Amber Archive Nov 2004 by thread
366 messages
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Starting
Sun Oct 31 2004 - 17:53:00 PST,
Ending
Wed Dec 01 2004 - 02:53:00 PST
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Re: AMBER: ptraj questions
Oliver Hucke
(Mon Nov 01 2004 - 09:59:06 PST)
AMBER: Building the parallel version in AMBER 8 and GIBBS
Ilyas Yildirim
(Tue Nov 09 2004 - 19:03:54 PST)
Re: AMBER: Building the parallel version in AMBER 8 and GIBBS
David A. Case
(Tue Nov 09 2004 - 21:07:05 PST)
AMBER: Amber7 installation error on Solaris 9
Joe Nolan
(Mon Nov 01 2004 - 12:03:25 PST)
Re: AMBER: Amber7 installation error on Solaris 9
David A. Case
(Mon Nov 01 2004 - 13:11:24 PST)
AMBER: MD & folding
bybaker.itsa.ucsf.edu
(Mon Nov 01 2004 - 23:03:42 PST)
Re: AMBER: MD & folding
Bimo Ario Tejo
(Mon Nov 01 2004 - 23:26:09 PST)
AMBER: about FEP
Xiao He
(Tue Nov 02 2004 - 00:29:43 PST)
Re: AMBER: about FEP
Annette Ho
(Tue Nov 02 2004 - 02:44:03 PST)
Re: AMBER: about FEP
david.evans.ulsop.ac.uk
(Tue Nov 02 2004 - 03:28:44 PST)
Re: AMBER: about FEP
Annette Höglund
(Tue Nov 02 2004 - 03:58:27 PST)
Re: AMBER: about FEP
david.evans.ulsop.ac.uk
(Tue Nov 02 2004 - 04:42:25 PST)
Re: AMBER: about FEP
Ray Luo
(Tue Nov 02 2004 - 06:05:41 PST)
Re: Re: AMBER: about FEP
Xiao He
(Tue Nov 02 2004 - 19:18:22 PST)
Re: Re: AMBER: about FEP
Thomas Steinbrecher
(Wed Nov 03 2004 - 00:07:51 PST)
AMBER: FEP and charges
Annette Höglund
(Wed Nov 03 2004 - 03:59:16 PST)
Re: AMBER: FEP and charges
Chunhu Tan
(Thu Nov 04 2004 - 14:23:16 PST)
AMBER: Solvation free energy of a charged molecule.
Chunhu Tan
(Thu Nov 11 2004 - 17:53:58 PST)
Re: AMBER: Solvation free energy of a charged molecule.
David A. Case
(Fri Nov 12 2004 - 08:11:15 PST)
Re: AMBER: Solvation free energy of a charged molecule.
Chunhu Tan
(Fri Nov 12 2004 - 10:43:32 PST)
AMBER: a quick question about carnal
Haijun Yang
(Fri Nov 12 2004 - 12:51:17 PST)
Re: AMBER: about FEP
David A. Case
(Tue Nov 02 2004 - 08:19:27 PST)
AMBER: ESP fitting from Gaussian03 cube files
Ye Mei
(Tue Nov 02 2004 - 01:01:40 PST)
AMBER: MD & folding
bybaker.itsa.ucsf.edu
(Tue Nov 02 2004 - 13:31:31 PST)
Re: AMBER: MD & folding
Carlos Simmerling
(Tue Nov 02 2004 - 15:03:41 PST)
AMBER: MD & folding
bybaker.itsa.ucsf.edu
(Tue Nov 02 2004 - 16:05:00 PST)
AMBER: Clustering in PTRAJ
Stephen.Titmuss.csiro.au
(Tue Nov 02 2004 - 17:38:31 PST)
AMBER: SANDER BOMB in subroutine nonbond_list
Marc Perea
(Tue Nov 02 2004 - 04:45:34 PST)
Re: AMBER: SANDER BOMB in subroutine nonbond_list
David A. Case
(Wed Nov 03 2004 - 10:05:15 PST)
AMBER: basis set
Yanze Zhang
(Tue Nov 02 2004 - 21:57:19 PST)
Re: AMBER: basis set
FyD
(Fri Nov 05 2004 - 11:55:06 PST)
: AMBER: basis set
ying xiong
(Tue Nov 02 2004 - 22:43:52 PST)
AMBER: ESPGEN problems to read G03 output files
Hernán Alonso
(Tue Nov 02 2004 - 23:03:12 PST)
Re: AMBER: ESPGEN problems to read G03 output files
Jiten
(Wed Nov 03 2004 - 00:33:04 PST)
Re: AMBER: ESPGEN problems to read G03 output files
FyD
(Fri Nov 05 2004 - 11:56:52 PST)
AMBER: Extracting torsional angles for specific conformation
Darian, Eva
(Wed Nov 03 2004 - 10:12:33 PST)
AMBER: gaff parameter ambiguities
Anthony Fejes
(Wed Nov 03 2004 - 15:16:07 PST)
AMBER: MD simulation at pH=1
Kijeong Kwac
(Wed Nov 03 2004 - 20:20:01 PST)
AMBER: Fluctuation in temperature
anshul.imtech.res.in
(Thu Nov 04 2004 - 14:09:58 PST)
Re: AMBER: Fluctuation in temperature
Oliver Hucke
(Thu Nov 04 2004 - 10:14:36 PST)
RE: AMBER: Fluctuation in temperature
Ross Walker
(Thu Nov 04 2004 - 12:05:57 PST)
AMBER: H-bonded waters selection
pl
(Thu Nov 04 2004 - 04:41:32 PST)
Re: AMBER: H-bonded waters selection
Thomas E. Cheatham, III
(Thu Nov 04 2004 - 21:05:24 PST)
Re: AMBER: H-bonded waters selection
pl
(Fri Nov 05 2004 - 02:42:01 PST)
AMBER: gaussian command line
Yanze Zhang
(Thu Nov 04 2004 - 11:40:27 PST)
Re: AMBER: gaussian command line
FyD
(Fri Nov 05 2004 - 12:02:45 PST)
AMBER:
Kara Wald
(Thu Nov 04 2004 - 13:05:42 PST)
AMBER: Re: Antechamber
Kara Wald
(Thu Nov 04 2004 - 13:13:28 PST)
RE: AMBER: Re: Antechamber
Ross Walker
(Thu Nov 04 2004 - 13:31:48 PST)
Re: AMBER: Re: Antechamber
Kara Wald
(Mon Nov 08 2004 - 13:49:13 PST)
AMBER: ptraj problem
Abd Ghani Abd Aziz
(Thu Nov 04 2004 - 17:53:39 PST)
Re: AMBER: ptraj problem
Thomas E. Cheatham, III
(Thu Nov 04 2004 - 18:13:51 PST)
Re: AMBER: ptraj problem
Abd Ghani Abd Aziz
(Thu Nov 04 2004 - 18:39:37 PST)
AMBER: constructing a small colecule
mathew k varghese
(Thu Nov 04 2004 - 20:41:58 PST)
Re: AMBER: constructing a small colecule
david.evans.ulsop.ac.uk
(Fri Nov 05 2004 - 01:53:07 PST)
AMBER: translational and rotational entropy
hj zou
(Thu Nov 04 2004 - 22:48:22 PST)
Re: AMBER: translational and rotational entropy
Andreas Svrcek-Seiler
(Thu Nov 04 2004 - 23:43:00 PST)
AMBER: end point contribution in MCTI
Cai, Yufeng
(Fri Nov 05 2004 - 06:12:11 PST)
Re: AMBER: end point contribution in MCTI
David A. Case
(Fri Nov 05 2004 - 08:36:31 PST)
AMBER: Amber7 compilation error
Joe Nolan
(Fri Nov 05 2004 - 07:17:39 PST)
Re: AMBER: Amber7 compilation error
David A. Case
(Fri Nov 05 2004 - 08:50:01 PST)
AMBER: Problems using mm_pbsa.perl
Daniel Wetzler
(Fri Nov 05 2004 - 08:28:15 PST)
Re: AMBER: Problems using mm_pbsa.perl
Holger Gohlke
(Fri Nov 05 2004 - 08:41:39 PST)
AMBER: ptraj radial
Sandro Fornili
(Fri Nov 05 2004 - 08:28:57 PST)
AMBER: Minimization failure: 1cbn
Harianto
(Fri Nov 05 2004 - 09:16:30 PST)
Re: AMBER: Minimization failure: 1cbn
Bimo Ario Tejo
(Fri Nov 05 2004 - 14:12:03 PST)
Re: AMBER: Minimization failure: 1cbn
Bill Ross
(Fri Nov 05 2004 - 14:32:41 PST)
AMBER: where is the VDW radius?
Cai, Yufeng
(Sat Nov 06 2004 - 07:42:29 PST)
Re: AMBER: where is the VDW radius?
Oliver Hucke
(Sat Nov 06 2004 - 11:16:00 PST)
AMBER: positive VDWAALS
John
(Sun Nov 07 2004 - 10:11:13 PST)
Re: AMBER: positive VDWAALS
Michael Crowley
(Sun Nov 07 2004 - 13:51:26 PST)
AMBER: mm_PBSA: problems calculating molecular surface for some snapshots
Magne Olufsen
(Mon Nov 08 2004 - 01:50:39 PST)
AMBER: time-averaged restraints
John
(Mon Nov 08 2004 - 12:21:51 PST)
AMBER: amber 7 nmode on osx
Knut Langsetmo
(Mon Nov 08 2004 - 15:26:26 PST)
AMBER: salt bridge detection
Ye Mei
(Mon Nov 08 2004 - 18:33:21 PST)
AMBER: error message about the input file of sander
Ru-Zhen Li
(Mon Nov 08 2004 - 18:23:23 PST)
Re: AMBER: error message about the input file of sander
Michael Crowley
(Mon Nov 08 2004 - 22:48:03 PST)
Re: AMBER: error message about the input file of sander
Ru-Zhen Li
(Tue Nov 09 2004 - 04:20:40 PST)
Re: AMBER: error message about the input file of sander
Ru-Zhen Li
(Tue Nov 09 2004 - 04:49:26 PST)
RE: AMBER: error message about the input file of sander
Ross Walker
(Tue Nov 09 2004 - 09:44:31 PST)
Re: AMBER: error message about the input file of sander
Ru-Zhen Li
(Tue Nov 09 2004 - 12:33:57 PST)
AMBER: Problem with Water solute during MD
Daniel Wetzler
(Tue Nov 09 2004 - 05:20:13 PST)
Re: AMBER: Problem with Water solute during MD
David A. Case
(Tue Nov 09 2004 - 08:06:31 PST)
Re: AMBER: Problem with Water solute during MD
Daniel Wetzler
(Wed Nov 10 2004 - 02:19:11 PST)
Re: AMBER: Problem with Water solute during MD
David A. Case
(Wed Nov 10 2004 - 07:42:50 PST)
Re: AMBER: Problem with Water solute during MD
Bill Ross
(Wed Nov 10 2004 - 07:20:23 PST)
AMBER: Leap
Greg Kellogg
(Tue Nov 09 2004 - 08:24:43 PST)
Re: AMBER: Leap
David A. Case
(Tue Nov 09 2004 - 09:00:38 PST)
Re: AMBER: Problem with Water solute during MD
Bill Ross
(Tue Nov 09 2004 - 09:36:22 PST)
AMBER: IBELLY
Harianto
(Tue Nov 09 2004 - 12:40:58 PST)
AMBER: Solaris f77 Machine file for Amber7?
Joe Nolan
(Tue Nov 09 2004 - 14:13:58 PST)
Re: AMBER: Solaris f77 Machine file for Amber7?
David A. Case
(Tue Nov 09 2004 - 16:57:24 PST)
Re: AMBER: Solaris f77 Machine file for Amber7?
Joe Nolan
(Wed Nov 10 2004 - 08:45:50 PST)
Re: AMBER: Solaris f77 Machine file for Amber7?
David A. Case
(Wed Nov 10 2004 - 09:07:13 PST)
Re: AMBER: Solaris f77 Machine file for Amber7?
Joe Nolan
(Wed Nov 10 2004 - 13:11:44 PST)
Re: AMBER: Solaris f77 Machine file for Amber7?
David A. Case
(Wed Nov 10 2004 - 13:49:47 PST)
Re: AMBER: Solaris f77 Machine file for Amber7?
Joe Nolan
(Wed Nov 10 2004 - 14:43:54 PST)
Re: AMBER: Solaris f77 Machine file for Amber7?
David A. Case
(Wed Nov 10 2004 - 16:15:32 PST)
Re: AMBER: Solaris f77 Machine file for Amber7?
Joe Nolan
(Thu Nov 11 2004 - 10:50:06 PST)
Re: AMBER: Solaris f77 Machine file for Amber7?
Joe Nolan
(Thu Nov 11 2004 - 14:00:33 PST)
AMBER: single strand simulation
ding
(Tue Nov 09 2004 - 16:12:17 PST)
Re: AMBER: single strand simulation
Thomas E. Cheatham, III
(Tue Nov 09 2004 - 16:32:58 PST)
AMBER: AMBER Parameter Database
Yanze Zhang
(Wed Nov 10 2004 - 07:35:32 PST)
AMBER: parameter set
Yanze Zhang
(Wed Nov 10 2004 - 11:56:54 PST)
Re: AMBER: parameter set
David A. Case
(Wed Nov 10 2004 - 12:10:40 PST)
Re: AMBER: parameter set
Bill Ross
(Wed Nov 10 2004 - 12:17:25 PST)
AMBER: About the parameter names
Ilyas Yildirim
(Wed Nov 10 2004 - 13:20:31 PST)
Re: AMBER: About the parameter names
David A. Case
(Wed Nov 10 2004 - 13:50:58 PST)
RE: AMBER: Can parallel simulation have a nonperiodic boundary condition?
Ross Walker
(Wed Nov 10 2004 - 16:26:27 PST)
AMBER: ptraj
MURAT CETINKAYA
(Thu Nov 11 2004 - 13:19:45 PST)
AMBER: glibc version
Ye Mei
(Thu Nov 11 2004 - 22:04:00 PST)
Re: AMBER: glibc version
David A. Case
(Fri Nov 12 2004 - 14:17:53 PST)
AMBER: AMBER 4 Manual?
Ru-Zhen Li
(Fri Nov 12 2004 - 09:02:16 PST)
Re: AMBER: AMBER 4 Manual?
David A. Case
(Fri Nov 12 2004 - 14:10:42 PST)
AMBER: Energy change for isomerization reaction of cyclic peptide
nlxc
(Fri Nov 12 2004 - 10:03:00 PST)
Re: AMBER: Energy change for isomerization reaction of cyclic peptide
David A. Case
(Fri Nov 12 2004 - 14:02:10 PST)
Re: AMBER: a quick question about carnal
Bill Ross
(Fri Nov 12 2004 - 13:53:41 PST)
Re: AMBER: a quick question about carnal
Haijun Yang
(Mon Nov 15 2004 - 09:31:53 PST)
AMBER: the energy difference between sander and nmode
xiaowei li
(Fri Nov 12 2004 - 13:52:57 PST)
Re: AMBER: the energy difference between sander and nmode
David A. Case
(Fri Nov 12 2004 - 14:43:28 PST)
AMBER: xleap problems
Kepa Koldo Burusco Goñi
(Fri Nov 12 2004 - 11:33:42 PST)
Re: AMBER: xleap problems
Mark Williamson
(Fri Nov 12 2004 - 15:58:05 PST)
Re: AMBER: xleap problems
Ilyas Yildirim
(Fri Nov 12 2004 - 15:58:21 PST)
AMBER: Parameters for new residue?
Satpal Virdee
(Sat Nov 13 2004 - 11:34:27 PST)
Re: AMBER: Parameters for new residue?
David A. Case
(Sat Nov 13 2004 - 17:30:39 PST)
AMBER: convert .pdb to .mol2
bybaker.itsa.ucsf.edu
(Sat Nov 13 2004 - 20:35:45 PST)
Re: AMBER: convert .pdb to .mol2
Ye Mei
(Sat Nov 13 2004 - 20:57:32 PST)
AMBER: Babel
bybaker.itsa.ucsf.edu
(Sat Nov 13 2004 - 23:29:40 PST)
Re: AMBER: Babel
Carlos Simmerling
(Sun Nov 14 2004 - 06:02:17 PST)
Re: AMBER: Babel
FyD
(Mon Nov 15 2004 - 15:07:11 PST)
AMBER: nmode:Number of atoms in -p and -c files do not agree!
myang.vitamin.uni.cc
(Sun Nov 14 2004 - 18:20:25 PST)
Re: AMBER: nmode:Number of atoms in -p and -c files do not agree!
David A. Case
(Mon Nov 15 2004 - 08:10:43 PST)
Re: AMBER: nmode:Number of atoms in -p and -c files do not agree!
myang.vitamin.uni.cc
(Mon Nov 15 2004 - 11:58:58 PST)
Re: AMBER: nmode:Number of atoms in -p and -c files do not agree!
David A. Case
(Mon Nov 15 2004 - 13:43:15 PST)
AMBER: ifort 8.0
Ilyas Yildirim
(Mon Nov 15 2004 - 14:41:28 PST)
Re: AMBER: ifort 8.0
Jack Lei
(Mon Nov 15 2004 - 14:46:01 PST)
RE: AMBER: ifort 8.0
Ross Walker
(Wed Nov 17 2004 - 10:39:49 PST)
Re: AMBER: nmode:Number of atoms in -p and -c files do not agree!
myang.vitamin.uni.cc
(Mon Nov 15 2004 - 17:26:17 PST)
AMBER: restraintmask problem in ptraj
Takanori TANAKA
(Mon Nov 15 2004 - 03:06:23 PST)
Re: AMBER: restraintmask problem in ptraj
Viktor Hornak
(Mon Nov 15 2004 - 05:37:24 PST)
AMBER: gibbs compilation error
Nelson Fonseca
(Mon Nov 15 2004 - 09:41:27 PST)
Re: AMBER: gibbs compilation error
David A. Case
(Mon Nov 15 2004 - 10:18:12 PST)
AMBER: AMBER8 parallel job
Emmanuel Giudice
(Sun Nov 14 2004 - 23:39:50 PST)
AMBER: Re: Amber Re: Antechamber problems
Kara Wald
(Mon Nov 15 2004 - 13:05:19 PST)
AMBER: Can xleap to handle homology model altogether X-ray structure?
Jack Lei
(Mon Nov 15 2004 - 14:39:55 PST)
AMBER: Can xleap handle homology model altogether with X-ray structure?
Jack Lei
(Mon Nov 15 2004 - 15:08:44 PST)
Re: AMBER: Can xleap to handle homology model altogether X-ray structure?
David A. Case
(Tue Nov 16 2004 - 08:13:11 PST)
Re: AMBER: Can xleap to handle homology model altogether X-ray structure?
Joachim Reichelt
(Tue Nov 16 2004 - 09:42:02 PST)
AMBER: Problem with a single aminoacid as inhibitor
Daniel Wetzler
(Wed Nov 17 2004 - 03:54:04 PST)
Re: AMBER: Problem with a single aminoacid as inhibitor
Carlos Simmerling
(Wed Nov 17 2004 - 04:43:08 PST)
AMBER: AMBER8 compiling error under Itanium 2.
qlu.notes.cc.sunysb.edu
(Mon Nov 15 2004 - 16:39:36 PST)
Re: AMBER: AMBER8 compiling error under Itanium 2.
Ye Mei
(Mon Nov 15 2004 - 17:46:52 PST)
Re: AMBER: AMBER8 compiling error under Itanium 2.
Jack Lei
(Tue Nov 16 2004 - 09:32:23 PST)
AMBER: constant pH simulations reference
Sergio E. Wong
(Mon Nov 15 2004 - 17:50:16 PST)
Re: AMBER: constant pH simulations reference
David A. Case
(Mon Nov 15 2004 - 18:23:42 PST)
AMBER: ambpdb segmentation fault
justin litchfield
(Mon Nov 15 2004 - 18:57:14 PST)
RE: AMBER: ambpdb segmentation fault
Ross Walker
(Wed Nov 17 2004 - 13:35:40 PST)
Re: AMBER: ambpdb segmentation fault
justin litchfield
(Wed Nov 17 2004 - 14:46:01 PST)
Re: AMBER: ambpdb segmentation fault
justin litchfield
(Sun Nov 21 2004 - 21:09:25 PST)
Re: AMBER: ambpdb segmentation fault
Bill Ross
(Sun Nov 21 2004 - 21:34:13 PST)
FWD: RE: AMBER: xleap problems
Kepa Koldo Burusco Goñi
(Tue Nov 16 2004 - 02:56:40 PST)
AMBER: SUSE 9.1 and AMBER 8
Ilyas Yildirim
(Tue Nov 16 2004 - 03:12:16 PST)
Re: AMBER: SUSE 9.1 and AMBER 8
Andreas Svrcek-Seiler
(Tue Nov 16 2004 - 05:10:44 PST)
INSTALLATION GUIDE FOR IFORT AND AMBER8 IN LINUX SUSE 9.1 ....Re: AMBER: SUSE 9.1 and AMBER 8
Cenk Andac
(Tue Nov 16 2004 - 06:19:03 PST)
AMBER: How to compile the downloadable RESP in UNIX
Yanze Zhang
(Tue Nov 16 2004 - 07:33:03 PST)
Re: AMBER: How to compile the downloadable RESP in UNIX
Satpal Virdee
(Tue Nov 16 2004 - 07:58:41 PST)
Re: AMBER: How to compile the downloadable RESP in UNIX
Yanze Zhang
(Wed Nov 17 2004 - 15:04:57 PST)
Re: AMBER: How to compile the downloadable RESP in UNIX
Satpal Virdee
(Thu Nov 18 2004 - 04:36:07 PST)
Re: AMBER: How to compile the downloadable RESP in UNIX
Yanze Zhang
(Thu Nov 18 2004 - 12:10:13 PST)
AMBER: restrained options
Toshifumi Yui
(Tue Nov 16 2004 - 08:42:22 PST)
AMBER: <dV/dL> fluctuations in TI
Nelson Fonseca
(Wed Nov 17 2004 - 03:39:01 PST)
Re: AMBER: <dV/dL> fluctuations in TI
Thomas Steinbrecher
(Wed Nov 17 2004 - 05:06:40 PST)
Re: AMBER: <dV/dL> fluctuations in TI
Chunhu Tan
(Thu Nov 18 2004 - 14:57:05 PST)
Re: AMBER: <dV/dL> fluctuations in TI
Chunhu Tan
(Fri Nov 19 2004 - 11:07:03 PST)
AMBER: Problem with a single aminoacid as inhibitor
Daniel Wetzler
(Wed Nov 17 2004 - 03:59:12 PST)
Re: AMBER: Problem with a single aminoacid as inhibitor
david.evans.ulsop.ac.uk
(Wed Nov 17 2004 - 04:55:58 PST)
Re: AMBER: Problem with a single aminoacid as inhibitor
M. L. Dodson
(Wed Nov 17 2004 - 07:29:26 PST)
Re: AMBER: Problem with a single aminoacid as inhibitor
Daniel Wetzler
(Wed Nov 17 2004 - 08:13:50 PST)
AMBER: Problem to update antechamber package.
Guillaume Bollot
(Wed Nov 17 2004 - 05:50:49 PST)
AMBER: RMS of energy in Minimization using SANDER
Jack Lei
(Wed Nov 17 2004 - 10:15:31 PST)
RE: AMBER: RMS of energy in Minimization using SANDER
Ross Walker
(Wed Nov 17 2004 - 10:36:25 PST)
AMBER: Fifth European Workshop in Drug Design
Andrea Tafi
(Thu Nov 18 2004 - 04:35:02 PST)
AMBER: Diastereoisomers of ATP
William Boxford
(Thu Nov 18 2004 - 07:18:42 PST)
AMBER: calcium van der Waals parameters
cailliez
(Thu Nov 18 2004 - 08:53:23 PST)
Re: AMBER: calcium van der Waals parameters
Bill Ross
(Mon Nov 22 2004 - 10:57:09 PST)
Re: AMBER: calcium van der Waals parameters
Piotr Cieplak
(Mon Nov 22 2004 - 11:03:57 PST)
Re: AMBER: calcium van der Waals parameters
Bill Ross
(Thu Nov 18 2004 - 10:25:49 PST)
Re: AMBER: calcium van der Waals parameters
cailliez
(Mon Nov 22 2004 - 09:10:30 PST)
AMBER: Problem with carnal on linux
Sébastien Fiorucci
(Fri Nov 19 2004 - 06:13:26 PST)
RE: AMBER: Problem with carnal on linux
Ross Walker
(Fri Nov 19 2004 - 09:36:08 PST)
AMBER: SHAKE probelm
Huang, Hai
(Fri Nov 19 2004 - 08:25:24 PST)
RE: AMBER: SHAKE probelm
Ross Walker
(Fri Nov 19 2004 - 09:35:18 PST)
RE: AMBER: SHAKE probelm
Huang, Hai
(Fri Nov 19 2004 - 14:56:54 PST)
RE: AMBER: SHAKE probelm
Ross Walker
(Fri Nov 19 2004 - 15:09:05 PST)
RE: AMBER: SHAKE probelm
Huang, Hai
(Tue Nov 23 2004 - 14:01:25 PST)
AMBER: amber8 compilation
lucian livadaru
(Fri Nov 19 2004 - 10:51:00 PST)
RE: AMBER: amber8 compilation
Ross Walker
(Fri Nov 19 2004 - 11:20:00 PST)
RE: AMBER: amber8 compilation
lucian livadaru
(Mon Nov 22 2004 - 14:22:43 PST)
RE: AMBER: amber8 compilation
Ross Walker
(Mon Nov 22 2004 - 14:48:03 PST)
AMBER: leap compiling problem on a 64-bit machine
xhu1.memphis.edu
(Fri Nov 19 2004 - 11:13:22 PST)
RE: AMBER: leap compiling problem on a 64-bit machine
Ross Walker
(Fri Nov 19 2004 - 11:32:01 PST)
Re: RE: AMBER: leap compiling problem on a 64-bit machine
xhu1.memphis.edu
(Fri Nov 19 2004 - 15:51:58 PST)
Re: RE: AMBER: leap compiling problem on a 64-bit machine
Tomas Linhart
(Fri Nov 19 2004 - 17:14:51 PST)
Re: RE: AMBER: leap compiling problem on a 64-bit machine
xhu1.memphis.edu
(Sat Nov 20 2004 - 12:19:27 PST)
Re: RE: AMBER: leap compiling problem on a 64-bit machine
Tomas Linhart
(Sat Nov 20 2004 - 14:15:44 PST)
Re: RE: AMBER: leap compiling problem on a 64-bit machine
xhu1.memphis.edu
(Sun Nov 21 2004 - 14:52:02 PST)
Re: RE: AMBER: leap compiling problem on a 64-bit machine
Tomas Linhart
(Sun Nov 21 2004 - 15:22:25 PST)
Re: RE: AMBER: leap compiling problem on a 64-bit machine
xhu1.memphis.edu
(Sun Nov 21 2004 - 19:31:53 PST)
AMBER: Electrolyte concentrations in MD
arubin.unmc.edu
(Fri Nov 19 2004 - 12:56:09 PST)
Re: AMBER: leap compiling problem on a 64-bit machine
Bill Ross
(Fri Nov 19 2004 - 13:14:07 PST)
AMBER: calculation of pKa values
Peter Trodler
(Mon Nov 22 2004 - 00:32:25 PST)
AMBER: sander, MD problems
Kepa Koldo Burusco Goñi
(Mon Nov 22 2004 - 04:00:37 PST)
Re: AMBER: sander, MD problems
Carlos Simmerling
(Mon Nov 22 2004 - 04:53:29 PST)
AMBER: problem solved: leap compiling problem on a 64-bit machine
xhu1.memphis.edu
(Mon Nov 22 2004 - 12:51:28 PST)
AMBER: New problem on our 64bit box: xleap Segmentation fault
xhu1.memphis.edu
(Mon Nov 22 2004 - 13:03:48 PST)
RE: AMBER: New problem on our 64bit box: xleap Segmentation fault
Ross Walker
(Mon Nov 22 2004 - 13:29:13 PST)
Re: RE: AMBER: New problem on our 64bit box: xleap Segmentation fault
xhu1.memphis.edu
(Mon Nov 22 2004 - 14:37:03 PST)
AMBER: LEaP compilation error on Solaris 9
Joe Nolan
(Mon Nov 22 2004 - 13:21:41 PST)
Re: AMBER: LEaP compilation error on Solaris 9
David A. Case
(Mon Nov 22 2004 - 14:02:35 PST)
Re: AMBER: LEaP compilation error on Solaris 9
Bill Ross
(Mon Nov 22 2004 - 14:16:10 PST)
Re: AMBER: New problem on our 64bit box: xleap Segmentation fault
Bill Ross
(Mon Nov 22 2004 - 13:27:21 PST)
Re: AMBER: New problem on our 64bit box: xleap Segmentation fault
xhu1.memphis.edu
(Mon Nov 22 2004 - 14:38:37 PST)
AMBER: generating parmfile containing topology and parameter information
Nitin Bhardwaj
(Mon Nov 22 2004 - 13:29:00 PST)
RE: AMBER: generating parmfile containing topology and parameter information
Ross Walker
(Mon Nov 22 2004 - 13:46:30 PST)
RE: AMBER: generating parmfile containing topology and parameter information
Nitin Bhardwaj
(Mon Nov 22 2004 - 15:53:07 PST)
Re: AMBER: generating parmfile containing topology and parameter information
David A. Case
(Mon Nov 22 2004 - 16:12:20 PST)
AMBER: questions on dummy atom types in FEP setup
Eric Hu
(Mon Nov 22 2004 - 13:37:54 PST)
Re: AMBER: questions on dummy atom types in FEP setup
Chunhu Tan
(Mon Nov 22 2004 - 15:37:57 PST)
Re: AMBER: questions on dummy atom types in FEP setup
Eric Hu
(Mon Nov 22 2004 - 18:22:45 PST)
AMBER: mm_pbsa +fillratio
Carsten Detering
(Mon Nov 22 2004 - 15:14:55 PST)
Re: AMBER: mm_pbsa +fillratio
David A. Case
(Mon Nov 22 2004 - 15:20:03 PST)
Re: AMBER: mm_pbsa +fillratio
Carsten Detering
(Mon Nov 22 2004 - 16:38:13 PST)
Re: AMBER: problem solved: leap compiling problem on a 64-bit machine
Bill Ross
(Mon Nov 22 2004 - 14:37:58 PST)
Re: AMBER: problem solved: leap compiling problem on a 64-bit machine
xhu1.memphis.edu
(Mon Nov 22 2004 - 15:48:43 PST)
AMBER: Problem with converting AMBER PREP to MOL2
Cenk Andac
(Mon Nov 22 2004 - 16:13:39 PST)
Re: AMBER: Problem with converting AMBER PREP to MOL2
David A. Case
(Tue Nov 23 2004 - 08:12:06 PST)
Re: AMBER: Problem with converting AMBER PREP to MOL2
david.evans.ulsop.ac.uk
(Tue Nov 23 2004 - 09:06:22 PST)
Re: AMBER: Problem with converting AMBER PREP to MOL2
Bill Ross
(Tue Nov 23 2004 - 10:00:31 PST)
AMBER: mm_pbsa + vertex atom mismatch
Carsten Detering
(Mon Nov 22 2004 - 19:01:28 PST)
AMBER: Resend: Problem with converting AMBER8 PREP to MOL2
Cenk Andac
(Tue Nov 23 2004 - 00:57:55 PST)
AMBER: langevin dynamic in sander
Stefano.Pieraccini.unimi.it
(Tue Nov 23 2004 - 01:33:08 PST)
Re: AMBER: langevin dynamic in sander
David A. Case
(Tue Nov 23 2004 - 08:21:30 PST)
AMBER: TI with electrostatic decoupling
Nelson Fonseca
(Tue Nov 23 2004 - 01:56:44 PST)
AMBER: Problem with minimisation of an protein-inhibitor complex
Daniel Wetzler
(Tue Nov 23 2004 - 02:31:33 PST)
Re: AMBER: TI with electrostatic decoupling
David A. Case
(Tue Nov 23 2004 - 08:42:16 PST)
Re: AMBER: TI with electrostatic decoupling
Chunhu Tan
(Tue Nov 23 2004 - 11:01:48 PST)
AMBER: restart calculation
tang kwa
(Tue Nov 23 2004 - 02:31:22 PST)
Re: AMBER: restart calculation
Tomas Linhart
(Tue Nov 23 2004 - 02:53:29 PST)
Re: AMBER: restart calculation
tang kwa
(Tue Nov 23 2004 - 03:44:45 PST)
Re: AMBER: restart calculation
David A. Case
(Tue Nov 23 2004 - 08:39:37 PST)
Re: AMBER: restart calculation
Carlos Simmerling
(Tue Nov 23 2004 - 04:45:28 PST)
RE: AMBER: restart calculation
Ross Walker
(Tue Nov 23 2004 - 10:02:12 PST)
AMBER: Problem with minimisation of an protein-inhibitor complex
Daniel Wetzler
(Tue Nov 23 2004 - 04:31:38 PST)
RE: AMBER: Problem with minimisation of an protein-inhibitor complex
Ross Walker
(Tue Nov 23 2004 - 10:16:04 PST)
AMBER: add dummy atoms
tang kwa
(Tue Nov 23 2004 - 06:27:05 PST)
Re: AMBER: add dummy atoms
David A. Case
(Tue Nov 23 2004 - 08:27:48 PST)
AMBER: Antechamber problems
Kara Wald
(Tue Nov 23 2004 - 10:49:43 PST)
AMBER: md.out & plot
bybaker.itsa.ucsf.edu
(Tue Nov 23 2004 - 14:23:41 PST)
Re: AMBER: md.out & plot
Luis Gracia
(Tue Nov 23 2004 - 14:43:33 PST)
RE: AMBER: md.out & plot
Ross Walker
(Tue Nov 23 2004 - 14:59:58 PST)
AMBER: cannot load frcmod file properly
Eric Hu
(Tue Nov 23 2004 - 15:10:17 PST)
Re: AMBER: cannot load frcmod file properly
Chunhu Tan
(Tue Nov 23 2004 - 18:12:42 PST)
Re: AMBER: cannot load frcmod file properly
Eric Hu
(Wed Nov 24 2004 - 10:28:02 PST)
Re: AMBER: cannot load frcmod file properly
Chunhu Tan
(Wed Nov 24 2004 - 12:37:46 PST)
AMBER: Re: md.out & plot
bybaker.itsa.ucsf.edu
(Tue Nov 23 2004 - 17:26:36 PST)
Re: AMBER: Re: md.out & plot
Furse, Kristina Elisabet
(Tue Nov 23 2004 - 20:29:37 PST)
Re: AMBER: Re: md.out & plot
Furse, Kristina Elisabet
(Tue Nov 23 2004 - 20:37:21 PST)
AMBER: build a cyclic peptide
Eric Hu
(Tue Nov 23 2004 - 17:34:13 PST)
Re: AMBER: build a cyclic peptide
Carlos Simmerling
(Tue Nov 23 2004 - 18:43:13 PST)
Re: AMBER: build a cyclic peptide
Eric Hu
(Wed Nov 24 2004 - 10:26:44 PST)
Re: AMBER: build a cyclic peptide
Carlos Simmerling
(Wed Nov 24 2004 - 10:56:57 PST)
Re: AMBER: build a cyclic peptide
Eric Hu
(Wed Nov 24 2004 - 12:11:18 PST)
Re: AMBER: build a cyclic peptide
Carlos Simmerling
(Wed Nov 24 2004 - 12:33:10 PST)
Re: AMBER: build a cyclic peptide
Bill Ross
(Wed Nov 24 2004 - 10:39:15 PST)
Re: AMBER: build a cyclic peptide
Bill Ross
(Wed Nov 24 2004 - 13:56:44 PST)
Re: AMBER: build a cyclic peptide
Bill Ross
(Tue Nov 23 2004 - 18:33:04 PST)
AMBER: Installation of AMBER8 on AMD cluster using pgf90
Hwankyu Lee
(Tue Nov 23 2004 - 18:41:13 PST)
Re: AMBER: Installation of AMBER8 on AMD cluster using pgf90
David A. Case
(Tue Nov 23 2004 - 23:03:55 PST)
Re: AMBER: Installation of AMBER8 on AMD cluster using pgf90
Hwankyu Lee
(Wed Nov 24 2004 - 06:03:28 PST)
AMBER: Re: md.out & plot
bybaker.itsa.ucsf.edu
(Tue Nov 23 2004 - 22:21:10 PST)
AMBER: missing XaLeap_wcl file
Nitin Bhardwaj
(Wed Nov 24 2004 - 10:22:04 PST)
AMBER: extracting energy from trajector?
MURAT CETINKAYA
(Wed Nov 24 2004 - 10:33:04 PST)
Re: AMBER: extracting energy from trajector?
Carlos Simmerling
(Wed Nov 24 2004 - 10:55:49 PST)
Re: AMBER: extracting energy from trajector?
Bill Ross
(Wed Nov 24 2004 - 11:33:29 PST)
Re: AMBER: extracting energy from trajector?
David Smith
(Wed Nov 24 2004 - 11:29:34 PST)
Re: AMBER: extracting energy from trajector?
MURAT CETINKAYA
(Sun Nov 28 2004 - 16:59:27 PST)
Re: AMBER: extracting energy from trajector?
David Smith
(Mon Nov 29 2004 - 04:37:41 PST)
Re: AMBER: extracting energy from trajector?
David Smith
(Mon Nov 29 2004 - 05:04:52 PST)
Re: AMBER: extracting energy from trajector?
MURAT CETINKAYA
(Mon Nov 29 2004 - 07:31:14 PST)
Re: AMBER: extracting energy from trajector?
David Smith
(Mon Nov 29 2004 - 08:54:53 PST)
Re: AMBER: extracting energy from trajector?
MURAT CETINKAYA
(Mon Nov 29 2004 - 09:20:12 PST)
Re: AMBER: extracting energy from trajector?
David Smith
(Mon Nov 29 2004 - 09:39:30 PST)
Re: AMBER: extracting energy from trajector?
Bill Ross
(Wed Nov 24 2004 - 10:50:30 PST)
Re: AMBER: extracting energy from trajector?
Carlos Simmerling
(Wed Nov 24 2004 - 11:07:12 PST)
AMBER: nucgen problem
opitz.che.udel.edu
(Wed Nov 24 2004 - 14:08:52 PST)
Re: AMBER: nucgen problem
david.evans.ulsop.ac.uk
(Thu Nov 25 2004 - 01:04:28 PST)
Re: AMBER: nucgen problem
Bill Ross
(Thu Nov 25 2004 - 09:08:14 PST)
AMBER: Regarding Dielectric Constant in AMBER8
pande.vineet.fc.up.pt
(Thu Nov 25 2004 - 07:22:41 PST)
Re: AMBER: Regarding Dielectric Constant in AMBER8
Carlos Simmerling
(Thu Nov 25 2004 - 07:50:12 PST)
Re: AMBER: Regarding Dielectric Constant in AMBER8
pande.vineet.fc.up.pt
(Thu Nov 25 2004 - 08:03:27 PST)
Re: AMBER: Regarding Dielectric Constant in AMBER8
Carlos Simmerling
(Thu Nov 25 2004 - 08:45:34 PST)
Re: AMBER: Regarding Dielectric Constant in AMBER8
pande.vineet.fc.up.pt
(Fri Nov 26 2004 - 00:45:50 PST)
Re: AMBER: Regarding Dielectric Constant in AMBER8
Carlos Simmerling
(Fri Nov 26 2004 - 06:02:56 PST)
Re: AMBER: Regarding Dielectric Constant in AMBER8
pande.vineet.fc.up.pt
(Fri Nov 26 2004 - 08:35:43 PST)
Re: AMBER: Regarding Dielectric Constant in AMBER8
pande.vineet.fc.up.pt
(Fri Nov 26 2004 - 08:45:47 PST)
Re: AMBER: Regarding Dielectric Constant in AMBER8
Carlos Simmerling
(Fri Nov 26 2004 - 08:55:48 PST)
Re: AMBER: Regarding Dielectric Constant in AMBER8
pande.vineet.fc.up.pt
(Fri Nov 26 2004 - 10:59:19 PST)
Re: AMBER: Regarding Dielectric Constant in AMBER8
Carlos Simmerling
(Fri Nov 26 2004 - 11:24:59 PST)
Re: AMBER: question about molsurf
Chris Page
(Thu Nov 25 2004 - 10:45:28 PST)
AMBER: combine crd files
bybaker.itsa.ucsf.edu
(Fri Nov 26 2004 - 14:54:43 PST)
Re: AMBER: combine crd files
Furse, Kristina Elisabet
(Fri Nov 26 2004 - 15:42:09 PST)
Re: AMBER: combine crd files
Carlos Simmerling
(Fri Nov 26 2004 - 16:03:28 PST)
AMBER: sander.QMMM on Mac
justin litchfield
(Fri Nov 26 2004 - 15:17:35 PST)
RE: AMBER: sander.QMMM on Mac
Ross Walker
(Fri Nov 26 2004 - 17:56:56 PST)
Re: AMBER: sander.QMMM on Mac
justin litchfield
(Sat Nov 27 2004 - 00:29:26 PST)
AMBER: Protein with maximum hydrogen bonds
anshul.imtech.res.in
(Sat Nov 27 2004 - 09:23:43 PST)
RE: AMBER: Protein with maximum hydrogen bonds
Ross Walker
(Fri Nov 26 2004 - 23:15:34 PST)
Re: AMBER: Protein with maximum hydrogen bonds
pande.vineet.fc.up.pt
(Sat Nov 27 2004 - 06:13:58 PST)
Re: AMBER: Protein with maximum hydrogen bonds
Sanjeev B.S.
(Sat Nov 27 2004 - 07:14:01 PST)
AMBER: About Disulfer bond
Xiao He
(Sat Nov 27 2004 - 00:11:00 PST)
Re: AMBER: About Disulfer bond
David A. Case
(Sat Nov 27 2004 - 10:05:28 PST)
Fwd: Re: AMBER: Protein with maximum hydrogen bonds
pande.vineet.fc.up.pt
(Sat Nov 27 2004 - 06:19:31 PST)
AMBER: xfl90 and xlc "C" compiler
Dr. Noah Allen
(Sat Nov 27 2004 - 12:05:28 PST)
Re: AMBER: xfl90 and xlc "C" compiler
justin litchfield
(Sat Nov 27 2004 - 12:42:22 PST)
AMBER: GO lie Amber simulation
Alena Shmygelska
(Sat Nov 27 2004 - 13:48:53 PST)
Re: AMBER: GO lie Amber simulation
David A. Case
(Sat Nov 27 2004 - 15:37:45 PST)
AMBER: saving trajectory parameters
Ed Pate
(Sat Nov 27 2004 - 16:17:40 PST)
RE: AMBER: saving trajectory parameters
Ross Walker
(Sat Nov 27 2004 - 16:52:03 PST)
AMBER: MD run: frozen
bybaker.itsa.ucsf.edu
(Sat Nov 27 2004 - 22:17:36 PST)
RE: AMBER: MD run: frozen
Ross Walker
(Sat Nov 27 2004 - 23:00:37 PST)
Re: AMBER: MD run: frozen
Carlos Simmerling
(Sun Nov 28 2004 - 07:32:25 PST)
Re: AMBER: MD run: frozen
bybaker.itsa.ucsf.edu
(Sun Nov 28 2004 - 16:39:30 PST)
AMBER: FEP - GIBBS of charged sidechains using IELPER
Annette Höglund
(Sun Nov 28 2004 - 09:26:06 PST)
Re: AMBER: FEP - GIBBS of charged sidechains using IELPER
David A. Case
(Sun Nov 28 2004 - 15:28:43 PST)
AMBER: question!
Marsita M
(Sun Nov 28 2004 - 19:01:41 PST)
AMBER: problem in quasih.f diagonalising matrix
Phineus Markwick
(Mon Nov 29 2004 - 05:14:35 PST)
Re: AMBER: problem in quasih.f diagonalising matrix
David A. Case
(Mon Nov 29 2004 - 08:38:46 PST)
AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem)
Hannes Barsch
(Mon Nov 29 2004 - 09:02:15 PST)
AMBER: Restrained minimization problem
opitz.che.udel.edu
(Mon Nov 29 2004 - 14:11:56 PST)
Re: AMBER: Restrained minimization problem
Bill Ross
(Mon Nov 29 2004 - 14:31:54 PST)
Re: AMBER: Restrained minimization problem
opitz.che.udel.edu
(Mon Nov 29 2004 - 14:50:14 PST)
Re: AMBER: Restrained minimization problem
opitz.che.udel.edu
(Mon Nov 29 2004 - 14:56:47 PST)
Re: AMBER: Restrained minimization problem
David A. Case
(Mon Nov 29 2004 - 15:27:41 PST)
AMBER: increasing the maximum value of NPHB parameter
Alena Shmygelska
(Mon Nov 29 2004 - 21:05:08 PST)
Re: AMBER: increasing the maximum value of NPHB parameter
David A. Case
(Tue Nov 30 2004 - 17:58:59 PST)
Re: AMBER: Restrained minimization problem
Thomas E. Cheatham, III
(Mon Nov 29 2004 - 15:02:44 PST)
Re: AMBER: Restrained minimization problem
Bill Ross
(Mon Nov 29 2004 - 15:25:58 PST)
Re: AMBER: Restrained minimization problem
Furse, Kristina Elisabet
(Mon Nov 29 2004 - 15:32:28 PST)
AMBER: Slowly releasing restraints
Marcin Krol
(Tue Nov 30 2004 - 03:12:37 PST)
Re: AMBER: Slowly releasing restraints
David A. Case
(Tue Nov 30 2004 - 11:55:40 PST)
AMBER: amber8 parallel installation with mpich
cailliez
(Tue Nov 30 2004 - 04:24:41 PST)
Re: AMBER: amber8 parallel installation with mpich
Marc Baaden
(Tue Nov 30 2004 - 04:00:26 PST)
Re: AMBER: amber8 parallel installation with mpich
Marc Baaden
(Tue Nov 30 2004 - 04:27:18 PST)
AMBER: problem loading mdcrd to VMD
Ru-Zhen Li
(Tue Nov 30 2004 - 04:59:40 PST)
Re: AMBER: problem loading mdcrd to VMD
Stefano.Pieraccini.unimi.it
(Tue Nov 30 2004 - 06:04:07 PST)
Re: AMBER: problem loading mdcrd to VMD
David Smith
(Tue Nov 30 2004 - 06:19:24 PST)
Re: AMBER: problem loading mdcrd to VMD
Ru-Zhen Li
(Tue Nov 30 2004 - 09:05:57 PST)
Re: AMBER: problem loading mdcrd to VMD
David Smith
(Tue Nov 30 2004 - 09:44:16 PST)
Re: AMBER: problem loading mdcrd to VMD
myang.vitamin.uni.cc
(Tue Nov 30 2004 - 10:48:43 PST)
Re: AMBER: problem loading mdcrd to VMD
Ru-Zhen Li
(Tue Nov 30 2004 - 15:17:08 PST)
AMBER: memory prolem of the nmode calculation
Xiao Jian Tan
(Tue Nov 30 2004 - 15:24:18 PST)
Re: AMBER: memory prolem of the nmode calculation
David A. Case
(Tue Nov 30 2004 - 17:40:29 PST)
Re: AMBER: problem loading mdcrd to VMD
David E. Konerding
(Tue Nov 30 2004 - 07:45:59 PST)
Re: AMBER: problem loading mdcrd to VMD
John Bushnell
(Tue Nov 30 2004 - 14:41:14 PST)
AMBER: Implicit 4r md
yen li
(Tue Nov 30 2004 - 08:58:34 PST)
AMBER: Re: AMBER: problem loading mdcrd to VMD
Dawsonzhu.aol.com
(Tue Nov 30 2004 - 15:03:46 PST)
Last message date
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Wed Dec 01 2004 - 02:53:00 PST
Archived on
: Wed Apr 17 2024 - 05:53:16 PDT
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