Amber Archive Nov 2002 by subject
234 messages
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Starting
Fri Nov 01 2002 - 01:08:20 PST,
Ending
Fri Nov 29 2002 - 13:06:36 PST
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(no subject)
Narang Manpreet Kaur
(Fri Nov 29 2002 - 02:54:03 PST)
CHAUMONT Alain
(Mon Nov 25 2002 - 07:32:50 PST)
Narang Manpreet Kaur
(Sat Nov 23 2002 - 02:40:12 PST)
Narang Manpreet Kaur
(Sat Nov 16 2002 - 02:17:02 PST)
Monica
(Wed Nov 13 2002 - 22:26:57 PST)
.top files read into xLeap?
David A. Case
(Mon Nov 11 2002 - 18:20:41 PST)
Arvid Soederhaell
(Mon Nov 11 2002 - 02:24:00 PST)
a second question
Ioana Cozmuta
(Mon Nov 25 2002 - 16:20:52 PST)
Amber on PC-Linux
Philippe Aplincourt
(Thu Nov 14 2002 - 07:22:20 PST)
amber on RH8
Scott Brozell
(Thu Nov 07 2002 - 13:13:14 PST)
Amber Perl module
Michael Ford
(Thu Nov 14 2002 - 15:26:24 PST)
Luis Gracia
(Thu Nov 14 2002 - 13:55:25 PST)
Tod Pascal
(Thu Nov 14 2002 - 13:33:01 PST)
Amber7/CYGWIN compiling
James W. Caldwell
(Tue Nov 12 2002 - 13:09:33 PST)
Are posters to the Amber list being spammed?
Nicholson, James D Mr ARO
(Sun Nov 17 2002 - 17:48:15 PST)
atom type not recognized by GB
eric hu
(Sun Nov 24 2002 - 18:30:17 PST)
David A. Case
(Sun Nov 24 2002 - 17:50:01 PST)
eric hu
(Sun Nov 24 2002 - 17:05:59 PST)
average and runningaverage in ptraj
Thomas Cheatham
(Wed Nov 06 2002 - 09:36:56 PST)
Holger Gohlke
(Wed Nov 06 2002 - 08:56:23 PST)
Vlad Cojocaru
(Wed Nov 06 2002 - 07:40:51 PST)
averaging with ptraj and carnal
Vlad Cojocaru
(Fri Nov 08 2002 - 04:31:03 PST)
belly and EWALD in amber7
Zhang Jian
(Sun Nov 10 2002 - 17:36:25 PST)
darden
(Sun Nov 10 2002 - 14:25:31 PST)
Zhang Jian
(Sat Nov 09 2002 - 19:04:14 PST)
belly and ivcap conflict in gibbs
David A. Case
(Sun Nov 10 2002 - 14:35:16 PST)
Break down energy contributions
Numan Oezguen
(Fri Nov 29 2002 - 13:06:36 PST)
Bugfixes
William Wei
(Wed Nov 06 2002 - 01:50:35 PST)
Bulk Email Sending & Bullet Proof Web Hosting
pposton
(Wed Nov 20 2002 - 14:25:53 PST)
C60 parameter
Pascal Bonnet
(Thu Nov 28 2002 - 04:12:19 PST)
vannajan_at_chiangmai.ac.th
(Thu Nov 28 2002 - 00:47:47 PST)
Calculating atomic charges for AMBER with Gaussian98W
M. L. Dodson
(Sat Nov 23 2002 - 07:36:27 PST)
Thomas Steinbrecher
(Sat Nov 23 2002 - 05:52:47 PST)
carnal
Stéphane Teletchéa
(Mon Nov 04 2002 - 02:09:10 PST)
carnal output trajectory
Francesca Mocci
(Fri Nov 01 2002 - 08:53:31 PST)
carnal7 produces memory fault and a core
Giulio Rastelli
(Sat Nov 09 2002 - 08:21:10 PST)
CCl4 as solvent
Aldo Jongejan
(Tue Nov 05 2002 - 05:44:02 PST)
choose dt in gibbs
sxzheng
(Sun Nov 17 2002 - 19:06:34 PST)
CMM method
David A. Case
(Wed Nov 13 2002 - 16:42:26 PST)
Ioana Cozmuta
(Wed Nov 13 2002 - 14:57:10 PST)
Conterions
David Case
(Sat Nov 16 2002 - 11:45:01 PST)
Monica
(Sat Nov 16 2002 - 00:10:15 PST)
creating a pdb trajectory with carnal
Vlad Cojocaru
(Mon Nov 18 2002 - 07:29:21 PST)
defining groups on dif. sets in carnal
Vlad Cojocaru
(Tue Nov 19 2002 - 02:59:06 PST)
drifting from average structure
Vlad Cojocaru
(Sat Nov 09 2002 - 08:17:38 PST)
entropy calcs in mm_pbsa
Holger Gohlke
(Tue Nov 05 2002 - 13:27:39 PST)
giulio_at_unimo.it
(Tue Nov 05 2002 - 12:21:00 PST)
Equilibration output Amber7
Thomas Cheatham
(Fri Nov 22 2002 - 09:49:55 PST)
Fredrick Robin Devadoss
(Fri Nov 22 2002 - 01:42:32 PST)
equilibrium problem about cut and belly
Thomas Steinbrecher
(Tue Nov 05 2002 - 09:24:54 PST)
David A. Case
(Tue Nov 05 2002 - 08:14:51 PST)
Error in Equilibration
Fredrick Robin Devadoss
(Tue Nov 26 2002 - 02:14:12 PST)
error in reading .crd file with GIBBS
hagop demirdjian
(Thu Nov 14 2002 - 07:40:32 PST)
Error running AMBER6 on Beowulf cluster
Carlos Simmerling
(Fri Nov 22 2002 - 15:33:49 PST)
arubin_at_unmc.edu
(Fri Nov 22 2002 - 13:38:12 PST)
David A. Case
(Thu Nov 21 2002 - 17:31:47 PST)
arubin_at_unmc.edu
(Thu Nov 21 2002 - 15:10:39 PST)
esp.sh problem
FyD
(Thu Nov 28 2002 - 00:03:33 PST)
David A. Case
(Wed Nov 27 2002 - 11:12:54 PST)
David Smith
(Wed Nov 27 2002 - 10:13:09 PST)
FyD
(Wed Nov 27 2002 - 09:17:40 PST)
Ewald
David A. Case
(Wed Nov 13 2002 - 08:09:08 PST)
Monica
(Wed Nov 13 2002 - 07:20:23 PST)
EWALD crash
David A. Case
(Mon Nov 18 2002 - 16:27:37 PST)
external electric field
Ioana Cozmuta
(Mon Nov 25 2002 - 15:18:38 PST)
external electric field/another try
James W. Caldwell
(Wed Nov 27 2002 - 15:31:24 PST)
darden
(Wed Nov 27 2002 - 15:27:32 PST)
Ioana Cozmuta
(Wed Nov 27 2002 - 14:13:08 PST)
FEP/Gibbs question
meiselba
(Tue Nov 19 2002 - 07:29:07 PST)
flag TREE_CHAIN_CLASSIFICATION in topology file from amber7
David A. Case
(Fri Nov 01 2002 - 05:51:26 PST)
Pascal Bonnet
(Fri Nov 01 2002 - 01:08:20 PST)
Forwarded mail....
David A. Case
(Sun Nov 10 2002 - 14:40:19 PST)
Narang Manpreet Kaur
(Sat Nov 09 2002 - 01:56:37 PST)
Frictional forces in gB
Kristina Furse
(Tue Nov 19 2002 - 15:41:32 PST)
GIBBS - Error message.
David A. Case
(Tue Nov 19 2002 - 09:09:09 PST)
Miguel de Federico
(Tue Nov 19 2002 - 08:00:25 PST)
GIBBS - ERROR: Restraint read error from RSTIN; Check format:
David A. Case
(Tue Nov 26 2002 - 15:30:52 PST)
Miguel de Federico
(Tue Nov 26 2002 - 01:14:19 PST)
help on VMD movie
Zhang Jian
(Wed Nov 13 2002 - 17:40:14 PST)
Zhang Jian
(Wed Nov 13 2002 - 07:21:30 PST)
Francesca Mocci
(Wed Nov 13 2002 - 06:28:06 PST)
Stéphane Teletchéa
(Wed Nov 13 2002 - 05:12:58 PST)
Zhang Jian
(Wed Nov 13 2002 - 04:44:36 PST)
help! Non bond list overflow!
Jian Zhang
(Wed Nov 13 2002 - 18:32:01 PST)
Zhang Jian
(Wed Nov 13 2002 - 18:10:02 PST)
David A. Case
(Wed Nov 13 2002 - 16:51:07 PST)
Zhang Jian
(Wed Nov 13 2002 - 02:56:39 PST)
How Amber calculates electrostatic energy?
Daniel Svozil
(Wed Nov 27 2002 - 06:47:11 PST)
Hydrophobic protein in water
Luo Liu
(Sun Nov 24 2002 - 14:52:20 PST)
input format for gibbs restraints
Jose Ramon Blas
(Wed Nov 13 2002 - 18:59:43 PST)
David A. Case
(Wed Nov 13 2002 - 17:53:27 PST)
Inquiry
software_at_kagaku.com
(Sun Nov 24 2002 - 19:44:51 PST)
intdiel & extdiel
Holger Gohlke
(Thu Nov 21 2002 - 07:55:15 PST)
Fredrick Robin Devadoss
(Wed Nov 20 2002 - 20:28:35 PST)
David A. Case
(Wed Nov 20 2002 - 07:51:44 PST)
Fredrick Robin Devadoss
(Wed Nov 20 2002 - 03:23:59 PST)
ion distances
Bill Ross
(Mon Nov 25 2002 - 16:51:46 PST)
Thomas E. Cheatham, III
(Thu Nov 21 2002 - 15:54:46 PST)
남기엽
(Thu Nov 21 2002 - 14:52:55 PST)
Marcela Madrid
(Thu Nov 21 2002 - 12:59:12 PST)
leap for peptide
Sichun Yang
(Fri Nov 22 2002 - 14:33:51 PST)
limit of RMSD value
Thomas Cheatham
(Tue Nov 19 2002 - 09:51:53 PST)
Bimo Ario Tejo
(Tue Nov 19 2002 - 05:57:40 PST)
Linmin question...
David A. Case
(Fri Nov 15 2002 - 00:12:20 PST)
Andrei Leitão
(Thu Nov 14 2002 - 10:13:01 PST)
Andrei Leitão
(Thu Nov 14 2002 - 10:10:21 PST)
makeDIST_RST?
David A. Case
(Mon Nov 18 2002 - 16:15:35 PST)
Sichun Yang
(Mon Nov 18 2002 - 15:44:09 PST)
MEP g98_option
Pascal Bonnet
(Mon Nov 11 2002 - 03:05:55 PST)
FyD
(Fri Nov 08 2002 - 22:35:22 PST)
molsurf reference
David A. Case
(Fri Nov 01 2002 - 05:46:21 PST)
Giulio Rastelli
(Fri Nov 01 2002 - 04:17:35 PST)
more about averaging
Bill Ross
(Fri Nov 08 2002 - 13:21:39 PST)
Vlad Cojocaru
(Fri Nov 08 2002 - 06:12:00 PST)
NATOM mismatch in coord and topology files.
Narang Manpreet Kaur
(Sun Nov 17 2002 - 22:49:46 PST)
nbflag
Ioana Cozmuta
(Wed Nov 06 2002 - 19:45:02 PST)
Ioana Cozmuta
(Wed Nov 06 2002 - 19:19:26 PST)
NMR restraints on a 10-mer DNA in Sander
David A. Case
(Tue Nov 12 2002 - 15:30:52 PST)
Michael G Cooney
(Tue Nov 12 2002 - 12:16:32 PST)
Jo.Vinje_at_kj.uib.no
(Tue Nov 12 2002 - 09:34:55 PST)
non-zero 10-12 coefficient
Anonymous
(Thu Nov 14 2002 - 16:18:34 PST)
nonpeoridic boundary + mm/gbsa
Holger Gohlke
(Mon Nov 11 2002 - 08:59:27 PST)
Yongjun Jiang
(Mon Nov 11 2002 - 04:49:03 PST)
ntx=7, irest=0
David A. Case
(Fri Nov 22 2002 - 18:36:28 PST)
Marcela Madrid
(Fri Nov 22 2002 - 15:56:00 PST)
ntx=7, irest=0, redux
David Case
(Fri Nov 22 2002 - 22:53:37 PST)
Nz-Acetyllysine parameters
Luis Gracia
(Tue Nov 19 2002 - 16:08:13 PST)
P.3 in antechamber
Giulio Rastelli
(Thu Nov 21 2002 - 03:02:16 PST)
P4_GLOBMEMSIZE problem
Ross Walker
(Tue Nov 05 2002 - 15:04:03 PST)
Jean-Christophe Ducom
(Tue Nov 05 2002 - 09:53:11 PST)
Ross Walker
(Tue Nov 05 2002 - 09:16:55 PST)
Jean-Christophe Ducom
(Mon Nov 04 2002 - 09:33:19 PST)
parameters for cyclic nucleotides
Thomas.Fox_at_bc.boehringer-ingelheim.com
(Fri Nov 29 2002 - 02:11:43 PST)
parmchk -p option
Thomas.Fox_at_bc.boehringer-ingelheim.com
(Fri Nov 29 2002 - 02:09:09 PST)
PARMSET
John Bushnell
(Thu Nov 21 2002 - 14:32:25 PST)
David A. Case
(Thu Nov 21 2002 - 08:13:38 PST)
Ross Walker
(Thu Nov 21 2002 - 06:30:36 PST)
sara nunez
(Thu Nov 21 2002 - 06:08:12 PST)
pdb file
Ioana Cozmuta
(Fri Nov 22 2002 - 17:44:22 PST)
Ioana Cozmuta
(Fri Nov 22 2002 - 16:41:01 PST)
periodic box
David A. Case
(Mon Nov 04 2002 - 10:32:11 PST)
Craig A Bayse
(Mon Nov 04 2002 - 08:49:53 PST)
Please help. Energy suddenly increase. Protein jump out
Yong Duan
(Wed Nov 27 2002 - 14:52:54 PST)
Carlos Simmerling
(Wed Nov 27 2002 - 13:35:15 PST)
Yong Duan
(Wed Nov 27 2002 - 10:42:39 PST)
David A. Case
(Wed Nov 27 2002 - 08:26:55 PST)
Lich Nguyen
(Tue Nov 26 2002 - 23:42:29 PST)
polarizabitlity
X. Tan
(Tue Nov 19 2002 - 10:08:31 PST)
David A. Case
(Mon Nov 18 2002 - 16:44:10 PST)
X. Tan
(Fri Nov 15 2002 - 17:41:37 PST)
Problem
David Case
(Fri Nov 29 2002 - 11:49:20 PST)
Monica
(Thu Nov 28 2002 - 22:35:19 PST)
problem about cut and cap
sxzheng
(Sun Nov 03 2002 - 04:40:25 PST)
problem in PME
David A. Case
(Tue Nov 12 2002 - 15:16:52 PST)
Kristina Furse
(Tue Nov 12 2002 - 08:43:03 PST)
David A. Case
(Tue Nov 12 2002 - 06:06:47 PST)
Monica
(Tue Nov 12 2002 - 05:42:21 PST)
problem in restrt
Thomas Cheatham
(Fri Nov 22 2002 - 09:55:27 PST)
Marcela Madrid
(Fri Nov 22 2002 - 08:37:53 PST)
Problem in run
David Case
(Fri Nov 08 2002 - 23:33:27 PST)
Monica Jain
(Fri Nov 08 2002 - 22:52:46 PST)
Monica
(Fri Nov 08 2002 - 20:41:52 PST)
procheck
David A. Case
(Tue Nov 05 2002 - 08:31:31 PST)
hung_at_atc.atccu.chula.ac.th
(Mon Nov 04 2002 - 22:53:56 PST)
pseudoatoms and NMR restraints
David A. Case
(Tue Nov 05 2002 - 08:06:07 PST)
david
(Tue Nov 05 2002 - 01:46:42 PST)
question
Stéphane Teletchéa
(Tue Nov 19 2002 - 04:43:04 PST)
Yong Duan
(Fri Nov 15 2002 - 20:40:56 PST)
Ioana Cozmuta
(Fri Nov 15 2002 - 19:22:13 PST)
David A. Case
(Fri Nov 15 2002 - 18:45:34 PST)
ramdomized start velocities
James W. Caldwell
(Fri Nov 08 2002 - 12:35:39 PST)
Andy Purkiss
(Fri Nov 08 2002 - 11:28:46 PST)
David A. Case
(Fri Nov 08 2002 - 11:20:54 PST)
Arvid Soederhaell
(Fri Nov 08 2002 - 04:35:23 PST)
residue cross-correlation
Stéphane Teletchéa
(Tue Nov 12 2002 - 02:57:10 PST)
Thomas Cheatham
(Fri Nov 08 2002 - 12:50:42 PST)
Andreas Svrcek-Seiler
(Fri Nov 08 2002 - 12:16:59 PST)
Bimo Ario Tejo
(Fri Nov 08 2002 - 10:57:48 PST)
Bimo Ario Tejo
(Fri Nov 08 2002 - 07:00:01 PST)
restart
David A. Case
(Mon Nov 04 2002 - 13:59:15 PST)
Ioana Cozmuta
(Mon Nov 04 2002 - 12:57:16 PST)
restart mm_pbsa
Pascal Bonnet
(Thu Nov 14 2002 - 07:13:06 PST)
Lepsa
(Thu Nov 14 2002 - 05:52:22 PST)
Layi Adekoya
(Thu Nov 14 2002 - 05:02:51 PST)
restarting simulation
Marcela Madrid
(Fri Nov 22 2002 - 14:07:47 PST)
Carlos Simmerling
(Fri Nov 22 2002 - 12:56:24 PST)
Marcela Madrid
(Fri Nov 22 2002 - 12:06:42 PST)
restrain a residue as center of mass
Carlos Simmerling
(Wed Nov 27 2002 - 13:38:57 PST)
Carlos Simmerling
(Wed Nov 27 2002 - 13:34:00 PST)
eric hu
(Wed Nov 27 2002 - 10:42:36 PST)
Carlos Simmerling
(Tue Nov 26 2002 - 16:17:58 PST)
eric hu
(Tue Nov 26 2002 - 15:36:19 PST)
Restraint Ambiguities
David A. Case
(Fri Nov 22 2002 - 08:33:34 PST)
Neema Salimi
(Thu Nov 21 2002 - 20:37:13 PST)
David A. Case
(Thu Nov 21 2002 - 18:08:04 PST)
Neema Salimi
(Thu Nov 21 2002 - 14:56:44 PST)
restrt format problem
Marcela Madrid
(Wed Nov 06 2002 - 14:48:02 PST)
Roar capabilities
M. L. Dodson
(Fri Nov 08 2002 - 09:37:48 PST)
RUNMIN
Ioana Cozmuta
(Mon Nov 04 2002 - 17:37:08 PST)
hung_at_atc.atccu.chula.ac.th
(Mon Nov 04 2002 - 17:04:23 PST)
Sander: check COM velocity, temp: 0.000000 0.00(Removed)
David Case
(Fri Nov 08 2002 - 23:17:18 PST)
Thomas Cheatham
(Fri Nov 08 2002 - 21:49:21 PST)
Miguel de Federico de la Rúa
(Fri Nov 08 2002 - 06:08:38 PST)
saveAmberParm of leap
David A. Case
(Mon Nov 11 2002 - 16:05:15 PST)
Sichun Yang
(Mon Nov 11 2002 - 11:27:16 PST)
simulating dna
David A. Case
(Mon Nov 18 2002 - 16:29:22 PST)
Tod Pascal
(Fri Nov 15 2002 - 17:23:54 PST)
Snapshot stuff
Layi Adekoya
(Tue Nov 05 2002 - 06:32:11 PST)
solvateOct
David A. Case
(Tue Nov 26 2002 - 15:51:31 PST)
Kristina Furse
(Tue Nov 26 2002 - 14:51:52 PST)
David A. Case
(Fri Nov 22 2002 - 18:31:03 PST)
Kristina Furse
(Fri Nov 22 2002 - 13:36:33 PST)
surface
Ioana Cozmuta
(Thu Nov 07 2002 - 13:03:56 PST)
targeted MD for more than 2 groups
Carlos Simmerling
(Thu Nov 21 2002 - 15:54:53 PST)
Sichun Yang
(Thu Nov 21 2002 - 13:20:44 PST)
the removal of global motion
David A. Case
(Tue Nov 12 2002 - 16:18:31 PST)
Ioana Cozmuta
(Tue Nov 12 2002 - 15:52:41 PST)
David A. Case
(Tue Nov 12 2002 - 15:25:09 PST)
Shixiang Yan
(Tue Nov 12 2002 - 08:44:38 PST)
the tree name?
David A. Case
(Wed Nov 27 2002 - 14:44:17 PST)
Sichun Yang
(Tue Nov 26 2002 - 19:29:27 PST)
time-averaged restraint developer
Jake Isaacs
(Wed Nov 06 2002 - 14:20:11 PST)
torsion restraints in GIBBS
Jose Ramon Blas
(Tue Nov 05 2002 - 16:35:44 PST)
David A. Case
(Tue Nov 05 2002 - 08:20:57 PST)
total energies during MM-PBSA
Lepsa
(Fri Nov 01 2002 - 09:29:33 PST)
using SHAKE for solvent only
David A. Case
(Mon Nov 25 2002 - 10:17:54 PST)
hagop demirdjian
(Mon Nov 25 2002 - 07:42:57 PST)
Visualizing AMBER coordinates trajectory in VMD
Tom Bishop
(Tue Nov 05 2002 - 03:36:41 PST)
David A. Case
(Mon Nov 04 2002 - 13:57:10 PST)
Pratul Agarwal
(Mon Nov 04 2002 - 12:54:57 PST)
your mail
David Case
(Fri Nov 29 2002 - 12:07:19 PST)
darden
(Sun Nov 24 2002 - 14:46:35 PST)
David Case
(Sat Nov 16 2002 - 07:43:29 PST)
David A. Case
(Thu Nov 14 2002 - 08:00:48 PST)
Last message date
:
Fri Nov 29 2002 - 13:06:36 PST
Archived on
: Fri Dec 13 2024 - 05:53:18 PST
234 messages
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