Amber Archive Jul 2002: by subject

"amber mail"
- jim caldwell (Thu Jul 25 2002 - 09:11:01 PDT)
"crd" file created with VMD
- Soonmin Jang (Wed Jul 24 2002 - 00:28:27 PDT)
- David Case (Wed Jul 24 2002 - 00:04:02 PDT)
- Carlos Simmerling (Tue Jul 23 2002 - 20:02:50 PDT)
- Carlos Simmerling (Tue Jul 23 2002 - 18:42:15 PDT)
- Soonmin Jang (Tue Jul 23 2002 - 17:47:04 PDT)
- Soonmin Jang (Tue Jul 23 2002 - 09:23:56 PDT)
'triangular' bond or angle
- Mahadevan Seetharaman (Tue Jul 30 2002 - 13:53:20 PDT)
(no subject)
- deepak rangaswamy (Wed Jul 24 2002 - 20:57:14 PDT)
- Carlos Simmerling (Tue Jul 23 2002 - 04:48:48 PDT)
- deepak rangaswamy (Tue Jul 23 2002 - 00:01:41 PDT)
- Narang Manpreet Kaur (Wed Jul 03 2002 - 08:08:40 PDT)
a water jumps
- David Case (Mon Jul 29 2002 - 22:13:16 PDT)
- Masaki Tomimoto (Mon Jul 29 2002 - 20:47:21 PDT)
about solvateOct
- Nikolai Smolin (Fri Jul 19 2002 - 01:22:20 PDT)
acetyl groups on protein fragments
- Laurent Chiche (Fri Jul 26 2002 - 00:43:03 PDT)
- Elizabeth K. White (Thu Jul 25 2002 - 11:55:04 PDT)
am1-bcc charges, antechamber
- M. L. Dodson (Thu Jul 25 2002 - 05:32:05 PDT)
- Giulio Rastelli (Thu Jul 25 2002 - 03:53:46 PDT)
- Laurent Chiche (Thu Jul 25 2002 - 02:17:58 PDT)
- M. L. Dodson (Wed Jul 24 2002 - 13:24:23 PDT)
- David A. Case (Wed Jul 24 2002 - 12:58:25 PDT)
- Sophia Kondratova (Wed Jul 24 2002 - 12:02:02 PDT)
AM1-BCC sensitivity to AM1 charges
- ajakalian_at_lav.Boehringer-Ingelheim.com (Tue Jul 30 2002 - 11:28:25 PDT)
- Matthew Lee (Tue Jul 30 2002 - 10:31:43 PDT)
Amber 7 Installation
- Joffre Heredia (Tue Jul 09 2002 - 23:17:45 PDT)
- Sanjeev B.S. (Tue Jul 09 2002 - 10:38:16 PDT)
- Rajesh Korde (Tue Jul 09 2002 - 09:45:36 PDT)
AMBER Machine Questions
- DTphonehome33_at_aol.com (Tue Jul 30 2002 - 10:00:33 PDT)
amber on sp3
- David A. Case (Wed Jul 17 2002 - 12:14:44 PDT)
amber-request.cgl.ucsf.edu
- Mihaly Mezei (Mon Jul 29 2002 - 11:42:22 PDT)
AMBER7 and Movie
- Y Fang (Mon Jul 22 2002 - 13:58:23 PDT)
- Carlos Simmerling (Mon Jul 22 2002 - 09:56:52 PDT)
- Pascal Bonnet (Mon Jul 22 2002 - 01:36:50 PDT)
- Snyder, James (Fri Jul 19 2002 - 15:25:37 PDT)
- Y Fang (Fri Jul 19 2002 - 14:03:22 PDT)
Anal in AMBER7
- Ting Wang (Mon Jul 22 2002 - 02:19:16 PDT)
anal in AMBER7 gives inconsistent results with itself
- Prabal Maiti (Sun Jul 07 2002 - 22:46:31 PDT)
- Prabal Maiti (Fri Jul 05 2002 - 16:00:55 PDT)
anal in AMBER7 gives inconsistent results with itself (fwd)
- Prabal Maiti (Fri Jul 12 2002 - 10:38:19 PDT)
Announcement: Optimally Partitioned Electric Properties - OPEP
- Chris Chipot (Wed Jul 10 2002 - 01:06:48 PDT)
antechamber created prep file--Problem in xleap
- Sarangan Ravichandran (Tue Jul 16 2002 - 06:54:45 PDT)
antechamber created prep file--Problem in xleap--additional info
- Sarangan Ravichandran (Tue Jul 16 2002 - 07:06:31 PDT)
are there inconsistencies in anal?
- David A. Case (Fri Jul 12 2002 - 11:58:02 PDT)
Benchmark
- St�phane Teletch�a (Mon Jul 22 2002 - 09:55:14 PDT)
BR parameters in AMBER
- Esther Kellenberger (Wed Jul 03 2002 - 07:24:26 PDT)
bug in .../sander/egb.f ?
- Sanjeev B.S. (Mon Jul 08 2002 - 12:08:09 PDT)
building general solvent boxes with leap
- Elsa de Sousa Henriques (Thu Jul 18 2002 - 20:41:25 PDT)
- Xavier Deupi (Thu Jul 18 2002 - 16:16:17 PDT)
- Bill Ross (Thu Jul 18 2002 - 12:18:57 PDT)
- David A. Case (Wed Jul 17 2002 - 13:14:40 PDT)
- Xavier Deupi (Wed Jul 17 2002 - 10:19:28 PDT)
building ss DNA/RNA
- David A. Case (Tue Jul 30 2002 - 15:29:19 PDT)
- Cozmuta (Tue Jul 30 2002 - 14:47:45 PDT)
C sp2 connected to OS
- Bimo Ario Tejo (Tue Jul 23 2002 - 01:23:03 PDT)
- Bimo Ario Tejo (Mon Jul 22 2002 - 10:37:27 PDT)
CA-OS parameter
- Bimo Ario Tejo (Tue Jul 23 2002 - 09:07:19 PDT)
CCl4 solvent box
- Bimo Ario Tejo (Wed Jul 24 2002 - 12:55:04 PDT)
- Bimo Ario Tejo (Wed Jul 24 2002 - 08:40:10 PDT)
China International Biology Projects Fair
- Genefax (Thu Jul 11 2002 - 22:40:19 PDT)
compiling MPICH
- Thomas Steinbrecher (Thu Jul 11 2002 - 05:46:12 PDT)
correction about solvateOct
- Michael Crowley (Fri Jul 19 2002 - 09:37:10 PDT)
- William Wei (Fri Jul 19 2002 - 08:18:53 PDT)
- Michael Jakusch (Fri Jul 19 2002 - 02:49:48 PDT)
- Nikolai Smolin (Fri Jul 19 2002 - 02:09:58 PDT)
counter-ions in FEP
- David A. Case (Fri Jul 12 2002 - 09:00:11 PDT)
- Christophe L M J Verlinde (Thu Jul 11 2002 - 09:37:41 PDT)
create new atom problem on xleap
- Bill Ross (Thu Jul 04 2002 - 13:58:59 PDT)
- yuann (Thu Jul 04 2002 - 13:04:01 PDT)
creating a solvent box
- Laurent Chiche (Thu Jul 25 2002 - 07:46:47 PDT)
- CUI, Guanglei (Thu Jul 25 2002 - 06:33:01 PDT)
- Bimo Ario Tejo (Thu Jul 25 2002 - 05:32:17 PDT)
Decrease the solvated system by removing the outside crystal water
- Ling Zhang (Mon Jul 15 2002 - 09:58:34 PDT)
Defining Restraints in Sander
- John Bushnell (Thu Jul 18 2002 - 17:44:16 PDT)
- Carlos Simmerling (Thu Jul 18 2002 - 14:29:22 PDT)
- Asif Rahaman (Thu Jul 18 2002 - 13:21:59 PDT)
dielectric constant for partialy solvated MD
- Carlos Simmerling (Wed Jul 31 2002 - 13:54:12 PDT)
- Miyashita, Osamu (Wed Jul 31 2002 - 11:55:58 PDT)
Distance dependent vaccum energy minimization in AMBER7
- Sarangan Ravichandran (Fri Jul 05 2002 - 08:29:40 PDT)
docking in xleap
- Bill Ross (Wed Jul 03 2002 - 21:25:50 PDT)
Dual AMD motherboards
- Ross Walker (Tue Jul 16 2002 - 00:31:56 PDT)
- Pietro Amodeo (Mon Jul 15 2002 - 01:36:34 PDT)
- Contractor-SIMTECH (Fri Jul 12 2002 - 08:33:54 PDT)
eedmeth variable in AMBER7
- David A. Case (Tue Jul 09 2002 - 08:31:59 PDT)
- Sarangan Ravichandran (Tue Jul 09 2002 - 07:30:28 PDT)
electrostatics truncation in AMBER
- David A. Case (Fri Jul 19 2002 - 08:26:20 PDT)
- Therese Malliavin (Fri Jul 19 2002 - 06:21:59 PDT)
Energies/coordinate files from mm_pbsa problem
- Peter Gannett (Tue Jul 30 2002 - 11:25:29 PDT)
Error decoding variable
- Carlos Simmerling (Wed Jul 31 2002 - 08:41:04 PDT)
- jim caldwell (Wed Jul 31 2002 - 07:43:56 PDT)
- Carlos Simmerling (Wed Jul 31 2002 - 05:37:46 PDT)
- Rukman Hertadi (Wed Jul 31 2002 - 03:52:02 PDT)
Format in a trajectory files is suddenly changed
- Masaki Tomimoto (Mon Jul 22 2002 - 09:54:44 PDT)
gaff and parm99
- Pascal Bonnet (Wed Jul 24 2002 - 08:51:30 PDT)
- David A. Case (Wed Jul 24 2002 - 08:13:48 PDT)
- Pascal Bonnet (Wed Jul 24 2002 - 06:11:36 PDT)
GENERALIZED BORN model on a protein with Fe
- David A. Case (Thu Jul 18 2002 - 10:41:53 PDT)
- Mahadevan Seetharaman (Thu Jul 18 2002 - 07:55:01 PDT)
Gibbs tutorial problem
- David A. Case (Thu Jul 25 2002 - 12:03:17 PDT)
- yuann (Wed Jul 24 2002 - 17:40:50 PDT)
heat up at constant pressure
- Qing Zhang (Mon Jul 08 2002 - 15:05:19 PDT)
How to decrease the solvated system in Amber6?
- Ling Zhang (Tue Jul 02 2002 - 08:30:19 PDT)
- David A. Case (Tue Jul 02 2002 - 04:38:50 PDT)
- Ling Zhang (Mon Jul 01 2002 - 09:28:51 PDT)
Including explicit waters in GB dynamics
- Kristina Furse (Sat Jul 20 2002 - 17:30:43 PDT)
increase lastist
- jim caldwell (Wed Jul 24 2002 - 15:45:43 PDT)
- David A. Case (Wed Jul 24 2002 - 14:41:48 PDT)
- Marcela Madrid (Wed Jul 24 2002 - 13:41:45 PDT)
installing MPICH for AMBER on Linux CLuster
- Thomas A. Spraggins (Mon Jul 08 2002 - 06:15:23 PDT)
- Walter Langel (Mon Jul 08 2002 - 05:26:36 PDT)
- root (Mon Jul 08 2002 - 03:02:52 PDT)
installing MPICH for AMBER on Linux CLuster update
- Thomas Steinbrecher (Mon Jul 08 2002 - 06:46:48 PDT)
LEaP gives "no sp2 improper torsion term" warnings
- David A. Case (Fri Jul 12 2002 - 13:25:35 PDT)
looking for frcmod in AMBER Tutorials
- yuann (Fri Jul 12 2002 - 02:19:45 PDT)
makeDIP_RST.dna
- Vickie Tsui (Wed Jul 24 2002 - 16:49:57 PDT)
- McAteer, Kathleen (Wed Jul 24 2002 - 12:24:42 PDT)
MAX_RSTACK
- Joffre Heredia (Wed Jul 10 2002 - 10:12:15 PDT)
- Jithesh (Tue Jul 09 2002 - 23:24:42 PDT)
md equilibration in chloroform
- Thomas.Fox_at_bc.boehringer-ingelheim.com (Thu Jul 11 2002 - 10:51:47 PDT)
- David A. Case (Mon Jul 08 2002 - 08:42:24 PDT)
- Sophia Kondratova (Mon Jul 08 2002 - 06:38:27 PDT)
Minimization in GB-SA-E-Spikes, LINMIN
- David A. Case (Wed Jul 17 2002 - 17:43:57 PDT)
- Sarangan Ravichandran (Tue Jul 16 2002 - 10:11:27 PDT)
- Andreas Svrcek-Seiler (Tue Jul 16 2002 - 09:00:55 PDT)
- Sarangan Ravichandran (Tue Jul 16 2002 - 08:02:58 PDT)
mol2 with antechamber
- David A. Case (Fri Jul 26 2002 - 08:54:08 PDT)
- Giulio Rastelli (Fri Jul 26 2002 - 03:57:22 PDT)
Net Charge is Different In The Sander Output!!
- David A. Case (Tue Jul 09 2002 - 20:53:47 PDT)
- Sarangan Ravichandran (Tue Jul 09 2002 - 18:19:00 PDT)
new problems compiling amber 7
- ramon kleber da rocha (Thu Jul 11 2002 - 10:30:07 PDT)
- Sanjeev B.S. (Wed Jul 10 2002 - 07:57:40 PDT)
- ramon kleber da rocha (Wed Jul 10 2002 - 06:11:52 PDT)
New Promotion Products at American Disc Corporation
- Service (Thu Jul 25 2002 - 12:56:47 PDT)
NON-BONDED INTERACTION
- Rosalia Pascual (Tue Jul 30 2002 - 07:41:49 PDT)
Not able to image a snapshot.
- St�phane Teletch�a (Thu Jul 11 2002 - 01:24:48 PDT)
- St�phane Teletch�a (Wed Jul 10 2002 - 08:28:12 PDT)
Origin300, Linux Cluster
- Dow Hurst (Mon Jul 08 2002 - 07:40:34 PDT)
- St�phane Teletch�a (Mon Jul 08 2002 - 05:37:37 PDT)
- St�phane Teletch�a (Fri Jul 05 2002 - 01:48:03 PDT)
- C. Klein (Thu Jul 04 2002 - 10:41:31 PDT)
- Jianhui Wu (Thu Jul 04 2002 - 09:04:07 PDT)
parallel jobs die with no error message from sander
- Joffre Heredia (Tue Jul 30 2002 - 10:46:37 PDT)
- Joffre Heredia (Mon Jul 29 2002 - 21:06:33 PDT)
- Scott Brozell (Mon Jul 29 2002 - 15:43:51 PDT)
- jim caldwell (Mon Jul 29 2002 - 13:08:50 PDT)
- lamon_at_lav.Boehringer-Ingelheim.com (Mon Jul 29 2002 - 10:48:20 PDT)
parameter file for MgGTP
- Holger Sondermann (Tue Jul 02 2002 - 18:34:24 PDT)
periodic box
- Thomas E. Cheatham, III (Wed Jul 31 2002 - 07:26:49 PDT)
- Peter Gannett (Sat Jul 27 2002 - 07:41:50 PDT)
- Jiyoung Heo (Fri Jul 26 2002 - 15:00:28 PDT)
Pictausch??
- nicolescholiz1_at_web.de (Mon Jul 08 2002 - 16:14:10 PDT)
PME in gibbs module
- X. Tan (Tue Jul 16 2002 - 13:29:27 PDT)
Pressure probs in MD
- jim caldwell (Thu Jul 25 2002 - 08:55:57 PDT)
- suvendu lomash (Thu Jul 25 2002 - 00:49:28 PDT)
prmtop file question.
- David A. Case (Wed Jul 17 2002 - 17:08:28 PDT)
- Carlos Andres Ramirez-Mondragon (Wed Jul 17 2002 - 14:15:59 PDT)
problem compiling roar (mop7mm) on alpha
- Chuck Schneider (Tue Jul 23 2002 - 10:09:37 PDT)
- Tru (Tue Jul 23 2002 - 10:05:08 PDT)
- hagop demirdjian (Tue Jul 23 2002 - 08:35:11 PDT)
Problem getting sander started
- Sanjeev B.S. (Wed Jul 10 2002 - 05:26:39 PDT)
- Thomas Steinbrecher (Wed Jul 10 2002 - 05:24:00 PDT)
problem in compiling amber7 in IBMSP3 cluster
- Michael Crowley (Fri Jul 05 2002 - 11:11:55 PDT)
- A.Madhumalar (Thu Jul 04 2002 - 09:29:50 PDT)
Problem with LEAP
- David A. Case (Tue Jul 16 2002 - 08:19:24 PDT)
- Miguel de Federico (Tue Jul 16 2002 - 03:53:37 PDT)
problem with make_crd_hg, mm_pbsa
- Jianhui Wu (Mon Jul 22 2002 - 11:28:29 PDT)
problemas running amber7 tests on a SP2 machine
- ramon kleber da rocha (Tue Jul 23 2002 - 13:33:28 PDT)
problems compiling Amber 7
- Thomas A. Spraggins (Fri Jul 05 2002 - 11:42:32 PDT)
- ramon kleber da rocha (Fri Jul 05 2002 - 10:52:45 PDT)
- ramon kleber da rocha (Tue Jul 02 2002 - 07:42:05 PDT)
ptraj
- Joseph Nachman (Fri Jul 26 2002 - 13:14:53 PDT)
- Joseph Nachman (Fri Jul 26 2002 - 12:43:36 PDT)
- Thomas Cheatham (Fri Jul 26 2002 - 12:15:04 PDT)
- David A. Case (Fri Jul 26 2002 - 12:08:54 PDT)
- Kristina Furse (Fri Jul 26 2002 - 11:32:38 PDT)
PTRAJ: radial distribution function
- Thomas Cheatham (Wed Jul 17 2002 - 14:47:24 PDT)
- A. Hungie (Wed Jul 17 2002 - 08:58:14 PDT)
Purine to Pyrimidine mutation
- Bernd Wellenzohn (Thu Jul 25 2002 - 05:29:27 PDT)
Question about error message about "lastist" and "virtual box"
- David A. Case (Fri Jul 12 2002 - 08:55:51 PDT)
- Masaki Tomimoto (Fri Jul 12 2002 - 08:19:12 PDT)
Questions about xleap ...
- Bill Ross (Tue Jul 23 2002 - 12:03:52 PDT)
Questions about xleap and mm_pbsa (cont.2)
- Salinthip Thipayang (Tue Jul 23 2002 - 08:21:23 PDT)
Questions about xleap and mm_pbsa(cont.)
- David A. Case (Tue Jul 23 2002 - 10:18:44 PDT)
- Salinthip Thipayang (Tue Jul 23 2002 - 07:46:20 PDT)
Questions about xleap and mm_pbsa]
- David A. Case (Fri Jul 19 2002 - 11:59:24 PDT)
- Salinthip Thipayang (Fri Jul 19 2002 - 10:49:08 PDT)
RDC restraints
- Richard Stefl (Mon Jul 08 2002 - 08:01:39 PDT)
Running TIP5P with PBC
- Sarah Tschampel (Tue Jul 09 2002 - 10:32:32 PDT)
- David Case (Wed Jul 03 2002 - 12:49:28 PDT)
- Sarah Tschampel (Wed Jul 03 2002 - 12:47:41 PDT)
sander crash
- K.Seshadri (Mon Jul 29 2002 - 01:40:57 PDT)
SANDER documentation for nmropt
- David A. Case (Mon Jul 29 2002 - 17:27:52 PDT)
sander mpirun hangs with 4 CPU, but not with 2
- lamon_at_lav.Boehringer-Ingelheim.com (Tue Jul 30 2002 - 10:06:05 PDT)
- Thomas Steinbrecher (Tue Jul 30 2002 - 08:09:03 PDT)
Segmentation fault
- Bimo Ario Tejo (Wed Jul 24 2002 - 02:42:26 PDT)
- David A. Case (Tue Jul 23 2002 - 15:44:02 PDT)
- Bimo Ario Tejo (Tue Jul 23 2002 - 12:44:58 PDT)
several questions
- Heather A Carlson (Tue Jul 23 2002 - 20:17:35 PDT)
- David A. Case (Tue Jul 23 2002 - 17:08:10 PDT)
- David Keller (Tue Jul 23 2002 - 15:24:04 PDT)
simulated annealing example
- Qing Zhang (Wed Jul 10 2002 - 19:59:20 PDT)
- Snyder, James (Wed Jul 10 2002 - 13:42:43 PDT)
simulation management tools
- Tom Bishop (Fri Jul 05 2002 - 08:58:59 PDT)
SS bond
- David A. Case (Wed Jul 24 2002 - 13:00:44 PDT)
- Masaki Tomimoto (Wed Jul 24 2002 - 12:04:21 PDT)
structure
- David Case (Tue Jul 30 2002 - 22:43:50 PDT)
- Cozmuta (Tue Jul 30 2002 - 20:34:44 PDT)
sulfonic group generated with antechamber
- Michael Jakusch (Thu Jul 25 2002 - 05:23:30 PDT)
Summary: make_crd_hp, mm_pbsa
- Jianhui Wu (Mon Jul 22 2002 - 14:45:32 PDT)
TEST
- Sarangan Ravichandran (Fri Jul 05 2002 - 05:43:37 PDT)
tests for amber
- jim caldwell (Tue Jul 30 2002 - 17:57:49 PDT)
- Cozmuta (Tue Jul 30 2002 - 16:47:18 PDT)
The 216 water box
- Mihaly Mezei (Thu Jul 18 2002 - 15:48:12 PDT)
This one with anal in amber6
- Prabal Maiti (Fri Jul 12 2002 - 11:09:39 PDT)
time scale to see the ion effect on DNA
- A.Madhumalar (Wed Jul 10 2002 - 23:40:52 PDT)
torsion angle constrains
- Marcela Madrid (Tue Jul 02 2002 - 14:22:09 PDT)
Trajectory files
- Carlos Simmerling (Wed Jul 24 2002 - 08:52:29 PDT)
- Laurent Chiche (Wed Jul 24 2002 - 08:26:36 PDT)
- David A. Case (Wed Jul 24 2002 - 08:15:55 PDT)
- Natasja Brooijmans (Wed Jul 24 2002 - 07:34:28 PDT)
- Miguel de Federico (Wed Jul 24 2002 - 05:10:51 PDT)
trajectory problem?
- David Case (Wed Jul 24 2002 - 22:22:57 PDT)
Umbrella sampling in AMBER
- David A. Case (Wed Jul 24 2002 - 14:44:35 PDT)
- Pratul Agarwal (Wed Jul 24 2002 - 13:53:54 PDT)
water box size
- eric hu (Thu Jul 25 2002 - 12:21:24 PDT)
- Shixiang Yan (Fri Jul 19 2002 - 16:02:32 PDT)
- eric hu (Fri Jul 19 2002 - 15:09:25 PDT)
Water molecule numbering
- Shixiang Yan (Thu Jul 25 2002 - 19:28:02 PDT)
- Masaki Tomimoto (Thu Jul 25 2002 - 17:32:19 PDT)
- Masaki Tomimoto (Thu Jul 25 2002 - 17:04:01 PDT)
- Shixiang Yan (Thu Jul 25 2002 - 16:25:08 PDT)
- Masaki Tomimoto (Thu Jul 25 2002 - 15:28:25 PDT)
water molecules diffuse during equilibration
- David A. Case (Tue Jul 16 2002 - 18:31:12 PDT)
- Qing Zhang (Tue Jul 16 2002 - 16:56:53 PDT)
your mail
- CUI, Guanglei (Thu Jul 25 2002 - 06:30:30 PDT)

Amber Archive Jul 2002 by subject