 - 10:43:33 CST)
Re: CCL:electrostatic potential calculations
Nathan A. Baker
(Mon Jan 13 2003 - 16:27:00 CST)
Re: electrostatic potential calculations
Peter Gannett
(Mon Jan 13 2003 - 11:32:19 CST)
Dummy atoms in free energy calculation
Lepsa
(Sat Jan 11 2003 - 12:18:44 CST)
Re: Dummy atoms in free energy calculation
David A. Case
(Mon Jan 13 2003 - 01:37:35 CST)
problem with antechamber
Craig A Bayse
(Sun Jan 12 2003 - 12:54:05 CST)
Re: problem with antechamber
David A. Case
(Sun Jan 12 2003 - 16:01:06 CST)
xleap crashes
Layi Adekoya
(Mon Jan 13 2003 - 01:54:20 CST)
Re: xleap crashes
David A. Case
(Mon Jan 13 2003 - 11:08:15 CST)
coordinates for quasih
Jake Isaacs
(Mon Jan 13 2003 - 08:43:54 CST)
Re: coordinates for quasih
Pratul Agarwal
(Mon Jan 13 2003 - 09:48:17 CST)
mm_pbsa -- COMPT must be specified (correctly)
William Wei
(Mon Jan 13 2003 - 12:00:10 CST)
Re: mm_pbsa -- COMPT must be specified (correctly)
Holger Gohlke
(Mon Jan 13 2003 - 11:01:10 CST)
RE: mm_pbsa -- COMPT must be specified (correctly)
William Wei
(Mon Jan 13 2003 - 11:32:36 CST)
Re: mm_pbsa -- COMPT must be specified (correctly)
Lepsa
(Tue Jan 14 2003 - 02:49:55 CST)
xleap crashes
Layi Adekoya
(Tue Jan 14 2003 - 02:46:49 CST)
chloroform, dichlormethane f.f.
Arvid Soederhaell
(Tue Jan 14 2003 - 04:24:33 CST)
Re: chloroform, dichlormethane f.f.
David A. Case
(Tue Jan 14 2003 - 10:19:24 CST)
Re: chloroform, dichlormethane f.f.
Jose Ramon Blas
(Tue Jan 14 2003 - 18:05:34 CST)
MEAD on SuSE 8.1
Vlad Cojocaru
(Tue Jan 14 2003 - 09:10:18 CST)
Re: CCL:MEAD on SuSE 8.1
Szilveszter Juhos
(Tue Jan 14 2003 - 10:22:08 CST)
Summary: mm_pbsa -- COMPT must be specified (correctly)
William Wei
(Tue Jan 14 2003 - 09:31:07 CST)
mm_gbsa: Unit 5 Error on OPEN: sander_com.in
William Wei
(Tue Jan 14 2003 - 11:19:36 CST)
Re: mm_gbsa: Unit 5 Error on OPEN: sander_com.in
Michael Ford
(Tue Jan 14 2003 - 11:34:33 CST)
Re: mm_gbsa: Unit 5 Error on OPEN: sander_com.in
Michael Ford
(Wed Jan 15 2003 - 12:00:34 CST)
Moil-view
Ling Zhang
(Tue Jan 14 2003 - 11:47:14 CST)
Re: Moil-view
CUI, Guanglei
(Tue Jan 14 2003 - 11:48:49 CST)
how to stop mapping of N- and C-terminal residues in xleap
Michael Ford
(Tue Jan 14 2003 - 13:37:27 CST)
Re: how to stop mapping of N- and C-terminal residues in xleap
David A. Case
(Tue Jan 14 2003 - 13:59:52 CST)
solvatecap
GUILLERMINA L ESTIU
(Tue Jan 14 2003 - 14:33:16 CST)
Re: solvatecap
David A. Case
(Tue Jan 14 2003 - 16:29:43 CST)
nscm
Kristina Furse
(Tue Jan 14 2003 - 18:21:52 CST)
Re: nscm
David A. Case
(Tue Jan 14 2003 - 18:55:14 CST)
RE: nscm
Kristina Furse
(Wed Jan 15 2003 - 13:13:00 CST)
compiling amber: Machine file for new 64 bit HP-Itanium II CPU
Ying-Chieh Sun
(Tue Jan 14 2003 - 19:40:40 CST)
solvatecap
GUILLERMINA L ESTIU
(Wed Jan 15 2003 - 08:48:05 CST)
Re: how to stop mapping of N- and C-terminal residues in xleap (The RTFM solution)
Michael Ford
(Wed Jan 15 2003 - 12:02:52 CST)
mail reflector
caldwell_at_heimdal.compchem.ucsf.edu
(Thu Jan 16 2003 - 15:07:10 CST)
solvent free energy, GB
Robert G. Endres
(Thu Jan 16 2003 - 15:33:36 CST)
Re: solvent free energy, GB
David A. Case
(Thu Jan 16 2003 - 18:25:16 CST)
terminal phosphate group in RNA
Mahadevan Seetharaman
(Thu Jan 16 2003 - 16:10:13 CST)
Polarization charges -geometry
Lepsa
(Fri Jan 17 2003 - 02:21:30 CST)
Re: Polarization charges -geometry
David A. Case
(Tue Jan 21 2003 - 10:56:07 CST)
pi-pi in AMBER
Lepsa
(Tue Jan 21 2003 - 11:53:27 CST)
octahedral volume
Peter Varnai
(Fri Jan 17 2003 - 04:26:58 CST)
Re: octahedral volume
David A. Case
(Tue Jan 21 2003 - 11:03:23 CST)
mm_pbsa Stop at statistics
William Wei
(Fri Jan 17 2003 - 12:52:48 CST)
UCSF Network changes to affect Amber Web site.
caldwell_at_heimdal.compchem.ucsf.edu
(Fri Jan 17 2003 - 13:41:19 CST)
RE: UCSF Network changes to affect Amber Web site.
Ross Walker
(Fri Jan 17 2003 - 14:07:29 CST)
Re: UCSF Network changes to affect Amber Web site.
David A. Case
(Fri Jan 17 2003 - 14:14:59 CST)
nucleic acid structures
Ioana Cozmuta
(Fri Jan 17 2003 - 19:12:35 CST)
Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold
John D. Chodera
(Sat Jan 18 2003 - 03:26:12 CST)
Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold
David A. Case
(Sat Jan 18 2003 - 12:53:54 CST)
Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold
David A. Case
(Mon Jan 20 2003 - 01:26:16 CST)
High temperature MD
A.Madhumalar
(Sun Jan 19 2003 - 10:02:41 CST)
Re: High temperature MD
Lepsa
(Thu Jan 30 2003 - 01:27:19 CST)
equilibrated solvent box
pu xuemei
(Mon Jan 20 2003 - 02:54:33 CST)
Re: equilibrated solvent box
David A. Case
(Wed Jan 22 2003 - 10:48:12 CST)
equilibrated solvent box
pu xuemei
(Mon Jan 20 2003 - 02:55:26 CST)
Has anyone ever used MEAD?
Vlad Cojocaru
(Mon Jan 20 2003 - 07:58:30 CST)
CARNAL
Lepsa
(Mon Jan 20 2003 - 09:22:22 CST)
Re: CARNAL
Lepsa
(Tue Jan 21 2003 - 03:33:37 CST)
Re: CARNAL
Lepsa
(Tue Jan 21 2003 - 12:07:18 CST)
Ewald error
Miguel de Federico
(Mon Jan 20 2003 - 09:32:21 CST)
Re: Ewald error
David A. Case
(Mon Jan 20 2003 - 11:31:49 CST)
morse potential
hagop demirdjian
(Mon Jan 20 2003 - 10:22:03 CST)
Re: morse potential
David A. Case
(Mon Jan 20 2003 - 11:29:59 CST)
script for Potential/kinectic energy
Layi Adekoya
(Mon Jan 20 2003 - 10:30:09 CST)
Re: script for Potential/kinectic energy
Holger Gohlke
(Mon Jan 20 2003 - 10:44:13 CST)
Re: script for Potential/kinectic energy
Luis Gracia
(Mon Jan 20 2003 - 12:16:52 CST)
scripts for compiling UHBD/MEAD with amber 7.0
eric hu
(Mon Jan 20 2003 - 11:54:37 CST)
SASA and H-bond over trajectories
Bimo Ario Tejo
(Mon Jan 20 2003 - 22:59:12 CST)
Amber tutorial crown-ether
Dvira Segal
(Tue Jan 21 2003 - 08:06:55 CST)
Re: Amber tutorial crown-ether
David A. Case
(Tue Jan 21 2003 - 10:48:47 CST)
(no subject)
Anke Eisenmann
(Tue Jan 21 2003 - 08:07:25 CST)
Re: your mail
David A. Case
(Tue Jan 21 2003 - 10:35:52 CST)
'hot-solvent' and 'cold solute' problem
Stefan Jungblut
(Tue Jan 21 2003 - 09:36:37 CST)
Re: 'hot-solvent' and 'cold solute' problem
David A. Case
(Tue Jan 21 2003 - 10:38:14 CST)
shake and H-O-H angle
Luis Gracia
(Tue Jan 21 2003 - 10:57:16 CST)
Re: shake and H-O-H angle
Andreas Svrcek-Seiler
(Tue Jan 21 2003 - 13:29:22 CST)
Probelm with the generation of topology file
Jash, Panchatapa
(Tue Jan 21 2003 - 12:01:45 CST)
reduce the disk space
eric hu
(Tue Jan 21 2003 - 12:48:14 CST)
average structure generated by carnal
eric hu
(Tue Jan 21 2003 - 12:53:49 CST)
Re: average structure generated by carnal
Peter Gannett
(Tue Jan 21 2003 - 14:14:38 CST)
Re: average structure generated by carnal
Andreas Svrcek-Seiler
(Wed Jan 22 2003 - 09:16:53 CST)