Amber Archive Sep 2002: by subject

(no subject)
- Apostoluk, Wlodzimierz K (Wed Sep 25 2002 - 12:09:53 PDT)
a freeware to display RMSD matrices
- CUI, Guanglei (Thu Sep 19 2002 - 06:42:29 PDT)
- Vlad Cojocaru (Thu Sep 19 2002 - 05:44:53 PDT)
about amber and charmm, thanks
- Zhang Jian (Sun Sep 08 2002 - 02:10:57 PDT)
additional info
- Ioana Cozmuta (Sun Sep 01 2002 - 11:44:32 PDT)
amber
- K.Veluraja (Sun Sep 15 2002 - 22:14:04 PDT)
Amber 7 and 6 topology files.
- James W. Caldwell (Mon Sep 30 2002 - 08:41:25 PDT)
- Miguel de Federico (Mon Sep 30 2002 - 08:08:36 PDT)
amber question
- James W. Caldwell (Mon Sep 16 2002 - 10:24:20 PDT)
- David A. Case (Mon Sep 16 2002 - 09:47:03 PDT)
- yao yong (Mon Sep 16 2002 - 04:03:16 PDT)
Amber Reflector
- James W. Caldwell (Thu Sep 26 2002 - 10:47:58 PDT)
amber7 compilation on irix6.4 mp
- K.Seshadri (Mon Sep 09 2002 - 10:44:13 PDT)
ambpdb?
- Lepsa (Wed Sep 25 2002 - 01:29:25 PDT)
- Arvid Soederhaell (Wed Sep 25 2002 - 00:38:34 PDT)
Anal Error : Group
- Lifeng Tian (Fri Sep 27 2002 - 15:35:23 PDT)
antechamber best practices/charge equivalence w/ AM1-BCC
- Bayly, Christopher (Tue Sep 24 2002 - 07:49:56 PDT)
- Tom Bishop (Mon Sep 23 2002 - 14:28:57 PDT)
assistance required
- amit kumar (Mon Sep 16 2002 - 09:25:05 PDT)
atoms coming too close during MD (with SHAKE on)
- Pratul Agarwal (Mon Sep 02 2002 - 18:01:18 PDT)
Beowulf killing jobs
- Ross Walker (Mon Sep 16 2002 - 07:46:45 PDT)
- Peter Gannett (Fri Sep 13 2002 - 14:03:19 PDT)
betaP,SURFOFF inconsistency
- Holger Gohlke (Sun Sep 22 2002 - 13:20:03 PDT)
binding site volume
- Michal Otyepka (Fri Sep 13 2002 - 00:13:08 PDT)
- Shixiang Yan (Thu Sep 12 2002 - 16:38:41 PDT)
BLOWUP after 100 ns???
- Randy M. Wadkins (Thu Sep 19 2002 - 18:41:16 PDT)
- David A. Case (Thu Sep 19 2002 - 17:29:58 PDT)
- Randy M. Wadkins (Thu Sep 19 2002 - 14:39:48 PDT)
- Randy M. Wadkins (Thu Sep 19 2002 - 13:51:28 PDT)
bondbydistance
- Nicholson, James D Mr ARO (Sat Sep 07 2002 - 17:16:28 PDT)
- case (Fri Sep 06 2002 - 17:04:02 PDT)
- eric hu (Thu Sep 05 2002 - 16:20:43 PDT)
BondEn shoots in solvent minimization
- suvendu lomash (Mon Sep 30 2002 - 08:50:39 PDT)
bug in New2oldparm
- David A. Case (Thu Sep 19 2002 - 08:28:30 PDT)
- Pascal Bonnet (Thu Sep 19 2002 - 03:35:46 PDT)
carnal averaging
- Holger Gohlke (Mon Sep 02 2002 - 13:43:52 PDT)
- Vlad Cojocaru (Mon Sep 02 2002 - 04:43:33 PDT)
Carnal+HBond confusion
- Sanjeev B.S. (Tue Sep 24 2002 - 05:13:05 PDT)
- Sanjeev B.S. (Wed Sep 18 2002 - 21:18:36 PDT)
Changing MAXINT
- Ross Walker (Mon Sep 16 2002 - 07:39:36 PDT)
- John Bushnell (Fri Sep 13 2002 - 15:38:52 PDT)
- Joel Konkle-Parker (Thu Sep 12 2002 - 16:21:13 PDT)
compile Moil-View, GL header files
- Renee olano (Tue Sep 03 2002 - 09:54:57 PDT)
- Jianhui Wu (Tue Sep 03 2002 - 08:20:09 PDT)
compiling amber 7 with Intel Fortran Compiler 6.0
- James W. Caldwell (Wed Sep 25 2002 - 13:58:04 PDT)
- James W. Caldwell (Wed Sep 25 2002 - 13:16:48 PDT)
- Scott Brozell (Wed Sep 25 2002 - 13:05:45 PDT)
- ramon kleber da rocha (Wed Sep 25 2002 - 12:23:21 PDT)
compiling amber 7 with Intel Fortran Compiler 6.0 (fwd)
- John Bushnell (Wed Sep 25 2002 - 13:10:50 PDT)
compiling amber on a linux box using DMEM-ALLOC
- James W. Caldwell (Fri Sep 06 2002 - 17:56:42 PDT)
- Scott Brozell (Fri Sep 06 2002 - 17:16:40 PDT)
- John Bushnell (Fri Sep 06 2002 - 16:43:12 PDT)
- ramon kleber da rocha (Fri Sep 06 2002 - 16:11:55 PDT)
- Florian Barth (Fri Sep 06 2002 - 15:13:31 PDT)
- Scott Brozell (Fri Sep 06 2002 - 15:01:27 PDT)
- ramon kleber da rocha (Fri Sep 06 2002 - 13:46:43 PDT)
compiling without ISTAR2
- Ross Walker (Thu Sep 19 2002 - 10:50:49 PDT)
Constant pressure equilibration in a system with a solvent cap
- David Smith (Fri Sep 27 2002 - 09:11:19 PDT)
- David A. Case (Fri Sep 27 2002 - 08:26:09 PDT)
- James W. Caldwell (Fri Sep 27 2002 - 06:54:46 PDT)
- dianah_at_unm.edu (Thu Sep 26 2002 - 18:04:38 PDT)
cut-off question
- case (Fri Sep 06 2002 - 17:01:28 PDT)
- Cozmuta (Fri Sep 06 2002 - 15:49:21 PDT)
- Ioana Cozmuta (Wed Sep 04 2002 - 12:43:38 PDT)
D-tryptophan
- James W. Caldwell (Sat Sep 14 2002 - 08:21:42 PDT)
- Perdita Barran (Sat Sep 14 2002 - 07:16:45 PDT)
Density during equilibration (sander)
- Pratul Agarwal (Thu Sep 26 2002 - 07:09:02 PDT)
- Marc Dobler (Wed Sep 18 2002 - 00:11:21 PDT)
- Carlos Simmerling (Tue Sep 17 2002 - 18:44:13 PDT)
- Marc Dobler (Tue Sep 17 2002 - 17:29:22 PDT)
- Pratul Agarwal (Tue Sep 17 2002 - 17:22:22 PDT)
- David A. Case (Tue Sep 17 2002 - 12:21:49 PDT)
- Pratul Agarwal (Tue Sep 17 2002 - 09:56:10 PDT)
different counterions for special type of DNA
- Vlad Cojocaru (Thu Sep 26 2002 - 05:59:31 PDT)
Distace dependent dielectric constant
- David A. Case (Thu Sep 12 2002 - 15:39:35 PDT)
- Lorenzo Gontrani (Mon Sep 09 2002 - 01:33:43 PDT)
divalent cations parameters
- Apostoluk, Wlodzimierz K (Mon Sep 30 2002 - 15:38:11 PDT)
DNA Tutorial Script
- Holger Gohlke (Wed Sep 04 2002 - 20:29:23 PDT)
- Joel Konkle-Parker (Wed Sep 04 2002 - 16:18:16 PDT)
Do I have to rerun 1ns MD??
- Lepsa (Mon Sep 23 2002 - 08:50:26 PDT)
- Holger Gohlke (Sun Sep 22 2002 - 12:30:40 PDT)
Dual Processor AMD vs. Single Processor
- St�phane Teletch�a (Thu Sep 12 2002 - 01:09:58 PDT)
- DeLano, Warren (Wed Sep 11 2002 - 17:34:47 PDT)
Dynamic Movement of Molecule
- Thomas Cheatham (Fri Sep 20 2002 - 12:01:39 PDT)
- Yuuki Komata (Fri Sep 20 2002 - 01:03:48 PDT)
ES40 hangs amber7 jobs.
- Sanjeev B.S. (Mon Sep 02 2002 - 19:29:45 PDT)
Escaping Atoms
- case (Thu Sep 05 2002 - 15:04:06 PDT)
- ch cureton (Wed Sep 04 2002 - 03:43:03 PDT)
example 1 problems
- David A. Case (Tue Sep 17 2002 - 07:45:31 PDT)
- James W. Caldwell (Tue Sep 17 2002 - 07:24:30 PDT)
- Alicia Hopkins (Tue Sep 17 2002 - 05:03:53 PDT)
- Natasja Brooijmans (Mon Sep 16 2002 - 09:40:38 PDT)
- David A. Case (Mon Sep 16 2002 - 09:25:54 PDT)
- Alicia Hopkins (Mon Sep 16 2002 - 08:57:23 PDT)
expression of V(lambda) in GIBBS
- David A. Case (Tue Sep 24 2002 - 07:14:01 PDT)
- hagop demirdjian (Tue Sep 24 2002 - 05:44:02 PDT)
GB tutorial
- David A. Case (Thu Sep 26 2002 - 08:31:19 PDT)
GBSA and surface crystal waters
- Raik Grunberg (Tue Sep 10 2002 - 07:44:20 PDT)
group selection for all heavy atoms ?
- Raik Grunberg (Fri Sep 06 2002 - 09:23:33 PDT)
groups in targeted md
- Christoph Brockmann (Mon Sep 30 2002 - 07:48:16 PDT)
- Carlos Simmerling (Mon Sep 30 2002 - 07:04:26 PDT)
- Christoph Brockmann (Mon Sep 30 2002 - 06:15:10 PDT)
Help using moilview to make animations of trajectories
- Nicholson, James D Mr ARO (Fri Sep 13 2002 - 15:15:33 PDT)
How to check whether the trajectory file matches the coordinates file or not?
- Kristina Furse (Mon Sep 09 2002 - 12:32:27 PDT)
- Shixiang Yan (Mon Sep 09 2002 - 11:53:04 PDT)
- Ling Zhang (Mon Sep 09 2002 - 11:31:13 PDT)
how to detect bad contact?
- X. Tan (Wed Sep 04 2002 - 12:14:40 PDT)
image
- David A. Case (Thu Sep 19 2002 - 10:43:32 PDT)
- X. Tan (Thu Sep 19 2002 - 10:32:15 PDT)
Image charges with the solvate cap command
- David A. Case (Mon Sep 30 2002 - 17:34:28 PDT)
- dkeller_at_unm.edu (Mon Sep 30 2002 - 08:52:11 PDT)
Is H-bonding really there?
- Ioana Cozmuta (Fri Sep 27 2002 - 15:04:37 PDT)
- Pratul Agarwal (Fri Sep 27 2002 - 13:58:25 PDT)
- Thomas Cheatham (Fri Sep 27 2002 - 13:53:24 PDT)
- suvendu lomash (Fri Sep 27 2002 - 12:59:48 PDT)
ISTAR2 - oops, just found the answer...
- Mahadevan Seetharaman (Wed Sep 25 2002 - 12:55:46 PDT)
just a test
- Vlad Cojocaru (Wed Sep 11 2002 - 06:39:59 PDT)
large energy fluctration
- eric hu (Fri Sep 20 2002 - 11:00:17 PDT)
- Carlos Simmerling (Thu Sep 12 2002 - 11:50:09 PDT)
- eric hu (Thu Sep 12 2002 - 11:05:10 PDT)
leap and topology file
- Lepsa (Fri Sep 13 2002 - 07:39:45 PDT)
- Marcela Madrid (Thu Sep 12 2002 - 09:12:20 PDT)
loadpdb error messages
- James W. Caldwell (Tue Sep 10 2002 - 16:49:48 PDT)
- Joel Konkle-Parker (Tue Sep 10 2002 - 15:58:07 PDT)
MD Primers
- Peter Gannett (Fri Sep 27 2002 - 16:34:40 PDT)
- Joel Konkle-Parker (Fri Sep 27 2002 - 12:54:03 PDT)
MDaemon Warning - Virus Found
- postmaster_at_96com.com (Fri Sep 13 2002 - 06:13:22 PDT)
- postmaster_at_96com.com (Fri Sep 13 2002 - 06:10:40 PDT)
- postmaster_at_96com.com (Tue Sep 10 2002 - 08:57:00 PDT)
- postmaster_at_96com.com (Mon Sep 09 2002 - 04:04:45 PDT)
- postmaster_at_96com.com (Fri Sep 06 2002 - 04:13:47 PDT)
- postmaster_at_96com.com (Wed Sep 04 2002 - 03:40:26 PDT)
- postmaster_at_96com.com (Tue Sep 03 2002 - 04:57:12 PDT)
- postmaster_at_96com.com (Mon Sep 02 2002 - 04:25:18 PDT)
- postmaster_at_96com.com (Mon Sep 02 2002 - 03:12:42 PDT)
memory allocation in mm_pbsa
- Holger Gohlke (Wed Sep 11 2002 - 08:55:07 PDT)
- James W. Caldwell (Wed Sep 11 2002 - 08:26:19 PDT)
- Giulio Rastelli (Wed Sep 11 2002 - 03:41:04 PDT)
MM-PBSA basics
- Lepsa (Mon Sep 30 2002 - 00:13:16 PDT)
- Holger Gohlke (Sun Sep 29 2002 - 19:44:52 PDT)
- Michael Ford (Fri Sep 27 2002 - 12:53:01 PDT)
mm_pbsa
- David A. Case (Mon Sep 23 2002 - 06:25:02 PDT)
- Mahadevan Seetharaman (Sun Sep 22 2002 - 19:07:27 PDT)
- Holger Gohlke (Sun Sep 22 2002 - 14:01:22 PDT)
- Sue Heavner (Fri Sep 20 2002 - 13:00:36 PDT)
mm_pbsa and statistic program
- David A. Case (Thu Sep 26 2002 - 08:37:15 PDT)
- Pascal Bonnet (Thu Sep 26 2002 - 03:50:52 PDT)
mm_pbsa output error
- Holger Gohlke (Mon Sep 23 2002 - 21:21:30 PDT)
- Michael Murray (Mon Sep 23 2002 - 10:26:11 PDT)
mm_pbsa positive binding energies
- David A. Case (Mon Sep 02 2002 - 10:50:30 PDT)
- Mathy Froeyen (Mon Sep 02 2002 - 02:11:34 PDT)
mm_pbsa question.
- wentaofu (Tue Sep 17 2002 - 08:35:59 PDT)
mol2 file format in the future of amber
- M. L. Dodson (Sun Sep 22 2002 - 08:34:06 PDT)
- David A. Case (Sun Sep 22 2002 - 08:10:42 PDT)
- M. L. Dodson (Fri Sep 20 2002 - 07:41:02 PDT)
Mopac509mn/linux
- James W. Caldwell (Tue Sep 24 2002 - 08:00:20 PDT)
mpirun
- Ross Walker (Sun Sep 01 2002 - 15:36:24 PDT)
- Ioana Cozmuta (Sun Sep 01 2002 - 11:32:08 PDT)
new2oldparm format (2)
- Pascal Bonnet (Thu Sep 19 2002 - 03:43:39 PDT)
nmanal help request
- David A. Case (Fri Sep 27 2002 - 08:38:23 PDT)
- Peter Fojan (Fri Sep 27 2002 - 06:59:11 PDT)
nmode compile question?
- James W. Caldwell (Tue Sep 10 2002 - 11:04:07 PDT)
- Holger Gohlke (Tue Sep 10 2002 - 09:17:24 PDT)
- Yongjun Jiang (Tue Sep 10 2002 - 05:46:18 PDT)
non-bonded metal ion in complex
- Pratul Agarwal (Tue Sep 17 2002 - 06:59:14 PDT)
- yuann (Mon Sep 16 2002 - 23:28:45 PDT)
NTX value
- giudice (Mon Sep 02 2002 - 00:05:45 PDT)
offset of temperature when running MD with CAP and no periodic conditions
- Andreas Svrcek-Seiler (Thu Sep 19 2002 - 10:11:31 PDT)
- Therese Malliavin (Thu Sep 19 2002 - 08:44:24 PDT)
old prmtop
- Peter Gannett (Wed Sep 04 2002 - 11:10:56 PDT)
- Holger Gohlke (Wed Sep 04 2002 - 09:21:32 PDT)
- C. Klein (Wed Sep 04 2002 - 09:21:18 PDT)
- Thomas Steinbrecher (Wed Sep 04 2002 - 08:56:47 PDT)
parameterization of a new class of compounds (nucleic acid base analogues)
- Vlad Cojocaru (Mon Sep 09 2002 - 02:40:05 PDT)
Parameters for AMBER
- David A. Case (Fri Sep 20 2002 - 06:53:18 PDT)
parameters for sugars
- Elsa de Sousa Henriques (Mon Sep 30 2002 - 09:42:24 PDT)
- A.Madhumalar (Sun Sep 29 2002 - 09:30:36 PDT)
Partial charge generation RESP/antechamber
- James W. Caldwell (Mon Sep 30 2002 - 15:27:37 PDT)
Periodicity Question
- DeLano, Warren (Fri Sep 20 2002 - 17:29:49 PDT)
Polarizability, a general question
- Michal Otyepka (Wed Sep 11 2002 - 01:56:32 PDT)
Problems during equilibration
- Pratul Agarwal (Wed Sep 11 2002 - 19:40:05 PDT)
- Pratul Agarwal (Wed Sep 11 2002 - 13:14:05 PDT)
- Pratul Agarwal (Wed Sep 11 2002 - 12:38:36 PDT)
problems on IBM AIX
- Carlos P. Sosa (Fri Sep 13 2002 - 08:47:31 PDT)
- David A. Case (Fri Sep 13 2002 - 07:42:14 PDT)
- Giovanni Fossati (Thu Sep 12 2002 - 18:43:52 PDT)
Problems with poly(A)-poly(T) tutorial...
- Andrei Leit�o (Mon Sep 30 2002 - 12:55:53 PDT)
protein minimization
- m.elizabeth sophia (Tue Sep 03 2002 - 09:01:35 PDT)
- CUI, Guanglei (Tue Sep 03 2002 - 06:19:39 PDT)
- Lepsa (Mon Sep 02 2002 - 23:13:54 PDT)
ptraj - BONDS_WITHOUT_HYDROGEN
- Sophia Kondratova (Wed Sep 25 2002 - 09:54:48 PDT)
ptraj rdf output
- Prabal Maiti (Fri Sep 20 2002 - 16:24:35 PDT)
ptraj-6.4/LES
- Peter Varnai (Mon Sep 23 2002 - 02:18:25 PDT)
PyMOL + AMBER Trajectories
- DeLano, Warren (Tue Sep 03 2002 - 10:51:57 PDT)
question
- Ioana Cozmuta (Tue Sep 03 2002 - 10:46:04 PDT)
Question about Antechamber
- David A. Case (Thu Sep 26 2002 - 08:28:51 PDT)
- Masaki Tomimoto (Wed Sep 25 2002 - 14:37:55 PDT)
Question about Counterions
- Markus Drumm (Thu Sep 19 2002 - 10:38:24 PDT)
question about nmode again.
- David A. Case (Tue Sep 17 2002 - 07:40:00 PDT)
- Yongjun Jiang (Tue Sep 17 2002 - 00:15:54 PDT)
question about using 10-12 in amber7/sander.
- Margaret Cheung (Sat Sep 28 2002 - 13:35:48 PDT)
- Margaret Cheung (Sat Sep 28 2002 - 12:53:56 PDT)
Question on Antechamber paper
- Nicholson, James D Mr ARO (Thu Sep 26 2002 - 10:18:17 PDT)
Qustion about calculation of pressure
- James W. Caldwell (Thu Sep 12 2002 - 09:43:25 PDT)
- Nikolai Smolin (Thu Sep 12 2002 - 03:01:44 PDT)
rdparm
- Joffre Heredia (Tue Sep 10 2002 - 11:07:26 PDT)
Request for help with Antechamber
- James W. Caldwell (Fri Sep 27 2002 - 22:54:24 PDT)
- Nicholson, James D Mr ARO (Fri Sep 27 2002 - 18:00:37 PDT)
- David A. Case (Fri Sep 27 2002 - 17:54:21 PDT)
- Nicholson, James D Mr ARO (Fri Sep 27 2002 - 16:58:58 PDT)
RMSD for heavy atoms only
- Pratul Agarwal (Wed Sep 25 2002 - 13:54:45 PDT)
sander.LES questions
- Carlos Simmerling (Thu Sep 12 2002 - 10:24:25 PDT)
- Peter Varnai (Thu Sep 12 2002 - 09:27:12 PDT)
sander_classic: Recompile without ISTAR2
- Mahadevan Seetharaman (Wed Sep 25 2002 - 12:53:59 PDT)
SETVEL, incorrect number of arguments?
- David A. Case (Tue Sep 17 2002 - 12:18:38 PDT)
- Giovanni Fossati (Mon Sep 16 2002 - 15:43:30 PDT)
sorry this is just a test
- Vlad Cojocaru (Thu Sep 12 2002 - 08:23:24 PDT)
Strange MD simulation results with GB solvation at high temp.
- Soonmin Jang (Thu Sep 12 2002 - 22:21:32 PDT)
- Carlos Simmerling (Wed Sep 11 2002 - 19:04:44 PDT)
- David A. Case (Wed Sep 11 2002 - 18:20:17 PDT)
- Soonmin Jang (Tue Sep 10 2002 - 08:56:53 PDT)
- Carlos Simmerling (Tue Sep 10 2002 - 05:07:58 PDT)
- Soonmin Jang (Tue Sep 10 2002 - 03:09:06 PDT)
the amino group of 2amino purine has strange behaviour
- Vlad Cojocaru (Thu Sep 12 2002 - 11:42:10 PDT)
Torsion driving
- ch cureton (Thu Sep 26 2002 - 09:00:34 PDT)
vlimit and vmax
- darden (Fri Sep 20 2002 - 12:27:10 PDT)
- Thomas Cheatham (Fri Sep 20 2002 - 12:14:11 PDT)
watershell in ptraj
- Thomas Cheatham (Tue Sep 24 2002 - 12:28:09 PDT)
- Michael Trieb (Tue Sep 24 2002 - 02:03:49 PDT)
who to address this to?...
- Michael Crowley (Mon Sep 09 2002 - 10:41:16 PDT)
- Holger Gohlke (Mon Sep 09 2002 - 09:25:00 PDT)
- Jessica Swanson (Sun Sep 08 2002 - 15:59:23 PDT)
why are the results so large difference calculating by mm_pbsa and mm_gbsa?
- Holger Gohlke (Tue Sep 10 2002 - 09:26:07 PDT)
- Yongjun Jiang (Tue Sep 10 2002 - 00:18:46 PDT)
why are the results so large difference calculating by mm_pbsaandmm_gbsa?
- Yongjun Jiang (Thu Sep 12 2002 - 00:25:32 PDT)
write problem on IBM-AIX
- Giovanni Fossati (Mon Sep 30 2002 - 08:51:54 PDT)
your mail
- David A. Case (Mon Sep 30 2002 - 09:35:06 PDT)
Z DNA
- Sue Heavner (Tue Sep 17 2002 - 12:55:04 PDT)

Amber Archive Sep 2002 by subject