Amber Archive May 2003: by subject

(no subject)
- 你的朋友 (Thu May 29 2003 - 23:15:53 PDT)
- smolnar.jadeinc.com (Sat May 03 2003 - 11:19:25 PDT)
- Narang Manpreet Kaur (Fri May 02 2003 - 22:02:20 PDT)
10-12 H-bond terms
- Ioana Cozmuta (Mon May 12 2003 - 16:32:19 PDT)
- David A. Case (Mon May 12 2003 - 14:58:52 PDT)
- Ioana Cozmuta (Mon May 12 2003 - 12:50:40 PDT)
- Andreas Svrcek-Seiler (Sat May 10 2003 - 16:13:08 PDT)
- Ioana Cozmuta (Fri May 09 2003 - 15:27:53 PDT)
2 questions
- David A. Case (Fri May 09 2003 - 08:54:41 PDT)
- Carlos Simmerling (Fri May 09 2003 - 04:08:51 PDT)
- FyD (Fri May 09 2003 - 03:02:41 PDT)
A question about AMBER, leaprc.ff02EP
- yuming chen (Wed May 14 2003 - 03:45:11 PDT)
- David A. Case (Tue May 13 2003 - 23:26:56 PDT)
- yuming chen (Tue May 13 2003 - 22:17:47 PDT)
a question about constructing a periodic box by PLEP.
- Margaret Shun Cheung (Tue May 20 2003 - 08:48:56 PDT)
a question about scale factor
- Carlos Simmerling (Sat May 10 2003 - 21:00:24 PDT)
- Ye Mei (Sat May 10 2003 - 19:53:45 PDT)
A question of how to choose a appropriate box size for imposing periodic boundary conditions in the simulations.
- Margaret Shun Cheung (Fri May 23 2003 - 08:18:39 PDT)
A simple question about offset, want to make sure
- Huang Zunnan (Sat May 31 2003 - 09:44:46 PDT)
about the dielectric
- Yong Duan (Wed May 28 2003 - 02:24:58 PDT)
- Ye Mei (Wed May 28 2003 - 00:57:49 PDT)
- Ye Mei (Wed May 28 2003 - 00:42:22 PDT)
Amber 7.xx installation on FreeBSD
- M. L. Dodson (Tue May 20 2003 - 14:19:21 PDT)
- Joseph Maxwell (Tue May 20 2003 - 13:27:11 PDT)
Amber on SGI with Itanium compilers for linux
- Sanjeev B.S. (Tue May 27 2003 - 06:58:17 PDT)
Amber on SGI with Itanium compilers for linux (fwd)
- Sanjeev B.S. (Tue May 27 2003 - 05:21:20 PDT)
AMD opteron
- Tru Huynh (Wed May 28 2003 - 09:52:18 PDT)
- Tru Huynh (Wed May 28 2003 - 06:08:51 PDT)
- Hai-Long Wang (Tue May 27 2003 - 08:57:39 PDT)
ANAL in AMBER
- David A. Case (Fri May 09 2003 - 09:11:33 PDT)
- A.Madhumalar (Tue May 06 2003 - 00:25:05 PDT)
anal, amber7 and resnum 0
- David A. Case (Fri May 16 2003 - 14:57:33 PDT)
- Sanjeev B.S. (Fri May 16 2003 - 15:23:04 PDT)
- Sanjeev B.S. (Fri May 16 2003 - 15:15:19 PDT)
antechamber read gaussian file
- quch quch (Thu May 29 2003 - 13:32:10 PDT)
- quch quch (Thu May 29 2003 - 13:32:14 PDT)
atomic positional fluctuation
- Holger Gohlke (Thu May 15 2003 - 13:38:07 PDT)
- pengyo.rwja.umdnj.edu (Thu May 15 2003 - 11:22:25 PDT)
bad atom type f(fluorine) in MM-PBSA?
- Lishan Yao (Wed May 21 2003 - 10:12:17 PDT)
- Holger Gohlke (Wed May 21 2003 - 08:49:20 PDT)
- Lishan Yao (Wed May 21 2003 - 06:29:01 PDT)
best force field for Protein+DNA
- Robert G. Endres (Fri May 23 2003 - 08:14:51 PDT)
Calcium in proteins
- David A. Case (Tue May 20 2003 - 07:40:06 PDT)
- Javier Cuervo (Mon May 19 2003 - 17:11:54 PDT)
can not minimize
- tang kwa (Mon May 05 2003 - 07:45:24 PDT)
- Guanglei Cui (Mon May 05 2003 - 07:07:39 PDT)
- tang kwa (Mon May 05 2003 - 06:57:40 PDT)
- tang kwa (Mon May 05 2003 - 06:49:31 PDT)
- Guanglei Cui (Mon May 05 2003 - 06:42:37 PDT)
- Carlos Simmerling (Mon May 05 2003 - 05:00:04 PDT)
- tang kwa (Mon May 05 2003 - 04:57:42 PDT)
center command
- Ioana Cozmuta (Fri May 23 2003 - 14:40:50 PDT)
CFP: Informatics Approaches in Structural Genomics at PSB 2004
- Sean Mooney (Wed May 28 2003 - 08:46:17 PDT)
charge fitting for c-term homocysteine.
- X. Tan (Thu May 22 2003 - 19:25:19 PDT)
clustering trajectories
- chernhoe (Wed May 28 2003 - 20:19:41 PDT)
coordinate files from carnal
- jaw3.cec.wustl.edu (Thu May 29 2003 - 07:13:25 PDT)
current AMBER citation?
- David A. Case (Thu May 08 2003 - 08:16:13 PDT)
- Jake Isaacs (Thu May 08 2003 - 07:08:38 PDT)
difference between iwrap and image?
- yuann (Sat May 10 2003 - 22:47:23 PDT)
distance-dependent dielectric function
- Shixiang Yan (Fri May 23 2003 - 09:39:04 PDT)
- Robert G. Endres (Fri May 23 2003 - 08:44:27 PDT)
DNA base-step distortion
- Jiri Sponer (Mon May 19 2003 - 02:56:00 PDT)
- kbyun.wesleyan.edu (Sun May 18 2003 - 16:43:59 PDT)
- kbyun.wesleyan.edu (Sun May 18 2003 - 12:37:12 PDT)
Does Anyone Have a Working MACHINE File for Solaris/SPARC?
- Chen, Ya (Wed May 28 2003 - 10:30:53 PDT)
Does Leap has a problem with Isoleucines?
- Holger Gohlke (Wed May 28 2003 - 09:14:47 PDT)
- Frederico.Miranda.ibmb.uib.no (Tue May 27 2003 - 23:28:21 PDT)
Etot is not constant in NVE ensemble
- darden (Fri May 09 2003 - 16:20:24 PDT)
- bishop (Fri May 09 2003 - 12:41:34 PDT)
- A. Hungie (Fri May 09 2003 - 09:08:56 PDT)
- Thomas Cheatham (Fri May 09 2003 - 08:49:18 PDT)
- Yong Duan (Fri May 09 2003 - 07:58:25 PDT)
- darden (Fri May 09 2003 - 07:38:53 PDT)
- A. Hungie (Fri May 09 2003 - 06:46:43 PDT)
EWALD BOMB
- Michael Crowley (Tue May 27 2003 - 08:45:22 PDT)
- tang kwa (Tue May 27 2003 - 08:38:31 PDT)
- Yong Duan (Mon May 26 2003 - 16:51:22 PDT)
- Holger Gohlke (Mon May 26 2003 - 12:58:00 PDT)
- tang kwa (Mon May 26 2003 - 07:27:07 PDT)
Ewald: coeff, error estimate
- darden (Thu May 01 2003 - 14:30:48 PDT)
- Paula Petrone (Thu May 01 2003 - 09:05:28 PDT)
Fluorine atom type in mm_pbsa?
- David A. Case (Tue May 20 2003 - 07:30:53 PDT)
- Lishan Yao (Tue May 20 2003 - 06:12:04 PDT)
- Lishan Yao (Mon May 19 2003 - 14:00:09 PDT)
force field parameters for torsions
- David A. Case (Mon May 19 2003 - 10:44:27 PDT)
- cailliez (Mon May 19 2003 - 08:19:36 PDT)
force field parameters for torsions (I am away)
- Charles Laughton (Mon May 19 2003 - 10:49:32 PDT)
From Dr. Ekaterina Nikitina
- Nikitina Ekaterina (Sun May 25 2003 - 03:26:09 PDT)
- David A. Case (Thu May 22 2003 - 10:16:58 PDT)
- caldwell.heimdal.compchem.ucsf.edu (Tue May 20 2003 - 09:27:04 PDT)
H-O-H angle
- Ioana Cozmuta (Tue May 13 2003 - 21:32:17 PDT)
- Luis Gracia (Tue May 13 2003 - 14:46:05 PDT)
- Ioana Cozmuta (Tue May 13 2003 - 13:17:54 PDT)
HBOND energies in sander
- Holger Gohlke (Mon May 26 2003 - 10:24:01 PDT)
- Francisco Blanco (Sun May 25 2003 - 04:37:52 PDT)
Heat of Vaporization
- David A. Case (Tue May 13 2003 - 08:12:41 PDT)
- Karl N. Kirschner (Mon May 12 2003 - 07:46:17 PDT)
help me switching from amber5 to amber6
- David A. Case (Wed May 07 2003 - 17:59:54 PDT)
- Asif Rahaman (Wed May 07 2003 - 17:18:01 PDT)
Help with Sander test output error
- Donald Keidel (Fri May 02 2003 - 10:38:11 PDT)
how to set up a carbon nanotube pdb file
- zhaoxc.puccini.che.pitt.edu (Mon May 05 2003 - 14:24:10 PDT)
Hybdrogen bonds and LJ 10-12
- David A. Case (Thu May 22 2003 - 10:21:18 PDT)
- Michal Otyepka (Wed May 21 2003 - 02:49:47 PDT)
I still have problems with parm99.dat
- cailliez (Wed May 21 2003 - 06:37:19 PDT)
Increase lastist in the &cntrl namelist
- Ioana Cozmuta (Tue May 13 2003 - 13:26:48 PDT)
- Dodi Heryadi (Tue May 13 2003 - 13:14:25 PDT)
- Ioana Cozmuta (Tue May 13 2003 - 11:58:09 PDT)
- GUILLERMINA L ESTIU (Tue May 13 2003 - 11:37:24 PDT)
- GUILLERMINA L ESTIU (Tue May 13 2003 - 11:16:09 PDT)
information
- aram joel panay (Thu May 29 2003 - 20:45:48 PDT)
initial velocity
- Carlos Simmerling (Fri May 02 2003 - 07:20:09 PDT)
- Natasja Brooijmans (Fri May 02 2003 - 07:18:26 PDT)
- Youyi Peng (Fri May 02 2003 - 07:22:52 PDT)
IR6 and makeDIST-RST
- Francisco Blanco (Sat May 24 2003 - 12:15:29 PDT)
Latest Leap Compile Errors
- Stephen P. Molnar, Ph.D. (Mon May 05 2003 - 06:18:35 PDT)
- David A. Case (Sun May 04 2003 - 14:02:05 PDT)
- smolnar.jadeinc.com (Sun May 04 2003 - 04:44:50 PDT)
leap complains!
- Kristina Furse (Thu May 22 2003 - 16:17:16 PDT)
- Jose Ramon Blas (Thu May 22 2003 - 15:03:02 PDT)
- Layi Adekoya (Thu May 22 2003 - 04:56:11 PDT)
LES analysis tool other than Moil-view
- Sameer P. Kawatkar (Wed May 28 2003 - 11:21:38 PDT)
Mainchain.dat
- Lepsa (Tue May 20 2003 - 06:34:36 PDT)
- tang kwa (Mon May 19 2003 - 09:16:12 PDT)
MD input file for MM-PBSA calculations
- Lepsa (Mon May 26 2003 - 02:03:02 PDT)
- Natasja Brooijmans (Sat May 24 2003 - 09:28:39 PDT)
- Thomas Steinbrecher (Sat May 24 2003 - 05:36:43 PDT)
MD problem
- Yong Duan (Thu May 29 2003 - 17:58:21 PDT)
- Guanglei Cui (Thu May 29 2003 - 14:28:07 PDT)
- Shuang Ding (Thu May 29 2003 - 14:30:54 PDT)
- Guanglei Cui (Thu May 29 2003 - 14:14:14 PDT)
- Shuang Ding (Thu May 29 2003 - 14:04:22 PDT)
- Carlos Simmerling (Thu May 29 2003 - 13:56:27 PDT)
- Shuang Ding (Thu May 29 2003 - 13:47:20 PDT)
MD steps limit in sander (Amber 6)
- Carlos Simmerling (Wed May 07 2003 - 08:51:01 PDT)
Minimisation - peek_ewald_inpcrd: SHOULD NOT BE HERE
- Omar Wahab (Mon May 12 2003 - 02:49:52 PDT)
minimizaiton in vacuum
- tang kwa (Tue May 06 2003 - 05:17:03 PDT)
- David A. Case (Mon May 05 2003 - 09:01:16 PDT)
Minimization problem w/ counter-ion !
- David A. Case (Thu May 22 2003 - 09:51:28 PDT)
minimization with restraints
- Carlos Simmerling (Tue May 20 2003 - 06:42:43 PDT)
- A. Hungie (Tue May 06 2003 - 05:57:22 PDT)
mm_gbsa question
- Holger Gohlke (Tue May 27 2003 - 18:40:36 PDT)
- Javier Cuervo (Tue May 27 2003 - 17:49:18 PDT)
mm_pbsa and B/Z DNA relative stabilities
- Robert G. Endres (Wed May 14 2003 - 06:36:14 PDT)
- Peter Gannett (Wed May 14 2003 - 04:54:47 PDT)
mm_pbsa with PBCAL = 0
- Holger Gohlke (Fri May 16 2003 - 14:34:41 PDT)
- wentaofu (Fri May 16 2003 - 12:14:42 PDT)
multiple timesteps
- Ioana Cozmuta (Fri May 02 2003 - 15:41:51 PDT)
Newton-Raphson minimization for large systems
- Qing Zhang (Wed May 14 2003 - 16:09:07 PDT)
no MD output
- Youyi Peng (Mon May 12 2003 - 12:01:47 PDT)
non bonded pairlist?
- Arvid Soederhaell (Wed May 07 2003 - 00:34:27 PDT)
non-periodic system
- Yong Duan (Wed May 21 2003 - 20:24:01 PDT)
- Yong Duan (Wed May 21 2003 - 20:17:03 PDT)
- Ioana Cozmuta (Wed May 21 2003 - 19:47:34 PDT)
- Michael Crowley (Wed May 21 2003 - 16:27:03 PDT)
- Ioana Cozmuta (Wed May 21 2003 - 15:50:18 PDT)
NOTIFICATION
- CLARK WOOD (Tue May 27 2003 - 06:40:26 PDT)
- CLARK WOOD (Tue May 27 2003 - 06:16:49 PDT)
- Jiten (Tue May 27 2003 - 17:31:10 PDT)
- Joseph Maxwell (Tue May 27 2003 - 09:11:36 PDT)
nucgen.dat
- Ioana Cozmuta (Thu May 15 2003 - 13:08:50 PDT)
- Maria Zavodszky (Thu May 15 2003 - 11:37:14 PDT)
off-diagonal VDW term
- David A. Case (Tue May 20 2003 - 07:43:33 PDT)
- Yong Duan (Tue May 20 2003 - 00:24:25 PDT)
- Ioana Cozmuta (Mon May 19 2003 - 18:24:34 PDT)
- Jiyoung Heo (Mon May 19 2003 - 18:01:13 PDT)
Order parameters
- Holger Gohlke (Tue May 27 2003 - 12:15:15 PDT)
- cailliez (Tue May 27 2003 - 01:25:30 PDT)
parameters for nitro group
- David A. Case (Tue May 13 2003 - 09:45:02 PDT)
- Shixiang Yan (Tue May 13 2003 - 08:30:49 PDT)
parm99
- Bayly, Christopher (Thu May 22 2003 - 06:36:18 PDT)
- Junmei Wang (Wed May 21 2003 - 11:30:18 PDT)
- David A. Case (Tue May 20 2003 - 15:37:32 PDT)
- cailliez (Tue May 20 2003 - 05:55:17 PDT)
Phosphorylated Serine Library
- Frederico.Miranda.ibmb.uib.no (Fri May 30 2003 - 01:01:31 PDT)
Phosphotyrosine parametrization
- Obdulia Rabal (Thu May 08 2003 - 00:51:19 PDT)
Pi-Pi stacking
- Fernando Martin (Tue May 06 2003 - 10:35:45 PDT)
Please help on xleap: FATAL ERROR
- Margaret Shun Cheung (Fri May 23 2003 - 07:06:10 PDT)
- John Bushnell (Thu May 22 2003 - 19:04:15 PDT)
- David A. Case (Thu May 22 2003 - 17:25:07 PDT)
- Margaret Shun Cheung (Thu May 22 2003 - 15:20:42 PDT)
problem about virtual box?
- Thomas E. Cheatham, III (Thu May 01 2003 - 10:33:49 PDT)
- Youyi Peng (Thu May 01 2003 - 10:42:47 PDT)
- Thomas Cheatham (Thu May 01 2003 - 10:07:52 PDT)
- pengyo.rwja.umdnj.edu (Thu May 01 2003 - 09:20:10 PDT)
- Carlos Simmerling (Thu May 01 2003 - 08:46:05 PDT)
- Youyi Peng (Thu May 01 2003 - 08:49:00 PDT)
problem on MD simulation of damage DNA
- Carlos Simmerling (Thu May 01 2003 - 13:20:02 PDT)
- Shuang Ding (Thu May 01 2003 - 13:11:04 PDT)
Problem with CMC/MD
- Sameer P. Kawatkar (Tue May 20 2003 - 08:35:16 PDT)
problems with anal in amber7
- Liliana Wroblewska (Fri May 23 2003 - 14:53:28 PDT)
protonate problem
- David A. Case (Wed May 14 2003 - 11:36:04 PDT)
- Venkata S Koppuravuri (Wed May 14 2003 - 10:17:39 PDT)
ptraj and rdf help
- tianxiao yang (Wed May 21 2003 - 15:54:59 PDT)
ptraj generated PDB files
- David A. Case (Fri May 16 2003 - 08:43:34 PDT)
- caldwell.heimdal.compchem.ucsf.edu (Fri May 16 2003 - 06:07:57 PDT)
- Fabian Boes (Fri May 16 2003 - 07:01:38 PDT)
ptraj rdf help
- Thomas Cheatham (Wed May 21 2003 - 21:12:57 PDT)
- tianxiao yang (Wed May 21 2003 - 15:28:26 PDT)
Question about BELLY NMODE
- Masaki Tomimoto (Fri May 02 2003 - 08:46:36 PDT)
- Masaki Tomimoto (Fri May 02 2003 - 08:30:36 PDT)
Questions about statistics output of mm_pbsa?
- Lishan Yao (Fri May 23 2003 - 06:31:44 PDT)
- Lishan Yao (Fri May 23 2003 - 06:22:07 PDT)
- David A. Case (Thu May 22 2003 - 17:32:15 PDT)
- Holger Gohlke (Thu May 22 2003 - 14:41:32 PDT)
- Lishan Yao (Thu May 22 2003 - 14:04:04 PDT)
Questoin about temperature
- Maverick (Thu May 01 2003 - 22:27:29 PDT)
Residual dipolar couplings
- McAteer, Kathleen (Wed May 21 2003 - 10:49:18 PDT)
- McAteer, Kathleen (Tue May 20 2003 - 14:03:58 PDT)
- David A. Case (Fri May 02 2003 - 10:21:53 PDT)
RESP, constraining Dipole Moment
- Artur Galstyan (Mon May 19 2003 - 03:06:51 PDT)
RMSD fluctuation too much
- Carlos Simmerling (Thu May 08 2003 - 08:26:41 PDT)
- Youyi Peng (Thu May 08 2003 - 08:02:43 PDT)
RMSF problem
- yuan bo (Sat May 10 2003 - 02:31:27 PDT)
rotational and translational motion
- Carlos Simmerling (Thu May 22 2003 - 05:54:51 PDT)
- Jean-François Taly (Thu May 22 2003 - 05:45:18 PDT)
Sander help
- David A. Case (Tue May 13 2003 - 17:51:12 PDT)
- tianxiao yang (Tue May 13 2003 - 16:47:17 PDT)
saveAmberParm problems in xleap
- Wayne Dawson (Thu May 08 2003 - 02:02:45 PDT)
- Ioana Cozmuta (Tue May 06 2003 - 13:54:49 PDT)
- Wayne Dawson (Tue May 06 2003 - 10:04:19 PDT)
- Guanglei Cui (Tue May 06 2003 - 06:42:13 PDT)
- caldwell.heimdal.compchem.ucsf.edu (Tue May 06 2003 - 05:45:36 PDT)
- Wayne Dawson (Tue May 06 2003 - 01:14:58 PDT)
School Amber Study
- Treakle, Kirk (Mon May 12 2003 - 10:00:33 PDT)
serine/tyrosine in charged states
- Layi Adekoya (Wed May 14 2003 - 05:26:55 PDT)
Simple math of memory calculation for nmode
- David A. Case (Thu May 01 2003 - 17:23:06 PDT)
- Masaki Tomimoto (Thu May 01 2003 - 11:26:08 PDT)
Simple question about sander parameter set
- Peng Tao (Tue May 13 2003 - 08:19:50 PDT)
- David A. Case (Tue May 13 2003 - 08:00:22 PDT)
- Peng Tao (Tue May 13 2003 - 07:44:40 PDT)
Simulation under physiological conditions
- Andreas Svrcek-Seiler (Thu May 15 2003 - 09:11:13 PDT)
- Michal Otyepka (Thu May 15 2003 - 08:50:44 PDT)
- Michal Otyepka (Thu May 15 2003 - 08:02:34 PDT)
SPC/E model -LJ parameters
- Ioana Cozmuta (Sun May 04 2003 - 14:55:53 PDT)
SPC/E water model
- Ioana Cozmuta (Wed May 07 2003 - 01:53:43 PDT)
- Holger Gohlke (Sun May 04 2003 - 16:27:01 PDT)
- Ioana Cozmuta (Sun May 04 2003 - 14:38:06 PDT)
translational and rotational motion (more information)
- Carlos Simmerling (Thu May 22 2003 - 06:35:13 PDT)
- Jean-François Taly (Thu May 22 2003 - 06:25:49 PDT)
unit of vlimit?
- Fabian Boes (Mon May 12 2003 - 07:36:25 PDT)
upper limited of memory for nmode
- wentaofu (Fri May 02 2003 - 17:06:06 PDT)
Use of Mg2+ in AMBER 7
- Peter Anderson (Thu May 08 2003 - 11:55:06 PDT)
using distance restraints in Sander (AIX 4.3 RS6000)
- David A. Case (Fri May 16 2003 - 13:42:18 PDT)
- Wayne Dawson (Fri May 16 2003 - 01:33:02 PDT)
Using GLYCAM in sander with a non-zero 10-12 coefficient
- Peng Tao (Wed May 14 2003 - 11:54:32 PDT)
water box distortion
- Holger Gohlke (Sat May 24 2003 - 18:26:21 PDT)
- GUILLERMINA L ESTIU (Sat May 24 2003 - 08:34:11 PDT)
- David A. Case (Fri May 23 2003 - 16:13:40 PDT)
- caldwell.heimdal.compchem.ucsf.edu (Fri May 23 2003 - 14:21:33 PDT)
- GUILLERMINA L ESTIU (Fri May 23 2003 - 13:36:17 PDT)
water residence time analysis
- Mahadevan Seetharaman (Tue May 13 2003 - 10:18:14 PDT)
What kind of interactions are ignored for end group interactions
- Carlos Simmerling (Fri May 09 2003 - 14:07:26 PDT)
- Huang Zunnan (Fri May 09 2003 - 13:41:10 PDT)
Xleap adding torsions
- Andrew Petersen (Tue May 20 2003 - 08:32:40 PDT)
Xleap: 'triangular' and 'square' bond
- Andreas Svrcek-Seiler (Thu May 22 2003 - 06:00:58 PDT)
- Christian Gossens (Thu May 22 2003 - 03:58:51 PDT)

Amber Archive May 2003 by subject