AMBER Archive (2002) - By Subject

2133 messages sorted by: [ author ] [ date ] [ thread ]
About this archive

Starting: Wed Jan 02 2002 - 16:22:14 CST
Ending: Tue Dec 31 2002 - 15:51:31 CST

Carlos Simmerling (Tue Jul 23 2002 - 06:48:48 CDT)

Lepsa (Wed Apr 17 2002 - 09:38:47 CDT)

Carlos Simmerling (Sat Apr 13 2002 - 07:06:29 CDT)

"amber mail"
- jim caldwell (Thu Jul 25 2002 - 11:11:01 CDT)
"crd" file created with VMD
- Soonmin Jang (Wed Jul 24 2002 - 02:28:27 CDT)
- David Case (Wed Jul 24 2002 - 02:04:02 CDT)
- Carlos Simmerling (Tue Jul 23 2002 - 22:02:50 CDT)
- Carlos Simmerling (Tue Jul 23 2002 - 20:42:15 CDT)
- Soonmin Jang (Tue Jul 23 2002 - 19:47:04 CDT)
- Soonmin Jang (Tue Jul 23 2002 - 11:23:56 CDT)
"flags" in .lib files
- Bill Ross (Wed Jan 23 2002 - 13:39:45 CST)
- Sue Heavner (Wed Jan 23 2002 - 10:22:08 CST)
"number of processors must be a power of two"
- Michael Crowley (Tue Aug 06 2002 - 12:31:50 CDT)
- Jim (Tue Aug 06 2002 - 12:29:48 CDT)
- David A. Case (Tue Aug 06 2002 - 11:40:33 CDT)
- Sanjeev B.S. (Tue Aug 06 2002 - 11:17:35 CDT)
- Jim (Tue Aug 06 2002 - 09:50:53 CDT)
"number of processors must be a power of two" (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:52:01 CDT)
"Unit 5 Error" with a Linux/MPICH Amber7
- Vincent BOSQUIER (Mon May 06 2002 - 11:44:09 CDT)
- Stéphane Teletchéa (Mon May 06 2002 - 11:22:42 CDT)
- David Case (Mon May 06 2002 - 11:18:24 CDT)
- Vincent BOSQUIER (Mon May 06 2002 - 10:50:07 CDT)
'triangular' bond or angle
- Mahadevan Seetharaman (Tue Jul 30 2002 - 15:53:20 CDT)
(no subject)
- Jennifer Hawkings (Sat Dec 07 2002 - 16:48:46 CST)
- Narang Manpreet Kaur (Fri Nov 29 2002 - 04:54:03 CST)
- CHAUMONT Alain (Mon Nov 25 2002 - 09:32:50 CST)
- Narang Manpreet Kaur (Sat Nov 23 2002 - 04:40:12 CST)
- Narang Manpreet Kaur (Sat Nov 16 2002 - 04:17:02 CST)
- Monica (Thu Nov 14 2002 - 00:26:57 CST)
- kbyun_at_wesleyan.edu (Tue Oct 08 2002 - 13:10:53 CDT)
- Ioana Cozmuta (Fri Oct 04 2002 - 19:12:44 CDT)
- Apostoluk, Wlodzimierz K (Wed Sep 25 2002 - 14:09:53 CDT)
- Prem Raj (Fri Sep 20 2002 - 11:42:14 CDT)
- Giulio Rastelli (Wed Aug 07 2002 - 04:07:21 CDT)
- sepideh ameli (Sun Aug 04 2002 - 14:01:20 CDT)
- deepak rangaswamy (Wed Jul 24 2002 - 22:57:14 CDT)
- deepak rangaswamy (Tue Jul 23 2002 - 02:01:41 CDT)
- Narang Manpreet Kaur (Wed Jul 03 2002 - 10:08:40 CDT)
- Christian.Pilger_at_bc.boehringer-ingelheim.com (Mon Jun 17 2002 - 05:09:11 CDT)
- Christian.Pilger_at_bc.boehringer-ingelheim.com (Fri Jun 14 2002 - 00:30:15 CDT)
- Snyder, James (Sun Jun 09 2002 - 19:45:03 CDT)
- Ishita sharma (Mon Jun 03 2002 - 06:07:38 CDT)
- SPEROLEEM_at_aol.com (Thu May 30 2002 - 17:51:26 CDT)
- Sophia Kondratova (Tue May 21 2002 - 13:37:24 CDT)
- Sophia Kondratova (Mon May 06 2002 - 08:13:53 CDT)
- Bill Ross (Tue Apr 23 2002 - 14:30:58 CDT)
- SPEROLEEM_at_aol.com (Mon Apr 22 2002 - 13:47:28 CDT)
- deepak rangaswamy (Sat Apr 20 2002 - 00:22:54 CDT)
- Filip Ryjacek (Wed Apr 17 2002 - 11:01:48 CDT)
- Mark Beardsell (Thu Apr 11 2002 - 08:36:29 CDT)
- Mark Hsieh (Wed Apr 10 2002 - 15:31:50 CDT)
- deepak rangaswamy (Tue Apr 02 2002 - 22:52:55 CST)
- Campbell, Matthew P (Tue Mar 05 2002 - 11:21:07 CST)
- deepak rangaswamy (Fri Mar 01 2002 - 05:00:51 CST)
- Ian Bates (Wed Feb 27 2002 - 15:23:17 CST)
- deepak rangaswamy (Tue Feb 26 2002 - 05:28:18 CST)
- Sophia Kondratova (Mon Jan 14 2002 - 12:28:01 CST)
- amutha ramaswamy (Thu Jan 10 2002 - 04:11:15 CST)
*.top file: "PARM-F-UHOSED, try again"
- Michael Ford (Thu Oct 31 2002 - 11:43:10 CST)
- David A. Case (Thu Oct 31 2002 - 11:19:06 CST)
- david (Thu Oct 31 2002 - 11:17:18 CST)
.OFF file format
- Bill Ross (Mon Feb 18 2002 - 14:26:16 CST)
- Dr Jan Rosenzweig (Mon Feb 18 2002 - 12:14:27 CST)
.top files read into xLeap?
- David A. Case (Mon Nov 11 2002 - 20:20:41 CST)
- Arvid Soederhaell (Mon Nov 11 2002 - 04:24:00 CST)
2D RMSd
- Luo Liu (Tue Oct 08 2002 - 03:32:34 CDT)
2nd restart
- CUI, Guanglei (Sun Oct 27 2002 - 11:02:30 CST)
4 Medicinal and Computational Chemistry Candidates
- medicinal and Compuatational Chemistry Resumes and Jobs (Tue Apr 16 2002 - 16:55:48 CDT)
64-bit Compilation SUN's forte compiler
- David A. Case (Mon Oct 28 2002 - 21:41:15 CST)
- Fernando Martin (Mon Oct 28 2002 - 18:24:21 CST)
- Scott Brozell (Mon Oct 28 2002 - 18:00:08 CST)
- Ioana Cozmuta (Mon Oct 28 2002 - 17:33:49 CST)
- Fernando Martin (Mon Oct 28 2002 - 17:15:52 CST)
a couple missing gaff angle terms
- Matthew Lee (Fri Aug 16 2002 - 16:55:44 CDT)
a freeware to display RMSD matrices
- CUI, Guanglei (Thu Sep 19 2002 - 08:42:29 CDT)
- Vlad Cojocaru (Thu Sep 19 2002 - 07:44:53 CDT)
a leap question
- David A. Case (Thu Oct 17 2002 - 10:35:01 CDT)
- CUI, Guanglei (Thu Oct 17 2002 - 08:43:24 CDT)
- Vlad Cojocaru (Thu Oct 17 2002 - 08:20:23 CDT)
a little bit confused with leap-frog algorithm...
- Margaret Cheung (Sat Mar 30 2002 - 21:35:36 CST)
- David Case (Thu Mar 28 2002 - 19:52:38 CST)
- Margaret Cheung (Thu Mar 28 2002 - 15:08:40 CST)
a missing variable
- Matthew Randolph Lee, Ph.D. (Wed Aug 28 2002 - 17:27:12 CDT)
- Vlad Cojocaru (Wed Aug 28 2002 - 15:43:04 CDT)
a more general question
- Vlad Cojocaru (Tue Apr 23 2002 - 09:20:34 CDT)
a more general question (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:41 CDT)
a more general question about ff (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:25 CDT)
a problem
- John Bushnell (Wed Apr 24 2002 - 16:02:31 CDT)
- Vlad Cojocaru (Mon Apr 22 2002 - 10:56:48 CDT)
a problem with AMBER7
- Vlad Cojocaru (Thu Jun 27 2002 - 05:12:58 CDT)
a question about .in files
- Bill Ross (Wed Mar 06 2002 - 13:16:53 CST)
- Vlad Cojocaru (Wed Mar 06 2002 - 09:00:02 CST)
a question about carnal
- Vlad Cojocaru (Wed Aug 14 2002 - 11:39:36 CDT)
a question about force field in AMBER
- David A. Case (Mon Dec 16 2002 - 19:56:29 CST)
- sychen (Sat Dec 14 2002 - 23:17:59 CST)
- jzhou (Sat Dec 14 2002 - 19:55:15 CST)
a second question
- Ioana Cozmuta (Mon Nov 25 2002 - 18:20:52 CST)
a water jumps
- David Case (Tue Jul 30 2002 - 00:13:16 CDT)
- Masaki Tomimoto (Mon Jul 29 2002 - 22:47:21 CDT)
about amber and charmm, thanks
- Zhang Jian (Sun Sep 08 2002 - 04:10:57 CDT)
about AMBER parallel edition
- Shimono Fumihiro (Thu Oct 03 2002 - 06:46:14 CDT)
- Shimono Fumihiro (Thu Oct 03 2002 - 06:07:36 CDT)
About counterions
- David A. Case (Thu Dec 05 2002 - 13:47:04 CST)
- Andrei Leitão (Thu Dec 05 2002 - 13:10:30 CST)
about dummy parameter of multiplicity
- David A. Case (Thu Oct 10 2002 - 13:37:40 CDT)
- sxzheng (Thu Oct 10 2002 - 02:55:15 CDT)
about ew_legal.h
- David Case (Wed May 01 2002 - 11:10:36 CDT)
- X. Tan (Tue Apr 30 2002 - 19:12:01 CDT)
About Group in Carnal
- William Wei (Thu Apr 25 2002 - 10:50:08 CDT)
About heating...
- David A. Case (Wed Dec 18 2002 - 13:42:51 CST)
- Andrei Leitão (Wed Dec 18 2002 - 12:23:43 CST)
about sander_classic AMBER6.0
- Nikolai Smolin (Mon May 20 2002 - 08:08:14 CDT)
about solvateOct
- Nikolai Smolin (Fri Jul 19 2002 - 03:22:20 CDT)
About the box info read error
- Bill Ross (Fri May 17 2002 - 15:33:51 CDT)
About the Memory allocation in MM_PBSA and SANDER
- Alan Leo (Fri Oct 04 2002 - 07:46:15 CDT)
About the sander_classic calculation
- John Bushnell (Thu Apr 04 2002 - 16:31:11 CST)
- Alan Leo (Thu Apr 04 2002 - 15:32:34 CST)
acetyl groups on protein fragments
- Laurent Chiche (Fri Jul 26 2002 - 02:43:03 CDT)
- Elizabeth K. White (Thu Jul 25 2002 - 13:55:04 CDT)
add DUMMY atom into coordinate file
- Alan Leo (Fri Aug 16 2002 - 14:51:35 CDT)
- yuann (Fri Aug 16 2002 - 04:12:04 CDT)
adding_hydrogens_to_pdb (fwd)
- David A. Case (Mon Aug 26 2002 - 19:34:36 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:07 CDT)
additional info
- Ioana Cozmuta (Sun Sep 01 2002 - 13:44:32 CDT)
adiabatic map
- franck chevalier (Wed Jan 09 2002 - 06:41:57 CST)
again about sander_classic Amber 6.0
- David Case (Wed May 22 2002 - 10:15:06 CDT)
- Nikolai Smolin (Wed May 22 2002 - 06:42:50 CDT)
again...Minimization of pentane holding a plane of carbon atoms
- Hungie Hungie (Wed Apr 17 2002 - 13:03:23 CDT)
allocation memory error
- Ioana Cozmuta (Tue Oct 22 2002 - 16:52:56 CDT)
- Ioana Cozmuta (Fri Oct 18 2002 - 14:50:22 CDT)
am1-bcc charges
- David A. Case (Tue Aug 06 2002 - 14:32:12 CDT)
- Sophia Kondratova (Tue Aug 06 2002 - 13:26:22 CDT)
am1-bcc charges, antechamber
- M. L. Dodson (Thu Jul 25 2002 - 07:32:05 CDT)
- Giulio Rastelli (Thu Jul 25 2002 - 05:53:46 CDT)
- Laurent Chiche (Thu Jul 25 2002 - 04:17:58 CDT)
- M. L. Dodson (Wed Jul 24 2002 - 15:24:23 CDT)
- David A. Case (Wed Jul 24 2002 - 14:58:25 CDT)
- Sophia Kondratova (Wed Jul 24 2002 - 14:02:02 CDT)
AM1-BCC sensitivity to AM1 charges
- ajakalian_at_lav.Boehringer-Ingelheim.com (Tue Jul 30 2002 - 13:28:25 CDT)
- Matthew Lee (Tue Jul 30 2002 - 12:31:43 CDT)
Amber
- vijay dasa (Mon Oct 28 2002 - 00:51:02 CST)
- K.Veluraja (Mon Sep 16 2002 - 00:14:04 CDT)
- shailendra singh (Mon Mar 18 2002 - 23:57:48 CST)
Amber 4 question
- Tod Pascal (Fri Oct 18 2002 - 17:42:40 CDT)
AMBER 5
- Monica (Wed Mar 27 2002 - 22:29:12 CST)
Amber 6 on IA64
- Karen Haskell (Wed Jan 09 2002 - 15:35:02 CST)
Amber 6.0 purchasing!!
- hathaimard pongkasem (Wed Jan 16 2002 - 02:15:03 CST)
- hathaimard pongkasem (Wed Jan 16 2002 - 02:14:48 CST)
amber 60 on Unicos Cray
- Cezary Czaplewski (Mon Mar 04 2002 - 11:56:36 CST)
AMBER 7 - more problems with leap
- Mark Beardsell (Wed May 01 2002 - 07:17:46 CDT)
Amber 7 and 6 topology files.
- James W. Caldwell (Mon Sep 30 2002 - 10:41:25 CDT)
- Miguel de Federico (Mon Sep 30 2002 - 10:08:36 CDT)
Amber 7 bugfix 27 !! urgent
- Holger Gohlke (Wed Dec 04 2002 - 15:18:48 CST)
- William Wei (Wed Dec 04 2002 - 14:45:13 CST)
Amber 7 Installation
- Joffre Heredia (Wed Jul 10 2002 - 01:17:45 CDT)
- Sanjeev B.S. (Tue Jul 09 2002 - 12:38:16 CDT)
- Rajesh Korde (Tue Jul 09 2002 - 11:45:36 CDT)
Amber 7 MM-PBSA for Amber 6 trajectories
- David A. Case (Sat Dec 14 2002 - 13:26:01 CST)
- Qing Zhang (Thu Dec 12 2002 - 13:52:23 CST)
Amber 7 timings?
- Jim (Mon Aug 05 2002 - 09:53:25 CDT)
AMBER 99
- Felipe Pineda (Fri Mar 01 2002 - 02:25:27 CST)
- John Finke (Thu Feb 28 2002 - 18:22:55 CST)
Amber Crd format
- Natasja Brooijmans (Tue Oct 22 2002 - 14:04:43 CDT)
- Tod Pascal (Tue Oct 22 2002 - 13:21:05 CDT)
Amber in a distributed environment
- Sudhakar Pamidighantam (Wed Apr 17 2002 - 08:55:34 CDT)
- Peter Gannett (Wed Apr 17 2002 - 07:07:56 CDT)
AMBER logo citation
- David Case (Wed Feb 20 2002 - 11:11:41 CST)
- Lepsa (Wed Feb 20 2002 - 03:02:15 CST)
- Pascal Bonnet (Wed Feb 20 2002 - 02:17:39 CST)
- FyD (Wed Feb 20 2002 - 01:53:18 CST)
AMBER Machine Questions
- DTphonehome33_at_aol.com (Tue Jul 30 2002 - 12:00:33 CDT)
amber on MAC OSX
- Tru (Mon Jun 10 2002 - 04:18:03 CDT)
- Randy M. Wadkins (Fri Jun 07 2002 - 14:29:58 CDT)
- case (Thu Jun 06 2002 - 19:22:44 CDT)
Amber on PC-Linux
- Philippe Aplincourt (Thu Nov 14 2002 - 09:22:20 CST)
amber on RH8
- Scott Brozell (Thu Nov 07 2002 - 15:13:14 CST)
- chernhoe (Wed Nov 06 2002 - 22:43:41 CST)
- chernhoe (Wed Nov 06 2002 - 01:23:18 CST)
amber on sp3
- David A. Case (Wed Jul 17 2002 - 14:14:44 CDT)
Amber on Tru64
- jim caldwell (Tue Jan 08 2002 - 13:51:06 CST)
- Sebastian Jayaraj (Tue Jan 08 2002 - 13:22:43 CST)
Amber Perl module
- Michael Ford (Thu Nov 14 2002 - 17:26:24 CST)
- Luis Gracia (Thu Nov 14 2002 - 15:55:25 CST)
- Tod Pascal (Thu Nov 14 2002 - 15:33:01 CST)
Amber PGF77 comilation error + MPICH problem
- Fabrice Yerly (Wed Jun 05 2002 - 03:31:26 CDT)
amber problem
- Carlos Simmerling (Wed Aug 28 2002 - 12:10:26 CDT)
Amber protein-ion problem
- Emma.Sigfridsson_at_astrazeneca.com (Tue Jun 11 2002 - 06:41:29 CDT)
amber question
- James W. Caldwell (Mon Sep 16 2002 - 12:24:20 CDT)
- David A. Case (Mon Sep 16 2002 - 11:47:03 CDT)
- yao yong (Mon Sep 16 2002 - 06:03:16 CDT)
Amber Reflector
- James W. Caldwell (Thu Sep 26 2002 - 12:47:58 CDT)
Amber Trajectories + VMD (fwd)
- Nicholson, James D Mr ARO (Tue Dec 03 2002 - 17:35:09 CST)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:58:00 CST)
amber trajectory
- Guanglei Cui (Wed Dec 18 2002 - 09:02:05 CST)
- Ioana Cozmuta (Tue Dec 17 2002 - 23:16:14 CST)
Amber trajectory movies in Powerpoint
- Elsa de Sousa Henriques (Tue Aug 06 2002 - 20:58:15 CDT)
- Cozmuta (Tue Aug 06 2002 - 13:25:31 CDT)
- mdk7p_at_cms.mail.virginia.edu (Tue Aug 06 2002 - 10:53:39 CDT)
Amber tutorial
- rino ragno (Sat Jun 15 2002 - 04:53:53 CDT)
Amber+Mosix
- Ross Walker (Sun Aug 11 2002 - 16:33:04 CDT)
- Jianhui Wu (Wed Aug 07 2002 - 15:40:15 CDT)
amber-request@cgl.ucsf.edu
- Mihaly Mezei (Mon Jul 29 2002 - 13:42:22 CDT)
Amber/Gentoo linux
- Margaret Cheung (Sun Aug 11 2002 - 18:31:02 CDT)
- Ross Walker (Sun Aug 11 2002 - 16:32:37 CDT)
- Jianhui Wu (Fri Aug 09 2002 - 14:53:16 CDT)
Amber6 & ES40 incompatability
- Sanjeev B.S. (Wed Mar 20 2002 - 01:01:17 CST)
Amber6 + IBM SP3
- Sanjeev B.S. (Sat Jan 19 2002 - 08:59:58 CST)
Amber6 and MPI
- Yu Chen (Wed Oct 23 2002 - 13:10:30 CDT)
AMBER6 on cluster
- Mako Furukawa (Mon Oct 07 2002 - 19:43:31 CDT)
- Mako Furukawa (Mon Oct 07 2002 - 19:12:28 CDT)
amber6 with parallel
- Khatcharin Siriwong (Mon Apr 22 2002 - 07:48:24 CDT)
Amber6, GB (Memory, MATOM, nmr.h)/Folding (mutation)
- David Case (Thu Mar 28 2002 - 12:40:16 CST)
- Wu, JianHui(IAF)(LAVAL) (Thu Mar 28 2002 - 11:56:04 CST)
AMBER7
- Michael Sattler (Thu May 30 2002 - 07:59:11 CDT)
AMBER7 and Movie
- Y Fang (Mon Jul 22 2002 - 15:58:23 CDT)
- Carlos Simmerling (Mon Jul 22 2002 - 11:56:52 CDT)
- Pascal Bonnet (Mon Jul 22 2002 - 03:36:50 CDT)
- Snyder, James (Fri Jul 19 2002 - 17:25:37 CDT)
- Y Fang (Fri Jul 19 2002 - 16:03:22 CDT)
amber7 and tip5p
- David Case (Wed Apr 24 2002 - 16:04:05 CDT)
Amber7 and VMD
- Thomas Cheatham (Wed Apr 10 2002 - 08:55:46 CDT)
- Soonmin Jang (Wed Apr 10 2002 - 03:40:37 CDT)
amber7 compilation on a beowulf cluster
- Peter Gannett (Sat Apr 20 2002 - 07:14:01 CDT)
- David Case (Fri Apr 19 2002 - 20:56:50 CDT)
- Bill Ross (Fri Apr 19 2002 - 17:26:19 CDT)
- John Bushnell (Fri Apr 19 2002 - 16:48:00 CDT)
- Peter Gannett (Fri Apr 19 2002 - 14:59:56 CDT)
Amber7 compilation on IBM sp3 machine
- Soonmin Jang (Tue Apr 30 2002 - 23:33:05 CDT)
amber7 compilation on irix6.4 mp
- K.Seshadri (Mon Sep 09 2002 - 12:44:13 CDT)
Amber7 nmode
- David Case (Wed May 01 2002 - 12:55:07 CDT)
- Sue Heavner (Wed May 01 2002 - 12:23:19 CDT)
amber7, gaff and minimization (fwd)
- David A. Case (Mon Aug 26 2002 - 20:35:26 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:50 CDT)
amber7, PME and anisotrop press.
- Arvid Soederhaell (Thu Apr 04 2002 - 03:46:58 CST)
Amber7, sander, restart, blast up
- Jianhui Wu (Wed Jun 05 2002 - 12:07:51 CDT)
Amber7/CYGWIN compiling
- James W. Caldwell (Tue Nov 12 2002 - 15:09:33 CST)
amber7: ES40s
- Sanjeev B.S. (Tue Aug 27 2002 - 08:08:49 CDT)
ambpdb
- David A. Case (Fri Dec 13 2002 - 22:46:12 CST)
- Holger Gohlke (Thu Dec 12 2002 - 18:44:44 CST)
- Vlad Cojocaru (Thu Dec 12 2002 - 16:01:23 CST)
ambpdb in AMBER7
- David Case (Wed May 22 2002 - 16:09:32 CDT)
- Matthew Lee (Wed May 22 2002 - 15:42:34 CDT)
ambpdb problem (fwd)
- David A. Case (Mon Aug 26 2002 - 20:27:08 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:32 CDT)
ambpdb?
- Lepsa (Wed Sep 25 2002 - 03:29:25 CDT)
- Arvid Soederhaell (Wed Sep 25 2002 - 02:38:34 CDT)
Amino acid unit "NHE" problem ?
- David Case (Thu Jan 17 2002 - 10:37:55 CST)
- Raik Grunberg (Thu Jan 17 2002 - 09:23:30 CST)
- Michael Jakusch (Thu Jan 17 2002 - 08:32:28 CST)
- S. Jang (Thu Jan 17 2002 - 06:27:19 CST)
Anal Error : Group
- Lifeng Tian (Fri Sep 27 2002 - 17:35:23 CDT)
Anal in AMBER7
- Ting Wang (Mon Jul 22 2002 - 04:19:16 CDT)
- Ting Wang (Tue May 21 2002 - 07:48:48 CDT)
- David Case (Sun May 19 2002 - 20:44:38 CDT)
anal in AMBER7 gives inconsistent results with itself
- Prabal Maiti (Mon Jul 08 2002 - 00:46:31 CDT)
- Prabal Maiti (Fri Jul 05 2002 - 18:00:55 CDT)
anal in AMBER7 gives inconsistent results with itself (fwd)
- Prabal Maiti (Fri Jul 12 2002 - 12:38:19 CDT)
anal input
- Prabal Maiti (Fri Feb 22 2002 - 18:31:58 CST)
analysis of Gibbs 2D run
- Asif Rahaman (Thu Jun 06 2002 - 23:46:34 CDT)
Analysis of LES simulation
- mer_at_chem.wayne.edu (Sun Jun 30 2002 - 17:40:39 CDT)
Announcement: Optimally Partitioned Electric Properties - OPEP
- Chris Chipot (Wed Jul 10 2002 - 03:06:48 CDT)
antechamber
- Carsten Detering (Wed Dec 18 2002 - 16:32:44 CST)
- Carsten Detering (Wed Dec 18 2002 - 13:38:16 CST)
- David Case (Wed May 22 2002 - 10:03:50 CDT)
- Giulio Rastelli (Wed May 22 2002 - 05:56:25 CDT)
antechamber best practices/charge equivalence w/ AM1-BCC
- Bayly, Christopher (Tue Sep 24 2002 - 09:49:56 CDT)
- Tom Bishop (Mon Sep 23 2002 - 16:28:57 CDT)
antechamber charges don't sum up to zero
- Michael Jakusch (Mon Jun 24 2002 - 14:38:15 CDT)
antechamber created prep file--Problem in xleap
- Sarangan Ravichandran (Tue Jul 16 2002 - 08:54:45 CDT)
antechamber created prep file--Problem in xleap--additional info
- Sarangan Ravichandran (Tue Jul 16 2002 - 09:06:31 CDT)
Antechamber generating bad charges w/ gaussian 98.
- Nicholson, James D Mr ARO (Wed Oct 23 2002 - 21:12:32 CDT)
- Nicholson, James D Mr ARO (Wed Oct 23 2002 - 21:00:47 CDT)
- James W. Caldwell (Wed Oct 23 2002 - 18:16:05 CDT)
- Nicholson, James D Mr ARO (Wed Oct 23 2002 - 16:50:56 CDT)
antechamber web page
- David A. Case (Tue Oct 01 2002 - 18:00:33 CDT)
- Ioana Cozmuta (Tue Oct 01 2002 - 17:33:36 CDT)
antechamber's prepc option
- David A. Case (Fri Aug 16 2002 - 15:10:55 CDT)
- Matthew Lee (Fri Aug 16 2002 - 14:20:59 CDT)
Antibody residue numbering
- Mark Hsieh (Tue Aug 20 2002 - 11:52:24 CDT)
- Mark Hsieh (Mon Aug 19 2002 - 20:00:03 CDT)
- David A. Case (Mon Aug 19 2002 - 16:15:45 CDT)
- Mark Hsieh (Mon Aug 19 2002 - 15:56:00 CDT)
Application of Amber
- Monica (Wed Jun 12 2002 - 10:24:49 CDT)
Are posters to the Amber list being spammed?
- Nicholson, James D Mr ARO (Sun Nov 17 2002 - 19:48:15 CST)
Are the programs sander and gibbs in Amber 7 parallel?
- ramon kleber da rocha (Wed Mar 06 2002 - 13:28:01 CST)
are there inconsistencies in anal?
- David A. Case (Fri Jul 12 2002 - 13:58:02 CDT)
assistance required
- amit kumar (Mon Sep 16 2002 - 11:25:05 CDT)
atom connection, .off file problem
- Uwe Richter (Wed Mar 20 2002 - 07:48:07 CST)
atom type not recognized by GB
- eric hu (Sun Nov 24 2002 - 20:30:17 CST)
- David A. Case (Sun Nov 24 2002 - 19:50:01 CST)
- eric hu (Sun Nov 24 2002 - 19:05:59 CST)
atomicfluct
- Bimo Ario Tejo (Thu Oct 03 2002 - 06:40:47 CDT)
atomicfluct in ptraj
- Kristina Furse (Thu Dec 19 2002 - 13:28:16 CST)
- David A. Case (Thu Dec 19 2002 - 11:28:43 CST)
- Kristina Furse (Wed Dec 18 2002 - 17:16:29 CST)
atoms coming too close during MD (with SHAKE on)
- Pratul Agarwal (Mon Sep 02 2002 - 20:01:18 CDT)
automated rescoring of ligands
- Vickie Tsui (Tue May 14 2002 - 16:23:29 CDT)
average and runningaverage in ptraj
- Thomas Cheatham (Wed Nov 06 2002 - 11:36:56 CST)
- Holger Gohlke (Wed Nov 06 2002 - 10:56:23 CST)
- Vlad Cojocaru (Wed Nov 06 2002 - 09:40:51 CST)
average of LES copies
- mer_at_chem.wayne.edu (Sun Aug 18 2002 - 20:00:22 CDT)
average position of water
- Elsa de Sousa Henriques (Tue Jan 08 2002 - 16:15:44 CST)
- Hungie Hungie (Tue Jan 08 2002 - 06:28:00 CST)
average structure
- Raja Swaminathan (Thu Sep 05 2002 - 12:16:03 CDT)
averaging with ptraj and carnal
- Vlad Cojocaru (Fri Nov 08 2002 - 06:31:03 CST)
azobenzene parameters
- Uwe Richter (Tue Jan 15 2002 - 04:18:03 CST)
B-factor
- Michal Otyepka (Thu Jan 31 2002 - 04:45:50 CST)
bad protein structure
- Guanglei Cui (Tue Dec 10 2002 - 23:07:20 CST)
- eric hu (Tue Dec 10 2002 - 19:30:52 CST)
beginners question
- dynamic group (Sun Dec 22 2002 - 23:17:52 CST)
belly and EWALD in amber7
- Zhang Jian (Sun Nov 10 2002 - 19:36:25 CST)
- darden (Sun Nov 10 2002 - 16:25:31 CST)
- Zhang Jian (Sat Nov 09 2002 - 21:04:14 CST)
belly and ivcap conflict in gibbs
- David A. Case (Sun Nov 10 2002 - 16:35:16 CST)
belly input
- Prabal Maiti (Tue Feb 12 2002 - 16:26:21 CST)
Benchmark
- Stéphane Teletchéa (Mon Jul 22 2002 - 11:55:14 CDT)
benchmark for Amber7
- A. Hungie (Fri Jun 07 2002 - 09:37:07 CDT)
Benchmarks
- Sanjeev B.S. (Sat Aug 03 2002 - 00:48:09 CDT)
Beowulf killing jobs
- Ross Walker (Mon Sep 16 2002 - 09:46:45 CDT)
- Peter Gannett (Fri Sep 13 2002 - 16:03:19 CDT)
betaP,SURFOFF inconsistency
- Holger Gohlke (Sun Sep 22 2002 - 15:20:03 CDT)
binding site volume
- Michal Otyepka (Fri Sep 13 2002 - 02:13:08 CDT)
- Shixiang Yan (Thu Sep 12 2002 - 18:38:41 CDT)
Binding site volume/Sander MD
- Jianhui Wu (Fri Aug 30 2002 - 16:20:09 CDT)
Biphasic box
- Gemma Kinsella (Wed Dec 04 2002 - 02:15:53 CST)
- David A. Case (Tue Dec 03 2002 - 17:09:50 CST)
Biphasic box (fwd)
- James W. Caldwell (Tue Dec 03 2002 - 17:15:50 CST)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:13:10 CST)
BLOWUP after 100 ns???
- Randy M. Wadkins (Thu Sep 19 2002 - 20:41:16 CDT)
- David A. Case (Thu Sep 19 2002 - 19:29:58 CDT)
- Randy M. Wadkins (Thu Sep 19 2002 - 16:39:48 CDT)
- Randy M. Wadkins (Thu Sep 19 2002 - 15:51:28 CDT)
bondbydistance
- Nicholson, James D Mr ARO (Sat Sep 07 2002 - 19:16:28 CDT)
- case (Fri Sep 06 2002 - 19:04:02 CDT)
- eric hu (Thu Sep 05 2002 - 18:20:43 CDT)
BondEn shoots in solvent minimization
- suvendu lomash (Mon Sep 30 2002 - 10:50:39 CDT)
box size & 1st equilibrium
- Carlos Simmerling (Fri Jun 28 2002 - 06:56:09 CDT)
- yuann (Fri Jun 28 2002 - 01:16:51 CDT)
box_size
- jim caldwell (Tue Jan 29 2002 - 09:56:23 CST)
- darden (Tue Jan 29 2002 - 09:38:55 CST)
- Susanna Monti (Tue Jan 29 2002 - 04:34:22 CST)
BR parameters in AMBER
- Esther Kellenberger (Wed Jul 03 2002 - 09:24:26 CDT)
Break down energy contributions
- Numan Oezguen (Fri Nov 29 2002 - 15:06:36 CST)
bug fixes
- David A. Case (Thu Dec 05 2002 - 10:41:02 CST)
- Filip Lankas (Thu Dec 05 2002 - 08:48:00 CST)
bug in .../sander/egb.f ?
- Sanjeev B.S. (Mon Jul 08 2002 - 14:08:09 CDT)
- Thomas A. Spraggins (Thu Jun 20 2002 - 12:45:28 CDT)
bug in New2oldparm
- David A. Case (Thu Sep 19 2002 - 10:28:30 CDT)
- Pascal Bonnet (Thu Sep 19 2002 - 05:35:46 CDT)
Bug in reading binary restart file with BOX parameters
- David A. Case (Wed Oct 16 2002 - 10:27:51 CDT)
- Vlad (Tue Oct 15 2002 - 21:58:54 CDT)
Bugfixes
- William Wei (Wed Nov 06 2002 - 03:50:35 CST)
building bcyd with tleap
- Itziar Maestre Asenjo (Wed Mar 20 2002 - 04:51:47 CST)
building general solvent boxes with leap
- Elsa de Sousa Henriques (Thu Jul 18 2002 - 22:41:25 CDT)
- Xavier Deupi (Thu Jul 18 2002 - 18:16:17 CDT)
- Bill Ross (Thu Jul 18 2002 - 14:18:57 CDT)
- David A. Case (Wed Jul 17 2002 - 15:14:40 CDT)
- Xavier Deupi (Wed Jul 17 2002 - 12:19:28 CDT)
building ss DNA/RNA
- David A. Case (Tue Jul 30 2002 - 17:29:19 CDT)
- Cozmuta (Tue Jul 30 2002 - 16:47:45 CDT)
Bulk Email Sending & Bullet Proof Web Hosting
- pposton (Wed Nov 20 2002 - 16:25:53 CST)
Business Cooperation (Inheritance Claim)
- Mr. Daniel Osondu (Fri Dec 13 2002 - 01:50:38 CST)
- Mr. Daniel Osondu (Thu Dec 12 2002 - 10:10:29 CST)
C sp2 connected to OS
- Bimo Ario Tejo (Tue Jul 23 2002 - 03:23:03 CDT)
- Bimo Ario Tejo (Mon Jul 22 2002 - 12:37:27 CDT)
C60 parameter
- Pascal Bonnet (Thu Nov 28 2002 - 06:12:19 CST)
- vannajan_at_chiangmai.ac.th (Thu Nov 28 2002 - 02:47:47 CST)
C=C=C bending parameters
- Jones de Andrade (Sun Jun 09 2002 - 15:55:33 CDT)
CA-OS parameter
- Bimo Ario Tejo (Tue Jul 23 2002 - 11:07:19 CDT)
Calculating atomic charges for AMBER with Gaussian98W
- M. L. Dodson (Sat Nov 23 2002 - 09:36:27 CST)
- Thomas Steinbrecher (Sat Nov 23 2002 - 07:52:47 CST)
can carnal do the job as anal ...)
- Michael Jakusch (Thu Aug 29 2002 - 06:56:12 CDT)
- Carlos Simmerling (Thu Aug 29 2002 - 05:54:15 CDT)
- Michael Jakusch (Thu Aug 29 2002 - 02:36:57 CDT)
can carnal do the job as anal to break down the energy?
- Haizhen Zhong (Wed Aug 28 2002 - 13:02:48 CDT)
can carnal do the job as anal to break down the energy?]
- Bill Ross (Wed Aug 28 2002 - 15:35:40 CDT)
- Holger Gohlke (Wed Aug 28 2002 - 13:36:51 CDT)
Can I use belly and ntr at the same time?
- David A. Case (Wed Oct 16 2002 - 10:45:49 CDT)
- sxzheng (Wed Oct 16 2002 - 10:21:10 CDT)
Can we get trajectories coordinates after FIT in Carnal?
- Bill Ross (Mon Aug 26 2002 - 18:54:25 CDT)
- William Wei (Wed Aug 14 2002 - 16:52:34 CDT)
- Holger Gohlke (Wed Aug 14 2002 - 16:29:41 CDT)
Can we get trajectories coordinates after FIT in Carnal? (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:03 CDT)
cannot deal with large trajectory?
- yuann (Mon Dec 30 2002 - 20:55:41 CST)
- yuann (Sat Dec 28 2002 - 21:17:23 CST)
cap option
- Ioana Cozmuta (Sun Dec 22 2002 - 19:21:01 CST)
cap water
- eric hu (Fri Jun 07 2002 - 13:39:22 CDT)
- eric hu (Wed Jun 05 2002 - 19:14:10 CDT)
Cap-atom-pointer in GIBBS
- Jose Ramon Blas (Thu Dec 05 2002 - 13:50:45 CST)
- James W. Caldwell (Thu Dec 05 2002 - 13:23:45 CST)
carnal
- Bill Ross (Fri Dec 06 2002 - 19:16:59 CST)
- Ioana Cozmuta (Fri Dec 06 2002 - 17:47:56 CST)
- Stéphane Teletchéa (Mon Nov 04 2002 - 04:09:10 CST)
- Ioana Cozmuta (Thu Oct 31 2002 - 12:30:35 CST)
- Vlad Cojocaru (Thu May 23 2002 - 05:35:29 CDT)
carnal amber 7.0
- Vlad Cojocaru (Mon Dec 02 2002 - 02:35:34 CST)
carnal and union
- Pascal Bonnet (Mon Mar 04 2002 - 03:00:20 CST)
carnal and union: solution
- Pascal Bonnet (Mon Mar 04 2002 - 06:33:17 CST)
carnal averaging
- Holger Gohlke (Mon Sep 02 2002 - 15:43:52 CDT)
- Vlad Cojocaru (Mon Sep 02 2002 - 06:43:33 CDT)
Carnal BUG??
- William Wei (Wed May 01 2002 - 22:19:03 CDT)
Carnal BUG?? --- How can I get the correct residue number?
- William Wei (Thu May 02 2002 - 12:48:10 CDT)
- William Wei (Thu May 02 2002 - 11:09:21 CDT)
Carnal coordinate averaging
- Bill Ross (Mon Feb 25 2002 - 16:44:17 CST)
- Michael G Cooney (Mon Feb 25 2002 - 16:01:26 CST)
carnal output trajectory
- Francesca Mocci (Fri Nov 01 2002 - 10:53:31 CST)
- Bill Ross (Wed Oct 30 2002 - 10:37:00 CST)
- Sanjeev B.S. (Wed Oct 30 2002 - 07:50:45 CST)
- Stéphane Teletchéa (Wed Oct 30 2002 - 07:50:19 CST)
- Vlad Cojocaru (Wed Oct 30 2002 - 07:25:36 CST)
- Vlad Cojocaru (Fri Oct 25 2002 - 04:50:55 CDT)
- Bill Ross (Thu Oct 24 2002 - 16:26:15 CDT)
- Margaret Cheung (Thu Oct 24 2002 - 15:57:50 CDT)
- Vlad Cojocaru (Thu Oct 24 2002 - 15:07:35 CDT)
Carnal RMSDs
- Bill Ross (Mon Aug 26 2002 - 18:56:50 CDT)
Carnal RMSDs (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:12 CDT)
carnal RST output format
- Andy Purkiss (Tue Mar 19 2002 - 14:45:00 CST)
- Bill Ross (Tue Mar 19 2002 - 13:32:36 CST)
- Pascal Bonnet (Tue Mar 19 2002 - 08:12:31 CST)
Carnal stream problem
- Vlad Cojocaru (Wed Aug 14 2002 - 09:45:04 CDT)
Carnal table output
- Holger Gohlke (Fri Oct 18 2002 - 10:20:57 CDT)
- Christoph Brockmann (Fri Oct 18 2002 - 03:48:37 CDT)
Carnal+HBond confusion
- Sanjeev B.S. (Tue Sep 24 2002 - 07:13:05 CDT)
- Sanjeev B.S. (Wed Sep 18 2002 - 23:18:36 CDT)
carnal7 produces memory fault and a core
- Giulio Rastelli (Sat Nov 09 2002 - 10:21:10 CST)
CCl4 as solvent
- Aldo Jongejan (Tue Nov 05 2002 - 07:44:02 CST)
CCl4 solvent box
- Bimo Ario Tejo (Wed Jul 24 2002 - 14:55:04 CDT)
- Bimo Ario Tejo (Wed Jul 24 2002 - 10:40:10 CDT)
CCL:Amber7 and partial charges
- David Case (Wed Dec 11 2002 - 12:07:10 CST)
CCL:freeware for RNA modeling on Linux (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:21 CST)
CH2Cl2 box
- Eric ARNOULT (Mon Oct 14 2002 - 12:51:21 CDT)
Chains, LEaP and ambpdb
- David A. Case (Tue Dec 17 2002 - 21:28:21 CST)
- Luis Gracia (Tue Dec 17 2002 - 15:23:55 CST)
- David A. Case (Tue Dec 17 2002 - 15:09:48 CST)
- Ioana Cozmuta (Tue Dec 17 2002 - 15:07:24 CST)
- Luis Gracia (Tue Dec 17 2002 - 13:47:59 CST)
change topology
- Bill Ross (Thu Mar 28 2002 - 03:45:49 CST)
- Michal Otyepka (Thu Mar 28 2002 - 02:44:38 CST)
Changing MAXINT
- Ross Walker (Mon Sep 16 2002 - 09:39:36 CDT)
- John Bushnell (Fri Sep 13 2002 - 17:38:52 CDT)
- Joel Konkle-Parker (Thu Sep 12 2002 - 18:21:13 CDT)
Charge export from Leap is rounded off
- jeff dyason (Sun May 26 2002 - 19:06:36 CDT)
charges
- David A. Case (Wed Aug 07 2002 - 20:35:07 CDT)
- Cozmuta (Tue Aug 06 2002 - 18:24:14 CDT)
- David Case (Thu May 23 2002 - 15:54:38 CDT)
- Marcela Madrid (Thu May 23 2002 - 15:25:43 CDT)
Charges derivation question!
- Lepsa (Thu Dec 12 2002 - 03:55:17 CST)
- Lepsa (Wed Dec 11 2002 - 10:21:23 CST)
- Marco Aurélio Correia Preto (Wed Oct 30 2002 - 10:39:24 CST)
charges for peptides
- Marcela Madrid (Fri Jun 07 2002 - 10:14:59 CDT)
charges-again
- Cozmuta (Wed Aug 07 2002 - 20:47:14 CDT)
CHARMm NPT input files
- Mahadevan Seetharaman (Sat Dec 07 2002 - 17:39:07 CST)
check-up question
- David A. Case (Tue Aug 06 2002 - 16:14:56 CDT)
- Cozmuta (Tue Aug 06 2002 - 14:13:31 CDT)
chesey@panther.gsu.edu
- Michael G Cooney (Mon Aug 12 2002 - 14:03:37 CDT)
China International Biology Projects Fair
- Genefax (Fri Jul 12 2002 - 00:40:19 CDT)
chirality.c failure - diagnosis, but no cure...
- Michael Ford (Thu Dec 19 2002 - 17:25:21 CST)
- Michael Ford (Thu Dec 19 2002 - 12:07:07 CST)
Cholesterol PREP file
- Stéphane Teletchéa (Thu Feb 28 2002 - 03:48:16 CST)
- samantha hughes (Wed Feb 27 2002 - 09:28:46 CST)
choose dt in gibbs
- sxzheng (Sun Nov 17 2002 - 21:06:34 CST)
choosing a forcefield
- nepenthes_at_vplaces.net (Thu Mar 07 2002 - 21:51:25 CST)
Clarification
- R.Sathyapriya (Tue Jun 04 2002 - 02:45:19 CDT)
CMM method
- David A. Case (Wed Nov 13 2002 - 18:42:26 CST)
- Ioana Cozmuta (Wed Nov 13 2002 - 16:57:10 CST)
cold belly run error
- eric hu (Tue Jun 11 2002 - 14:42:19 CDT)
- eric hu (Tue Jun 11 2002 - 12:41:47 CDT)
- Asim Okur (Mon Jun 10 2002 - 23:58:30 CDT)
- eric hu (Sun Jun 09 2002 - 17:55:47 CDT)
combinig two trajectory files.
- Pascal Bonnet (Mon Dec 02 2002 - 06:50:26 CST)
- Carlos Simmerling (Mon Dec 02 2002 - 06:49:21 CST)
- Yongjun Jiang (Mon Dec 02 2002 - 06:18:29 CST)
combining trajectory file
- Thomas Cheatham (Tue Mar 12 2002 - 12:30:51 CST)
- CUI, Guanglei (Tue Mar 12 2002 - 10:24:44 CST)
- Natasja Brooijmans (Tue Mar 12 2002 - 10:00:38 CST)
- Rukman Hertadi (Tue Mar 12 2002 - 03:48:49 CST)
Comparing simulations using Amber 5 and Amber 6
- Rebecca Perlow (Thu May 30 2002 - 09:18:36 CDT)
compilation for Hitachi SR8000
- A. Hungie (Sun May 26 2002 - 12:25:17 CDT)
compilation of sander on Alpha/Linux clusters
- jim caldwell (Fri May 24 2002 - 16:41:00 CDT)
Compilation on RedHat-7.2 with MPICH
- Vincent BOSQUIER (Thu May 02 2002 - 11:29:32 CDT)
Compilation ov Amber 7
- Sanjeev B.S. (Sun Jun 30 2002 - 12:42:28 CDT)
- Dov Barak (Fri Jun 21 2002 - 11:40:58 CDT)
compile AMBER on cygwin?
- quch quch (Thu Feb 07 2002 - 13:46:43 CST)
compile Moil-View, GL header files
- Renee olano (Tue Sep 03 2002 - 11:54:57 CDT)
- Viktor Hornak (Tue Sep 03 2002 - 11:12:22 CDT)
- Jianhui Wu (Tue Sep 03 2002 - 10:20:09 CDT)
Compiler & Hardware requirement of AMBER7 ?
- yuann (Tue Oct 22 2002 - 09:30:34 CDT)
- David Case (Tue Oct 15 2002 - 00:51:43 CDT)
- yuann (Mon Oct 14 2002 - 23:08:12 CDT)
compiling amber 6.0 in a Sun starfire ENT10000
- ramon kleber da rocha (Tue Apr 16 2002 - 14:08:54 CDT)
compiling amber 7 with Intel Fortran Compiler 6.0
- James W. Caldwell (Wed Sep 25 2002 - 15:58:04 CDT)
- James W. Caldwell (Wed Sep 25 2002 - 15:16:48 CDT)
- Scott Brozell (Wed Sep 25 2002 - 15:05:45 CDT)
- ramon kleber da rocha (Wed Sep 25 2002 - 14:23:21 CDT)
compiling amber 7 with Intel Fortran Compiler 6.0 (fwd)
- John Bushnell (Wed Sep 25 2002 - 15:10:50 CDT)
compiling amber on a linux box using DMEM-ALLOC
- James W. Caldwell (Fri Sep 06 2002 - 19:56:42 CDT)
- Scott Brozell (Fri Sep 06 2002 - 19:16:40 CDT)
- John Bushnell (Fri Sep 06 2002 - 18:43:12 CDT)
- ramon kleber da rocha (Fri Sep 06 2002 - 18:11:55 CDT)
- Florian Barth (Fri Sep 06 2002 - 17:13:31 CDT)
- Scott Brozell (Fri Sep 06 2002 - 17:01:27 CDT)
- ramon kleber da rocha (Fri Sep 06 2002 - 15:46:43 CDT)
Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system.
- Sanjeev B.S. (Wed Aug 07 2002 - 23:46:08 CDT)
- jeff dyason (Wed Aug 07 2002 - 23:45:49 CDT)
Compiling Amber7 on a Beowulf Cluster - Compiling Error
- Peter Gannett (Sat Apr 13 2002 - 08:59:29 CDT)
- David Case (Fri Apr 12 2002 - 19:37:01 CDT)
- Peter Gannett (Fri Apr 12 2002 - 18:59:38 CDT)
compiling error.
- Bill Ross (Mon Apr 01 2002 - 01:30:24 CST)
- Margaret Cheung (Sun Mar 31 2002 - 22:44:07 CST)
- Carlos Simmerling (Sun Mar 31 2002 - 09:24:19 CST)
- Margaret Cheung (Sun Mar 31 2002 - 01:26:53 CST)
compiling MPICH
- Thomas Steinbrecher (Thu Jul 11 2002 - 07:46:12 CDT)
Compiling on HP-UX 11.00
- Hagedorn, Dan N (Fri Aug 09 2002 - 13:45:00 CDT)
compiling SGI/mpi
- David A. Case (Fri Oct 04 2002 - 10:07:23 CDT)
- Ioana Cozmuta (Thu Oct 03 2002 - 22:09:02 CDT)
- David A. Case (Thu Oct 03 2002 - 20:50:11 CDT)
- Ioana Cozmuta (Thu Oct 03 2002 - 20:16:38 CDT)
compiling without ISTAR2
- Ross Walker (Thu Sep 19 2002 - 12:50:49 CDT)
- Prem Raj (Thu Sep 19 2002 - 12:27:48 CDT)
Computational alchemy
- Aldo Jongejan (Tue Oct 15 2002 - 05:52:12 CDT)
concentrated system
- Jerry wu (Mon Mar 04 2002 - 02:36:21 CST)
confusing error messages
- David A. Case (Wed Oct 16 2002 - 13:42:15 CDT)
Constant pressure equilibration in a system with a solvent cap
- David Smith (Fri Sep 27 2002 - 11:11:19 CDT)
- David A. Case (Fri Sep 27 2002 - 10:26:09 CDT)
- James W. Caldwell (Fri Sep 27 2002 - 08:54:46 CDT)
- dianah_at_unm.edu (Thu Sep 26 2002 - 20:04:38 CDT)
Constant pressure MD problems (sander)
- David A. Case (Mon Aug 12 2002 - 10:47:10 CDT)
- Pratul Agarwal (Mon Aug 12 2002 - 09:45:15 CDT)
Constraints in Amber
- David A. Case (Tue Dec 03 2002 - 17:16:02 CST)
Constraints in Amber (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:30 CST)
Conterions
- David Case (Sat Nov 16 2002 - 13:45:01 CST)
- Monica (Sat Nov 16 2002 - 02:10:15 CST)
convergence of MD simulations
- darden (Mon Apr 08 2002 - 15:08:10 CDT)
- Andreas Svrcek-Seiler (Fri Apr 05 2002 - 04:12:11 CST)
- Sue Heavner (Thu Apr 04 2002 - 16:24:05 CST)
- Sue Heavner (Sat Mar 30 2002 - 17:02:16 CST)
converting some files
- Vlad Cojocaru (Thu Mar 07 2002 - 05:00:00 CST)
correction about solvateOct
- Michael Crowley (Fri Jul 19 2002 - 11:37:10 CDT)
- William Wei (Fri Jul 19 2002 - 10:18:53 CDT)
- Michael Jakusch (Fri Jul 19 2002 - 04:49:48 CDT)
- Nikolai Smolin (Fri Jul 19 2002 - 04:09:58 CDT)
correlated motions in a protein!
- Pradipta Bandyopadhyay (Wed Feb 27 2002 - 17:52:55 CST)
corrupted trajectory
- CUI, Guanglei (Tue Dec 03 2002 - 20:04:13 CST)
- Shixiang Yan (Tue Dec 03 2002 - 17:36:37 CST)
- Guanglei Cui (Tue Dec 03 2002 - 17:07:46 CST)
counter-ions in FEP
- David A. Case (Fri Jul 12 2002 - 11:00:11 CDT)
- Christophe L M J Verlinde (Thu Jul 11 2002 - 11:37:41 CDT)
crdgrow
- David A. Case (Tue Oct 08 2002 - 20:17:45 CDT)
- Sanjeev B.S. (Tue Oct 08 2002 - 12:24:09 CDT)
- Ioana Cozmuta (Tue Oct 08 2002 - 12:19:23 CDT)
- Vlad Cojocaru (Sat May 04 2002 - 15:06:32 CDT)
create new atom problem on xleap
- Bill Ross (Thu Jul 04 2002 - 15:58:59 CDT)
- yuann (Thu Jul 04 2002 - 15:04:01 CDT)
creating a pdb trajectory with carnal
- Vlad Cojocaru (Mon Nov 18 2002 - 09:29:21 CST)
creating a solvent box
- David A. Case (Tue Aug 06 2002 - 13:53:50 CDT)
- Bimo Ario Tejo (Tue Aug 06 2002 - 12:23:13 CDT)
- Laurent Chiche (Thu Jul 25 2002 - 09:46:47 CDT)
- CUI, Guanglei (Thu Jul 25 2002 - 08:33:01 CDT)
- Bimo Ario Tejo (Thu Jul 25 2002 - 07:32:17 CDT)
creating a unit wth xleap
- Bill Ross (Tue Mar 19 2002 - 13:43:25 CST)
- Marcela Madrid (Tue Mar 19 2002 - 13:07:30 CST)
cut-off question
- case (Fri Sep 06 2002 - 19:01:28 CDT)
- Cozmuta (Fri Sep 06 2002 - 17:49:21 CDT)
- Ioana Cozmuta (Wed Sep 04 2002 - 14:43:38 CDT)
cutoffs in GB
- David A. Case (Thu Oct 17 2002 - 16:08:16 CDT)
Cyclodextrin
- Toshikazu Matsuoka (Wed May 29 2002 - 01:48:19 CDT)
D-tryptophan
- James W. Caldwell (Sat Sep 14 2002 - 10:21:42 CDT)
- Perdita Barran (Sat Sep 14 2002 - 09:16:45 CDT)
Decrease the solvated system by removing the outside crystal water
- Ling Zhang (Mon Jul 15 2002 - 11:58:34 CDT)
deep energetics problem
- David A. Case (Thu Dec 05 2002 - 13:55:40 CST)
- eric hu (Thu Dec 05 2002 - 12:42:42 CST)
default GB radii
- Andreas Svrcek-Seiler (Sat Dec 07 2002 - 06:02:09 CST)
- David A. Case (Fri Dec 06 2002 - 15:11:13 CST)
- Robert G. Endres (Fri Dec 06 2002 - 15:00:31 CST)
defining groups on dif. sets in carnal
- Vlad Cojocaru (Tue Nov 19 2002 - 04:59:06 CST)
Defining Restraints in Sander
- John Bushnell (Thu Jul 18 2002 - 19:44:16 CDT)
- Carlos Simmerling (Thu Jul 18 2002 - 16:29:22 CDT)
- Asif Rahaman (Thu Jul 18 2002 - 15:21:59 CDT)
Density during equilibration (sander)
- Pratul Agarwal (Thu Sep 26 2002 - 09:09:02 CDT)
- Marc Dobler (Wed Sep 18 2002 - 02:11:21 CDT)
- Carlos Simmerling (Tue Sep 17 2002 - 20:44:13 CDT)
- Marc Dobler (Tue Sep 17 2002 - 19:29:22 CDT)
- Pratul Agarwal (Tue Sep 17 2002 - 19:22:22 CDT)
- David A. Case (Tue Sep 17 2002 - 14:21:49 CDT)
- Pratul Agarwal (Tue Sep 17 2002 - 11:56:10 CDT)
dG of wild type/mutant
- FyD (Thu Mar 07 2002 - 05:26:31 CST)
DIANA like files
- Vlad Cojocaru (Wed Dec 04 2002 - 14:24:12 CST)
Dielectric constant for interior of proteins
- Pratul Agarwal (Thu Oct 10 2002 - 14:25:51 CDT)
- David A. Case (Thu Oct 10 2002 - 13:33:19 CDT)
- Pratul Agarwal (Thu Oct 10 2002 - 12:53:59 CDT)
dielectric constant for partialy solvated MD
- Carlos Simmerling (Wed Jul 31 2002 - 15:54:12 CDT)
- Miyashita, Osamu (Wed Jul 31 2002 - 13:55:58 CDT)
difference 94 99 force field
- Carlos Simmerling (Tue Aug 27 2002 - 09:34:50 CDT)
- Vlad Cojocaru (Tue Aug 27 2002 - 08:34:11 CDT)
difference in energy in amber6 and amber7
- David A. Case (Wed Dec 11 2002 - 09:40:48 CST)
- Prabal Maiti (Mon Dec 09 2002 - 20:07:15 CST)
different counterions for special type of DNA
- Vlad Cojocaru (Thu Sep 26 2002 - 07:59:31 CDT)
Different numbers on different architectures.
- David A. Case (Fri Oct 04 2002 - 11:26:07 CDT)
- David Smith (Fri Oct 04 2002 - 08:33:24 CDT)
dihedral parameter for conjugated double bonds in GAFF
- Giulio Rastelli (Fri Aug 16 2002 - 11:37:03 CDT)
- Giulio Rastelli (Wed Aug 14 2002 - 03:37:50 CDT)
Distace dependent dielectric constant
- David A. Case (Thu Sep 12 2002 - 17:39:35 CDT)
- Lorenzo Gontrani (Mon Sep 09 2002 - 03:33:43 CDT)
Distance dependent vaccum energy minimization in AMBER7
- Sarangan Ravichandran (Fri Jul 05 2002 - 10:29:40 CDT)
distance restraint stuff
- CUI, Guanglei (Thu Aug 01 2002 - 10:44:25 CDT)
- Layi Adekoya (Thu Aug 01 2002 - 10:24:50 CDT)
disulfide bond link between two chains
- Natasja Brooijmans (Mon Dec 16 2002 - 07:49:46 CST)
- pu xuemei (Mon Dec 16 2002 - 06:50:35 CST)
divalent cations parameters
- Apostoluk, Wlodzimierz K (Mon Sep 30 2002 - 17:38:11 CDT)
DME and Carnal with AMBER6
- Katherine W. Abold (Tue Apr 23 2002 - 09:48:04 CDT)
DNA shifts during MD; C.O.M. removing and ptraj doesn't help...
- Filip Ryjacek (Thu Apr 18 2002 - 10:17:12 CDT)
DNA structure get distorted
- David Case (Fri Apr 12 2002 - 11:27:10 CDT)
- Monica (Thu Apr 11 2002 - 03:00:48 CDT)
DNA Tutorial Script
- Holger Gohlke (Wed Sep 04 2002 - 22:29:23 CDT)
- Joel Konkle-Parker (Wed Sep 04 2002 - 18:18:16 CDT)
DNA Tutorial: min_ntr.in
- Joel Konkle-Parker (Fri Oct 11 2002 - 17:28:47 CDT)
Do I have to rerun 1ns MD??
- Lepsa (Mon Sep 23 2002 - 10:50:26 CDT)
- Holger Gohlke (Sun Sep 22 2002 - 14:30:40 CDT)
do I need to mutate H1 atoms to HC in a "not really" perturbed part of a molecule ?
- hagop demirdjian (Tue Oct 08 2002 - 09:51:50 CDT)
DOCK
- Peter Gannett (Thu Jan 24 2002 - 08:48:52 CST)
docking in amber?
- Sichun Yang (Thu Oct 10 2002 - 18:44:45 CDT)
docking in xleap
- Bill Ross (Wed Jul 03 2002 - 23:25:50 CDT)
does PME function without charge neutralization?
- darden (Tue Apr 02 2002 - 16:23:02 CST)
- Ian R Bates (Tue Apr 02 2002 - 12:30:41 CST)
drifting from average structure
- Vlad Cojocaru (Sat Nov 09 2002 - 10:17:38 CST)
Dual AMD ASUS A7M266-D Solved
- jim caldwell (Mon Mar 18 2002 - 20:37:19 CST)
Dual AMD motherboards
- Ross Walker (Tue Jul 16 2002 - 02:31:56 CDT)
- Pietro Amodeo (Mon Jul 15 2002 - 03:36:34 CDT)
- Greaves, Greg (Contractor-SIMTECH) (Fri Jul 12 2002 - 10:33:54 CDT)
- jim caldwell (Mon Mar 18 2002 - 20:04:24 CST)
- Demchuk, Eugene (Mon Mar 18 2002 - 18:52:55 CST)
- jim caldwell (Mon Mar 18 2002 - 17:47:12 CST)
dual H-bonding of bridging waters - CARNAL
- Michael Ford (Tue Dec 10 2002 - 18:16:24 CST)
Dual Processor AMD vs. Single Processor
- Stéphane Teletchéa (Thu Sep 12 2002 - 03:09:58 CDT)
- DeLano, Warren (Wed Sep 11 2002 - 19:34:47 CDT)
dummy atoms.
- Yongjun Jiang (Sat Apr 20 2002 - 22:20:44 CDT)
Dummy atoms...
- David A. Case (Wed Oct 23 2002 - 11:35:31 CDT)
- Miguel de Federico (Wed Oct 23 2002 - 02:44:34 CDT)
dummy parameters
- Pierre Mignon (Wed Oct 16 2002 - 02:10:46 CDT)
dummy torsional parameters
- David A. Case (Thu Jun 27 2002 - 10:38:49 CDT)
- Giulio Rastelli (Thu Jun 27 2002 - 05:31:50 CDT)
dummy torsional parameters again.
- David A. Case (Thu Oct 17 2002 - 12:58:38 CDT)
- X. Tan (Thu Oct 17 2002 - 11:52:05 CDT)
Dummy torsions
- David A. Case (Tue Oct 15 2002 - 10:25:41 CDT)
- Aldo Jongejan (Tue Oct 15 2002 - 08:33:02 CDT)
dump coordinate into mdcrd
- A. Hungie (Fri Aug 30 2002 - 03:03:17 CDT)
Dynamic Movement of Molecule
- Thomas Cheatham (Fri Sep 20 2002 - 14:01:39 CDT)
- Yuuki Komata (Fri Sep 20 2002 - 03:03:48 CDT)
E going up and down???
- David A. Case (Wed Aug 14 2002 - 17:16:05 CDT)
- Jiyoung Heo (Wed Aug 14 2002 - 16:13:44 CDT)
eedmeth variable in AMBER7
- David A. Case (Tue Jul 09 2002 - 10:31:59 CDT)
- Sarangan Ravichandran (Tue Jul 09 2002 - 09:30:28 CDT)
EGB = NaNQ
- Pratul Agarwal (Fri Oct 04 2002 - 15:26:47 CDT)
- Andreas Svrcek-Seiler (Fri Oct 04 2002 - 10:30:50 CDT)
- Pratul Agarwal (Thu Oct 03 2002 - 16:05:55 CDT)
electrostatics truncation in AMBER
- David A. Case (Fri Jul 19 2002 - 10:26:20 CDT)
- Therese Malliavin (Fri Jul 19 2002 - 08:21:59 CDT)
Energies/coordinate files from mm_pbsa problem
- Peter Gannett (Tue Jul 30 2002 - 13:25:29 CDT)
Energy conservation in NVE simulation ?
- Soonmin Jang (Tue May 21 2002 - 00:42:40 CDT)
Energy decomposition with ANAL
- Numan Oezguen (Mon Dec 16 2002 - 09:49:08 CST)
- Natasja Brooijmans (Fri Dec 06 2002 - 11:24:21 CST)
- Numan Oezguen (Fri Dec 06 2002 - 11:08:20 CST)
Energy decomposition with ANAL (fwd)
- David A. Case (Wed Dec 04 2002 - 10:31:52 CST)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:58:05 CST)
Energy problem during dynamics with amber 7
- David Case (Wed May 15 2002 - 12:29:55 CDT)
- Florence CASSET (Wed May 15 2002 - 04:48:23 CDT)
entropy calcs in mm_pbsa
- Holger Gohlke (Tue Nov 05 2002 - 15:27:39 CST)
- giulio_at_unimo.it (Tue Nov 05 2002 - 14:21:00 CST)
entropy calculation
- case (Tue Jun 11 2002 - 08:56:37 CDT)
- X. Tan (Mon Jun 10 2002 - 18:42:59 CDT)
Equilibration output Amber7
- Thomas Cheatham (Fri Nov 22 2002 - 11:49:55 CST)
- Guanglei Cui (Fri Nov 22 2002 - 08:42:02 CST)
- Fredrick Robin Devadoss (Fri Nov 22 2002 - 03:42:32 CST)
equilibrium problem about cut and belly
- Thomas Steinbrecher (Tue Nov 05 2002 - 11:24:54 CST)
- David A. Case (Tue Nov 05 2002 - 10:14:51 CST)
err in specifying disulphide bridge using xleap!
- James W. Caldwell (Mon Dec 02 2002 - 13:07:07 CST)
- David A. Case (Mon Dec 02 2002 - 11:05:01 CST)
- A.Madhumalar (Mon Dec 02 2002 - 10:25:30 CST)
Error decoding variable
- Rukman Hertadi (Wed Jul 31 2002 - 20:50:27 CDT)
- Carlos Simmerling (Wed Jul 31 2002 - 10:41:04 CDT)
- jim caldwell (Wed Jul 31 2002 - 09:43:56 CDT)
- Carlos Simmerling (Wed Jul 31 2002 - 07:37:46 CDT)
- Rukman Hertadi (Wed Jul 31 2002 - 05:52:02 CDT)
ERROR from RESNBA
- X. Tan (Tue Feb 19 2002 - 19:39:21 CST)
Error in Antechamber program in ammber7
- David A. Case (Wed Oct 16 2002 - 10:04:40 CDT)
- Narang Manpreet Kaur (Wed Oct 16 2002 - 00:01:45 CDT)
- David A. Case (Tue Oct 15 2002 - 10:33:09 CDT)
- Lepsa (Tue Oct 15 2002 - 10:07:57 CDT)
- Narang Manpreet Kaur (Tue Oct 15 2002 - 09:49:52 CDT)
Error in Equilibration
- Fredrick Robin Devadoss (Tue Nov 26 2002 - 04:14:12 CST)
error in reading .crd file with GIBBS
- hagop demirdjian (Thu Nov 14 2002 - 09:40:32 CST)
error in rMD
- Monica (Fri Jun 28 2002 - 08:35:34 CDT)
- Guanglei Cui (Fri Jun 28 2002 - 08:22:35 CDT)
error message
- Bill Ross (Wed Oct 16 2002 - 14:22:44 CDT)
- Andreas Svrcek-Seiler (Wed Oct 16 2002 - 12:58:18 CDT)
- Margaret Cheung (Wed Oct 16 2002 - 12:56:50 CDT)
- Natasja Brooijmans (Wed Oct 16 2002 - 12:48:41 CDT)
- Holger Gohlke (Wed Oct 16 2002 - 12:38:34 CDT)
- Vlad Cojocaru (Wed Oct 16 2002 - 12:25:01 CDT)
Error running AMBER6 on Beowulf cluster
- Carlos Simmerling (Fri Nov 22 2002 - 17:33:49 CST)
- arubin_at_unmc.edu (Fri Nov 22 2002 - 15:38:12 CST)
- David A. Case (Thu Nov 21 2002 - 19:31:47 CST)
- arubin_at_unmc.edu (Thu Nov 21 2002 - 17:10:39 CST)
ERROR TERMINATION DUE TO SHAKE OR TORCON
- sxzheng (Fri Jan 11 2002 - 21:21:30 CST)
ES40 hangs amber7 jobs.
- Sanjeev B.S. (Mon Sep 02 2002 - 21:29:45 CDT)
- James W. Caldwell (Fri Aug 30 2002 - 11:07:11 CDT)
- Sanjeev B.S. (Thu Aug 29 2002 - 22:09:13 CDT)
Escaping Atoms
- case (Thu Sep 05 2002 - 17:04:06 CDT)
- ch cureton (Wed Sep 04 2002 - 05:43:03 CDT)
esp.sh problem
- FyD (Thu Nov 28 2002 - 02:03:33 CST)
- David A. Case (Wed Nov 27 2002 - 13:12:54 CST)
- David Smith (Wed Nov 27 2002 - 12:13:09 CST)
- FyD (Wed Nov 27 2002 - 11:17:40 CST)
Etot drops after restarting MD in sander
- Pratul Agarwal (Fri Aug 16 2002 - 13:18:58 CDT)
Etot drops after restarting MD in sander (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:16 CDT)
Europium force field parms
- Peter Gannett (Sun Mar 10 2002 - 14:07:44 CST)
even more van der Waals explosion
- Arvid Soederhaell (Fri Jun 21 2002 - 04:23:17 CDT)
Ewald
- David A. Case (Wed Nov 13 2002 - 10:09:08 CST)
- Monica (Wed Nov 13 2002 - 09:20:23 CST)
ewald bomb
- David A. Case (Fri Aug 30 2002 - 14:13:14 CDT)
- Vlad Cojocaru (Fri Aug 30 2002 - 08:38:49 CDT)
EWALD BOMB (The system has extended beyond ...)
- Michael Jakusch (Fri Jun 28 2002 - 04:17:20 CDT)
ewald bomb in md equilibration
- Sophia Kondratova (Mon Aug 26 2002 - 17:54:37 CDT)
ewald bomb in md equilibration (fwd)
- David A. Case (Mon Aug 26 2002 - 20:23:52 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:14 CDT)
EWALD crash
- David A. Case (Mon Nov 18 2002 - 18:27:37 CST)
example 1 problems
- David A. Case (Tue Sep 17 2002 - 09:45:31 CDT)
- James W. Caldwell (Tue Sep 17 2002 - 09:24:30 CDT)
- Alicia Hopkins (Tue Sep 17 2002 - 07:03:53 CDT)
- Natasja Brooijmans (Mon Sep 16 2002 - 11:40:38 CDT)
- David A. Case (Mon Sep 16 2002 - 11:25:54 CDT)
- Alicia Hopkins (Mon Sep 16 2002 - 10:57:23 CDT)
example gibbs file for the methane tutorial
- Andreas Kerzmann (Fri Aug 30 2002 - 05:18:06 CDT)
expression of V(lambda) in GIBBS
- David A. Case (Tue Sep 24 2002 - 09:14:01 CDT)
- hagop demirdjian (Tue Sep 24 2002 - 07:44:02 CDT)
external electric field
- Ioana Cozmuta (Mon Nov 25 2002 - 17:18:38 CST)
external electric field/another try
- James W. Caldwell (Wed Nov 27 2002 - 17:31:24 CST)
- darden (Wed Nov 27 2002 - 17:27:32 CST)
- Ioana Cozmuta (Wed Nov 27 2002 - 16:13:08 CST)
Extra points
- David A. Case (Thu Aug 15 2002 - 18:01:21 CDT)
- jim caldwell (Thu Aug 15 2002 - 16:54:21 CDT)
- Sarah Tschampel (Thu Aug 15 2002 - 15:25:45 CDT)
Extra points (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:49 CDT)
Fail message:Segmantation fault and Bus error?
- William Wei (Mon Apr 29 2002 - 14:38:48 CDT)
FEP - ligand to nothing (or water)??
- David A. Case (Tue Oct 29 2002 - 08:24:47 CST)
- Aldo Jongejan (Tue Oct 29 2002 - 03:50:54 CST)
FEP/Gibbs question
- Lepsa (Tue Dec 10 2002 - 09:59:39 CST)
- meiselba (Tue Nov 19 2002 - 09:29:07 CST)
FEP/Gibbs question to valine alanine tutorial
- meiselba (Sat Dec 14 2002 - 10:58:12 CST)
file
- David A. Case (Thu Aug 01 2002 - 15:46:52 CDT)
- Cozmuta (Thu Aug 01 2002 - 12:24:13 CDT)
flag TREE_CHAIN_CLASSIFICATION in topology file from amber7
- David A. Case (Fri Nov 01 2002 - 07:51:26 CST)
- Pascal Bonnet (Fri Nov 01 2002 - 03:08:20 CST)
Floating Invalid
- lifang xu (Wed Jun 12 2002 - 22:02:21 CDT)
- jim caldwell (Tue Jun 11 2002 - 09:43:49 CDT)
- Bill Ross (Tue Jun 11 2002 - 00:36:16 CDT)
flying monomers...
- Margaret Cheung (Fri Feb 15 2002 - 17:58:39 CST)
Follow distances during MD
- Raik Grunberg (Thu Apr 11 2002 - 07:49:16 CDT)
- Francois Dupradeau (Thu Apr 11 2002 - 05:19:02 CDT)
follow-up post on missing gaff terms
- Matthew Randolph Lee, Ph.D. (Tue Aug 20 2002 - 12:21:50 CDT)
force field name
- Peter Gannett (Thu Aug 15 2002 - 18:03:52 CDT)
- Yong Duan (Thu Aug 15 2002 - 11:11:19 CDT)
- A. Hungie (Thu Aug 15 2002 - 08:50:48 CDT)
Format in a trajectory files is suddenly changed
- Masaki Tomimoto (Mon Jul 22 2002 - 11:54:44 CDT)
Format of prep input files
- David A. Case (Tue Aug 13 2002 - 13:13:47 CDT)
- dianah_at_unm.edu (Tue Aug 13 2002 - 12:42:11 CDT)
Forwarded mail....
- David A. Case (Sun Nov 10 2002 - 16:40:19 CST)
- Narang Manpreet Kaur (Sat Nov 09 2002 - 03:56:37 CST)
frcmod file format
- Lepsa (Tue Feb 12 2002 - 01:05:54 CST)
- CUI, Guanglei (Mon Feb 11 2002 - 12:38:37 CST)
- Sophia Kondratova (Mon Feb 11 2002 - 12:16:23 CST)
free energy for binding
- Qing Zhang (Fri Jun 14 2002 - 17:50:54 CDT)
freeware for RNA modeling on Linux (fwd)
- James W. Caldwell (Tue Dec 17 2002 - 13:09:37 CST)
- Joerg-Gerald Siebers (Mon Dec 16 2002 - 20:43:05 CST)
- David A. Case (Tue Dec 03 2002 - 17:11:48 CST)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:10 CST)
Frictional forces in gB
- Kristina Furse (Tue Nov 19 2002 - 17:41:32 CST)
Fwd: NPT-MD
- David Case (Fri May 31 2002 - 09:56:43 CDT)
- Antonio J. Díaz Quintana (Fri May 31 2002 - 04:17:55 CDT)
gaff and parm99
- Pascal Bonnet (Wed Jul 24 2002 - 10:51:30 CDT)
- David A. Case (Wed Jul 24 2002 - 10:13:48 CDT)
- Pascal Bonnet (Wed Jul 24 2002 - 08:11:36 CDT)
GB in amber6
- CUI, Guanglei (Fri Aug 16 2002 - 08:25:52 CDT)
- David Case (Fri Aug 16 2002 - 00:23:23 CDT)
- CUI, Guanglei (Thu Aug 15 2002 - 21:33:27 CDT)
- Prabal Maiti (Thu Aug 15 2002 - 19:26:22 CDT)
GB in Amber7
- David A. Case (Wed Aug 14 2002 - 10:33:57 CDT)
- Jithesh (Wed Aug 14 2002 - 03:37:54 CDT)
GB model and belly
- David Case (Tue Mar 26 2002 - 17:07:33 CST)
- dkon_at_email.arizona.edu (Tue Mar 26 2002 - 15:46:40 CST)
GB simulation
- Giulio Rastelli (Mon Mar 04 2002 - 10:32:28 CST)
- CUI, Guanglei (Mon Mar 04 2002 - 09:41:53 CST)
GB tutorial
- David A. Case (Thu Sep 26 2002 - 10:31:19 CDT)
gB vs. explicit
- David A. Case (Wed Dec 04 2002 - 10:28:43 CST)
gB vs. explicit (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:53 CST)
GBSA and surface crystal waters
- Raik Grunberg (Tue Sep 10 2002 - 09:44:20 CDT)
GBSA with IGB=2, setting the PBradii bondi
- David Case (Sat Aug 31 2002 - 12:58:35 CDT)
- Sarangan Ravichandran (Fri Aug 30 2002 - 16:55:28 CDT)
Generalized Born and OPLS potential
- David A. Case (Mon Aug 05 2002 - 10:51:30 CDT)
- Soonmin Jang (Sat Aug 03 2002 - 03:05:27 CDT)
GENERALIZED BORN model on a protein with Fe
- David A. Case (Thu Jul 18 2002 - 12:41:53 CDT)
- Mahadevan Seetharaman (Thu Jul 18 2002 - 09:55:01 CDT)
generating left-handed A-DNA
- David Case (Wed Apr 24 2002 - 11:09:07 CDT)
- Marcela Madrid (Tue Apr 23 2002 - 19:41:08 CDT)
Gentoo vs. Redhat Linux, shared/distributed filesystem
- Jianhui Wu (Thu Aug 08 2002 - 14:44:53 CDT)
geometry optimization/turning off Elec and Vdw terms
- Margaret Cheung (Mon Oct 07 2002 - 17:26:01 CDT)
- Tom Bishop (Mon Oct 07 2002 - 15:17:52 CDT)
gibbs
- sara nunez (Wed Aug 28 2002 - 14:52:56 CDT)
Gibbs (FEP) (fwd)
- David A. Case (Mon Aug 26 2002 - 20:30:28 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:36 CDT)
GIBBS - end-of-file during read
- Miguel de Federico (Fri Dec 13 2002 - 04:12:48 CST)
GIBBS - Error message.
- David A. Case (Tue Nov 19 2002 - 11:09:09 CST)
- Miguel de Federico (Tue Nov 19 2002 - 10:00:25 CST)
GIBBS - ERROR: Restraint read error from RSTIN; Check format:
- David A. Case (Tue Nov 26 2002 - 17:30:52 CST)
- Miguel de Federico (Tue Nov 26 2002 - 03:14:19 CST)
GIBBS - Routine TORCON (internal constraints) failed
- Miguel de Federico (Tue Dec 17 2002 - 09:29:04 CST)
Gibbs Question
- Bernd Wellenzohn (Mon Feb 18 2002 - 14:47:15 CST)
Gibbs tutorial problem
- David A. Case (Thu Jul 25 2002 - 14:03:17 CDT)
- yuann (Wed Jul 24 2002 - 19:40:50 CDT)
glucose
- Carlos Simmerling (Tue May 28 2002 - 10:50:59 CDT)
- Yuguang Mu (Tue May 28 2002 - 10:05:10 CDT)
group input in ANAL
- Mite51 (Sat Jan 26 2002 - 15:09:46 CST)
- Elizabeth K. White (Fri Jan 25 2002 - 16:11:13 CST)
group selection for all heavy atoms ?
- Raik Grunberg (Fri Sep 06 2002 - 11:23:33 CDT)
GROUP Specification - Error decoding variable
- Yongjun Jiang (Thu May 30 2002 - 03:23:57 CDT)
- yuann (Thu May 30 2002 - 02:43:02 CDT)
groups in targeted md
- Christoph Brockmann (Mon Sep 30 2002 - 09:48:16 CDT)
- Carlos Simmerling (Mon Sep 30 2002 - 09:04:26 CDT)
- Christoph Brockmann (Mon Sep 30 2002 - 08:15:10 CDT)
H-bond
- Dmitry Pavlov (Fri May 31 2002 - 03:01:42 CDT)
heat up at constant pressure
- Qing Zhang (Mon Jul 08 2002 - 17:05:19 CDT)
helix analysis
- Prabal Maiti (Mon May 20 2002 - 14:20:45 CDT)
helix analysis (fwd)
- David Case (Thu May 23 2002 - 16:41:00 CDT)
- Prabal Maiti (Thu May 23 2002 - 16:30:33 CDT)
Hello Amber,
- vijay dasa (Mon Oct 28 2002 - 04:20:24 CST)
help ..problem about antechamber
- Yi ming Cheng (Sat Apr 13 2002 - 00:30:26 CDT)
Help needed about mm_pbsa
- Holger Gohlke (Thu Aug 15 2002 - 12:04:03 CDT)
help on parameters.
- X. Tan (Mon Feb 04 2002 - 19:40:52 CST)
help on VMD movie
- Zhang Jian (Wed Nov 13 2002 - 19:40:14 CST)
- Zhang Jian (Wed Nov 13 2002 - 09:21:30 CST)
- Francesca Mocci (Wed Nov 13 2002 - 08:28:06 CST)
- Stéphane Teletchéa (Wed Nov 13 2002 - 07:12:58 CST)
- Zhang Jian (Wed Nov 13 2002 - 06:44:36 CST)
help please :)
- Richard Kho (Fri Mar 15 2002 - 18:59:23 CST)
Help using moilview to make animations of trajectories
- Nicholson, James D Mr ARO (Fri Sep 13 2002 - 17:15:33 CDT)
help! Non bond list overflow!
- Jian Zhang (Wed Nov 13 2002 - 20:32:01 CST)
- Zhang Jian (Wed Nov 13 2002 - 20:10:02 CST)
- David A. Case (Wed Nov 13 2002 - 18:51:07 CST)
- Zhang Jian (Wed Nov 13 2002 - 04:56:39 CST)
Help! Sander run error: Bus error
- David Case (Tue Apr 16 2002 - 00:32:16 CDT)
help/suggestions needed with PROFEC
- Salinthip Thipayang (Fri May 03 2002 - 10:03:47 CDT)
- Salinthip Thipayang (Fri May 03 2002 - 09:40:41 CDT)
help: nmode compile question!!!
- Andreas Svrcek-Seiler (Wed May 15 2002 - 06:30:12 CDT)
heterochirical peptides ?
- David Case (Tue Apr 30 2002 - 13:21:38 CDT)
- Yuguang Mu (Tue Apr 30 2002 - 10:43:39 CDT)
high electrostatic energy
- thenmalar rathinavelan (Thu Mar 07 2002 - 23:13:40 CST)
HIS residues
- Natasja Brooijmans (Thu Oct 24 2002 - 18:09:55 CDT)
- Ioana Cozmuta (Thu Oct 24 2002 - 16:51:40 CDT)
How Amber calculates electrostatic energy?
- Daniel Svozil (Wed Nov 27 2002 - 08:47:11 CST)
How can I get the correct residue number?
- Bill Ross (Thu May 02 2002 - 15:38:24 CDT)
- Bill Ross (Thu May 02 2002 - 15:26:45 CDT)
How to check whether the trajectory file matches the coordinates file or not?
- Kristina Furse (Mon Sep 09 2002 - 14:32:27 CDT)
- Shixiang Yan (Mon Sep 09 2002 - 13:53:04 CDT)
- Ling Zhang (Mon Sep 09 2002 - 13:31:13 CDT)
How to choose the box and cap size
- sxzheng (Thu Oct 31 2002 - 00:42:27 CST)
How to convert oldparmtop to newparmtop?
- A.Madhumalar (Thu Oct 17 2002 - 12:05:29 CDT)
- Michael Ford (Wed Oct 16 2002 - 14:47:57 CDT)
- David A. Case (Wed Oct 16 2002 - 13:04:59 CDT)
- A.Madhumalar (Wed Oct 16 2002 - 12:18:35 CDT)
How to decrease the solvated system in Amber6?
- Ling Zhang (Tue Jul 02 2002 - 10:30:19 CDT)
- David A. Case (Tue Jul 02 2002 - 06:38:50 CDT)
- Ling Zhang (Mon Jul 01 2002 - 11:28:51 CDT)
How to define a sphere to minimize?
- Bill Ross (Mon Oct 21 2002 - 10:11:19 CDT)
- David Smith (Mon Oct 21 2002 - 06:00:03 CDT)
- Guillermo Mulliert Carlín (Mon Oct 21 2002 - 01:46:57 CDT)
how to detect bad contact?
- X. Tan (Wed Sep 04 2002 - 14:14:40 CDT)
How to do 2dRMS in ptraj
- Ying Zhao (Thu Oct 10 2002 - 14:33:43 CDT)
How to generate PNA structure?
- A. Hungie (Mon Oct 07 2002 - 03:51:53 CDT)
how to keep aromatic ring flat
- Bill Ross (Fri Jun 14 2002 - 18:34:42 CDT)
- Qing Zhang (Fri Jun 14 2002 - 18:00:51 CDT)
how to make mpeg files from amber trajectories
- Anke Eisenmann (Tue Aug 27 2002 - 09:41:01 CDT)
How to make mpeg files from amber trajectories (fwd)
- Michal Otyepka (Wed Aug 28 2002 - 02:22:54 CDT)
- Jake Isaacs (Tue Aug 27 2002 - 08:48:24 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:07 CDT)
how to neutralise the system?
- David Case (Mon Jan 14 2002 - 13:35:00 CST)
- X. Tan (Mon Jan 14 2002 - 13:18:14 CST)
How to run the leap module
- John Bushnell (Tue Apr 30 2002 - 12:46:35 CDT)
- Sanjeev B.S. (Tue Apr 30 2002 - 05:37:11 CDT)
- param_at_ibab.ac.in (Tue Apr 30 2002 - 04:34:32 CDT)
How to set the dielctric constant equals 1, when running MD simulations in real solvent water?
- Ling Zhang (Thu Jun 13 2002 - 15:54:53 CDT)
How to specify the counterion positions using xleap?
- M. L. Dodson (Wed Oct 16 2002 - 19:10:22 CDT)
- Ioana Cozmuta (Wed Oct 16 2002 - 12:45:06 CDT)
- James W. Caldwell (Wed Oct 16 2002 - 10:28:06 CDT)
- David A. Case (Wed Oct 16 2002 - 10:09:21 CDT)
- A.Madhumalar (Wed Oct 16 2002 - 07:54:41 CDT)
Hydrogen bond energy using Anal
- A.Madhumalar (Tue Mar 26 2002 - 04:23:34 CST)
Hydrophobic protein in water
- Luo Liu (Sun Nov 24 2002 - 16:52:20 CST)
I can not see text in xleap !
- S. Jang (Wed Jan 16 2002 - 00:56:04 CST)
IBELLY and NMROPT in sander
- Tom Bishop (Thu Oct 10 2002 - 11:54:43 CDT)
IDECOMP
- Holger Gohlke (Wed Oct 30 2002 - 14:11:13 CST)
- Mark Hsieh (Wed Oct 30 2002 - 12:11:02 CST)
IFBOX=0 error in amber7
- Bill Ross (Wed May 01 2002 - 00:15:05 CDT)
- Eva Darian (Tue Apr 30 2002 - 23:43:31 CDT)
IFTRES option in sander and gibbs
- Alexander Issanin (Tue Feb 12 2002 - 15:09:52 CST)
IGB =4 with GAFF and bugfix24 incomplete?
- David A. Case (Wed Oct 16 2002 - 13:55:24 CDT)
- Tom Bishop (Wed Oct 16 2002 - 13:12:37 CDT)
igb problem in sander
- Emma.Sigfridsson_at_astrazeneca.com (Wed Jun 12 2002 - 04:11:20 CDT)
igb=2 in amber7
- Randy M. Wadkins (Fri Aug 02 2002 - 17:28:48 CDT)
igb=2,gbsa=1,antechamber,bad atom type
- Jianhui Wu (Fri May 17 2002 - 14:20:14 CDT)
Im lost
- David A. Case (Tue Aug 20 2002 - 10:15:29 CDT)
- Sankha Subhra Som (Tue Aug 20 2002 - 00:16:00 CDT)
image
- David A. Case (Thu Sep 19 2002 - 12:43:32 CDT)
- X. Tan (Thu Sep 19 2002 - 12:32:15 CDT)
Image charges with the solvate cap command
- David A. Case (Mon Sep 30 2002 - 19:34:28 CDT)
- dkeller_at_unm.edu (Mon Sep 30 2002 - 10:52:11 CDT)
image command
- Sophia Kondratova (Thu Aug 29 2002 - 12:46:01 CDT)
Imaging & fitting in carnal
- Sanjeev B.S. (Thu Oct 17 2002 - 06:01:55 CDT)
ImagingAtom
- Bill Ross (Thu Feb 07 2002 - 04:41:57 CST)
- eric ARNOULT (Wed Feb 06 2002 - 10:07:04 CST)
Import of CHARMM force field and GB potential parameters into Amber7
- David Case (Mon Aug 05 2002 - 00:25:28 CDT)
- Soonmin Jang (Sun Aug 04 2002 - 21:19:20 CDT)
Including explicit waters in GB dynamics
- Kristina Furse (Fri Aug 02 2002 - 15:32:52 CDT)
- Kristina Furse (Sat Jul 20 2002 - 19:30:43 CDT)
increase lastist
- jim caldwell (Wed Jul 24 2002 - 17:45:43 CDT)
- David A. Case (Wed Jul 24 2002 - 16:41:48 CDT)
- Marcela Madrid (Wed Jul 24 2002 - 15:41:45 CDT)
increasing the number of processors
- Ioana Cozmuta (Tue Dec 03 2002 - 18:17:58 CST)
increasing the number of processors (fwd)
- Ioana Cozmuta (Tue Dec 03 2002 - 18:19:24 CST)
Information request - where to buy software
- Claire Edmonds (Mon Aug 05 2002 - 08:23:59 CDT)
Initial Amber 7 benchmark timings
- Stéphane Teletchéa (Thu Apr 04 2002 - 03:36:23 CST)
- David Case (Wed Apr 03 2002 - 20:33:14 CST)
input files
- Carlos Simmerling (Wed Apr 03 2002 - 07:40:30 CST)
- Monica (Wed Apr 03 2002 - 07:00:42 CST)
input format for gibbs restraints
- Jose Ramon Blas (Wed Nov 13 2002 - 20:59:43 CST)
- David A. Case (Wed Nov 13 2002 - 19:53:27 CST)
Inquiry
- software_at_kagaku.com (Sun Nov 24 2002 - 21:44:51 CST)
inquiry regarding AMBER
- David Case (Thu Jan 10 2002 - 16:51:54 CST)
- xz27 (Thu Jan 10 2002 - 15:24:08 CST)
install leap not working
- Bill Ross (Tue Apr 30 2002 - 14:21:01 CDT)
- nepenthes_at_vplaces.net (Tue Apr 30 2002 - 02:52:07 CDT)
installing MPICH for AMBER on Linux CLuster
- Thomas A. Spraggins (Mon Jul 08 2002 - 08:15:23 CDT)
- Walter Langel (Mon Jul 08 2002 - 07:26:36 CDT)
- root (Mon Jul 08 2002 - 05:02:52 CDT)
installing MPICH for AMBER on Linux CLuster update
- Thomas Steinbrecher (Mon Jul 08 2002 - 08:46:48 CDT)
intdiel & extdiel
- Holger Gohlke (Thu Nov 21 2002 - 09:55:15 CST)
- Fredrick Robin Devadoss (Wed Nov 20 2002 - 22:28:35 CST)
- David A. Case (Wed Nov 20 2002 - 09:51:44 CST)
- Fredrick Robin Devadoss (Wed Nov 20 2002 - 05:23:59 CST)
Intel ifc Compiler
- Joachim Reichelt (Mon Jun 03 2002 - 01:51:54 CDT)
- David Case (Fri May 31 2002 - 09:51:21 CDT)
- David Case (Thu May 30 2002 - 09:00:55 CDT)
- Robert Duke (Thu May 30 2002 - 08:13:59 CDT)
- Joachim Reichelt (Thu May 30 2002 - 04:23:21 CDT)
Intel Kernel Math Library
- Joffre Heredia (Thu Jun 06 2002 - 14:46:32 CDT)
- case (Thu Jun 06 2002 - 10:02:25 CDT)
Interaction table from minimization
- kiyean.nam_at_pharma.novartis.com (Fri Jun 28 2002 - 16:40:59 CDT)
Interface and Amber 7.0
- David Pearlman (Tue Aug 27 2002 - 11:35:19 CDT)
- David A. Case (Tue Aug 27 2002 - 06:53:45 CDT)
- Nigel D Priestley (Mon Aug 26 2002 - 21:45:55 CDT)
INTPRT and PMF
- David Pearlman (Tue Apr 23 2002 - 15:05:12 CDT)
- Sophia Kondratova (Tue Apr 23 2002 - 13:23:36 CDT)
ion distances
- Bill Ross (Mon Nov 25 2002 - 18:51:46 CST)
- Thomas E. Cheatham, III (Thu Nov 21 2002 - 17:54:46 CST)
- ë‚¨ê¸°ì—½ (Thu Nov 21 2002 - 16:52:55 CST)
- Marcela Madrid (Thu Nov 21 2002 - 14:59:12 CST)
Is H-bonding really there?
- Ioana Cozmuta (Tue Oct 01 2002 - 16:44:55 CDT)
- Ioana Cozmuta (Fri Sep 27 2002 - 17:04:37 CDT)
- Pratul Agarwal (Fri Sep 27 2002 - 15:58:25 CDT)
- Thomas Cheatham (Fri Sep 27 2002 - 15:53:24 CDT)
- suvendu lomash (Fri Sep 27 2002 - 14:59:48 CDT)
ISTAR2 - oops, just found the answer...
- Mahadevan Seetharaman (Wed Sep 25 2002 - 14:55:46 CDT)
iwrap and image
- James W. Caldwell (Wed Aug 28 2002 - 09:35:50 CDT)
- Sophia Kondratova (Wed Aug 28 2002 - 07:55:36 CDT)
iwrap set in sander of Amber6
- Ling Zhang (Thu Jun 27 2002 - 15:43:41 CDT)
j3 coupling
- David A. Case (Fri Jun 21 2002 - 09:49:40 CDT)
- Yuguang Mu (Fri Jun 21 2002 - 05:38:31 CDT)
Junmei et al. 1999
- David Case (Wed May 22 2002 - 10:05:23 CDT)
- Yuguang Mu (Wed May 22 2002 - 04:30:29 CDT)
- Lepsa (Wed May 22 2002 - 03:58:41 CDT)
- Michal Otyepka (Wed May 22 2002 - 02:57:11 CDT)
just a test
- Vlad Cojocaru (Wed Sep 11 2002 - 08:39:59 CDT)
large energy fluctration
- eric hu (Fri Sep 20 2002 - 13:00:17 CDT)
- Carlos Simmerling (Thu Sep 12 2002 - 13:50:09 CDT)
- eric hu (Thu Sep 12 2002 - 13:05:10 CDT)
Latest parm + getting parm98 as default in LEaP
- David Case (Tue Jan 22 2002 - 10:14:55 CST)
- Bill Ross (Tue Jan 22 2002 - 01:07:39 CST)
- Lepsa (Tue Jan 22 2002 - 00:39:59 CST)
- Andreas Svrcek-Seiler (Mon Jan 21 2002 - 04:01:49 CST)
- Sanjeev B.S. (Mon Jan 21 2002 - 00:43:42 CST)
LEAP - Introducing dummy atoms
- James W. Caldwell (Mon Dec 02 2002 - 13:11:27 CST)
- Miguel de Federico (Mon Dec 02 2002 - 10:42:49 CST)
leap - sander information flow
- David A. Case (Mon Oct 28 2002 - 15:44:28 CST)
- Wiktor Jurkowski (Mon Oct 28 2002 - 06:34:51 CST)
leap and topology file
- Lepsa (Fri Sep 13 2002 - 09:39:45 CDT)
- Marcela Madrid (Thu Sep 12 2002 - 11:12:20 CDT)
leap bugfix
- Bill Ross (Sun Apr 21 2002 - 16:55:34 CDT)
leap calculation
- Itziar Maestre Asenjo (Wed Mar 06 2002 - 11:43:44 CST)
leap calculation (loadamberprep)
- Bill Ross (Wed Mar 06 2002 - 13:22:33 CST)
Leap error: PDB file with more than 10000 residues
- jim caldwell (Tue Aug 06 2002 - 16:57:34 CDT)
- Pratul Agarwal (Tue Aug 06 2002 - 16:47:00 CDT)
- David A. Case (Tue Aug 06 2002 - 16:13:30 CDT)
- Pratul Agarwal (Tue Aug 06 2002 - 14:50:04 CDT)
leap for peptide
- Sichun Yang (Fri Nov 22 2002 - 16:33:51 CST)
LEaP gives "no sp2 improper torsion term" warnings
- David A. Case (Fri Jul 12 2002 - 15:25:35 CDT)
LEaP: The parm and coord files disagree on the number of atoms
- James W. Caldwell (Tue Oct 29 2002 - 09:50:26 CST)
- Miguel de Federico (Tue Oct 29 2002 - 02:24:58 CST)
leap:segmentation fault
- Sanjeev B.S. (Tue Feb 26 2002 - 10:30:45 CST)
leaprc file (fwd)
- David A. Case (Mon Aug 26 2002 - 20:09:22 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:44 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:29 CDT)
LIMIN Faliure/Energies per residue for B-DNA etc.
- darden (Thu Jan 31 2002 - 15:11:19 CST)
- Prabal Maiti (Thu Jan 31 2002 - 13:49:00 CST)
limit of RMSD value
- Thomas Cheatham (Tue Nov 19 2002 - 11:51:53 CST)
- Bimo Ario Tejo (Tue Nov 19 2002 - 07:57:40 CST)
limit of written files with ptraj
- Carles Ferrer (Mon Mar 11 2002 - 14:54:16 CST)
Linking to its own image
- Miguel Angel Rodriguez Carvajal (Thu Feb 14 2002 - 08:15:52 CST)
LINMIN FAILURE
- David A. Case (Tue Oct 08 2002 - 20:33:07 CDT)
- hung_at_atc.atccu.chula.ac.th (Tue Oct 08 2002 - 19:41:00 CDT)
LINMIN failure during minimization
- David A. Case (Fri Aug 09 2002 - 11:09:09 CDT)
- Giulio Rastelli (Fri Aug 09 2002 - 03:46:18 CDT)
Linmin question...
- David A. Case (Fri Nov 15 2002 - 02:12:20 CST)
- Andrei Leitão (Thu Nov 14 2002 - 12:13:01 CST)
- Andrei Leitão (Thu Nov 14 2002 - 12:10:21 CST)
Linux Parallel compilation Linux Mpich PGI
- Viktor Hornak (Mon May 27 2002 - 09:56:24 CDT)
- Fabrice Yerly (Mon May 27 2002 - 07:31:09 CDT)
linux?
- Carlos Simmerling (Fri Jan 04 2002 - 07:55:15 CST)
- Shixiang Yan (Thu Jan 03 2002 - 20:17:46 CST)
Lipid simulation, DMPC
- Samantha (Wed Feb 13 2002 - 10:24:20 CST)
literature for NVE
- Khatcharin Siriwong (Mon Aug 12 2002 - 11:19:03 CDT)
- David A. Case (Mon Aug 12 2002 - 10:38:45 CDT)
- Khatcharin Siriwong (Mon Aug 12 2002 - 04:07:05 CDT)
loadpdb error messages
- James W. Caldwell (Tue Sep 10 2002 - 18:49:48 CDT)
- Joel Konkle-Parker (Tue Sep 10 2002 - 17:58:07 CDT)
look for benchmark with myrinet vs. 100-BT
- C. Klein (Sun Aug 04 2002 - 03:21:29 CDT)
- Margaret Cheung (Fri Aug 02 2002 - 13:20:22 CDT)
- Jianhui Wu (Fri Aug 02 2002 - 12:15:29 CDT)
looking for frcmod in AMBER Tutorials
- yuann (Fri Jul 12 2002 - 04:19:45 CDT)
loss of disulfide bonds
- David A. Case (Mon Oct 14 2002 - 13:10:50 CDT)
- Richard Henchman (Mon Oct 14 2002 - 12:44:30 CDT)
- James W. Caldwell (Mon Oct 14 2002 - 12:28:15 CDT)
- Carlos Simmerling (Mon Oct 14 2002 - 11:49:15 CDT)
- Natasja Brooijmans (Mon Oct 14 2002 - 11:46:54 CDT)
- David A. Case (Mon Oct 14 2002 - 11:04:30 CDT)
- Holger Gohlke (Mon Oct 14 2002 - 10:51:01 CDT)
- Nicolas Le Novere (Mon Oct 14 2002 - 10:31:23 CDT)
Mac OS X compiliation?
- Randy M. Wadkins (Thu Jun 06 2002 - 16:58:18 CDT)
MACHINE file for Tru64 ES45
- CUI, Guanglei (Tue Oct 08 2002 - 08:47:16 CDT)
- Chuck Schneider (Tue Oct 08 2002 - 06:28:45 CDT)
- CUI, Guanglei (Mon Oct 07 2002 - 14:20:19 CDT)
Machine_file for Hitachi SR8000
- A. Hungie (Wed Jun 05 2002 - 06:09:03 CDT)
MacOS X
- David Bevan (Tue Jan 29 2002 - 10:15:12 CST)
Magnesium as a DNA counterion in AMBER 6.0
- Mike Keller (Thu Mar 28 2002 - 09:31:29 CST)
mail host switchover
- jim caldwell (Mon Aug 19 2002 - 16:58:11 CDT)
mail reflector
- James W. Caldwell (Mon Aug 26 2002 - 17:35:53 CDT)
makeDIP_RST.dna
- Vickie Tsui (Wed Jul 24 2002 - 18:49:57 CDT)
- McAteer, Kathleen (Wed Jul 24 2002 - 14:24:42 CDT)
makeDIST_RST?
- David A. Case (Mon Nov 18 2002 - 18:15:35 CST)
- Sichun Yang (Mon Nov 18 2002 - 17:44:09 CST)
Matching Patterns
- Tali (Wed Apr 10 2002 - 16:57:59 CDT)
MAX_RSTACK
- Joffre Heredia (Wed Jul 10 2002 - 12:12:15 CDT)
- Jithesh (Wed Jul 10 2002 - 01:24:42 CDT)
max_rstack requested
- Albert Codony (Sun Apr 28 2002 - 17:39:58 CDT)
Maxwell Boltzmann Distribution
- Stéphane Teletchéa (Thu Jan 17 2002 - 08:48:02 CST)
md equilibration in chloroform
- Thomas.Fox_at_bc.boehringer-ingelheim.com (Thu Jul 11 2002 - 12:51:47 CDT)
- David A. Case (Mon Jul 08 2002 - 10:42:24 CDT)
- Sophia Kondratova (Mon Jul 08 2002 - 08:38:27 CDT)
MD in alcohol
- Marc DOBLER (Mon Aug 05 2002 - 03:46:17 CDT)
- David Case (Mon Aug 05 2002 - 00:31:40 CDT)
- Marc DOBLER (Sun Aug 04 2002 - 21:33:52 CDT)
MD on cytochrome
- Mahadevan Seetharaman (Thu Aug 01 2002 - 16:15:52 CDT)
MD Primers
- Peter Gannett (Fri Sep 27 2002 - 18:34:40 CDT)
- Joel Konkle-Parker (Fri Sep 27 2002 - 14:54:03 CDT)
MD with simulated annealing
- Giulio Rastelli (Fri Feb 22 2002 - 12:39:56 CST)
MDaemon Warning - Virus Found
- postmaster_at_bydnet.com.pl (Wed Dec 04 2002 - 21:49:28 CST)
- postmaster_at_96com.com (Fri Sep 13 2002 - 08:13:22 CDT)
- postmaster_at_96com.com (Fri Sep 13 2002 - 08:10:40 CDT)
- postmaster_at_96com.com (Tue Sep 10 2002 - 10:57:00 CDT)
- postmaster_at_96com.com (Mon Sep 09 2002 - 06:04:45 CDT)
- postmaster_at_96com.com (Fri Sep 06 2002 - 06:13:47 CDT)
- postmaster_at_96com.com (Wed Sep 04 2002 - 05:40:26 CDT)
- postmaster_at_96com.com (Tue Sep 03 2002 - 06:57:12 CDT)
- postmaster_at_96com.com (Mon Sep 02 2002 - 06:25:18 CDT)
- postmaster_at_96com.com (Mon Sep 02 2002 - 05:12:42 CDT)
- postmaster_at_96com.com (Fri Aug 30 2002 - 05:59:25 CDT)
- postmaster_at_96com.com (Fri Aug 30 2002 - 05:08:15 CDT)
- postmaster_at_96com.com (Thu Aug 29 2002 - 12:02:23 CDT)
- postmaster_at_96com.com (Thu Aug 29 2002 - 07:20:52 CDT)
- postmaster_at_96com.com (Thu Aug 29 2002 - 05:14:06 CDT)
mdcrd to arc
- Ian R Bates (Sat Mar 23 2002 - 10:46:21 CST)
memory allocation in mm_pbsa
- Holger Gohlke (Wed Sep 11 2002 - 10:55:07 CDT)
- James W. Caldwell (Wed Sep 11 2002 - 10:26:19 CDT)
- Giulio Rastelli (Wed Sep 11 2002 - 05:41:04 CDT)
Memory and swap in sander
- David A. Case (Mon Aug 12 2002 - 10:55:55 CDT)
- William Wei (Mon Aug 12 2002 - 10:11:35 CDT)
memory problem on gibbs
- X. Tan (Thu Feb 14 2002 - 18:24:55 CST)
MEP g98_option
- Pascal Bonnet (Mon Nov 11 2002 - 05:05:55 CST)
- FyD (Sat Nov 09 2002 - 00:35:22 CST)
message during minimization
- David A. Case (Thu Dec 19 2002 - 10:05:00 CST)
- Ioana Cozmuta (Wed Dec 18 2002 - 20:02:26 CST)
- darden (Wed Dec 18 2002 - 18:32:21 CST)
- Ioana Cozmuta (Wed Dec 18 2002 - 17:09:05 CST)
- darden (Wed Dec 18 2002 - 10:24:48 CST)
- Ioana Cozmuta (Tue Dec 17 2002 - 23:31:52 CST)
min output
- James W. Caldwell (Thu Oct 24 2002 - 11:01:15 CDT)
- David A. Case (Wed Oct 23 2002 - 18:51:06 CDT)
- Ioana Cozmuta (Wed Oct 23 2002 - 18:26:44 CDT)
minimising WATBOX216
- Michael G Cooney (Tue Jan 15 2002 - 15:38:58 CST)
- sara nunez (Tue Jan 15 2002 - 13:11:04 CST)
minimization in amber7 for nonperiodic systems
- David A. Case (Wed Aug 14 2002 - 10:28:21 CDT)
- Giulio Rastelli (Wed Aug 14 2002 - 10:03:11 CDT)
- David Case (Wed Aug 14 2002 - 00:47:43 CDT)
Minimization in GB-SA-E-Spikes, LINMIN
- David A. Case (Wed Jul 17 2002 - 19:43:57 CDT)
- Sarangan Ravichandran (Tue Jul 16 2002 - 12:11:27 CDT)
- Andreas Svrcek-Seiler (Tue Jul 16 2002 - 11:00:55 CDT)
- Sarangan Ravichandran (Tue Jul 16 2002 - 10:02:58 CDT)
Minimization of pentane holding a plane of carbon atoms
- Hungie Hungie (Wed Apr 17 2002 - 12:32:28 CDT)
minimization problem
- Andreas Svrcek-Seiler (Tue Mar 19 2002 - 07:33:19 CST)
- Uwe Richter (Tue Mar 19 2002 - 06:22:06 CST)
minimization probs
- case (Tue Jun 11 2002 - 12:36:57 CDT)
- Amesh Patel (Tue Jun 11 2002 - 10:57:12 CDT)
minimization to fix up hydrogen positions
- yuann (Wed May 29 2002 - 02:33:23 CDT)
minimum image cut-off
- Nikolai Smolin (Wed Jun 26 2002 - 06:05:08 CDT)
misdirected message
- Michael G Cooney (Mon Aug 12 2002 - 14:35:35 CDT)
missing residues
- Mark Hsieh (Sun May 05 2002 - 02:15:31 CDT)
mm pbsa: generate snapshots
- Mathy Froeyen (Thu Apr 18 2002 - 02:19:35 CDT)
- Mark Hsieh (Wed Apr 17 2002 - 16:52:41 CDT)
MM-GBSA and counterions
- David A. Case (Thu Oct 03 2002 - 15:43:35 CDT)
- Michael Ford (Thu Oct 03 2002 - 14:27:27 CDT)
MM-PBSA and Insight's version of Delphi
- Emma.Sigfridsson_at_astrazeneca.com (Mon Oct 14 2002 - 02:47:21 CDT)
MM-PBSA basics
- Lepsa (Mon Sep 30 2002 - 02:13:16 CDT)
- Holger Gohlke (Sun Sep 29 2002 - 21:44:52 CDT)
- Michael Ford (Fri Sep 27 2002 - 14:53:01 CDT)
MM-PBSA philosophy
- David Case (Wed Mar 20 2002 - 10:10:05 CST)
- Felipe Pineda (Wed Mar 20 2002 - 08:25:05 CST)
- Michal Otyepka (Wed Mar 20 2002 - 06:34:24 CST)
MM-PBSA tutorial
- Lepsa (Mon Oct 14 2002 - 02:14:47 CDT)
- Holger Gohlke (Thu Oct 10 2002 - 13:57:41 CDT)
- Giulio Rastelli (Thu Oct 10 2002 - 09:22:59 CDT)
MM-PBSA: .crg file for Delphi
- Holger Gohlke (Wed Dec 11 2002 - 12:31:07 CST)
- Thomas Steinbrecher (Wed Dec 11 2002 - 12:08:40 CST)
MM-PGBSA Question!!
- David A. Case (Tue Oct 22 2002 - 09:45:20 CDT)
- Bernd Wellenzohn (Tue Oct 22 2002 - 07:46:29 CDT)
mm_pbsa
- David A. Case (Mon Sep 23 2002 - 08:25:02 CDT)
- Mahadevan Seetharaman (Sun Sep 22 2002 - 21:07:27 CDT)
- Holger Gohlke (Sun Sep 22 2002 - 16:01:22 CDT)
- Sue Heavner (Fri Sep 20 2002 - 15:00:36 CDT)
- Lepsa (Fri May 24 2002 - 09:27:21 CDT)
- X. Tan (Mon May 20 2002 - 18:04:52 CDT)
mm_pbsa and statistic program
- David A. Case (Thu Sep 26 2002 - 10:37:15 CDT)
- Pascal Bonnet (Thu Sep 26 2002 - 05:50:52 CDT)
mm_pbsa curious output of coordinates and resulting errors...
- Michael Ford (Tue Oct 29 2002 - 16:01:43 CST)
mm_pbsa error message (warning?)
- Michael Ford (Tue Oct 29 2002 - 16:47:02 CST)
mm_pbsa error message!
- Michael Ford (Wed Dec 18 2002 - 11:37:57 CST)
- William Wei (Wed Dec 18 2002 - 11:17:16 CST)
mm_pbsa for uhbd
- Mark Hsieh (Fri Apr 19 2002 - 20:56:18 CDT)
mm_pbsa in parallel system
- David Case (Mon Jun 03 2002 - 09:49:08 CDT)
mm_pbsa in parallel system (fwd)
- Jianhui Wu (Mon Jun 03 2002 - 11:03:12 CDT)
mm_pbsa output error
- Holger Gohlke (Mon Sep 23 2002 - 23:21:30 CDT)
- Michael Murray (Mon Sep 23 2002 - 12:26:11 CDT)
mm_pbsa positive binding energies
- David A. Case (Mon Sep 02 2002 - 12:50:30 CDT)
- Mathy Froeyen (Mon Sep 02 2002 - 04:11:34 CDT)
mm_pbsa question.
- wentaofu (Tue Sep 17 2002 - 10:35:59 CDT)
mm_pbsa-amber7
- Sue Heavner (Tue Oct 22 2002 - 14:06:01 CDT)
Mn parameters!!!
- navjot_at_bioinfo.ernet.in (Mon Jun 17 2002 - 04:19:12 CDT)
model molecules for getting charges of DNA
- Qing Zhang (Sun Jun 09 2002 - 14:47:04 CDT)
- Jiyoung Heo (Sat Jun 08 2002 - 19:20:10 CDT)
mol2 file format in the future of amber
- M. L. Dodson (Sun Sep 22 2002 - 10:34:06 CDT)
- David A. Case (Sun Sep 22 2002 - 10:10:42 CDT)
- M. L. Dodson (Fri Sep 20 2002 - 09:41:02 CDT)
mol2 with antechamber
- David A. Case (Fri Jul 26 2002 - 10:54:08 CDT)
- Giulio Rastelli (Fri Jul 26 2002 - 05:57:22 CDT)
mol2_to_off
- Matthew Randolph Lee, Ph.D. (Fri Aug 16 2002 - 17:15:41 CDT)
Molecular Dynamic procedure...
- Andrei Leitão (Wed Oct 16 2002 - 10:48:10 CDT)
Molecular dynamic protocol...
- David A. Case (Fri Dec 27 2002 - 13:25:51 CST)
- Andrei Leitão (Fri Dec 27 2002 - 12:40:26 CST)
molsurf reference
- David A. Case (Fri Nov 01 2002 - 07:46:21 CST)
- Giulio Rastelli (Fri Nov 01 2002 - 06:17:35 CST)
mopac
- Pascal Bonnet (Fri Jun 28 2002 - 03:49:11 CDT)
- David A. Case (Thu Jun 27 2002 - 13:34:34 CDT)
- David.Rilett_at_astrazeneca.com (Thu Jun 27 2002 - 12:50:41 CDT)
Mopac509mn/linux
- James W. Caldwell (Tue Sep 24 2002 - 10:00:20 CDT)
more about averaging
- Bill Ross (Fri Nov 08 2002 - 15:21:39 CST)
- Vlad Cojocaru (Fri Nov 08 2002 - 08:12:00 CST)
More GB/Belly
- dkon_at_email.arizona.edu (Tue Mar 26 2002 - 16:00:23 CST)
more information about the previous email
- Vlad Cojocaru (Wed Oct 16 2002 - 12:26:43 CDT)
more van der Waals explosion
- Arvid Soederhaell (Fri Jun 21 2002 - 04:00:59 CDT)
MP_Lite
- Stéphane Teletchéa (Thu Jan 24 2002 - 11:44:40 CST)
MPI (parallel) version of GIBBS
- Etienne ENGLER (Mon Jan 07 2002 - 06:13:45 CST)
MPI sander
- Uwe Richter (Thu Feb 21 2002 - 07:13:52 CST)
mpi version of sander in Amber 6.0 with constraints
- Stefan Andreev Andreev (Wed Aug 14 2002 - 17:13:26 CDT)
MPI_BCAST error
- Nathan A. Baker (Wed Dec 18 2002 - 19:31:47 CST)
- Scott Brozell (Wed Dec 18 2002 - 15:24:55 CST)
- Nathan A. Baker (Wed Dec 18 2002 - 09:51:02 CST)
MPICH and AMBER 7
- Mark Hsieh (Thu Apr 18 2002 - 18:12:58 CDT)
MPich error
- Stéphane Teletchéa (Wed May 29 2002 - 09:00:44 CDT)
- Fabrice Yerly (Wed May 29 2002 - 07:46:29 CDT)
mpich, I/O, Master node, filesystem
- David Case (Thu Aug 08 2002 - 00:14:25 CDT)
- Jianhui Wu (Wed Aug 07 2002 - 23:24:13 CDT)
MPICH/LAM on sparc
- Sanjeev B.S. (Sat Feb 16 2002 - 06:23:26 CST)
mpirun
- Ross Walker (Sun Sep 01 2002 - 17:36:24 CDT)
- Ioana Cozmuta (Sun Sep 01 2002 - 13:32:08 CDT)
MS program ...
- Samantha (Sat Mar 23 2002 - 11:09:14 CST)
- A. Ababou (Sat Mar 23 2002 - 10:21:15 CST)
multiple improper torsion terms
- Thijs Beuming (Fri Jan 11 2002 - 21:37:58 CST)
Mutations - Molecular Dynamics
- William Wei (Mon May 27 2002 - 10:21:04 CDT)
- William Wei (Thu May 16 2002 - 18:11:36 CDT)
MXVAR
- Guanglei Cui (Thu Dec 12 2002 - 10:34:17 CST)
NaCl concentration
- Peter Gannett (Tue Apr 30 2002 - 14:34:38 CDT)
NAD parameters
- Andy Purkiss (Thu Jan 17 2002 - 13:42:21 CST)
namelist error with sander
- Andreas Kerzmann (Mon Aug 12 2002 - 07:40:12 CDT)
- David A. Case (Fri Aug 09 2002 - 10:50:27 CDT)
- Andreas Kerzmann (Fri Aug 09 2002 - 03:47:53 CDT)
Nanotubes with AMBER
- David Case (Sun Aug 11 2002 - 23:13:23 CDT)
- Stefan Andreev Andreev (Sun Aug 11 2002 - 18:59:26 CDT)
NATOM mismatch in coord and topology files.
- Narang Manpreet Kaur (Mon Nov 18 2002 - 00:49:46 CST)
NAV detected a virus in a document YOU sent to webmaster@nctimes.com.
- Mercury (Thu Oct 31 2002 - 21:12:51 CST)
nbflag
- Ioana Cozmuta (Wed Nov 06 2002 - 21:45:02 CST)
- Ioana Cozmuta (Wed Nov 06 2002 - 21:19:26 CST)
Net Charge is Different In The Sander Output!!
- David A. Case (Tue Jul 09 2002 - 22:53:47 CDT)
- Sarangan Ravichandran (Tue Jul 09 2002 - 20:19:00 CDT)
new on the Amber web pages...
- David A. Case (Tue Dec 31 2002 - 15:51:31 CST)
new problems compiling amber 7
- ramon kleber da rocha (Thu Jul 11 2002 - 12:30:07 CDT)
- Sanjeev B.S. (Wed Jul 10 2002 - 09:57:40 CDT)
- ramon kleber da rocha (Wed Jul 10 2002 - 08:11:52 CDT)
New Promotion Products at American Disc Corporation
- Service (Thu Jul 25 2002 - 14:56:47 CDT)
New Residue
- Monica (Mon Jun 24 2002 - 10:01:42 CDT)
new residues
- Vlad Cojocaru (Thu Apr 04 2002 - 07:03:37 CST)
new RNA residues
- Vlad Cojocaru (Thu May 02 2002 - 14:07:32 CDT)
new telescopes-Maksutov-Cassegrain, reflector, refractor
- wang lan (Tue Oct 15 2002 - 06:42:50 CDT)
- wang lan (Tue Oct 15 2002 - 06:13:49 CDT)
new units
- Vlad Cojocaru (Fri Mar 08 2002 - 08:35:46 CST)
new2oldparm format (2)
- Pascal Bonnet (Thu Sep 19 2002 - 05:43:39 CDT)
Nitro parameters
- Jerry Matthew Parks (Wed Aug 21 2002 - 16:28:48 CDT)
nmanal help request
- David A. Case (Fri Sep 27 2002 - 10:38:23 CDT)
- Peter Fojan (Fri Sep 27 2002 - 08:59:11 CDT)
Nmode
- James Caldwell (Thu Dec 19 2002 - 15:17:31 CST)
- Pratul Agarwal (Thu Dec 19 2002 - 15:07:47 CST)
nmode compile question?
- James W. Caldwell (Tue Sep 10 2002 - 13:04:07 CDT)
- Holger Gohlke (Tue Sep 10 2002 - 11:17:24 CDT)
- Yongjun Jiang (Tue Sep 10 2002 - 07:46:18 CDT)
nmode memory requirements
- David Case (Fri Jan 18 2002 - 11:50:29 CST)
- Michael Jakusch (Fri Jan 18 2002 - 10:15:52 CST)
nmode segmentation fault
- Haizhen Zhong (Fri Aug 09 2002 - 08:46:19 CDT)
- jim caldwell (Thu Aug 08 2002 - 13:21:03 CDT)
- Holger Gohlke (Thu Aug 08 2002 - 13:16:11 CDT)
- zhongh_at_umich.edu (Thu Aug 08 2002 - 08:56:08 CDT)
nmode vectors
- Thijs Beuming (Mon Jan 21 2002 - 06:24:48 CST)
nmr and positional restraint in input
- Christoph Brockmann (Thu Oct 10 2002 - 04:12:49 CDT)
- Peter Varnai (Wed Oct 09 2002 - 12:44:03 CDT)
NMR refinement
- A. Hungie (Thu May 16 2002 - 10:02:17 CDT)
- David Case (Wed May 15 2002 - 12:09:27 CDT)
- Jake Isaacs (Tue May 14 2002 - 14:16:37 CDT)
NMR restrains
- Marcela Madrid (Mon Dec 09 2002 - 14:33:31 CST)
NMR restraints on a 10-mer DNA in Sander
- David A. Case (Tue Nov 12 2002 - 17:30:52 CST)
- Michael G Cooney (Tue Nov 12 2002 - 14:16:32 CST)
- Jo.Vinje_at_kj.uib.no (Tue Nov 12 2002 - 11:34:55 CST)
nmropt problem in AMBER7
- Rukman Hertadi (Mon Mar 25 2002 - 03:51:22 CST)
no mdcrd, no mden file
- Arvid Soederhaell (Fri Jun 07 2002 - 06:43:30 CDT)
noesy intensity input in DNA
- Monica (Thu Apr 11 2002 - 03:03:50 CDT)
NON-BONDED INTERACTION
- David A. Case (Tue Oct 01 2002 - 10:28:00 CDT)
- Rosalia Pascual (Tue Jul 30 2002 - 09:41:49 CDT)
non-bonded metal ion in complex
- Pratul Agarwal (Tue Sep 17 2002 - 08:59:14 CDT)
- yuann (Tue Sep 17 2002 - 01:28:45 CDT)
non-zero 10-12 coefficient
- Anonymous (Thu Nov 14 2002 - 18:18:34 CST)
nonpeoridic boundary + mm/gbsa
- Holger Gohlke (Mon Nov 11 2002 - 10:59:27 CST)
- Yongjun Jiang (Mon Nov 11 2002 - 06:49:03 CST)
Not able to do parallel run (again)
- Stéphane Teletchéa (Tue Jan 08 2002 - 10:21:07 CST)
- Stéphane Teletchéa (Mon Jan 07 2002 - 11:08:17 CST)
Not able to image a snapshot.
- Stéphane Teletchéa (Thu Jul 11 2002 - 03:24:48 CDT)
- Stéphane Teletchéa (Wed Jul 10 2002 - 10:28:12 CDT)
Not able to use xleap ...
- CUI, Guanglei (Mon Oct 21 2002 - 10:33:23 CDT)
- Stéphane Teletchéa (Mon Oct 21 2002 - 10:02:25 CDT)
- CUI, Guanglei (Mon Oct 21 2002 - 08:43:51 CDT)
- Stéphane Teletchéa (Mon Oct 21 2002 - 02:08:12 CDT)
- Ross Walker (Sat Oct 19 2002 - 04:51:30 CDT)
- Stéphane Teletchéa (Fri Oct 18 2002 - 12:24:38 CDT)
- CUI, Guanglei (Fri Oct 18 2002 - 12:14:24 CDT)
- David A. Case (Fri Oct 18 2002 - 11:38:23 CDT)
- CUI, Guanglei (Fri Oct 18 2002 - 11:26:47 CDT)
- Stéphane Teletchéa (Fri Oct 18 2002 - 10:58:21 CDT)
not compiled with -DHAS_10_12!!
- Carlos Simmerling (Thu Dec 05 2002 - 11:03:08 CST)
- Sarah Tschampel (Thu Dec 05 2002 - 10:43:40 CST)
- William Wei (Thu Dec 05 2002 - 10:29:22 CST)
npairs
- Prem Raj (Thu Sep 19 2002 - 17:22:42 CDT)
NTT=5?
- Jake Isaacs (Wed May 01 2002 - 14:47:09 CDT)
- Jung-Hsing Lin (Tue Apr 30 2002 - 15:36:45 CDT)
- David Case (Tue Apr 30 2002 - 13:16:04 CDT)
- Jung-Hsing Lin (Tue Apr 30 2002 - 11:10:46 CDT)
- David Case (Tue Apr 30 2002 - 00:32:20 CDT)
- Jung-Hsing Lin (Mon Apr 29 2002 - 18:10:30 CDT)
ntwv saves v(t) or v(t+dt/2) ?
- David A. Case (Thu Dec 19 2002 - 11:24:33 CST)
- hagop demirdjian (Thu Dec 19 2002 - 10:04:55 CST)
NTX / IREST inconsistency
- David A. Case (Fri Oct 04 2002 - 10:35:07 CDT)
- Bimo Ario Tejo (Fri Oct 04 2002 - 10:11:59 CDT)
NTX value
- giudice (Mon Sep 02 2002 - 02:05:45 CDT)
- David A. Case (Fri Aug 30 2002 - 14:07:44 CDT)
- James W. Caldwell (Fri Aug 30 2002 - 13:35:30 CDT)
- James W. Caldwell (Fri Aug 30 2002 - 11:10:10 CDT)
- giudice (Fri Aug 30 2002 - 05:31:19 CDT)
ntx=7, irest=0
- David A. Case (Fri Nov 22 2002 - 20:36:28 CST)
- Marcela Madrid (Fri Nov 22 2002 - 17:56:00 CST)
ntx=7, irest=0, redux
- David Case (Sat Nov 23 2002 - 00:53:37 CST)
number of H-bonds
- Sanjeev B.S. (Sun Oct 20 2002 - 00:14:32 CDT)
- Bimo Ario Tejo (Sat Oct 19 2002 - 23:54:44 CDT)
Number of WATBOX
- David Smith (Thu Apr 25 2002 - 08:25:40 CDT)
- yuann (Thu Apr 25 2002 - 00:54:02 CDT)
Nz-Acetyllysine parameters
- Luis Gracia (Tue Nov 19 2002 - 18:08:13 CST)
Octane Box (equilibrated)
- samantha hughes (Wed Jul 24 2002 - 10:27:53 CDT)
off-to-mol2
- David A. Case (Wed Dec 18 2002 - 12:03:48 CST)
- Anke Eisenmann (Wed Dec 18 2002 - 10:49:22 CST)
offset of temperature when running MD with CAP and no periodic conditions
- Andreas Svrcek-Seiler (Thu Sep 19 2002 - 12:11:31 CDT)
- Therese Malliavin (Thu Sep 19 2002 - 10:44:24 CDT)
old prmtop
- Peter Gannett (Wed Sep 04 2002 - 13:10:56 CDT)
- Holger Gohlke (Wed Sep 04 2002 - 11:21:32 CDT)
- C. Klein (Wed Sep 04 2002 - 11:21:18 CDT)
- Thomas Steinbrecher (Wed Sep 04 2002 - 10:56:47 CDT)
once again: residue cross-correlation
- Bimo Ario Tejo (Fri Oct 25 2002 - 09:39:40 CDT)
One question about how to use the amber
- Zhe SUN (Tue Mar 26 2002 - 06:49:35 CST)
Open position: Postdoctoral Scientist
- Joachim Reichelt (Wed Jan 16 2002 - 09:57:07 CST)
Order of a protein, bound waters and ligand in saveamberparm
- Masaki Tomimoto (Thu Aug 15 2002 - 17:04:18 CDT)
- Masaki Tomimoto (Thu Aug 15 2002 - 15:25:45 CDT)
order parameters?
- Arvid Soederhaell (Fri Apr 12 2002 - 07:55:33 CDT)
Origin300, Linux Cluster
- Dow Hurst (Mon Jul 08 2002 - 09:40:34 CDT)
- Stéphane Teletchéa (Mon Jul 08 2002 - 07:37:37 CDT)
- Stéphane Teletchéa (Fri Jul 05 2002 - 03:48:03 CDT)
- C. Klein (Thu Jul 04 2002 - 12:41:31 CDT)
- Jianhui Wu (Thu Jul 04 2002 - 11:04:07 CDT)
Overwrite files
- Yong Duan (Thu Dec 05 2002 - 20:41:37 CST)
- Scott Brozell (Thu Dec 05 2002 - 15:39:23 CST)
- Long Hai (Thu Dec 05 2002 - 15:33:53 CST)
- Joffre Heredia (Thu Dec 05 2002 - 14:25:33 CST)
P.3 in antechamber
- Giulio Rastelli (Thu Nov 21 2002 - 05:02:16 CST)
P4_GLOBMEMSIZE problem
- Ross Walker (Tue Nov 05 2002 - 17:04:03 CST)
- Jean-Christophe Ducom (Tue Nov 05 2002 - 11:53:11 CST)
- Ross Walker (Tue Nov 05 2002 - 11:16:55 CST)
- Jean-Christophe Ducom (Mon Nov 04 2002 - 11:33:19 CST)
pairlist limit
- Guanglei Cui (Fri Jan 04 2002 - 22:56:39 CST)
- Laila Abou Zeid (Fri Jan 04 2002 - 08:32:57 CST)
Parallel Amber on Solaris 2.6
- William Gropp (Mon Jun 03 2002 - 14:20:26 CDT)
- Thomas A. Spraggins (Mon Jun 03 2002 - 09:49:45 CDT)
parallel jobs die with no error message from sander
- Joffre Heredia (Tue Jul 30 2002 - 12:46:37 CDT)
- Joffre Heredia (Mon Jul 29 2002 - 23:06:33 CDT)
- Scott Brozell (Mon Jul 29 2002 - 17:43:51 CDT)
- jim caldwell (Mon Jul 29 2002 - 15:08:50 CDT)
- lamon_at_lav.Boehringer-Ingelheim.com (Mon Jul 29 2002 - 12:48:20 CDT)
parallel sander on T3E
- Natasja Brooijmans (Sat May 25 2002 - 10:44:34 CDT)
- Peter Gannett (Sat May 25 2002 - 09:46:37 CDT)
parallel sander?
- Mark Hsieh (Tue Apr 23 2002 - 14:35:44 CDT)
- Mark Hsieh (Tue Apr 23 2002 - 14:31:55 CDT)
parameter estimation
- Lepsa (Fri Mar 08 2002 - 03:52:50 CST)
- Vlad Cojocaru (Thu Mar 07 2002 - 12:32:25 CST)
parameter file for MgGTP
- Holger Sondermann (Tue Jul 02 2002 - 20:34:24 CDT)
parameterization of a new class of compounds (nucleic acid base analogues)
- Vlad Cojocaru (Mon Sep 09 2002 - 04:40:05 CDT)
Parameters
- Marta Murcia (Wed Jan 16 2002 - 09:59:26 CST)
Parameters for AMBER
- David A. Case (Fri Sep 20 2002 - 08:53:18 CDT)
parameters for cyclic nucleotides
- Thomas.Fox_at_bc.boehringer-ingelheim.com (Fri Nov 29 2002 - 04:11:43 CST)
Parameters for hexachloroethane
- Bjorn-Olav Brandsdal (Wed Jun 05 2002 - 04:13:54 CDT)
parameters for sugars
- Elsa de Sousa Henriques (Mon Sep 30 2002 - 11:42:24 CDT)
- A.Madhumalar (Sun Sep 29 2002 - 11:30:36 CDT)
parameters for zn2+ bond to cys-
- lamon_at_lav.Boehringer-Ingelheim.com (Thu Jun 20 2002 - 08:17:38 CDT)
- X. Tan (Wed Jun 19 2002 - 19:23:16 CDT)
parm94.dat file
- x357l (Tue Feb 12 2002 - 12:21:44 CST)
parmchk -p option
- Thomas.Fox_at_bc.boehringer-ingelheim.com (Fri Nov 29 2002 - 04:09:09 CST)
parmjoin
- David Case (Mon Apr 29 2002 - 13:26:26 CDT)
- Vlad Cojocaru (Mon Apr 29 2002 - 11:53:01 CDT)
PARMSET
- John Bushnell (Thu Nov 21 2002 - 16:32:25 CST)
- David A. Case (Thu Nov 21 2002 - 10:13:38 CST)
- Ross Walker (Thu Nov 21 2002 - 08:30:36 CST)
- sara nunez (Thu Nov 21 2002 - 08:08:12 CST)
Partial charge generation RESP/antechamber
- James W. Caldwell (Mon Sep 30 2002 - 17:27:37 CDT)
partial charges
- David A. Case (Mon Jun 24 2002 - 20:52:47 CDT)
- Carlos Simmerling (Mon Jun 24 2002 - 20:38:35 CDT)
- Osvaldo Santos-Filho (Mon Jun 24 2002 - 19:33:15 CDT)
Passing arguments with SP2 LoadLeveler
- Thomas A. Spraggins (Mon Jun 24 2002 - 09:41:26 CDT)
Patching AMBER7 with #24
- Lepsa (Wed Oct 23 2002 - 10:23:14 CDT)
- Lepsa (Wed Oct 23 2002 - 02:49:07 CDT)
pbc in amber
- Xiang Mao (Thu Aug 29 2002 - 08:00:04 CDT)
PC (principal component) analysis
- Soonmin Jang (Tue Aug 20 2002 - 03:02:24 CDT)
pdb file
- Ioana Cozmuta (Fri Nov 22 2002 - 19:44:22 CST)
- Ioana Cozmuta (Fri Nov 22 2002 - 18:41:01 CST)
PDB file with CONECT record
- Prabal Maiti (Tue Apr 16 2002 - 00:48:00 CDT)
- Miguel Angel (Fri Apr 12 2002 - 05:03:09 CDT)
- Bill Ross (Fri Apr 12 2002 - 02:27:37 CDT)
- Prabal Maiti (Fri Apr 12 2002 - 01:27:15 CDT)
- Bill Ross (Wed Apr 10 2002 - 01:09:36 CDT)
- Bill Ross (Mon Apr 08 2002 - 15:02:21 CDT)
- Prabal Maiti (Mon Apr 08 2002 - 14:06:21 CDT)
PDB file with CONECT record (fwd)
- David Case (Tue Apr 09 2002 - 22:30:38 CDT)
- Prabal Maiti (Tue Apr 09 2002 - 20:04:50 CDT)
penalty function in NMR refinement
- Mahadevan Seetharaman (Mon Dec 02 2002 - 11:09:05 CST)
pentane minimization
- Hungie Hungie (Thu Apr 18 2002 - 04:16:46 CDT)
- Hungie Hungie (Thu Apr 18 2002 - 04:15:33 CDT)
pentane minimization...again
- Hungie Hungie (Thu Apr 18 2002 - 11:30:15 CDT)
period boundary
- Shunzhou Wan (Fri Oct 11 2002 - 10:50:39 CDT)
periodic box
- David A. Case (Mon Nov 04 2002 - 12:32:11 CST)
- Craig A Bayse (Mon Nov 04 2002 - 10:49:53 CST)
- Thomas E. Cheatham, III (Wed Jul 31 2002 - 09:26:49 CDT)
- Peter Gannett (Sat Jul 27 2002 - 09:41:50 CDT)
- Jiyoung Heo (Fri Jul 26 2002 - 17:00:28 CDT)
Periodic water box
- Thomas Cheatham (Wed Jun 19 2002 - 22:57:04 CDT)
- Rudesh Toofanny (Fri Jun 14 2002 - 07:41:01 CDT)
Periodicity Question
- DeLano, Warren (Fri Sep 20 2002 - 19:29:49 CDT)
Persistence length
- Bernd Wellenzohn (Thu Feb 28 2002 - 09:39:11 CST)
perturbation of gln to glu
- M. L. Dodson (Sun Oct 13 2002 - 19:02:00 CDT)
Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd)
- David A. Case (Mon Aug 26 2002 - 20:21:06 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:02 CDT)
perturbed type DH not found
- Mao Xiang (Wed Jun 12 2002 - 05:47:19 CDT)
Pictausch??
- nicolescholiz1_at_web.de (Mon Jul 08 2002 - 18:14:10 CDT)
Please give me a hand on understanding AMBER/MPI and locmem.
- Margaret Cheung (Sat Aug 03 2002 - 17:23:50 CDT)
- David Case (Sat Aug 03 2002 - 15:02:42 CDT)
- Margaret Cheung (Sat Aug 03 2002 - 01:49:46 CDT)
Please help. Energy suddenly increase. Protein jump out
- Yong Duan (Wed Nov 27 2002 - 16:52:54 CST)
- Carlos Simmerling (Wed Nov 27 2002 - 15:35:15 CST)
- Yong Duan (Wed Nov 27 2002 - 12:42:39 CST)
- David A. Case (Wed Nov 27 2002 - 10:26:55 CST)
- Lich Nguyen (Wed Nov 27 2002 - 01:42:29 CST)
plep question
- FyD (Wed Jun 26 2002 - 02:28:23 CDT)
plotting electrostatic potential surface
- Ioana Cozmuta (Fri Dec 13 2002 - 17:18:17 CST)
PME & cutoff
- darden (Sun May 26 2002 - 12:03:30 CDT)
- A. Hungie (Sat May 25 2002 - 08:12:48 CDT)
PME box ?
- Long Hai (Wed Jun 05 2002 - 11:07:29 CDT)
- David Smith (Wed Jun 05 2002 - 09:15:44 CDT)
- Yi ming Cheng (Wed Jun 05 2002 - 07:11:15 CDT)
PME in gibbs module
- X. Tan (Tue Jul 16 2002 - 15:29:27 CDT)
PMF calculations
- David Pearlman (Thu Apr 25 2002 - 13:36:41 CDT)
- David Pearlman (Thu Apr 25 2002 - 13:30:24 CDT)
- David Smith (Thu Apr 25 2002 - 10:13:23 CDT)
- Sophia Kondratova (Thu Apr 25 2002 - 08:30:11 CDT)
PMF with sander module
- David A. Case (Fri Aug 16 2002 - 14:23:16 CDT)
- Pratul Agarwal (Wed Aug 14 2002 - 22:49:34 CDT)
- mer_at_gordon.chem.wayne.edu (Wed Aug 14 2002 - 18:23:25 CDT)
polarizabilities
- Lepsa (Tue Mar 26 2002 - 03:12:09 CST)
Polarizabilities, charge scaling and ions
- Michal Otyepka (Wed Mar 27 2002 - 03:42:29 CST)
Polarizability, a general question
- Michal Otyepka (Wed Sep 11 2002 - 03:56:32 CDT)
polarizabitlity
- X. Tan (Tue Nov 19 2002 - 12:08:31 CST)
- David A. Case (Mon Nov 18 2002 - 18:44:10 CST)
- X. Tan (Fri Nov 15 2002 - 19:41:37 CST)
positional restraints
- David A. Case (Fri Dec 06 2002 - 10:05:02 CST)
- Vlad Cojocaru (Fri Dec 06 2002 - 06:55:05 CST)
Post-doctoral position
- Wolfe, Jennifer (Mon Mar 18 2002 - 10:33:11 CST)
Potential bug in gbsa.h of sander-7
- Vlad (Mon Oct 14 2002 - 19:35:58 CDT)
Potential Energy and RMS-Deviation Issues
- David A. Case (Thu Aug 01 2002 - 11:25:57 CDT)
- Thomas Cheatham (Thu Aug 01 2002 - 11:08:09 CDT)
- CUI, Guanglei (Thu Aug 01 2002 - 10:38:36 CDT)
- mdk7p_at_cms.mail.virginia.edu (Thu Aug 01 2002 - 10:01:07 CDT)
Power Point slides
- Krishna Bisetty (Mon Feb 18 2002 - 01:11:22 CST)
Pressure probs in MD
- jim caldwell (Thu Jul 25 2002 - 10:55:57 CDT)
- suvendu lomash (Thu Jul 25 2002 - 02:49:28 CDT)
pressure variation coupled with taup value
- Vlad Cojocaru (Mon Oct 14 2002 - 04:36:42 CDT)
prmtop file question.
- David A. Case (Wed Jul 17 2002 - 19:08:28 CDT)
- Carlos Andres Ramirez-Mondragon (Wed Jul 17 2002 - 16:15:59 CDT)
probelms in install of amber (fwd)
- Marcelo Roitburd (Thu Jun 27 2002 - 17:47:41 CDT)
- Marcelo Roitburd (Thu Jun 27 2002 - 17:23:29 CDT)
- Marcelo Roitburd (Thu Jun 27 2002 - 15:59:35 CDT)
Problem
- David Case (Fri Nov 29 2002 - 13:49:20 CST)
- Monica (Fri Nov 29 2002 - 00:35:19 CST)
problem about cut and cap
- sxzheng (Sun Nov 03 2002 - 06:40:25 CST)
problem compiling roar (mop7mm) on alpha
- Chuck Schneider (Tue Jul 23 2002 - 12:09:37 CDT)
- Tru (Tue Jul 23 2002 - 12:05:08 CDT)
- hagop demirdjian (Tue Jul 23 2002 - 10:35:11 CDT)
Problem getting sander started
- Sanjeev B.S. (Wed Jul 10 2002 - 07:26:39 CDT)
- Thomas Steinbrecher (Wed Jul 10 2002 - 07:24:00 CDT)
Problem in amber
- David Case (Thu Jun 27 2002 - 09:38:30 CDT)
- Monica (Thu Jun 27 2002 - 00:28:21 CDT)
problem in compiling amber7 in IBMSP3 cluster
- Michael Crowley (Fri Jul 05 2002 - 13:11:55 CDT)
- A.Madhumalar (Thu Jul 04 2002 - 11:29:50 CDT)
problem in MD
- Carlos Simmerling (Tue Aug 27 2002 - 20:40:06 CDT)
- Xiang Mao (Tue Aug 27 2002 - 19:05:11 CDT)
problem in PME
- David A. Case (Tue Nov 12 2002 - 17:16:52 CST)
- Kristina Furse (Tue Nov 12 2002 - 10:43:03 CST)
- David A. Case (Tue Nov 12 2002 - 08:06:47 CST)
- Monica (Tue Nov 12 2002 - 07:42:21 CST)
problem in restrt
- Thomas Cheatham (Fri Nov 22 2002 - 11:55:27 CST)
- Marcela Madrid (Fri Nov 22 2002 - 10:37:53 CST)
Problem in run
- David Case (Sat Nov 09 2002 - 01:33:27 CST)
- Monica Jain (Sat Nov 09 2002 - 00:52:46 CST)
- Monica (Fri Nov 08 2002 - 22:41:52 CST)
problem in running MM-PBSA script
- David Case (Thu Feb 14 2002 - 10:42:52 CST)
problem in sander
- David A. Case (Fri Oct 11 2002 - 10:00:53 CDT)
- Ioana Cozmuta (Thu Oct 10 2002 - 21:11:06 CDT)
problem reading rstrnt file with pgf77
- Michael Petersen (Fri Aug 16 2002 - 08:23:48 CDT)
problem reading rstrnt file with pgf77 compiled sander
- Michael Petersen (Wed Aug 14 2002 - 05:13:24 CDT)
Problem with 2D Gibbs run
- Asif Rahaman (Wed May 22 2002 - 17:32:49 CDT)
problem with amber7 compiling on SGI
- Chris Switzer (Wed Aug 14 2002 - 20:26:54 CDT)
problem with amber7 mpi
- Shixiang Yan (Thu Aug 01 2002 - 08:29:58 CDT)
- Carlos Simmerling (Thu Aug 01 2002 - 07:34:43 CDT)
- Bimo Ario Tejo (Thu Aug 01 2002 - 05:50:32 CDT)
Problem with atom type
- Bill Ross (Thu Mar 28 2002 - 18:14:16 CST)
- rhertadi_at_bio.titech.ac.jp (Thu Mar 28 2002 - 15:55:33 CST)
problem with gibbs !!!!
- James W. Caldwell (Tue Oct 22 2002 - 09:34:23 CDT)
- Asif Rahaman (Mon Oct 21 2002 - 21:18:10 CDT)
Problem with Gibbs 2D run
- Asif Rahaman (Sun Jun 02 2002 - 22:29:38 CDT)
Problem with LEAP
- David A. Case (Tue Jul 16 2002 - 10:19:24 CDT)
- Miguel de Federico (Tue Jul 16 2002 - 05:53:37 CDT)
problem with make_crd_hg, mm_pbsa
- Jianhui Wu (Mon Jul 22 2002 - 13:28:29 CDT)
problemas running amber7 tests on a SP2 machine
- ramon kleber da rocha (Tue Jul 23 2002 - 15:33:28 CDT)
problems compiling Amber 7
- Thomas A. Spraggins (Fri Jul 05 2002 - 13:42:32 CDT)
- ramon kleber da rocha (Fri Jul 05 2002 - 12:52:45 CDT)
- ramon kleber da rocha (Tue Jul 02 2002 - 09:42:05 CDT)
- David A. Case (Thu Jun 27 2002 - 13:27:09 CDT)
- ramon kleber da rocha (Thu Jun 27 2002 - 12:18:50 CDT)
Problems during equilibration
- Pratul Agarwal (Wed Sep 11 2002 - 21:40:05 CDT)
- Pratul Agarwal (Wed Sep 11 2002 - 15:14:05 CDT)
- Pratul Agarwal (Wed Sep 11 2002 - 14:38:36 CDT)
problems on IBM AIX
- Carlos P. Sosa (Fri Sep 13 2002 - 10:47:31 CDT)
- David A. Case (Fri Sep 13 2002 - 09:42:14 CDT)
- Giovanni Fossati (Thu Sep 12 2002 - 20:43:52 CDT)
problems runing gibbs on a IBM SP2 machine
- ramon kleber da rocha (Fri Aug 09 2002 - 09:48:11 CDT)
problems using Link
- John Finke (Tue Mar 26 2002 - 14:39:59 CST)
Problems with AMBER7 and Multiple Processors on SGI servers
- Vincent BOSQUIER (Thu May 02 2002 - 03:55:45 CDT)
- David Case (Tue Apr 30 2002 - 11:02:30 CDT)
- Vincent BOSQUIER (Tue Apr 30 2002 - 04:59:11 CDT)
- Ian bates (Fri Apr 26 2002 - 10:17:52 CDT)
- Carlos Simmerling (Fri Apr 26 2002 - 07:05:52 CDT)
- Vincent BOSQUIER (Fri Apr 26 2002 - 03:39:35 CDT)
Problems with parallel computing in Amber7
- Vincent BOSQUIER (Tue May 14 2002 - 09:28:10 CDT)
problems with parallel sander on linux clusters?
- David Case (Sun Aug 04 2002 - 13:34:20 CDT)
Problems with poly(A)-poly(T) tutorial...
- Andrei Leitão (Mon Sep 30 2002 - 14:55:53 CDT)
Problems with tes.antechamber
- Chen, Ya (Tue Oct 29 2002 - 19:21:59 CST)
procheck
- David A. Case (Tue Nov 05 2002 - 10:31:31 CST)
- hung_at_atc.atccu.chula.ac.th (Tue Nov 05 2002 - 00:53:56 CST)
propeller twist of ideal B-DNA
- A. Hungie (Wed Jun 19 2002 - 11:37:29 CDT)
Protein jump out, please help
- Lich Nguyen (Thu Oct 24 2002 - 22:21:40 CDT)
- Michael G Cooney (Thu Oct 24 2002 - 13:51:52 CDT)
- Lich Nguyen (Thu Oct 24 2002 - 04:45:45 CDT)
protein minimization
- m.elizabeth sophia (Tue Sep 03 2002 - 11:01:35 CDT)
- CUI, Guanglei (Tue Sep 03 2002 - 08:19:39 CDT)
- Lepsa (Tue Sep 03 2002 - 01:13:54 CDT)
PROTON_INFO
- Qing Zhang (Sat Aug 03 2002 - 20:12:24 CDT)
- Cozmuta (Fri Aug 02 2002 - 22:25:37 CDT)
proton_info/PS
- Cozmuta (Thu Aug 01 2002 - 12:29:02 CDT)
Protonate doesn-t recognize by pdb input file
- Stéphane Teletchéa (Thu May 23 2002 - 07:23:31 CDT)
- David Case (Wed May 22 2002 - 11:20:20 CDT)
Protonate doesn-t recognize my pdb input file
- Stéphane Teletchéa (Wed May 22 2002 - 06:41:08 CDT)
Protonated database
- Andrew Petersen (Tue Jun 11 2002 - 14:12:28 CDT)
protonation pH dependent
- David A. Case (Thu Aug 08 2002 - 17:05:25 CDT)
- Cozmuta (Thu Aug 08 2002 - 16:14:46 CDT)
pseudoatoms and NMR restraints
- David A. Case (Tue Nov 05 2002 - 10:06:07 CST)
- david (Tue Nov 05 2002 - 03:46:42 CST)
ptraj
- Joseph Nachman (Fri Jul 26 2002 - 15:14:53 CDT)
- Joseph Nachman (Fri Jul 26 2002 - 14:43:36 CDT)
- Thomas Cheatham (Fri Jul 26 2002 - 14:15:04 CDT)
- David A. Case (Fri Jul 26 2002 - 14:08:54 CDT)
- Kristina Furse (Fri Jul 26 2002 - 13:32:38 CDT)
ptraj - BONDS_WITHOUT_HYDROGEN
- Sophia Kondratova (Wed Sep 25 2002 - 11:54:48 CDT)
ptraj and compressed files
- Michael G Cooney (Mon Jan 14 2002 - 10:48:40 CST)
ptraj cannot use compressed files?
- Michael G Cooney (Mon Jan 14 2002 - 10:17:03 CST)
ptraj problem
- Thomas Cheatham (Mon Jun 24 2002 - 12:24:30 CDT)
- Vlad Cojocaru (Mon Jun 24 2002 - 10:54:32 CDT)
- Prabal Maiti (Tue May 21 2002 - 18:51:22 CDT)
- Jake Isaacs (Tue May 21 2002 - 16:20:02 CDT)
ptraj rdf output
- Prabal Maiti (Fri Sep 20 2002 - 18:24:35 CDT)
ptraj rmsd calculation
- Thomas Steinbrecher (Thu Dec 05 2002 - 14:15:40 CST)
ptraj-6.4/LES
- Peter Varnai (Mon Sep 23 2002 - 04:18:25 CDT)
PTRAJ: radial distribution function
- Thomas Cheatham (Wed Jul 17 2002 - 16:47:24 CDT)
- A. Hungie (Wed Jul 17 2002 - 10:58:14 CDT)
pukering of DNA bases?
- A.Madhumalar (Sat Jan 12 2002 - 23:03:50 CST)
Purine to Pyrimidine mutation
- Bernd Wellenzohn (Thu Jul 25 2002 - 07:29:27 CDT)
PyMOL + AMBER Trajectories
- DeLano, Warren (Tue Sep 03 2002 - 12:51:57 CDT)
- DeLano, Warren (Thu Aug 29 2002 - 13:27:01 CDT)
Q: waters in NPT & periodic boundary condition
- David A. Case (Wed Aug 14 2002 - 11:45:46 CDT)
- Masaki Tomimoto (Wed Aug 14 2002 - 11:06:15 CDT)
quasih
- Pratul Agarwal (Mon Oct 28 2002 - 16:25:02 CST)
- CUI, Guanglei (Wed Feb 06 2002 - 09:53:55 CST)
- Sue Heavner (Wed Feb 06 2002 - 09:16:25 CST)
Query regarding Gamess
- Nitin Kumar Singh (Tue Jun 25 2002 - 10:23:09 CDT)
question
- Stéphane Teletchéa (Tue Nov 19 2002 - 06:43:04 CST)
- Yong Duan (Fri Nov 15 2002 - 22:40:56 CST)
- Ioana Cozmuta (Fri Nov 15 2002 - 21:22:13 CST)
- David A. Case (Fri Nov 15 2002 - 20:45:34 CST)
- Ioana Cozmuta (Tue Sep 03 2002 - 12:46:04 CDT)
- Sankha Subhra Som (Tue Aug 27 2002 - 01:24:32 CDT)
- jim caldwell (Tue Jun 18 2002 - 17:52:19 CDT)
- Craig A Bayse (Tue Jun 18 2002 - 17:04:47 CDT)
- TL Poulos (Wed Jun 05 2002 - 10:49:10 CDT)
- Masamichi Fujinami 4029 (Wed May 15 2002 - 00:49:03 CDT)
- Kang, Jonghoon (Wed Jan 02 2002 - 16:22:14 CST)
Question about Antechamber
- David A. Case (Thu Sep 26 2002 - 10:28:51 CDT)
- Masaki Tomimoto (Wed Sep 25 2002 - 16:37:55 CDT)
question about antibodies
- Ioana Cozmuta (Thu Oct 10 2002 - 15:05:25 CDT)
Question about Counterions
- Markus Drumm (Thu Sep 19 2002 - 12:38:24 CDT)
Question about error message about "lastist" and "virtual box"
- David A. Case (Fri Jul 12 2002 - 10:55:51 CDT)
- Masaki Tomimoto (Fri Jul 12 2002 - 10:19:12 CDT)
question about nmode again.
- David A. Case (Tue Sep 17 2002 - 09:40:00 CDT)
- Yongjun Jiang (Tue Sep 17 2002 - 02:15:54 CDT)
Question about obtaining amber!
- Peter Fojan (Thu Mar 21 2002 - 07:19:59 CST)
question about using 10-12 in amber7/sander.
- Margaret Cheung (Sat Sep 28 2002 - 15:35:48 CDT)
- Margaret Cheung (Sat Sep 28 2002 - 14:53:56 CDT)
Question on 2 stage RESP fit
- M. L. Dodson (Thu Dec 12 2002 - 07:05:15 CST)
- Ambarish Nag (Thu Dec 12 2002 - 00:39:08 CST)
Question on Antechamber paper
- Nicholson, James D Mr ARO (Thu Sep 26 2002 - 12:18:17 CDT)
question on belly and restraint
- Sichun Yang (Wed Oct 30 2002 - 14:54:37 CST)
question on Gibbs calculation
- X. Tan (Tue Mar 12 2002 - 15:50:24 CST)
question on ouput of sander
- David A. Case (Mon Oct 21 2002 - 13:59:27 CDT)
- Sichun Yang (Mon Oct 21 2002 - 13:45:29 CDT)
- CUI, Guanglei (Mon Oct 21 2002 - 13:43:40 CDT)
- Sichun Yang (Mon Oct 21 2002 - 13:19:17 CDT)
question regarding ntwv.
- David Case (Fri Feb 01 2002 - 00:43:51 CST)
- Margaret Cheung (Thu Jan 31 2002 - 19:55:58 CST)
Question to perturbation charge
- meiselba (Tue Dec 10 2002 - 07:35:38 CST)
question: velocity units
- Pascal Bonnet (Wed Jan 09 2002 - 11:57:58 CST)
- Martina Roeselova (Wed Jan 09 2002 - 11:46:00 CST)
questions about resp
- X. Tan (Tue Mar 12 2002 - 15:02:22 CST)
- X. Tan (Tue Jan 08 2002 - 10:31:55 CST)
Questions about xleap ...
- Bill Ross (Tue Jul 23 2002 - 14:03:52 CDT)
Questions about xleap and mm_pbsa (cont.2)
- Salinthip Thipayang (Tue Jul 23 2002 - 10:21:23 CDT)
Questions about xleap and mm_pbsa(cont.)
- David A. Case (Tue Jul 23 2002 - 12:18:44 CDT)
- Salinthip Thipayang (Tue Jul 23 2002 - 09:46:20 CDT)
Questions about xleap and mm_pbsa]
- David A. Case (Fri Jul 19 2002 - 13:59:24 CDT)
- Salinthip Thipayang (Fri Jul 19 2002 - 12:49:08 CDT)
Questions on crosslinking residues
- David A. Case (Thu Oct 03 2002 - 10:04:18 CDT)
- M. L. Dodson (Thu Oct 03 2002 - 07:42:08 CDT)
- Nicholson, James D Mr ARO (Wed Oct 02 2002 - 20:03:47 CDT)
- David A. Case (Wed Oct 02 2002 - 18:34:47 CDT)
- Nicholson, James D Mr ARO (Tue Oct 01 2002 - 16:59:19 CDT)
QUICK HELP! Parameters for neutral amino acids (fwd)
- David A. Case (Mon Aug 26 2002 - 20:32:50 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:43 CDT)
Qustion about calculation of pressure
- James W. Caldwell (Thu Sep 12 2002 - 11:43:25 CDT)
- Nikolai Smolin (Thu Sep 12 2002 - 05:01:44 CDT)
ramdomized start velocities
- James W. Caldwell (Fri Nov 08 2002 - 14:35:39 CST)
- Andy Purkiss (Fri Nov 08 2002 - 13:28:46 CST)
- David A. Case (Fri Nov 08 2002 - 13:20:54 CST)
- Arvid Soederhaell (Fri Nov 08 2002 - 06:35:23 CST)
RDC restraints
- Richard Stefl (Mon Jul 08 2002 - 10:01:39 CDT)
rdparm
- Elsa de Sousa Henriques (Tue Oct 08 2002 - 21:40:58 CDT)
- Ioana Cozmuta (Tue Oct 08 2002 - 12:33:41 CDT)
- Joffre Heredia (Tue Sep 10 2002 - 13:07:26 CDT)
rdparm error message
- Rukman Hertadi (Sun Mar 10 2002 - 02:46:53 CST)
Re Europium force field parms
- Marc Baaden (Mon Mar 11 2002 - 05:52:40 CST)
- Fabrice Yerly (Mon Mar 11 2002 - 01:32:59 CST)
reaction field energy of a ligand in MM-PBSA
- Giulio Rastelli (Wed Oct 09 2002 - 13:04:10 CDT)
- Lepsa (Wed Oct 09 2002 - 08:19:56 CDT)
Recalculating energies
- Carlos Simmerling (Wed Apr 17 2002 - 06:39:27 CDT)
- John Finke (Tue Apr 16 2002 - 19:45:23 CDT)
recursively calling sander?
- David Pearlman (Mon Feb 25 2002 - 21:10:22 CST)
- Jeff Ames (Mon Feb 25 2002 - 10:32:54 CST)
redius of B-DNA duplex
- A.Madhumalar (Mon Feb 25 2002 - 11:41:42 CST)
- Hungie Hungie (Mon Feb 25 2002 - 10:49:26 CST)
reference
- Marcela Madrid (Wed Jun 05 2002 - 10:48:55 CDT)
Reference for GB model 2
- Andreas Svrcek-Seiler (Thu Oct 17 2002 - 15:34:40 CDT)
- Jianhui Wu (Thu Oct 17 2002 - 14:26:18 CDT)
Reference, GB 2, Amber7
- Jianhui Wu (Thu Oct 17 2002 - 14:34:12 CDT)
Reflector problems
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 17:05:02 CST)
reg: MAC OS
- Prem Raj (Mon Oct 21 2002 - 13:19:40 CDT)
- Mengjuei Hsieh (Mon Oct 21 2002 - 13:13:35 CDT)
- David A. Case (Mon Oct 21 2002 - 11:11:56 CDT)
regarding RESP run from gamess output (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:55 CDT)
regarding resp-doubts
- James W. Caldwell (Thu Oct 03 2002 - 11:35:26 CDT)
- David A. Case (Thu Oct 03 2002 - 11:10:48 CDT)
- Miguel de Federico (Thu Oct 03 2002 - 11:01:23 CDT)
- Wiktor Jurkowski (Thu Oct 03 2002 - 10:41:13 CDT)
- thenmalar rathinavelan (Thu Oct 03 2002 - 03:21:51 CDT)
Release of Amber, version 7 (fwd)
- SPEROLEEM_at_aol.com (Tue Mar 05 2002 - 16:16:27 CST)
- amber mail account (Sun Mar 03 2002 - 17:13:26 CST)
remove COM velocity in Amber7
- Peter VARNAI (Thu Jun 20 2002 - 07:03:07 CDT)
- Peter VARNAI (Mon Jun 17 2002 - 07:16:27 CDT)
removing rotational motion
- Jianxin Guo (Fri Feb 22 2002 - 16:32:48 CST)
- Stéphane Teletchéa (Tue Feb 19 2002 - 07:15:10 CST)
- Raik Grunberg (Tue Feb 19 2002 - 06:30:00 CST)
- Raik Grunberg (Tue Feb 19 2002 - 06:30:00 CST)
- Andreas Svrcek-Seiler (Tue Feb 19 2002 - 06:27:18 CST)
- John Finke (Tue Feb 19 2002 - 03:44:08 CST)
removing rotational motion in MD
- Stéphane Teletchéa (Thu Jan 10 2002 - 02:35:54 CST)
- Sanjeev B.S. (Wed Jan 09 2002 - 12:54:55 CST)
- Stéphane Teletchéa (Wed Jan 09 2002 - 12:04:30 CST)
- Michael G Cooney (Wed Jan 09 2002 - 11:41:26 CST)
Reorder water in amber7
- Peter VARNAI (Tue Jun 11 2002 - 12:16:00 CDT)
- case (Tue Jun 11 2002 - 08:53:59 CDT)
- Carlos Simmerling (Tue Jun 11 2002 - 06:36:04 CDT)
- Peter Varnai (Tue Jun 11 2002 - 03:38:32 CDT)
reorder water with nmropt
- David A. Case (Fri Aug 02 2002 - 11:01:22 CDT)
- Peter Varnai (Fri Aug 02 2002 - 07:24:59 CDT)
replacing fft routines
- David A. Case (Tue Oct 22 2002 - 17:58:34 CDT)
- Florian Barth (Tue Oct 22 2002 - 15:08:14 CDT)
Request for help with Antechamber
- James W. Caldwell (Sat Sep 28 2002 - 00:54:24 CDT)
- Nicholson, James D Mr ARO (Fri Sep 27 2002 - 20:00:37 CDT)
- David A. Case (Fri Sep 27 2002 - 19:54:21 CDT)
- Nicholson, James D Mr ARO (Fri Sep 27 2002 - 18:58:58 CDT)
Resending: Medicinal and Computational Chemistry Job Market
- Computational Chemistry Job Market (Mon Mar 25 2002 - 14:05:03 CST)
residual dipolar coupling restraints
- Jake Isaacs (Thu Feb 14 2002 - 13:37:42 CST)
residue cross-correlation
- Stéphane Teletchéa (Tue Nov 12 2002 - 04:57:10 CST)
- Thomas Cheatham (Fri Nov 08 2002 - 14:50:42 CST)
- Andreas Svrcek-Seiler (Fri Nov 08 2002 - 14:16:59 CST)
- Bimo Ario Tejo (Fri Nov 08 2002 - 12:57:48 CST)
- Bimo Ario Tejo (Fri Nov 08 2002 - 09:00:01 CST)
- Bimo Ario Tejo (Thu Oct 24 2002 - 16:15:50 CDT)
resizing and recompiling sander
- UMEMOTO kimiko (Mon Jan 14 2002 - 19:12:02 CST)
RESP
- jim caldwell (Mon Apr 22 2002 - 10:04:25 CDT)
- Vlad Cojocaru (Mon Apr 22 2002 - 05:17:17 CDT)
- cfrenz_at_aecom.yu.edu (Thu Apr 18 2002 - 10:55:55 CDT)
RESP charges
- Ross Walker (Wed Apr 17 2002 - 10:28:58 CDT)
- jim caldwell (Wed Apr 17 2002 - 09:22:04 CDT)
- Ross Walker (Wed Apr 17 2002 - 08:21:37 CDT)
- Vlad Cojocaru (Wed Apr 17 2002 - 07:36:43 CDT)
- Lepsa (Wed Apr 17 2002 - 07:26:27 CDT)
- Vlad Cojocaru (Wed Apr 17 2002 - 05:53:27 CDT)
RESP charges for phosphorylated residues
- Uwe Richter (Tue May 28 2002 - 11:05:05 CDT)
RESP Crash
- Mike Keller (Thu Feb 14 2002 - 09:24:51 CST)
RESP gaussian job crashing
- David Smith (Fri Oct 04 2002 - 07:08:53 CDT)
- Carlos P. Sosa (Thu Oct 03 2002 - 17:39:59 CDT)
- Nicholson, James D Mr ARO (Thu Oct 03 2002 - 16:57:46 CDT)
- James W. Caldwell (Thu Oct 03 2002 - 09:04:59 CDT)
- Nicholson, James D Mr ARO (Wed Oct 02 2002 - 20:22:59 CDT)
Resp Multiconformational charge fitting!
- Pascal Bonnet (Wed Dec 18 2002 - 04:21:46 CST)
- Marco Aurélio Correia Preto (Wed Oct 30 2002 - 05:50:52 CST)
RESP Multiconformer Fitting
- Miguel de Federico (Thu Jun 20 2002 - 18:05:11 CDT)
RESP on Deoxy-ADE
- Qing Zhang (Tue Apr 23 2002 - 20:34:23 CDT)
- Qing Zhang (Tue Apr 23 2002 - 20:34:23 CDT)
RESP tutorial
- David Case (Tue Apr 23 2002 - 19:41:49 CDT)
- Michael G Cooney (Tue Apr 23 2002 - 12:15:51 CDT)
RESP-group constraint
- Marco Preto (Wed Oct 30 2002 - 10:50:21 CST)
RESP-ivary
- John Bushnell (Fri Apr 19 2002 - 13:16:40 CDT)
- Qing Zhang (Fri Apr 19 2002 - 11:15:27 CDT)
- Vlad Cojocaru (Fri Apr 19 2002 - 06:26:22 CDT)
restart
- David A. Case (Mon Nov 04 2002 - 15:59:15 CST)
- Ioana Cozmuta (Mon Nov 04 2002 - 14:57:16 CST)
restart md simulation
- Michael G Cooney (Tue Jan 29 2002 - 10:44:03 CST)
- Uwe Richter (Tue Jan 29 2002 - 03:35:50 CST)
restart mm_pbsa
- Pascal Bonnet (Thu Nov 14 2002 - 09:13:06 CST)
- Lepsa (Thu Nov 14 2002 - 07:52:22 CST)
- Layi Adekoya (Thu Nov 14 2002 - 07:02:51 CST)
restart without velocities
- Sanjeev B.S. (Wed Oct 02 2002 - 02:44:57 CDT)
- Michal Otyepka (Wed Oct 02 2002 - 02:39:02 CDT)
RESTARTED DUE TO LINMIN FAILURE
- Natasja Brooijmans (Thu Dec 19 2002 - 15:16:44 CST)
- William Wei (Thu Dec 19 2002 - 13:33:07 CST)
restarting simulation
- Marcela Madrid (Fri Nov 22 2002 - 16:07:47 CST)
- Carlos Simmerling (Fri Nov 22 2002 - 14:56:24 CST)
- Guanglei Cui (Fri Nov 22 2002 - 14:50:05 CST)
- Marcela Madrid (Fri Nov 22 2002 - 14:06:42 CST)
restrain a residue as center of mass
- Carlos Simmerling (Wed Nov 27 2002 - 15:38:57 CST)
- Carlos Simmerling (Wed Nov 27 2002 - 15:34:00 CST)
- eric hu (Wed Nov 27 2002 - 12:42:36 CST)
- Carlos Simmerling (Tue Nov 26 2002 - 18:17:58 CST)
- eric hu (Tue Nov 26 2002 - 17:36:19 CST)
restrained MD
- Vlad Cojocaru (Wed Dec 04 2002 - 12:18:54 CST)
restraining atoms
- Ioana Cozmuta (Thu Oct 17 2002 - 12:54:37 CDT)
- Lepsa (Thu Oct 17 2002 - 01:56:17 CDT)
- Ioana Cozmuta (Wed Oct 16 2002 - 12:56:10 CDT)
Restraint Ambiguities
- David A. Case (Fri Nov 22 2002 - 10:33:34 CST)
- Neema Salimi (Thu Nov 21 2002 - 22:37:13 CST)
- David A. Case (Thu Nov 21 2002 - 20:08:04 CST)
- Neema Salimi (Thu Nov 21 2002 - 16:56:44 CST)
restraints in parm in amber7
- Carlos Simmerling (Tue Aug 27 2002 - 20:38:59 CDT)
- Sarah Tschampel (Tue Aug 27 2002 - 16:57:33 CDT)
restrt format problem
- Marcela Madrid (Wed Nov 06 2002 - 16:48:02 CST)
restrt problem
- Sanjeev B.S. (Tue Feb 19 2002 - 07:50:41 CST)
rms and watershell (in ptraj)
- dkon_at_email.arizona.edu (Wed Feb 20 2002 - 18:54:58 CST)
RMSD by residue (fwd)
- Carlos Simmerling (Mon Aug 26 2002 - 20:10:41 CDT)
- Holger Gohlke (Mon Aug 26 2002 - 20:08:35 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:49:39 CDT)
RMSD calculation question
- Soonmin Jang (Fri Oct 04 2002 - 02:02:37 CDT)
RMSD for heavy atoms only
- Pratul Agarwal (Wed Sep 25 2002 - 15:54:45 CDT)
Roar 2.1 with Amber7
- Ross Walker (Wed Apr 10 2002 - 00:48:43 CDT)
- Soonmin Jang (Tue Apr 09 2002 - 22:39:07 CDT)
Roar capabilities
- M. L. Dodson (Fri Nov 08 2002 - 11:37:48 CST)
roar-cp problems
- M. L. Dodson (Wed Dec 18 2002 - 15:00:37 CST)
RST file for nonstandard residue
- vannajan_at_chiangmai.ac.th (Tue Dec 17 2002 - 03:07:04 CST)
RUNMIN
- Ioana Cozmuta (Mon Nov 04 2002 - 19:37:08 CST)
- hung_at_atc.atccu.chula.ac.th (Mon Nov 04 2002 - 19:04:23 CST)
Running amber7 and nab on FreeBSD
- bdodson_at_scms.utmb.EDU (Wed Jun 05 2002 - 15:31:24 CDT)
Running amber7 on Param10000
- Jithesh (Thu Aug 15 2002 - 02:35:46 CDT)
- Sanjeev B.S. (Wed Aug 14 2002 - 10:38:34 CDT)
running sander_classic for amber6 using different version of mpi
- Asif Rahaman (Mon Dec 09 2002 - 17:01:35 CST)
Running TIP5P with PBC
- Sarah Tschampel (Tue Jul 09 2002 - 12:32:32 CDT)
- David Case (Wed Jul 03 2002 - 14:49:28 CDT)
- Sarah Tschampel (Wed Jul 03 2002 - 14:47:41 CDT)
s-matrix format and ftnmr
- Shixiang Yan (Wed Mar 27 2002 - 15:49:50 CST)
SAMUEL METU
- sam_008_at_www.com (Thu Oct 03 2002 - 20:46:51 CDT)
- sam_008_at_www.com (Thu Oct 03 2002 - 20:46:50 CDT)
sander & prmtop file generated from antechamber input ?
- David Case (Wed Apr 24 2002 - 10:59:14 CDT)
- jeff dyason (Tue Apr 23 2002 - 22:33:58 CDT)
sander (Amber5) vs sander_classic (Amber6)
- Uwe Richter (Wed Jan 16 2002 - 05:33:32 CST)
sander (CAP) chokes on efc (Itanium2/Linux)
- Tadashi Takemori (Wed Dec 18 2002 - 03:38:25 CST)
- Karen Haskell (Tue Dec 17 2002 - 16:05:31 CST)
- Tadashi Takemori (Tue Dec 17 2002 - 01:11:14 CST)
sander crash
- K.Seshadri (Mon Jul 29 2002 - 03:40:57 CDT)
SANDER documentation for nmropt
- David A. Case (Mon Jul 29 2002 - 19:27:52 CDT)
sander input for a newbie
- Randy M. Wadkins (Wed Jun 12 2002 - 08:04:55 CDT)
- Randy M. Wadkins (Tue Jun 11 2002 - 18:21:22 CDT)
sander minimizations failing
- John Bushnell (Tue Aug 13 2002 - 19:03:12 CDT)
sander mpich hangs
- Mark Hsieh (Fri Apr 26 2002 - 14:08:48 CDT)
- Stéphane Teletchéa (Fri Apr 26 2002 - 06:54:01 CDT)
- Mark Hsieh (Thu Apr 25 2002 - 17:01:26 CDT)
sander mpirun hangs with 4 CPU, but not with 2
- lamon_at_lav.Boehringer-Ingelheim.com (Tue Jul 30 2002 - 12:06:05 CDT)
- Thomas Steinbrecher (Tue Jul 30 2002 - 10:09:03 CDT)
Sander multiprocessors running problem with MPI
- William Wei (Wed Oct 02 2002 - 13:09:49 CDT)
- Ross Walker (Wed Oct 02 2002 - 12:52:27 CDT)
sander on NEC-SX5
- Karen Haskell (Thu Aug 15 2002 - 11:38:57 CDT)
- C. Klein (Thu Aug 15 2002 - 11:12:24 CDT)
sander parallel
- Stéphane Teletchéa (Fri Jun 14 2002 - 03:58:53 CDT)
- eric hu (Thu Jun 13 2002 - 17:05:13 CDT)
- Joffre Heredia (Thu Jun 13 2002 - 12:39:55 CDT)
- eric hu (Wed Jun 12 2002 - 16:11:24 CDT)
Sander Recompilation for the Biotin-Streptavidin Tutorial?
- Thomas Steinbrecher (Wed Oct 30 2002 - 09:46:30 CST)
Sander rfree error
- James Caldwell (Mon Dec 30 2002 - 18:36:45 CST)
- kxg2248_at_njit.edu (Mon Dec 30 2002 - 16:58:19 CST)
Sander segmentation fault
- Joel Konkle-Parker (Thu Oct 17 2002 - 14:28:48 CDT)
Sander, Setup for Parallel SMP Linux Cluster
- Joffre Heredia (Thu May 16 2002 - 13:01:16 CDT)
- Tru (Wed May 15 2002 - 14:40:45 CDT)
- Jianhui Wu (Wed May 15 2002 - 14:02:27 CDT)
Sander-Gibbs
- Kidley N J (Mon Apr 08 2002 - 10:34:49 CDT)
sander.LES questions
- Carlos Simmerling (Thu Sep 12 2002 - 12:24:25 CDT)
- Peter Varnai (Thu Sep 12 2002 - 11:27:12 CDT)
sander6 running and crashing at PSC?
- CUI, Guanglei (Thu Oct 17 2002 - 12:17:40 CDT)
sander7 on IBM 7040-681 under AIX 5.1
- Peter Varnai (Fri Aug 30 2002 - 08:01:07 CDT)
sander7: MPI_COMM_RANK problem
- Carlos P. Sosa (Mon Oct 21 2002 - 14:44:56 CDT)
- Matteo Dal Peraro (Mon Oct 21 2002 - 14:17:14 CDT)
Sander: check COM velocity, temp: 0.000000 0.00(Removed)
- David Case (Sat Nov 09 2002 - 01:17:18 CST)
- Thomas Cheatham (Fri Nov 08 2002 - 23:49:21 CST)
- Miguel de Federico de la Rúa (Fri Nov 08 2002 - 08:08:38 CST)
sander_classic, erratic on IBM
- Giovanni Fossati (Thu May 30 2002 - 12:05:22 CDT)
- David Case (Thu May 30 2002 - 09:13:44 CDT)
- Giovanni Fossati (Thu May 30 2002 - 01:17:07 CDT)
sander_classic: Recompile without ISTAR2
- Mahadevan Seetharaman (Wed Sep 25 2002 - 14:53:59 CDT)
Save from LEaP to a PDBQ file ?
- Bill Ross (Fri Apr 12 2002 - 01:16:28 CDT)
- jeff dyason (Thu Apr 11 2002 - 22:50:32 CDT)
saveAmberParm of leap
- David A. Case (Mon Nov 11 2002 - 18:05:15 CST)
- Sichun Yang (Mon Nov 11 2002 - 13:27:16 CST)
scaleCharges
- David Case (Mon Mar 11 2002 - 11:37:51 CST)
- Vojta Klusak (Mon Mar 11 2002 - 03:45:54 CST)
scaling of amber with number of atoms
- Marcela Madrid (Mon Oct 21 2002 - 14:23:59 CDT)
Scaling of Sander on Linux Clusters (fwd)
- Sanjeev B.S. (Tue Aug 27 2002 - 12:59:51 CDT)
- Stéphane Teletchéa (Tue Aug 27 2002 - 04:31:16 CDT)
- Sanjeev B.S. (Tue Aug 27 2002 - 03:56:15 CDT)
- Stéphane Teletchéa (Tue Aug 27 2002 - 03:41:06 CDT)
- Peter Gannett (Mon Aug 26 2002 - 19:56:06 CDT)
- Pratul Agarwal (Mon Aug 26 2002 - 19:32:24 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:57 CDT)
SCEE parameter
- Sophia Kondratova (Wed Jan 09 2002 - 10:49:36 CST)
SDS forcefield?
- Arvid Soederhaell (Thu Oct 24 2002 - 04:25:58 CDT)
secondary structure
- Ian R Bates (Tue Mar 26 2002 - 13:49:48 CST)
segmentation fault
- Vlad Cojocaru (Tue Aug 20 2002 - 16:21:30 CDT)
- Bimo Ario Tejo (Wed Jul 24 2002 - 04:42:26 CDT)
- David A. Case (Tue Jul 23 2002 - 17:44:02 CDT)
- Bimo Ario Tejo (Tue Jul 23 2002 - 14:44:58 CDT)
selection of residues
- Ioana Cozmuta (Fri Dec 20 2002 - 18:51:52 CST)
seperate_solute_output
- Mirjam Lerch (Fri Jan 11 2002 - 03:02:31 CST)
SETVEL, incorrect number of arguments?
- David A. Case (Tue Sep 17 2002 - 14:18:38 CDT)
- Giovanni Fossati (Mon Sep 16 2002 - 17:43:30 CDT)
several questions
- Heather A Carlson (Tue Jul 23 2002 - 22:17:35 CDT)
- David A. Case (Tue Jul 23 2002 - 19:08:10 CDT)
- David Keller (Tue Jul 23 2002 - 17:24:04 CDT)
SHAKE (actually: new atom types)
- Bill Ross (Mon Jun 24 2002 - 14:22:02 CDT)
SHAKE problem
- Pratul Agarwal (Wed Oct 09 2002 - 08:39:55 CDT)
- Rosalia Pascual (Wed Aug 07 2002 - 10:13:12 CDT)
SHAKE troubles
- Arvid Soederhaell (Tue Jun 04 2002 - 03:22:40 CDT)
- Stéphane Teletchéa (Fri May 31 2002 - 04:45:48 CDT)
- Arvid Soederhaell (Fri May 31 2002 - 03:50:01 CDT)
- Lepsa (Wed May 29 2002 - 09:02:15 CDT)
- Yong Duan (Wed May 29 2002 - 07:33:14 CDT)
- Stéphane Teletchéa (Wed May 29 2002 - 05:50:12 CDT)
- Arvid Soederhaell (Wed May 29 2002 - 05:07:17 CDT)
SHAKE...
- Arvid Soederhaell (Mon Jun 24 2002 - 06:25:05 CDT)
simulated annealing example
- Qing Zhang (Wed Jul 10 2002 - 21:59:20 CDT)
- Snyder, James (Wed Jul 10 2002 - 15:42:43 CDT)
simulating dna
- David A. Case (Mon Nov 18 2002 - 18:29:22 CST)
- Tod Pascal (Fri Nov 15 2002 - 19:23:54 CST)
simulation management tools
- Tom Bishop (Fri Jul 05 2002 - 10:58:59 CDT)
Sir,
- Venkanna Belde (Thu Oct 17 2002 - 04:33:18 CDT)
Snapshot stuff
- Layi Adekoya (Tue Nov 05 2002 - 08:32:11 CST)
solvatebox
- Luis Gracia (Wed Dec 18 2002 - 09:58:47 CST)
- Luis Gracia (Tue Dec 17 2002 - 18:52:07 CST)
Solvated DNA using Amber 7
- Nicholson, James D Mr ARO (Thu Aug 01 2002 - 16:32:13 CDT)
solvated time-averaged restraint refinement of DNA
- Jake Isaacs (Wed Jun 19 2002 - 11:52:35 CDT)
solvateOct
- David A. Case (Mon Dec 02 2002 - 09:40:02 CST)
- Kristina Furse (Sun Dec 01 2002 - 15:57:13 CST)
- David A. Case (Tue Nov 26 2002 - 17:51:31 CST)
- Kristina Furse (Tue Nov 26 2002 - 16:51:52 CST)
- David A. Case (Fri Nov 22 2002 - 20:31:03 CST)
- Kristina Furse (Fri Nov 22 2002 - 15:36:33 CST)
solvating a protein with large cavity
- M. L. Dodson (Sat Dec 14 2002 - 10:23:15 CST)
- Tom Bishop (Sat Dec 14 2002 - 09:42:38 CST)
solved: nmr and positional restraint in input
- Peter Varnai (Thu Oct 10 2002 - 10:26:27 CDT)
Solvent exposed surface area over a trajectory
- Natasja Brooijmans (Thu Oct 17 2002 - 14:35:34 CDT)
- Sanjeev B.S. (Thu Oct 17 2002 - 14:18:56 CDT)
- Michael Ford (Thu Oct 17 2002 - 14:09:17 CDT)
- Rebecca Perlow (Thu Oct 17 2002 - 13:20:03 CDT)
Some error message on Leap
- Ioana Cozmuta (Thu Oct 10 2002 - 17:22:51 CDT)
- Michael Ford (Thu Oct 10 2002 - 16:27:03 CDT)
- Sichun Yang (Thu Oct 10 2002 - 15:15:43 CDT)
sorry this is just a test
- Vlad Cojocaru (Thu Sep 12 2002 - 10:23:24 CDT)
sorry!!!!maybe another stupid question
- Pratul Agarwal (Wed Aug 28 2002 - 20:45:28 CDT)
- Vlad Cojocaru (Wed Aug 28 2002 - 17:48:03 CDT)
specification for memory requirement
- Carlos Simmerling (Fri Oct 25 2002 - 20:55:42 CDT)
- yuann (Fri Oct 25 2002 - 19:37:13 CDT)
SS bond
- David A. Case (Wed Jul 24 2002 - 15:00:44 CDT)
- Masaki Tomimoto (Wed Jul 24 2002 - 14:04:21 CDT)
statistical analysis of MD trajectories
- Jake Isaacs (Thu Mar 07 2002 - 11:24:03 CST)
still having ptraj problems
- Jake Isaacs (Wed May 22 2002 - 10:50:11 CDT)
- Jake Isaacs (Wed May 22 2002 - 10:19:06 CDT)
Still no bench
- Stéphane Teletchéa (Tue Mar 19 2002 - 09:17:45 CST)
Strange MD simulation results with GB solvation at high temp.
- Soonmin Jang (Fri Sep 13 2002 - 00:21:32 CDT)
- Carlos Simmerling (Wed Sep 11 2002 - 21:04:44 CDT)
- David A. Case (Wed Sep 11 2002 - 20:20:17 CDT)
- Soonmin Jang (Tue Sep 10 2002 - 10:56:53 CDT)
- Carlos Simmerling (Tue Sep 10 2002 - 07:07:58 CDT)
- Soonmin Jang (Tue Sep 10 2002 - 05:09:06 CDT)
Stretching Constants
- Daniel Flint (Thu Jan 17 2002 - 05:21:52 CST)
structure
- David Case (Wed Jul 31 2002 - 00:43:50 CDT)
- Cozmuta (Tue Jul 30 2002 - 22:34:44 CDT)
Studying in Australia
- John Pritchard (Tue Dec 17 2002 - 22:36:07 CST)
subdomain moving as a rigid unit during MD
- Marcela Madrid (Fri May 24 2002 - 10:59:40 CDT)
Suggestion to Bill and Case
- William Wei (Fri Jun 07 2002 - 15:49:10 CDT)
- Bill Ross (Fri Jun 07 2002 - 15:16:30 CDT)
sulfate and sulfamate parameters
- jeff dyason (Wed Mar 27 2002 - 22:28:55 CST)
sulfonic group generated with antechamber
- Michael Jakusch (Thu Jul 25 2002 - 07:23:30 CDT)
Summary: make_crd_hp, mm_pbsa
- Jianhui Wu (Mon Jul 22 2002 - 16:45:32 CDT)
SUMMARY: solvating a protein with large cavity
- Ioana Cozmuta (Wed Dec 18 2002 - 19:21:23 CST)
- Richard Henchman (Wed Dec 18 2002 - 13:56:20 CST)
- Tom Bishop (Wed Dec 18 2002 - 09:03:27 CST)
surface
- Ioana Cozmuta (Thu Nov 07 2002 - 15:03:56 CST)
SURFTEN for GB
- Lepsa (Fri Oct 25 2002 - 08:55:12 CDT)
- Lepsa (Fri Oct 25 2002 - 08:51:30 CDT)
syntax
- David A. Case (Wed Oct 16 2002 - 13:57:44 CDT)
- Ioana Cozmuta (Wed Oct 16 2002 - 13:14:54 CDT)
Targeted MD
- Carlos Simmerling (Mon Oct 28 2002 - 17:09:19 CST)
- Giulio Rastelli (Mon Oct 28 2002 - 15:44:05 CST)
- Peter VARNAI (Sat Oct 19 2002 - 09:26:30 CDT)
- Carlos Simmerling (Fri Oct 18 2002 - 10:45:33 CDT)
- David A. Case (Fri Oct 18 2002 - 10:32:14 CDT)
- Giulio Rastelli (Fri Oct 18 2002 - 09:28:48 CDT)
targeted MD for more than 2 groups
- Carlos Simmerling (Thu Nov 21 2002 - 17:54:53 CST)
- Sichun Yang (Thu Nov 21 2002 - 15:20:44 CST)
targeted MD sample
- eric hu (Thu Dec 26 2002 - 14:25:36 CST)
taupt: time constant for heat bath coupling for the SOLUTE
- David A. Case (Fri Jun 21 2002 - 19:28:38 CDT)
- Qing Zhang (Fri Jun 21 2002 - 18:44:55 CDT)
temperature control
- Michael G Cooney (Tue Feb 05 2002 - 13:15:58 CST)
- Jerry wu (Mon Jan 14 2002 - 21:55:16 CST)
test
- James W. Caldwell (Mon Aug 26 2002 - 17:04:35 CDT)
- Sarangan Ravichandran (Fri Jul 05 2002 - 07:43:37 CDT)
test mail
- Jim Caldwell (Tue Dec 03 2002 - 16:48:07 CST)
test of mm_pbsa
- Yongjun Jiang (Tue Jun 11 2002 - 22:08:23 CDT)
tests for amber
- jim caldwell (Tue Jul 30 2002 - 19:57:49 CDT)
- Cozmuta (Tue Jul 30 2002 - 18:47:18 CDT)
Thanks
- FyD (Fri Apr 12 2002 - 02:04:53 CDT)
Thanks to all
- Albert Codony (Sat May 04 2002 - 10:38:12 CDT)
The 216 water box
- Mihaly Mezei (Thu Jul 18 2002 - 17:48:12 CDT)
the amino group of 2amino purine has strange behaviour
- Vlad Cojocaru (Thu Sep 12 2002 - 13:42:10 CDT)
The atom number mismatch in coord and topology file in AMBER6.
- Robert Duke (Fri Jun 14 2002 - 11:27:00 CDT)
- Ling Zhang (Fri Jun 14 2002 - 09:58:45 CDT)
The atom number mismatch in coord and topology file.
- Carlos Simmerling (Thu Jun 13 2002 - 17:27:38 CDT)
- Ling Zhang (Thu Jun 13 2002 - 16:41:08 CDT)
The crystal water is solute or solvent during solvation
- Ling Zhang (Fri Jun 28 2002 - 13:58:08 CDT)
The link is out
- David Case (Wed Feb 20 2002 - 11:20:00 CST)
- Carlos Simmerling (Tue Feb 19 2002 - 14:53:45 CST)
- Stéphane Teletchéa (Tue Feb 19 2002 - 10:58:44 CST)
the removal of global motion
- David A. Case (Tue Nov 12 2002 - 18:18:31 CST)
- Ioana Cozmuta (Tue Nov 12 2002 - 17:52:41 CST)
- David A. Case (Tue Nov 12 2002 - 17:25:09 CST)
- Shixiang Yan (Tue Nov 12 2002 - 10:44:38 CST)
the tree name?
- David A. Case (Wed Nov 27 2002 - 16:44:17 CST)
- Sichun Yang (Tue Nov 26 2002 - 21:29:27 CST)
This is a test for amber reflector - please ignore
- Lorenzo Gontrani (Thu May 23 2002 - 03:34:38 CDT)
- Asif Rahaman (Wed May 22 2002 - 17:17:29 CDT)
this is a test of the amber reflector. Please ignore. Marcela
- Marcela Madrid (Wed May 22 2002 - 08:59:24 CDT)
This one with anal in amber6
- Prabal Maiti (Fri Jul 12 2002 - 13:09:39 CDT)
TI integration
- Joe Fernandez (Sat May 04 2002 - 08:59:57 CDT)
TI using sander on cluster
- Joe Fernandez (Mon May 06 2002 - 09:52:50 CDT)
time averaged restraint parameters
- Jake Isaacs (Thu Oct 17 2002 - 15:09:59 CDT)
time correlation function
- David A. Case (Thu Oct 31 2002 - 09:21:28 CST)
- Bimo Ario Tejo (Fri Oct 25 2002 - 09:47:28 CDT)
time scale to see the ion effect on DNA
- A.Madhumalar (Thu Jul 11 2002 - 01:40:52 CDT)
time-averaged restraint developer
- Jake Isaacs (Wed Nov 06 2002 - 16:20:11 CST)
timescale of deoxyribose ring repuckering
- Jake Isaacs (Tue Jan 22 2002 - 10:43:40 CST)
timings?
- David A. Case (Fri Dec 06 2002 - 09:46:27 CST)
- Arvid Soederhaell (Fri Dec 06 2002 - 02:51:10 CST)
TIP4P
- David Case (Fri May 31 2002 - 09:44:19 CDT)
- SEKIJIMA Masakazu (Fri May 31 2002 - 02:32:08 CDT)
- SEKIJIMA Masakazu (Thu May 30 2002 - 03:43:14 CDT)
TIP4P parameters
- David Case (Tue Apr 30 2002 - 00:17:49 CDT)
- Ge Zhou (Mon Apr 29 2002 - 21:03:54 CDT)
TIP4P water with AMBER6
- jim caldwell (Wed May 22 2002 - 15:25:00 CDT)
- Noriaki Okimoto (Wed May 22 2002 - 13:01:35 CDT)
tleap error for systems with 64-bit pointers
- Karen Haskell (Fri Jun 14 2002 - 14:55:16 CDT)
To PROFEC users
- Salinthip Thipayang (Fri Apr 19 2002 - 09:13:11 CDT)
Topology file format in AMBER 7
- David Case (Tue May 14 2002 - 16:33:15 CDT)
- Joffre Heredia (Tue May 14 2002 - 16:14:55 CDT)
topology file generation
- Carlos Simmerling (Mon May 06 2002 - 07:27:06 CDT)
- Sanjeev B.S. (Mon May 06 2002 - 07:24:30 CDT)
- Andreas Svrcek-Seiler (Mon May 06 2002 - 07:11:54 CDT)
- Sanjeev B.S. (Mon May 06 2002 - 00:36:36 CDT)
torsion angle constrains
- Marcela Madrid (Tue Jul 02 2002 - 16:22:09 CDT)
Torsion driving
- ch cureton (Thu Sep 26 2002 - 11:00:34 CDT)
Torsion restraint between center of mass groups
- Pratul Agarwal (Mon Aug 26 2002 - 16:51:33 CDT)
torsion restraints in GIBBS
- Jose Ramon Blas (Tue Nov 05 2002 - 18:35:44 CST)
- David A. Case (Tue Nov 05 2002 - 10:20:57 CST)
torsional fit
- Fabrizio Giordanetto (Fri Jan 25 2002 - 04:34:55 CST)
total energies during MM-PBSA
- Lepsa (Fri Nov 01 2002 - 11:29:33 CST)
- Giulio Rastelli (Sun Oct 27 2002 - 12:20:19 CST)
Trajectory file converted in pdb file
- Yongjun Jiang (Sun Dec 29 2002 - 19:13:38 CST)
trajectory file limit???
- Ross Walker (Thu Aug 15 2002 - 16:48:30 CDT)
- Pratul Agarwal (Thu Aug 15 2002 - 16:12:35 CDT)
- jim caldwell (Thu Aug 15 2002 - 14:26:13 CDT)
- David A. Case (Thu Aug 15 2002 - 12:26:34 CDT)
- Vlad Cojocaru (Thu Aug 15 2002 - 11:43:54 CDT)
Trajectory files
- Carlos Simmerling (Wed Jul 24 2002 - 10:52:29 CDT)
- Laurent Chiche (Wed Jul 24 2002 - 10:26:36 CDT)
- David A. Case (Wed Jul 24 2002 - 10:15:55 CDT)
- Natasja Brooijmans (Wed Jul 24 2002 - 09:34:28 CDT)
- Miguel de Federico (Wed Jul 24 2002 - 07:10:51 CDT)
trajectory problem?
- David Case (Thu Jul 25 2002 - 00:22:57 CDT)
transferring structures
- Matt Hartings (Wed Jun 26 2002 - 15:58:11 CDT)
- Bill Ross (Wed Jun 26 2002 - 14:47:02 CDT)
- Matt Hartings (Wed Jun 26 2002 - 12:24:23 CDT)
triNAG parameters?4
- Michael Ford (Tue Jan 22 2002 - 11:19:21 CST)
- Andrea Bernini (Mon Jan 21 2002 - 09:13:26 CST)
trouble with snapshots GC option of MM_PBSA
- Michael Ford (Thu Oct 10 2002 - 09:31:05 CDT)
- Michael Ford (Thu Oct 10 2002 - 09:23:24 CDT)
trouble with snapshots GC option of MM_PBSA - Now no output for lig and rec
- Michael Ford (Thu Oct 10 2002 - 10:10:35 CDT)
trouble with snapshots GC option of MM_PBSA]
- Holger Gohlke (Thu Oct 10 2002 - 11:15:39 CDT)
Truncated Octahedron Box
- giudice (Thu Oct 17 2002 - 08:06:28 CDT)
turning off ewald (fwd)
- David A. Case (Mon Aug 26 2002 - 20:12:29 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:21 CDT)
turning PME off in AMBER7
- David A. Case (Thu Jun 20 2002 - 08:49:33 CDT)
- Arvid Soederhaell (Thu Jun 20 2002 - 08:45:25 CDT)
- lamon_at_lav.Boehringer-Ingelheim.com (Thu Jun 20 2002 - 08:28:30 CDT)
Tutorial Error Message
- Holger Gohlke (Thu Aug 29 2002 - 10:22:25 CDT)
- Joel Konkle-Parker (Wed Aug 28 2002 - 18:19:48 CDT)
tutorial on plastocyanin
- David A. Case (Wed Oct 02 2002 - 09:48:27 CDT)
- Ioana Cozmuta (Wed Oct 02 2002 - 01:04:37 CDT)
Umbrella sampling in AMBER
- David A. Case (Wed Jul 24 2002 - 16:44:35 CDT)
- Pratul Agarwal (Wed Jul 24 2002 - 15:53:54 CDT)
unsuscribe
- Ivan Beà (Wed Jan 16 2002 - 09:25:38 CST)
Using a trucated octahedral box in Amber6
- Ling Zhang (Wed Jun 26 2002 - 20:28:46 CDT)
using belly with GB
- David A. Case (Wed Aug 07 2002 - 20:36:18 CDT)
Using GBSA for a DNA-PROTEIN complex (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:52:06 CDT)
using SHAKE for solvent only
- David A. Case (Mon Nov 25 2002 - 12:17:54 CST)
- hagop demirdjian (Mon Nov 25 2002 - 09:42:57 CST)
Using the new2oldparm command
- Pascal Bonnet (Fri Aug 02 2002 - 03:17:54 CDT)
- Karen Haskell (Thu Aug 01 2002 - 15:55:28 CDT)
- Holger Gohlke (Thu Aug 01 2002 - 15:52:23 CDT)
- dianah_at_unm.edu (Thu Aug 01 2002 - 15:18:32 CDT)
Using TIP4P water
- S. Yamasaki (Thu Jun 13 2002 - 20:05:48 CDT)
valine to alanine example
- Sophia Kondratova (Tue Apr 30 2002 - 10:23:21 CDT)
Valine to alanine Gibbs tutorial
- Lepsa (Mon Dec 16 2002 - 07:20:26 CST)
van der Waals explosion
- David A. Case (Fri Jun 21 2002 - 09:55:26 CDT)
- Arvid Soederhaell (Fri Jun 21 2002 - 03:54:05 CDT)
van der Waals, hydrogen bond energy
- Andreas Svrcek-Seiler (Sat Jun 29 2002 - 07:29:38 CDT)
- jim caldwell (Fri Jun 28 2002 - 19:24:21 CDT)
- Carlos Simmerling (Fri Jun 28 2002 - 18:41:11 CDT)
- Qing Zhang (Fri Jun 28 2002 - 17:57:10 CDT)
vanadium
- Natasja Brooijmans (Sun May 19 2002 - 21:35:27 CDT)
Vanderbilt Biomolecular Modeling Symposium
- Douglas Kojetin (Fri Aug 30 2002 - 14:22:19 CDT)
- Jarrod Smith (Fri Aug 30 2002 - 13:00:40 CDT)
visualizaion program for NMODE!
- Yuguang Mu (Thu Feb 28 2002 - 02:56:44 CST)
- Pradipta Bandyopadhyay (Wed Feb 27 2002 - 16:48:30 CST)
Visualizing AMBER coordinates trajectory in VMD
- Tom Bishop (Tue Nov 05 2002 - 05:36:41 CST)
- David A. Case (Mon Nov 04 2002 - 15:57:10 CST)
- Pratul Agarwal (Mon Nov 04 2002 - 14:54:57 CST)
vlimit and vmax
- darden (Fri Sep 20 2002 - 14:27:10 CDT)
- Thomas Cheatham (Fri Sep 20 2002 - 14:14:11 CDT)
- Prem Raj (Fri Sep 20 2002 - 12:27:07 CDT)
vlimit exceed
- David Case (Sun Feb 24 2002 - 00:03:24 CST)
- Yuguang Mu (Fri Feb 22 2002 - 01:44:53 CST)
- Prabal Maiti (Thu Feb 21 2002 - 21:23:39 CST)
vlimit exceeded
- Thomas Cheatham (Wed Jun 12 2002 - 14:35:53 CDT)
- Carlos Simmerling (Wed Jun 12 2002 - 06:42:14 CDT)
- A. Hungie (Wed Jun 12 2002 - 04:49:44 CDT)
volume of ucell too big!!
- sxzheng (Fri Oct 11 2002 - 10:06:52 CDT)
Vulgar Models Do Everything And Love It!!!
- telesales (Mon Apr 15 2002 - 19:03:45 CDT)
water box size
- eric hu (Thu Jul 25 2002 - 14:21:24 CDT)
- Shixiang Yan (Fri Jul 19 2002 - 18:02:32 CDT)
- eric hu (Fri Jul 19 2002 - 17:09:25 CDT)
water box,
- darden (Wed Dec 18 2002 - 18:45:55 CST)
- David A. Case (Wed Dec 18 2002 - 18:17:31 CST)
- Ioana Cozmuta (Wed Dec 18 2002 - 17:37:41 CST)
- darden (Wed Dec 18 2002 - 10:33:07 CST)
- Carlos Simmerling (Wed Dec 18 2002 - 07:18:18 CST)
- Ioana Cozmuta (Tue Dec 17 2002 - 17:18:31 CST)
water box-nonperiodic
- David Case (Sat Aug 03 2002 - 00:16:18 CDT)
- Cozmuta (Fri Aug 02 2002 - 22:14:35 CDT)
Water molecule numbering
- Shixiang Yan (Thu Jul 25 2002 - 21:28:02 CDT)
- Masaki Tomimoto (Thu Jul 25 2002 - 19:32:19 CDT)
- Masaki Tomimoto (Thu Jul 25 2002 - 19:04:01 CDT)
- Shixiang Yan (Thu Jul 25 2002 - 18:25:08 CDT)
- Masaki Tomimoto (Thu Jul 25 2002 - 17:28:25 CDT)
water molecules diffuse during equilibration
- David A. Case (Tue Jul 16 2002 - 20:31:12 CDT)
- Qing Zhang (Tue Jul 16 2002 - 18:56:53 CDT)
water/nonTIP3P
- Ioana Cozmuta (Wed Dec 18 2002 - 20:17:24 CST)
- Ioana Cozmuta (Wed Dec 18 2002 - 19:33:23 CST)
watershell in ptraj
- Thomas Cheatham (Tue Sep 24 2002 - 14:28:09 CDT)
- Michael Trieb (Tue Sep 24 2002 - 04:03:49 CDT)
WG:
- Christian.Pilger_at_bc.boehringer-ingelheim.com (Tue Jun 18 2002 - 00:48:01 CDT)
what are "end group interactions"?
- C. Klein (Mon Oct 07 2002 - 03:43:00 CDT)
What is the atoms limit for Amber 7?
- David Case (Wed Mar 27 2002 - 17:45:44 CST)
- William Wei (Wed Mar 27 2002 - 16:19:34 CST)
What's this "interface" the tutorial talks about?
- David Pearlman (Wed Aug 28 2002 - 14:49:57 CDT)
- priestle (Wed Aug 28 2002 - 14:02:52 CDT)
- Andreas Kerzmann (Wed Aug 28 2002 - 07:41:01 CDT)
who to address this to?...
- Michael Crowley (Mon Sep 09 2002 - 12:41:16 CDT)
- Holger Gohlke (Mon Sep 09 2002 - 11:25:00 CDT)
- Jessica Swanson (Sun Sep 08 2002 - 17:59:23 CDT)
why are the results so large difference calculating by mm_pbsa and mm_gbsa?
- Holger Gohlke (Tue Sep 10 2002 - 11:26:07 CDT)
- Yongjun Jiang (Tue Sep 10 2002 - 02:18:46 CDT)
why are the results so large difference calculating by mm_pbsaandmm_gbsa?
- Yongjun Jiang (Thu Sep 12 2002 - 02:25:32 CDT)
why is mm_pbsa broken ? (fwd)
- Holger Gohlke (Tue Aug 27 2002 - 12:12:17 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:59 CDT)
- amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:27 CDT)
write problem on IBM-AIX
- Nicolas Grima (Tue Oct 01 2002 - 04:40:07 CDT)
- Giovanni Fossati (Mon Sep 30 2002 - 10:51:54 CDT)
xaLeap make fails on AIX
- Bill Ross (Mon Jun 10 2002 - 13:19:47 CDT)
- Thomas A. Spraggins (Mon Jun 10 2002 - 11:13:01 CDT)
xleap
- Marcela Madrid (Tue May 28 2002 - 16:21:39 CDT)
- x357l (Tue Feb 19 2002 - 10:03:11 CST)
- sara nunez (Fri Jan 04 2002 - 17:28:14 CST)
xleap and carbohydrates and stuff
- Amesh Patel (Wed Feb 27 2002 - 08:43:23 CST)
xleap and modified sugar residues
- Holger Gohlke (Thu Oct 31 2002 - 13:54:23 CST)
- Michael Ford (Thu Oct 31 2002 - 13:22:17 CST)
xleap and PDB file
- Prabal Maiti (Tue Jan 29 2002 - 01:28:23 CST)
xleap on a SGI Fuel
- David A. Case (Mon Oct 07 2002 - 21:50:33 CDT)
- Giulio Rastelli (Mon Oct 07 2002 - 09:50:39 CDT)
xleap problem
- David A. Case (Thu Jun 27 2002 - 10:33:16 CDT)
- FyD (Thu Jun 27 2002 - 03:20:53 CDT)
- John Bushnell (Thu May 30 2002 - 00:53:05 CDT)
- Donald Thomas (Wed May 29 2002 - 23:42:04 CDT)
xleap XENVIRONMENT
- Mark C. Ballew (Thu Oct 03 2002 - 16:09:25 CDT)
- Lepsa (Thu Oct 03 2002 - 02:47:39 CDT)
- David A. Case (Wed Oct 02 2002 - 18:55:31 CDT)
- Mark C. Ballew (Wed Oct 02 2002 - 17:34:09 CDT)
xmkmf: not found
- Bill Ross (Thu Jun 27 2002 - 17:29:08 CDT)
your mail
- David Case (Fri Nov 29 2002 - 14:07:19 CST)
- darden (Sun Nov 24 2002 - 16:46:35 CST)
- David Case (Sat Nov 16 2002 - 09:43:29 CST)
- David A. Case (Thu Nov 14 2002 - 10:00:48 CST)
- David A. Case (Mon Sep 30 2002 - 11:35:06 CDT)
- darden (Wed Aug 07 2002 - 06:58:17 CDT)
- CUI, Guanglei (Thu Jul 25 2002 - 08:30:30 CDT)
- deepak rangaswamy (Tue Apr 30 2002 - 07:06:06 CDT)
- David Case (Sat Apr 20 2002 - 11:06:32 CDT)
- Andreas Svrcek-Seiler (Thu Apr 11 2002 - 09:33:22 CDT)
- jim caldwell (Mon Jan 14 2002 - 13:01:44 CST)
Z DNA
- Sue Heavner (Tue Sep 17 2002 - 14:55:04 CDT)
Zn/Mg Counterion placement around DNA
- mdk7p_at_cms.mail.virginia.edu (Fri Jun 28 2002 - 14:46:11 CDT)

Last message date: Tue Dec 31 2002 - 15:51:31 CST
Archived on: Thu May 05 2005 - 14:17:25 CDT

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