Amber Archive Oct 2001: by subject

(no subject)
- Bill Ross (Fri Oct 26 2001 - 15:51:36 PDT)
5-methyl deoxycytosine parameters
- Jake Isaacs (Fri Oct 12 2001 - 06:13:59 PDT)
?s: Xeon vs. Athlon, latency
- R. M. Fesinmeyer (Mon Oct 08 2001 - 10:15:39 PDT)
- Stephane (Fri Oct 05 2001 - 01:34:15 PDT)
- R. M. Fesinmeyer (Wed Oct 03 2001 - 20:36:38 PDT)
[Fwd: ?s: Xeon vs. Athlon, latency]
- Stephane (Mon Oct 08 2001 - 00:43:24 PDT)
adding water
- Bill Ross (Sat Oct 13 2001 - 21:44:47 PDT)
- Rozita Dara (Sat Oct 13 2001 - 19:40:22 PDT)
Amber 6 MDCRD Files > 2GB in 32 bit Linux.
- Ross Walker (Mon Oct 08 2001 - 04:49:14 PDT)
Amber6 on SuSE Linux
- jim caldwell (Wed Oct 17 2001 - 10:00:06 PDT)
- Toshikazu Matsuoka (Wed Oct 17 2001 - 01:56:49 PDT)
ANAL
- Bill Ross (Mon Oct 15 2001 - 11:17:23 PDT)
- Elizabeth K. White (Mon Oct 15 2001 - 10:45:18 PDT)
analysis problem
- Eoin Galligan (Mon Oct 08 2001 - 06:12:22 PDT)
Aqvist LJ parameters
- Samantha (Thu Oct 18 2001 - 11:34:46 PDT)
belly with GB term
- Tomoshi Kameda (Thu Oct 25 2001 - 12:54:22 PDT)
Binary mdcrd
- Halima Amer (Tue Oct 02 2001 - 23:43:41 PDT)
Can amber calculate the gibbs perturb energy when a ligand added a group
- Bill Ross (Sat Oct 13 2001 - 21:50:14 PDT)
charges for non-standard AAs
- Uwe Richter (Wed Oct 31 2001 - 05:46:15 PST)
Code modification.
- John Finke (Mon Oct 08 2001 - 16:16:44 PDT)
color in xleap
- Soonmin Jang (Sat Oct 20 2001 - 19:35:30 PDT)
Define flexible residues during MD simulation
- Bill Ross (Tue Oct 23 2001 - 21:14:35 PDT)
- wentaofu (Tue Oct 23 2001 - 14:59:59 PDT)
distribution of Na+ around DNA
- Bill Ross (Wed Oct 17 2001 - 07:32:02 PDT)
- Xiaolin Chuang (Wed Oct 17 2001 - 05:04:54 PDT)
DNA strands separated...
- Jithesh P.V. (Mon Oct 22 2001 - 00:07:09 PDT)
Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards
- Ross Walker (Thu Oct 18 2001 - 12:29:56 PDT)
- DeLano, Warren (Thu Oct 18 2001 - 09:48:53 PDT)
- David Konerding (Thu Oct 18 2001 - 08:30:38 PDT)
- Ross Walker (Thu Oct 18 2001 - 07:00:48 PDT)
energy decomposition
- Bill Ross (Sat Oct 13 2001 - 12:10:18 PDT)
- Elizabeth K. White (Sat Oct 13 2001 - 06:51:40 PDT)
Err in equilibration run
- A.Madhumalar (Sun Oct 28 2001 - 02:02:55 PST)
- Bill Ross (Mon Oct 22 2001 - 00:03:38 PDT)
- A.Madhumalar (Sun Oct 21 2001 - 23:22:09 PDT)
GB and Ions, 2nd try
- Andreas Svrcek-Seiler (Tue Oct 02 2001 - 08:43:39 PDT)
generation of small organic molecules on xleap
- Bill Ross (Sun Oct 21 2001 - 21:48:53 PDT)
- Soonmin Jang (Sun Oct 21 2001 - 16:55:17 PDT)
h-bond energy
- Min Wu (Sun Oct 21 2001 - 07:07:15 PDT)
help
- seema namboori (Wed Oct 17 2001 - 06:50:53 PDT)
help for restrained minimization
- Bill Ross (Mon Oct 29 2001 - 01:32:16 PST)
- Stephane (Mon Oct 29 2001 - 00:39:21 PST)
- xin.hu_at_ndsu.nodak.edu (Fri Oct 26 2001 - 21:10:19 PDT)
how to add Zn Ca parameters
- Eva Darian (Thu Oct 25 2001 - 14:29:50 PDT)
- Bill Ross (Wed Oct 24 2001 - 17:04:58 PDT)
- Xin Hu (Wed Oct 24 2001 - 16:08:51 PDT)
How to turn off PME?
- Hungie Hungie (Tue Oct 30 2001 - 07:49:45 PST)
image command of ptraj
- Xiaolin Chuang (Wed Oct 17 2001 - 05:22:20 PDT)
IMPORTANT Amber mail list announcement
- jim caldwell (Tue Oct 30 2001 - 11:44:48 PST)
Interface and Sander_classic
- David Pearlman (Tue Oct 30 2001 - 12:13:42 PST)
- David Pearlman (Tue Oct 30 2001 - 10:34:31 PST)
- Sophia Kondratova (Tue Oct 30 2001 - 05:06:03 PST)
Interface program installation
- David Pearlman (Fri Oct 19 2001 - 14:22:45 PDT)
- Sophia Kondratova (Fri Oct 19 2001 - 10:25:19 PDT)
ISTAR option and performance
- Jarrod Smith (Tue Oct 09 2001 - 11:30:22 PDT)
- Anton B. Guliaev (Tue Oct 09 2001 - 10:39:10 PDT)
iwrap
- Xiaolin Chuang (Wed Oct 17 2001 - 05:27:39 PDT)
LINMIN Failure
- Michael Jakusch (Mon Oct 01 2001 - 08:17:17 PDT)
MAX_RSTACK
- Dr David R V Buckley (Fri Oct 26 2001 - 10:44:02 PDT)
Maxwell-Boltzmann distribution of velocities
- Andreas Svrcek-Seiler (Fri Oct 26 2001 - 03:46:36 PDT)
- Marcela Madrid (Thu Oct 25 2001 - 12:23:08 PDT)
Methane minimization using Interface
- Sophia Kondratova (Wed Oct 24 2001 - 07:17:36 PDT)
MM-PBSA; E(internal)
- Michal Otyepka (Wed Oct 10 2001 - 09:58:19 PDT)
NAN errors during production runs
- Oliver Zerbe (Wed Oct 03 2001 - 09:45:10 PDT)
Need some help with Amber/Linux
- John Nicholas (Fri Oct 26 2001 - 09:19:11 PDT)
- David Pearlman (Thu Oct 25 2001 - 18:04:23 PDT)
- John Nicholas (Thu Oct 25 2001 - 14:42:52 PDT)
NFFT
- darden (Tue Oct 30 2001 - 10:03:22 PST)
- Michael Crowley (Tue Oct 30 2001 - 08:24:38 PST)
- Hungie Hungie (Tue Oct 30 2001 - 06:43:48 PST)
NPSCAL parameter
- Bill Ross (Mon Oct 08 2001 - 08:36:10 PDT)
- Nikolai Smolin (Mon Oct 08 2001 - 04:20:24 PDT)
NPT to NVE ensemble
- Hungie Hungie (Wed Oct 31 2001 - 05:31:20 PST)
NSCM setting to remove center of mass motion
- Sanjeev B.S. (Thu Oct 25 2001 - 20:44:41 PDT)
- Michael G Cooney (Thu Oct 25 2001 - 09:52:09 PDT)
P4 benchmarks posted
- Robert Matthew Fesinmeyer (Thu Oct 11 2001 - 13:10:14 PDT)
param CT-CT-CT-OH
- Michal Otyepka (Wed Oct 24 2001 - 11:54:56 PDT)
parameters
- Didier Rognan (Fri Oct 12 2001 - 09:12:37 PDT)
possible bug in carnal in AMBER5
- Bill Ross (Wed Oct 17 2001 - 14:09:00 PDT)
- Michael G Cooney (Wed Oct 17 2001 - 14:00:01 PDT)
Possible error in AMBER parm94 file?
- John D. Chodera (Mon Oct 01 2001 - 17:01:37 PDT)
post-processing of energy analysis
- Katherine Wallis Abold (Sun Oct 07 2001 - 13:58:30 PDT)
problem in a short MD with protein fixed
- Michael G Cooney (Wed Oct 17 2001 - 11:52:30 PDT)
- dwang (Tue Oct 16 2001 - 18:00:26 PDT)
Problem in GIBBS!
- PRADIPTA Bandyopadhyay (Fri Oct 19 2001 - 13:43:41 PDT)
problem with ambpdb
- Bill Ross (Wed Oct 03 2001 - 01:16:23 PDT)
prowat test difficulties
- C. Singer (Tue Oct 02 2001 - 11:37:39 PDT)
question about implicit solvation model with AMBER
- Howard Feldman (Tue Oct 23 2001 - 07:55:36 PDT)
R: color in xleap
- Lorenzo Gontrani (Sat Oct 20 2001 - 13:21:07 PDT)
RESP charges
- Lepsa (Tue Oct 09 2001 - 00:56:49 PDT)
- Eva Darian (Mon Oct 08 2001 - 14:44:16 PDT)
RESP charges (correction)
- Lepsa (Wed Oct 31 2001 - 08:01:30 PST)
- Lepsa (Wed Oct 10 2001 - 00:15:53 PDT)
- Eva Darian (Tue Oct 09 2001 - 08:54:49 PDT)
RESP charges!
- PRADIPTA Bandyopadhyay (Fri Oct 26 2001 - 13:24:45 PDT)
roar-cp crashed
- Yuguang Mu (Wed Oct 24 2001 - 14:25:38 PDT)
sander_classic
- Carlos Simmerling (Wed Oct 31 2001 - 12:57:43 PST)
- wentaofu (Wed Oct 31 2001 - 11:57:07 PST)
substracting of MM nonbondeb potential from QM curve
- Michal Otyepka (Tue Oct 23 2001 - 10:24:44 PDT)
Temperature and pressure couplings
- David Case (Wed Oct 03 2001 - 08:57:33 PDT)
- Filip Lankas (Wed Oct 03 2001 - 08:38:56 PDT)
torsional profile
- Giulio Rastelli (Thu Oct 18 2001 - 08:29:12 PDT)
torsional profile with MD
- Bill Ross (Mon Oct 15 2001 - 10:17:12 PDT)
- Bill Ross (Mon Oct 15 2001 - 10:12:21 PDT)
- Giulio Rastelli (Mon Oct 15 2001 - 09:17:34 PDT)
trajectory analysis
- Bill Ross (Sat Oct 13 2001 - 12:50:04 PDT)
- Sue Heavner (Sat Oct 13 2001 - 12:26:41 PDT)
unusual parameters
- pascal bonnet (Fri Oct 26 2001 - 01:06:26 PDT)
what should change in the parameter?
- backy_at_ibms.sinica.edu.tw (Wed Oct 31 2001 - 01:52:10 PST)
Xeon vs. Athlon, latency
- Yong Duan (Thu Oct 04 2001 - 10:19:29 PDT)
Xleap, PDB file format
- Bill Ross (Fri Oct 26 2001 - 09:31:16 PDT)
- David Case (Fri Oct 26 2001 - 08:59:14 PDT)
- Jarrod Smith (Fri Oct 26 2001 - 08:12:49 PDT)
- Sophia Kondratova (Fri Oct 26 2001 - 08:00:26 PDT)
xleap: japanese keyboad
- Toshikazu Matsuoka (Sun Oct 21 2001 - 22:41:02 PDT)

Amber Archive Oct 2001 by subject