Amber Archive Nov 2002: by author

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

Amber Archive Nov 2002 by author