Amber Archive Nov 2002: by subject

(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
- St�phane Teletch�a (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)
- St�phane Teletch�a (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 Leit�o (Thu Nov 14 2002 - 10:13:01 PST)
- Andrei Leit�o (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
- St�phane Teletch�a (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
- St�phane Teletch�a (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 R�a (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)

Amber Archive Nov 2002 by subject