Amber Archive Apr 2003: by subject

(no subject)
- Khanh.Dao.iac.uib.no (Mon Apr 21 2003 - 09:35:02 PDT)
- Carolina Salvador-Morales (Mon Apr 07 2003 - 06:22:27 PDT)
- dicksmit.umich.edu (Wed Apr 02 2003 - 11:32:37 PST)
A problem in opening the file
- Khanh.Dao.iac.uib.no (Tue Apr 15 2003 - 00:19:58 PDT)
- David A. Case (Mon Apr 14 2003 - 23:50:04 PDT)
- Khanh.Dao.iac.uib.no (Mon Apr 14 2003 - 22:01:11 PDT)
A problem in Sander production dynamics
- Thomas Cheatham (Mon Apr 14 2003 - 14:24:31 PDT)
- Carlos Simmerling (Mon Apr 14 2003 - 04:21:04 PDT)
- yuann (Mon Apr 14 2003 - 01:37:50 PDT)
A weird antechamber error
- David A. Case (Wed Apr 02 2003 - 07:24:12 PST)
- Yuhui Cheng (Tue Apr 01 2003 - 20:21:46 PST)
a-Helix direction?
- William Wei (Mon Apr 07 2003 - 13:26:40 PDT)
About electrostatic force calculations
- Soonmin Jang (Tue Apr 01 2003 - 21:58:38 PST)
about molecular dynamics
- Carlos Simmerling (Tue Apr 29 2003 - 20:30:06 PDT)
- Carlos Simmerling (Tue Apr 29 2003 - 18:14:39 PDT)
- ronnie (Tue Apr 29 2003 - 18:09:25 PDT)
Adding ACE to chopped protein
- Karl N. Kirschner (Wed Apr 16 2003 - 13:08:45 PDT)
addles
- Carlos Simmerling (Mon Apr 14 2003 - 09:22:29 PDT)
- Samy Name_removed_after_user_request (Tue Apr 08 2003 - 09:56:44 PDT)
ALA-scan problem with mm_pbsa.pl
- Natasja Brooijmans (Wed Apr 16 2003 - 11:14:55 PDT)
- Holger Gohlke (Wed Apr 16 2003 - 10:40:44 PDT)
- Natasja Brooijmans (Sun Apr 13 2003 - 15:21:03 PDT)
AMBER
- chandran karunakaran (Sun Apr 20 2003 - 18:13:32 PDT)
- chandran karunakaran (Tue Apr 15 2003 - 18:25:08 PDT)
- David A. Case (Tue Apr 15 2003 - 17:38:59 PDT)
- CUI, Guanglei (Tue Apr 15 2003 - 17:32:12 PDT)
- chandran karunakaran (Tue Apr 15 2003 - 16:55:16 PDT)
Amber on Linux
- Wen Li (Sun Apr 13 2003 - 08:06:52 PDT)
- Viktor Hornak (Sat Apr 12 2003 - 16:41:41 PDT)
- Wen Li (Sat Apr 12 2003 - 10:00:46 PDT)
Amber on Parallel Sun?
- Bengt Svensson (Mon Apr 28 2003 - 14:59:14 PDT)
AMBER pdb help - lost atoms
- kxg2248.njit.edu (Tue Apr 01 2003 - 11:39:27 PST)
- David A. Case (Tue Apr 01 2003 - 18:17:41 PST)
- Ioana Cozmuta (Tue Apr 01 2003 - 14:21:46 PST)
- David A. Case (Tue Apr 01 2003 - 12:19:35 PST)
AMBER pdb help - lost atoms - Part 2
- kxg2248.njit.edu (Thu Apr 03 2003 - 09:50:29 PST)
- David A. Case (Thu Apr 03 2003 - 09:23:41 PST)
Amber7 and mpirun on Linux
- Scott Brozell (Fri Apr 11 2003 - 12:40:38 PDT)
- Francesc Corcho (Fri Apr 11 2003 - 04:28:32 PDT)
- Scott Brozell (Thu Apr 10 2003 - 12:28:00 PDT)
- Wen Li (Thu Apr 10 2003 - 11:14:59 PDT)
ambpdb
- Venkata S Koppuravuri (Fri Apr 18 2003 - 09:14:34 PDT)
- Florian Barth (Wed Apr 16 2003 - 04:59:42 PDT)
- Luis Gracia (Tue Apr 15 2003 - 21:40:57 PDT)
- Youyi Peng (Tue Apr 15 2003 - 18:32:22 PDT)
ambpdb and protonate in AMBER7
- Francisco Blanco (Thu Apr 17 2003 - 04:38:29 PDT)
anal question
- Hai-Long Wang (Thu Apr 03 2003 - 13:48:11 PST)
Annealing blown up
- David A. Case (Thu Apr 24 2003 - 16:21:53 PDT)
- Nick Polfer (Thu Apr 24 2003 - 12:02:38 PDT)
any one has references to parallelization aspects of AMBER
- Harikrishnan (Tue Apr 29 2003 - 04:54:51 PDT)
- Satish Kumar (Tue Apr 29 2003 - 02:59:05 PDT)
anyone have AMBER benchmarks with gigabit ethernet?
- Ross Walker (Thu Apr 24 2003 - 06:20:07 PDT)
- Ross Walker (Thu Apr 24 2003 - 02:42:57 PDT)
- Carlos Simmerling (Wed Apr 23 2003 - 11:37:07 PDT)
atom position restraints
- Yuuki Komata (Tue Apr 29 2003 - 18:34:06 PDT)
- Yuuki Komata (Tue Apr 29 2003 - 05:44:25 PDT)
Beyond 1,000,000 atoms
- Vlad (Wed Apr 02 2003 - 14:45:21 PST)
Bugfixes
- Natasja Brooijmans (Fri Apr 11 2003 - 09:49:59 PDT)
- Francesc Corcho (Fri Apr 11 2003 - 04:40:08 PDT)
carnal hbond
- Hai-Long Wang (Wed Apr 30 2003 - 11:03:39 PDT)
CCL:MPI run problem
- Carlos Simmerling (Wed Apr 16 2003 - 13:26:42 PDT)
characteristics of nucleic acids homopolymers
- Ioana Cozmuta (Tue Apr 08 2003 - 11:33:03 PDT)
converting amber to gromos format
- Jake Isaacs (Wed Apr 23 2003 - 06:59:19 PDT)
CYS and HIS
- caldwell.heimdal.compchem.ucsf.edu (Wed Apr 16 2003 - 07:55:55 PDT)
- Youyi Peng (Wed Apr 16 2003 - 07:20:40 PDT)
debug leap
- Scott Brozell (Sat Apr 19 2003 - 16:40:03 PDT)
- vze6jslz.verizon.net (Sat Apr 19 2003 - 11:52:40 PDT)
Description of ATOM type in GLYCAM
- FyD (Tue Apr 29 2003 - 14:07:35 PDT)
- Peng Tao (Tue Apr 29 2003 - 12:14:52 PDT)
diffusion coefficients
- Thomas Cheatham (Mon Apr 14 2003 - 14:34:39 PDT)
- David A. Case (Sun Apr 13 2003 - 23:03:15 PDT)
- Yong Duan (Sun Apr 13 2003 - 20:50:48 PDT)
- yuan bo (Sun Apr 13 2003 - 19:34:25 PDT)
Examples for Energy Minimisation methods
- Carlos P. Sosa (Tue Apr 01 2003 - 10:08:27 PST)
- S.Swaminathan (Tue Apr 01 2003 - 12:35:41 PST)
force field parameters for phosphoserine
- David A. Case (Tue Apr 29 2003 - 07:56:48 PDT)
- Christoph Kluck (Tue Apr 29 2003 - 07:07:59 PDT)
frcmod file
- Wen Li (Thu Apr 03 2003 - 12:04:34 PST)
frcmod file for Free energy perturbation tutorial of valine to alanine
- dicksmit.umich.edu (Fri Apr 04 2003 - 10:06:37 PST)
free energy calculations
- Joseph Fernandez (Fri Apr 04 2003 - 13:18:25 PST)
free energy in sander
- Joseph Fernandez (Thu Apr 10 2003 - 19:58:30 PDT)
- David A. Case (Thu Apr 10 2003 - 15:45:05 PDT)
- Joseph Fernandez (Thu Apr 10 2003 - 14:32:52 PDT)
Future of structural biology conference
- David Cowburn (Thu Apr 24 2003 - 11:58:23 PDT)
Future of Structural Biology Conference, 2003, http://futurestructuralbiology.org
- David Cowburn (Tue Apr 29 2003 - 13:04:27 PDT)
GB/SA
- Robert G. Endres (Wed Apr 30 2003 - 12:57:31 PDT)
- Robert G. Endres (Mon Apr 28 2003 - 11:10:56 PDT)
- David A. Case (Wed Apr 23 2003 - 12:36:56 PDT)
- Robert G. Endres (Wed Apr 23 2003 - 09:26:14 PDT)
general minimisation methods
- S.Swaminathan (Fri Apr 04 2003 - 16:26:48 PST)
Groups defenition
- David A. Case (Wed Apr 09 2003 - 08:59:11 PDT)
- Javier Cuervo (Tue Apr 08 2003 - 13:31:27 PDT)
growing side chains
- Robert G. Endres (Mon Apr 07 2003 - 11:37:30 PDT)
how to restrain base pair
- David A. Case (Mon Apr 28 2003 - 12:14:49 PDT)
- Shuang Ding (Mon Apr 28 2003 - 11:59:58 PDT)
How to use GLYCAM force field in AMBER
- David A. Case (Wed Apr 23 2003 - 14:51:30 PDT)
- Peng Tao (Tue Apr 22 2003 - 08:08:06 PDT)
Hydrogen bond energy
- David A. Case (Thu Apr 03 2003 - 09:26:04 PST)
- Dr.K.Veluraja (Thu Apr 03 2003 - 02:37:02 PST)
ibelly and ntr
- Kristina Furse (Wed Apr 16 2003 - 12:51:43 PDT)
- sychen (Tue Apr 15 2003 - 20:03:57 PDT)
- David A. Case (Tue Apr 15 2003 - 16:13:11 PDT)
- Youyi Peng (Tue Apr 15 2003 - 14:59:59 PDT)
id_torus(): Could not find torus for atoms 1878 and 1894
- Yunfeng Hu (Mon Apr 14 2003 - 15:26:18 PDT)
job stopped
- CUI, Guanglei (Thu Apr 24 2003 - 13:32:29 PDT)
- Youyi Peng (Thu Apr 24 2003 - 13:33:37 PDT)
- Natasja Brooijmans (Thu Apr 24 2003 - 11:55:06 PDT)
- Youyi Peng (Thu Apr 24 2003 - 11:49:47 PDT)
- CUI, Guanglei (Thu Apr 24 2003 - 11:06:25 PDT)
- Youyi Peng (Thu Apr 24 2003 - 10:52:12 PDT)
leap problem
- yuan bo (Wed Apr 23 2003 - 20:49:36 PDT)
makeDIST_RST
- David A. Case (Thu Apr 17 2003 - 09:50:14 PDT)
- Youyi Peng (Wed Apr 16 2003 - 19:24:19 PDT)
MD went crazy
- Youyi Peng (Fri Apr 18 2003 - 12:28:14 PDT)
- Carlos Simmerling (Fri Apr 18 2003 - 12:04:49 PDT)
- Youyi Peng (Fri Apr 18 2003 - 11:55:51 PDT)
- Youyi Peng (Fri Apr 18 2003 - 11:33:26 PDT)
- Carlos Simmerling (Fri Apr 18 2003 - 10:31:41 PDT)
- Michael Crowley (Fri Apr 18 2003 - 10:30:53 PDT)
- Youyi Peng (Fri Apr 18 2003 - 10:36:35 PDT)
- Carlos Simmerling (Fri Apr 18 2003 - 09:17:11 PDT)
- Youyi Peng (Fri Apr 18 2003 - 09:17:24 PDT)
- Carlos Simmerling (Fri Apr 18 2003 - 08:20:07 PDT)
- Youyi Peng (Fri Apr 18 2003 - 08:20:25 PDT)
Metalloprotein
- chandran karunakaran (Mon Apr 14 2003 - 18:18:39 PDT)
MM-GBSA question
- Javier Cuervo (Fri Apr 18 2003 - 13:39:23 PDT)
mm_pbsa & nmode
- FyD (Tue Apr 08 2003 - 08:04:38 PDT)
mm_pbsa nmode calculation
- kbyun.wesleyan.edu (Wed Apr 23 2003 - 13:33:55 PDT)
- Holger Gohlke (Wed Apr 23 2003 - 12:12:51 PDT)
- kbyun.wesleyan.edu (Wed Apr 23 2003 - 11:33:17 PDT)
mm_pbsa_statistics.pm
- kbyun.wesleyan.edu (Tue Apr 22 2003 - 09:40:10 PDT)
MPI run problem
- William Wei (Wed Apr 16 2003 - 09:36:31 PDT)
mutating residues
- Craig A Bayse (Tue Apr 08 2003 - 09:09:38 PDT)
New Machine.sgi_mpi file
- Roberto Gomperts (Thu Apr 03 2003 - 10:33:35 PST)
Nitro group introduction in tyrosine residue
- chandran karunakaran (Mon Apr 07 2003 - 12:23:33 PDT)
nmode and mm_pbsa questions?
- Holger Gohlke (Fri Apr 25 2003 - 15:21:05 PDT)
- wentaofu (Fri Apr 25 2003 - 13:47:48 PDT)
nmode for S calculation
- wentaofu (Tue Apr 08 2003 - 16:22:47 PDT)
No statistical output for MM-PBSA?
- Holger Gohlke (Wed Apr 16 2003 - 11:05:38 PDT)
- Lishan Yao (Tue Apr 15 2003 - 19:25:22 PDT)
non bonded pair list
- David A. Case (Thu Apr 24 2003 - 16:24:37 PDT)
- Jean-François Taly (Thu Apr 24 2003 - 09:22:08 PDT)
old prmtop format in AMBER 6 differs from what is presented in AMBER 7 manual
- Filip Ryj�cek (Wed Apr 02 2003 - 04:29:07 PST)
Organic Solvents
- Jose Ramon Blas (Tue Apr 22 2003 - 15:00:58 PDT)
- Petrodler.aol.com (Tue Apr 22 2003 - 03:57:11 PDT)
- Carlos P. Sosa (Thu Apr 17 2003 - 08:17:54 PDT)
Periodic Boundary Condition in AMBER7 (the sander module)!
- David A. Case (Tue Apr 08 2003 - 15:25:53 PDT)
- Dat H. Nguyen (Tue Apr 08 2003 - 14:44:37 PDT)
phi and psi angles analysis
- Guanglei Cui (Tue Apr 29 2003 - 20:31:11 PDT)
- Holger Gohlke (Tue Apr 29 2003 - 16:48:50 PDT)
- Xiao Jian Tan (Tue Apr 29 2003 - 16:27:17 PDT)
please kindly help
- David A. Case (Mon Apr 07 2003 - 08:34:21 PDT)
- S.Swaminathan (Mon Apr 07 2003 - 19:03:34 PDT)
PME box information
- Khanh.Dao.iac.uib.no (Tue Apr 15 2003 - 02:56:38 PDT)
Polarizable simulation2
- David A. Case (Tue Apr 01 2003 - 13:49:39 PST)
- Lepsa (Tue Apr 01 2003 - 04:25:22 PST)
Problem Finishing Tutorial
- Ioana Cozmuta (Mon Apr 21 2003 - 16:41:13 PDT)
- Derek Smith (Mon Apr 21 2003 - 16:31:00 PDT)
Problem of Hbond in CARNAL
- sychen (Tue Apr 01 2003 - 06:23:11 PST)
- yuann (Tue Apr 01 2003 - 04:08:59 PST)
problem with tleap
- David A. Case (Tue Apr 08 2003 - 09:12:34 PDT)
- S.Swaminathan (Tue Apr 08 2003 - 18:56:44 PDT)
problem_namelist_reading
- Khanh.Dao.iac.uib.no (Tue Apr 29 2003 - 22:26:58 PDT)
- David A. Case (Tue Apr 29 2003 - 08:12:01 PDT)
- Khanh.Dao.iac.uib.no (Mon Apr 28 2003 - 23:19:46 PDT)
Problem_to_open_PROTON_INFO_file
- Venkata S Koppuravuri (Thu Apr 24 2003 - 12:43:59 PDT)
- David A. Case (Thu Apr 24 2003 - 08:30:32 PDT)
- Khanh.Dao.iac.uib.no (Thu Apr 24 2003 - 01:46:10 PDT)
Proper Restraint usage
- CUI, Guanglei (Tue Apr 15 2003 - 14:30:22 PDT)
- David A. Case (Tue Apr 15 2003 - 14:04:50 PDT)
- Steve Seibold (Tue Apr 15 2003 - 13:42:59 PDT)
Protein - DNA complex simulation - protocol
- Pratul Agarwal (Tue Apr 29 2003 - 07:39:18 PDT)
- Harikrishnan (Tue Apr 29 2003 - 06:16:25 PDT)
- Andreas Svrcek-Seiler (Tue Apr 29 2003 - 01:50:22 PDT)
- Harikrishnan (Mon Apr 28 2003 - 21:40:39 PDT)
protonate
- David A. Case (Tue Apr 08 2003 - 09:06:21 PDT)
- S.Swaminathan (Tue Apr 08 2003 - 12:14:50 PDT)
PSC Summer Workshop: Modeling from Protein Sequence to Structure
- Troy Wymore (Thu Apr 24 2003 - 10:33:39 PDT)
ptraj problem
- Sophia Kondratova (Fri Apr 04 2003 - 06:00:46 PST)
quasih
- cailliez (Thu Apr 17 2003 - 08:35:26 PDT)
question about H-bond in carnal?
- Sanjeev B.S. (Mon Apr 28 2003 - 23:59:15 PDT)
- Lishan Yao (Sun Apr 27 2003 - 17:37:13 PDT)
- Bill Ross (Fri Apr 25 2003 - 11:57:20 PDT)
- Sanjeev B.S. (Fri Apr 25 2003 - 08:53:35 PDT)
- Lishan Yao (Fri Apr 25 2003 - 08:24:56 PDT)
- Sanjeev B.S. (Fri Apr 25 2003 - 08:35:58 PDT)
- Lishan Yao (Fri Apr 25 2003 - 07:44:55 PDT)
question about MM-PBSA?
- Lepsa (Mon Apr 21 2003 - 23:50:42 PDT)
- Lishan Yao (Fri Apr 18 2003 - 07:10:24 PDT)
- Holger Gohlke (Thu Apr 17 2003 - 18:31:31 PDT)
- Lishan Yao (Thu Apr 17 2003 - 12:15:38 PDT)
- Lishan Yao (Tue Apr 08 2003 - 10:21:20 PDT)
Question: Nmode with counter ions.
- David A. Case (Thu Apr 24 2003 - 16:16:22 PDT)
- Masaki Tomimoto (Thu Apr 24 2003 - 10:09:02 PDT)
Request for Amber7 (fwd)
- Rajendra P. OJHA (Tue Apr 22 2003 - 02:53:12 PDT)
Request for Amber7 (xleap problem)
- John Bushnell (Tue Apr 22 2003 - 15:30:41 PDT)
Residual dipolar couplings
- McAteer, Kathleen (Wed Apr 30 2003 - 10:56:34 PDT)
sander & prmtop file generated from antechamber input ?
- David A. Case (Sun Apr 06 2003 - 22:28:58 PDT)
- sychen (Sun Apr 06 2003 - 09:12:44 PDT)
SANDER Source Code Documentation
- Jones, Garth A (Thu Apr 10 2003 - 00:07:13 PDT)
Side-chain/main-chain decomposition in MM-GBSA
- Holger Gohlke (Thu Apr 03 2003 - 14:46:52 PST)
- Lepsa (Thu Apr 03 2003 - 00:24:35 PST)
size of a simulation system
- Pratul Agarwal (Wed Apr 02 2003 - 12:02:29 PST)
- Ioana Cozmuta (Wed Apr 02 2003 - 10:37:40 PST)
- Pratul Agarwal (Wed Apr 02 2003 - 06:32:44 PST)
- Kristina Furse (Tue Apr 01 2003 - 14:36:01 PST)
- David A. Case (Tue Apr 01 2003 - 13:44:14 PST)
- Wen Li (Tue Apr 01 2003 - 07:49:42 PST)
solvents aren't loading
- Mac Brown (Tue Apr 15 2003 - 13:20:15 PDT)
SSBonds and charge problems
- David A. Case (Fri Apr 11 2003 - 22:29:53 PDT)
- caldwell.heimdal.compchem.ucsf.edu (Fri Apr 11 2003 - 12:50:04 PDT)
- Steve Seibold (Fri Apr 11 2003 - 12:54:23 PDT)
test
- Dr.Rajendra Joshi (Mon Apr 28 2003 - 18:58:57 PDT)
The error in the trajectory file
- Ling Zhang (Tue Apr 08 2003 - 09:37:58 PDT)
Tleap
- David A. Case (Tue Apr 08 2003 - 18:09:46 PDT)
- chandran karunakaran (Tue Apr 08 2003 - 16:01:21 PDT)
Tleap-metalloprotein
- Yong Duan (Thu Apr 10 2003 - 19:42:53 PDT)
- chandran karunakaran (Thu Apr 10 2003 - 18:20:40 PDT)
To: amber as a Nicer Person
- Dr. Carter, President (Mon Apr 14 2003 - 01:16:06 PDT)
topology file in large systems
- caldwell.heimdal.compchem.ucsf.edu (Thu Apr 17 2003 - 15:25:49 PDT)
- GUILLERMINA L ESTIU (Thu Apr 17 2003 - 14:58:35 PDT)
Trouble with AMBER 7
- Shafinaz (Mon Apr 07 2003 - 13:59:52 PDT)
trouble with OFF files
- M. L. Dodson (Mon Apr 21 2003 - 13:13:24 PDT)
- Mac Brown (Mon Apr 21 2003 - 12:07:32 PDT)
troubles on RS6000
- Wayne Dawson (Mon Apr 28 2003 - 02:37:50 PDT)
Trying to understand parm99.dat
- Yong Duan (Tue Apr 08 2003 - 18:48:48 PDT)
- Sichun Yang (Tue Apr 08 2003 - 17:44:32 PDT)
Unit of velocity
- A. Hungie (Thu Apr 03 2003 - 09:46:18 PST)
- David A. Case (Thu Apr 03 2003 - 09:18:11 PST)
- A. Hungie (Thu Apr 03 2003 - 05:38:59 PST)
unsubscribe from the mail list
- Xiaoqin Huang (Thu Apr 17 2003 - 05:15:11 PDT)
Using MPI, PBS
- Carlos Simmerling (Wed Apr 02 2003 - 11:29:41 PST)
- Ioana Cozmuta (Wed Apr 02 2003 - 11:13:01 PST)
- Venkata S Koppuravuri (Wed Apr 02 2003 - 10:58:23 PST)
Usubscribe
- Miguel de Federico (Fri Apr 11 2003 - 01:17:04 PDT)
velocity auto-correlation function
- A. Hungie (Wed Apr 16 2003 - 09:25:32 PDT)
very important
- CUI, Guanglei (Tue Apr 08 2003 - 07:47:55 PDT)
- Shafinaz (Tue Apr 08 2003 - 07:19:18 PDT)

Amber Archive Apr 2003 by subject