Amber Archive Feb 2005: by subject

Amber 8 with lam compilation problem
- Robert Duke (Thu Feb 24 2005 - 05:54:08 PST)
- Maciej (Wed Feb 23 2005 - 23:43:53 PST)
- Amber admin (Wed Feb 23 2005 - 12:39:02 PST)
- Ross Walker (Wed Feb 23 2005 - 10:02:47 PST)
- Maciej KA (Wed Feb 23 2005 - 00:07:37 PST)
- Ross Walker (Tue Feb 22 2005 - 23:20:54 PST)
- Maciej KA (Tue Feb 22 2005 - 23:08:16 PST)
AMBER:
- Austin B. Yongye (Fri Feb 25 2005 - 13:43:56 PST)
- David A. Case (Wed Feb 16 2005 - 08:49:18 PST)
- Beale, John (Wed Feb 16 2005 - 05:42:26 PST)
- Carlos Simmerling (Wed Feb 16 2005 - 04:55:57 PST)
- Gustavo Pierdominici Sottile (Wed Feb 16 2005 - 04:22:59 PST)
- Ross Walker (Mon Feb 14 2005 - 09:03:52 PST)
- S.Sundar Raman (Mon Feb 14 2005 - 01:03:27 PST)
AMBER: (no subject)
- yen li (Sun Feb 20 2005 - 10:16:32 PST)
AMBER: AIX problem
- Mayumi Haga (Mon Feb 21 2005 - 16:45:33 PST)
- David A. Case (Mon Feb 21 2005 - 16:05:40 PST)
- Mayumi Haga (Sun Feb 20 2005 - 21:17:29 PST)
AMBER: AMBER 8 : Water cap problem
- Ross Walker (Mon Feb 14 2005 - 09:07:21 PST)
- Guillaume Bollot (Mon Feb 14 2005 - 05:14:20 PST)
AMBER: amber 8 system requirements
- Ross Walker (Wed Feb 02 2005 - 10:47:55 PST)
- dkohen.carleton.edu (Wed Feb 02 2005 - 10:28:48 PST)
AMBER: Amber 8 with lam compilation problem
- Ross Walker (Mon Feb 21 2005 - 01:20:21 PST)
- m m (Mon Feb 21 2005 - 00:55:49 PST)
AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem
- praveena moldy (Sun Feb 27 2005 - 21:36:36 PST)
AMBER: Amber7 nmropt
- Robert Duke (Wed Feb 16 2005 - 15:05:37 PST)
- Ross Walker (Wed Feb 16 2005 - 13:55:40 PST)
- David A. Case (Wed Feb 16 2005 - 13:53:19 PST)
- Markus W. Germann (Wed Feb 16 2005 - 13:40:46 PST)
- Ross Walker (Wed Feb 16 2005 - 13:32:05 PST)
- Markus W. Germann (Wed Feb 16 2005 - 13:09:08 PST)
AMBER: amber8 and moil-view
- Carlos Simmerling (Fri Feb 18 2005 - 12:13:03 PST)
- Lihua Wang (Thu Feb 17 2005 - 12:14:04 PST)
- Carlos Simmerling (Thu Feb 17 2005 - 12:06:42 PST)
- Lihua Wang (Thu Feb 17 2005 - 11:52:08 PST)
- Carlos Simmerling (Thu Feb 17 2005 - 11:42:13 PST)
- Lihua Wang (Thu Feb 17 2005 - 11:26:32 PST)
AMBER: amber8 in IBM-SP4
- Jiten (Mon Jan 31 2005 - 19:32:28 PST)
AMBER: Amber8 installation test possible failures
- Ross Walker (Tue Feb 08 2005 - 12:17:40 PST)
- David A. Case (Tue Feb 08 2005 - 12:02:54 PST)
- Joe Nolan (Tue Feb 08 2005 - 11:55:39 PST)
AMBER: Amber8 Solaris installation failure
- David A. Case (Mon Feb 28 2005 - 14:42:21 PST)
- M. L. Dodson (Mon Feb 28 2005 - 12:55:47 PST)
- Joe Nolan (Mon Feb 28 2005 - 12:24:28 PST)
- M. L. Dodson (Tue Feb 22 2005 - 18:33:31 PST)
- David A. Case (Tue Feb 22 2005 - 16:52:13 PST)
- Bill Ross (Tue Feb 22 2005 - 16:08:37 PST)
- Ross Walker (Tue Feb 22 2005 - 15:55:17 PST)
- Joe Nolan (Tue Feb 22 2005 - 15:34:50 PST)
- Atro Tossavainen (Tue Feb 22 2005 - 12:19:31 PST)
- Joe Nolan (Tue Feb 22 2005 - 12:12:02 PST)
- David A. Case (Thu Feb 17 2005 - 18:31:00 PST)
- Joe Nolan (Thu Feb 17 2005 - 12:27:12 PST)
AMBER: Amber: sander error segmentation fault.
- Ross Walker (Fri Feb 18 2005 - 22:34:22 PST)
- S.Sundar Raman (Fri Feb 18 2005 - 22:03:50 PST)
AMBER: ambpdb radii
- David A. Case (Fri Feb 25 2005 - 10:15:57 PST)
- Harianto (Fri Feb 25 2005 - 10:41:59 PST)
- David A. Case (Fri Feb 25 2005 - 08:09:53 PST)
- Harianto (Fri Feb 25 2005 - 08:20:31 PST)
- David A. Case (Thu Feb 24 2005 - 16:56:40 PST)
- Harianto (Thu Feb 24 2005 - 11:24:39 PST)
AMBER: Another question about surface area calculation
- michael chen (Wed Feb 09 2005 - 22:26:00 PST)
AMBER: Antechamber help needed
- Kara Di Giorgio (Thu Feb 17 2005 - 09:24:34 PST)
AMBER: Antechamber/formatting question
- FyD (Sun Feb 27 2005 - 20:43:23 PST)
- FyD (Sun Feb 27 2005 - 20:12:37 PST)
- Kara Di Giorgio (Sun Feb 27 2005 - 17:13:19 PST)
- Ross Walker (Sun Feb 27 2005 - 11:56:18 PST)
- Kara Di Giorgio (Fri Feb 25 2005 - 18:02:40 PST)
- Ilyas Yildirim (Fri Feb 25 2005 - 17:31:46 PST)
- Kara Di Giorgio (Fri Feb 25 2005 - 16:43:36 PST)
- YoungJin Cho (Mon Feb 21 2005 - 08:15:32 PST)
- Kara Di Giorgio (Fri Feb 18 2005 - 10:20:40 PST)
- David A. Case (Sat Feb 05 2005 - 11:17:24 PST)
- Kara Di Giorgio (Fri Feb 04 2005 - 15:05:18 PST)
AMBER: archive
- Gustavo Pierdominici Sottile (Fri Feb 11 2005 - 06:58:33 PST)
AMBER: blows up
- Gustavo Pierdominici Sottile (Tue Feb 15 2005 - 11:11:43 PST)
AMBER: Can REM be used as multiple normal sander jobs on parallel machine
- Carlos Simmerling (Wed Feb 09 2005 - 16:03:55 PST)
- qlu.notes.cc.sunysb.edu (Wed Feb 09 2005 - 15:15:59 PST)
AMBER: Carnal in Amber8
- Bill Ross (Tue Feb 01 2005 - 11:57:19 PST)
- Bill Ross (Tue Feb 01 2005 - 11:47:15 PST)
- David A. Case (Tue Feb 01 2005 - 09:27:25 PST)
- Vlad Cojocaru (Tue Feb 01 2005 - 08:11:09 PST)
AMBER: change of prmtop file
- David A. Case (Wed Feb 02 2005 - 10:21:34 PST)
- Guanglei Cui (Wed Feb 02 2005 - 10:03:53 PST)
- Gustavo Pierdominici Sottile (Wed Feb 02 2005 - 07:43:34 PST)
AMBER: check in leap
- David A. Case (Tue Feb 15 2005 - 13:17:07 PST)
- Gustavo Pierdominici Sottile (Tue Feb 15 2005 - 11:34:21 PST)
AMBER: classes
- Vineet Pande (Thu Feb 24 2005 - 06:29:19 PST)
- Gustavo Pierdominici Sottile (Wed Feb 23 2005 - 13:00:47 PST)
AMBER: clusters
- Germán Sciaini (Fri Feb 04 2005 - 04:36:48 PST)
AMBER: Compilation problem at dual processor linux !
- Ross Walker (Wed Feb 02 2005 - 09:52:10 PST)
- Pradipta Bandyopadhyay (Wed Feb 02 2005 - 04:32:52 PST)
AMBER: compile amber8 on RHEL4
- Tru Huynh (Fri Feb 25 2005 - 05:09:33 PST)
- Ye MEI (Fri Feb 25 2005 - 04:01:17 PST)
- HuiZhe Li (Thu Feb 24 2005 - 23:59:02 PST)
AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD)
- David A. Case (Thu Feb 17 2005 - 23:56:20 PST)
- David A. Case (Thu Feb 17 2005 - 23:41:23 PST)
- M. L. Dodson (Thu Feb 17 2005 - 18:21:29 PST)
- Greg Recine (Thu Feb 17 2005 - 16:23:01 PST)
AMBER: constrains
- Ross Walker (Mon Feb 14 2005 - 09:10:42 PST)
- Vineet Pande (Mon Feb 14 2005 - 07:48:39 PST)
- Gustavo Pierdominici Sottile (Mon Feb 14 2005 - 06:53:18 PST)
AMBER: Controlling number of water residues...
- Pavan G (Mon Feb 28 2005 - 23:14:51 PST)
AMBER: convert one functional group to another with TI
- Eric Hu (Wed Feb 23 2005 - 15:18:29 PST)
- David A. Case (Wed Feb 23 2005 - 15:01:42 PST)
- David A. Case (Wed Feb 23 2005 - 14:46:55 PST)
- Eric Hu (Tue Feb 22 2005 - 22:36:03 PST)
- David A. Case (Tue Feb 22 2005 - 21:44:41 PST)
- Eric Hu (Tue Feb 22 2005 - 17:29:42 PST)
AMBER: Convert to Pdb
- M. L. Dodson (Wed Feb 09 2005 - 11:28:22 PST)
- Ross Walker (Wed Feb 09 2005 - 11:19:15 PST)
- Peter Gannett (Wed Feb 09 2005 - 11:07:07 PST)
- Beale, John (Wed Feb 09 2005 - 11:03:27 PST)
AMBER: correlation
- David A. Case (Mon Feb 28 2005 - 09:32:54 PST)
- Gustavo Pierdominici Sottile (Thu Feb 24 2005 - 11:48:50 PST)
AMBER: correlation along PCA modes
- Vlad Cojocaru (Mon Feb 07 2005 - 03:35:44 PST)
AMBER: creating a new residue
- Amber admin (Mon Feb 28 2005 - 08:44:59 PST)
AMBER: Creating an input file for GRASP using AMBER 8
- FyD (Mon Feb 07 2005 - 14:45:05 PST)
- Ilyas Yildirim (Mon Feb 07 2005 - 14:24:24 PST)
- FyD (Mon Feb 07 2005 - 11:52:42 PST)
- Bill Ross (Mon Feb 07 2005 - 11:40:33 PST)
- Ilyas Yildirim (Mon Feb 07 2005 - 11:07:29 PST)
AMBER: cross-correlation
- Xin Hu (Thu Feb 24 2005 - 08:40:54 PST)
AMBER: Cu++ and RED
- FyD (Tue Feb 15 2005 - 10:19:16 PST)
- Cenk Andac (Mon Feb 14 2005 - 21:30:47 PST)
- FyD (Fri Feb 11 2005 - 09:23:53 PST)
- Cenk Andac (Fri Feb 11 2005 - 01:46:13 PST)
AMBER: Cyclic peptide
- Carlos Simmerling (Wed Feb 16 2005 - 05:00:29 PST)
- Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Wed Feb 16 2005 - 01:48:19 PST)
- arubin.unmc.edu (Tue Feb 15 2005 - 13:12:28 PST)
AMBER: desc NEWRES and blank unit type
- David A. Case (Fri Feb 11 2005 - 14:24:25 PST)
- Stern, Julie (Wed Feb 09 2005 - 18:07:00 PST)
AMBER: dihedral driver?
- Beale, John (Tue Feb 22 2005 - 08:26:26 PST)
AMBER: DIVCON optimization
- David A. Case (Wed Feb 09 2005 - 18:22:07 PST)
- Kara Wald (Wed Feb 09 2005 - 15:30:07 PST)
- David A. Case (Wed Feb 09 2005 - 12:22:59 PST)
- Kara Di Giorgio (Wed Feb 09 2005 - 11:46:03 PST)
AMBER: DNA melting free energy calculation
- lei jia (Thu Feb 03 2005 - 16:39:57 PST)
AMBER: DNA Tutorial
- David A. Case (Mon Feb 21 2005 - 15:52:21 PST)
- Dwayne Hoobler (Mon Feb 21 2005 - 12:26:37 PST)
- Ross Walker (Fri Feb 18 2005 - 17:15:31 PST)
- Dwayne Hoobler (Fri Feb 18 2005 - 15:07:34 PST)
AMBER: Does delta.charge mean "final charge" for a dummy atom?
- Eric Hu (Fri Feb 25 2005 - 16:38:05 PST)
- David A. Case (Thu Feb 24 2005 - 18:31:04 PST)
- Eric Hu (Thu Feb 24 2005 - 17:22:23 PST)
AMBER: doubts with a new aminoacid
- Bill Ross (Tue Feb 01 2005 - 16:36:38 PST)
- David A. Case (Tue Feb 01 2005 - 15:35:36 PST)
- Gustavo Pierdominici Sottile (Tue Feb 01 2005 - 12:28:52 PST)
AMBER: dppsv returns error code: 29
- David A. Case (Fri Feb 04 2005 - 14:48:38 PST)
- Xiaowei (David) Li (Fri Feb 04 2005 - 09:58:56 PST)
AMBER: Dummy Atom Types on both states
- David A. Case (Tue Feb 15 2005 - 14:26:21 PST)
- david.evans.ulsop.ac.uk (Tue Feb 15 2005 - 10:13:57 PST)
- david.evans.ulsop.ac.uk (Tue Feb 15 2005 - 09:29:39 PST)
- Julien Michel (Tue Feb 15 2005 - 08:10:34 PST)
- yipinl.umich.edu (Tue Feb 15 2005 - 07:31:56 PST)
- Thomas Steinbrecher (Tue Feb 15 2005 - 01:04:06 PST)
- Ilyas Yildirim (Mon Feb 14 2005 - 18:29:03 PST)
AMBER: Dynamics error
- S.Sundar Raman (Tue Feb 08 2005 - 06:09:04 PST)
- Carlos Simmerling (Tue Feb 08 2005 - 04:59:04 PST)
- S.Sundar Raman (Tue Feb 08 2005 - 03:25:07 PST)
- S.Sundar Raman (Tue Feb 08 2005 - 03:10:19 PST)
AMBER: energy plot in minimization
- Ross Walker (Wed Feb 09 2005 - 10:10:13 PST)
- Gustavo Pierdominici Sottile (Wed Feb 09 2005 - 09:36:25 PST)
AMBER: EWALD and belly not strictly correct
- David A. Case (Wed Feb 16 2005 - 08:52:20 PST)
- darden (Wed Feb 16 2005 - 09:08:31 PST)
- Stern, Julie (Tue Feb 15 2005 - 21:41:49 PST)
AMBER: External Electric Field
- David A. Case (Wed Feb 02 2005 - 10:08:59 PST)
- Brandon Tefft (Tue Feb 01 2005 - 13:30:22 PST)
AMBER: Formatting Questions
- Bill Ross (Tue Feb 22 2005 - 16:03:26 PST)
- Kara Di Giorgio (Tue Feb 22 2005 - 13:48:46 PST)
- Kara Di Giorgio (Mon Feb 21 2005 - 18:03:37 PST)
- David A. Case (Mon Feb 21 2005 - 17:33:34 PST)
- Kara Di Giorgio (Mon Feb 21 2005 - 11:09:44 PST)
AMBER: Free energy extimate for the same structure but different conformers
- David A. Case (Mon Feb 21 2005 - 16:00:39 PST)
- claudio (Mon Feb 21 2005 - 12:56:10 PST)
AMBER: gaff frcmod file for TI calculation
- Eric Hu (Wed Feb 02 2005 - 17:47:32 PST)
- David A. Case (Wed Feb 02 2005 - 16:44:13 PST)
- Eric Hu (Wed Feb 02 2005 - 15:50:00 PST)
AMBER: gaussian output file
- Junmei Wang (Tue Feb 01 2005 - 15:03:22 PST)
AMBER: GB solvation and "boxed" environment simulation
- Soo (Thu Feb 17 2005 - 21:32:38 PST)
AMBER: GBSA calculation
- David A. Case (Mon Feb 28 2005 - 09:48:24 PST)
- Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon Feb 28 2005 - 02:59:23 PST)
AMBER: generate charmm paramater file from amber parm file
- David E. Konerding DSD staff (Wed Feb 16 2005 - 10:13:23 PST)
- david.evans.ulsop.ac.uk (Wed Feb 16 2005 - 10:02:07 PST)
- HL Eastwood (Wed Feb 16 2005 - 09:19:56 PST)
AMBER: How to build dynamics input for guanine with tleap ?
- Vineet Pande (Thu Feb 24 2005 - 06:35:23 PST)
- Maciej (Thu Feb 24 2005 - 05:44:37 PST)
AMBER: How to calculate RESTRAINT value
- Carlos Simmerling (Tue Feb 08 2005 - 05:01:46 PST)
- Mayumi Haga (Mon Feb 07 2005 - 20:09:25 PST)
AMBER: How to converts a binary mdcrd file
- thanyarat Udom (Fri Feb 11 2005 - 00:00:10 PST)
- thanyarat Udom (Thu Feb 10 2005 - 23:02:21 PST)
AMBER: huge bond distances in new residue
- David A. Case (Sat Feb 05 2005 - 10:57:37 PST)
- Stern, Julie (Fri Feb 04 2005 - 15:48:14 PST)
AMBER: ico(i)=-1?
- Guanglei Cui (Sat Feb 26 2005 - 07:42:08 PST)
- Xiao He (Fri Feb 25 2005 - 19:49:46 PST)
AMBER: inconsistent ordering in an improper dihedral of TRP
- Bill Ross (Fri Feb 11 2005 - 17:56:10 PST)
- Carlos Simmerling (Fri Feb 11 2005 - 15:41:26 PST)
- David A. Case (Fri Feb 11 2005 - 14:19:03 PST)
- Sanghyun Park (Sun Feb 06 2005 - 20:38:03 PST)
AMBER: installation of amber 8 on windows
- David Mathews (Sat Feb 19 2005 - 08:01:54 PST)
- anshul.imtech.res.in (Fri Feb 18 2005 - 06:33:40 PST)
- David Mathews (Thu Feb 17 2005 - 08:42:05 PST)
- anshul.imtech.res.in (Thu Feb 17 2005 - 12:17:11 PST)
AMBER: Is droplet boundary condition option possible ?
- David A. Case (Sat Feb 05 2005 - 10:53:53 PST)
- Soo (Fri Feb 04 2005 - 22:18:36 PST)
AMBER: Joining residues/units
- FyD (Fri Feb 25 2005 - 09:13:29 PST)
- Bogos Agianian (Thu Feb 24 2005 - 13:22:07 PST)
- David A. Case (Thu Feb 24 2005 - 12:54:37 PST)
- Bogos Agianian (Thu Feb 24 2005 - 06:58:55 PST)
AMBER: lastrst
- Furse, Kristina Elisabet (Wed Feb 23 2005 - 13:36:08 PST)
- Stern, Julie (Wed Feb 23 2005 - 13:03:57 PST)
- David A. Case (Tue Feb 22 2005 - 21:53:28 PST)
- Ilyas Yildirim (Tue Feb 22 2005 - 18:36:00 PST)
- Carlos Simmerling (Tue Feb 22 2005 - 17:39:37 PST)
- Stern, Julie (Tue Feb 22 2005 - 17:21:00 PST)
- Stern, Julie (Tue Feb 22 2005 - 15:06:24 PST)
AMBER: leap bond angle building
- Bill Ross (Tue Feb 08 2005 - 16:00:12 PST)
- Stern, Julie (Tue Feb 08 2005 - 15:44:39 PST)
AMBER: leap saveamberparm chain types response
- Bill Ross (Thu Feb 17 2005 - 17:15:20 PST)
- Stern, Julie (Thu Feb 17 2005 - 15:16:50 PST)
AMBER: Linux Enterprise
- Ross Walker (Tue Feb 08 2005 - 11:59:43 PST)
- David A. Case (Tue Feb 08 2005 - 11:59:15 PST)
- S. Frank Yan (Tue Feb 08 2005 - 11:45:40 PST)
- Beale, John (Tue Feb 08 2005 - 11:39:54 PST)
AMBER: loading pdb in leap to create parmeter files
- David A. Case (Sat Feb 05 2005 - 14:29:13 PST)
- mrbroad.ilstu.edu (Sat Feb 05 2005 - 13:24:04 PST)
AMBER: Mainchain example needed
- Kara Wald (Mon Feb 14 2005 - 13:43:06 PST)
AMBER: make test.lmod error
- David A. Case (Fri Feb 25 2005 - 09:41:32 PST)
- yuann (Fri Feb 25 2005 - 08:45:11 PST)
AMBER: Minimization
- Beale, John (Tue Feb 08 2005 - 11:30:52 PST)
AMBER: minimization.out
- David A. Case (Wed Feb 09 2005 - 11:53:41 PST)
- Gustavo Pierdominici Sottile (Wed Feb 09 2005 - 11:32:01 PST)
AMBER: minimize a ptraj average pdb structure
- Bill Ross (Wed Feb 09 2005 - 11:39:27 PST)
- Vineet Pande (Wed Feb 09 2005 - 02:05:14 PST)
- Eric Hu (Tue Feb 08 2005 - 17:48:26 PST)
AMBER: minimizing structures before MM-PBSA?
- Carlos Simmerling (Tue Feb 22 2005 - 17:37:18 PST)
- scopio (Tue Feb 22 2005 - 17:23:37 PST)
AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel
- David A. Case (Tue Feb 08 2005 - 11:28:23 PST)
- Fabien Cailliez (Tue Feb 08 2005 - 09:16:51 PST)
AMBER: Moil view trajectory clusters
- Austin B. Yongye (Thu Feb 17 2005 - 13:31:37 PST)
- Carlos Simmerling (Thu Feb 17 2005 - 10:19:50 PST)
- Austin B. Yongye (Thu Feb 17 2005 - 09:36:15 PST)
AMBER: moil-view
- Carlos Simmerling (Thu Feb 17 2005 - 08:28:15 PST)
- Beale, John (Thu Feb 17 2005 - 07:56:30 PST)
AMBER: molecule blowing apart during equilibration
- Carlos Simmerling (Fri Feb 18 2005 - 12:11:49 PST)
- Ross Walker (Fri Feb 18 2005 - 08:56:30 PST)
- Stern, Julie (Thu Feb 17 2005 - 23:12:16 PST)
AMBER: MPI for sander8
- James W. Caldwell (Tue Feb 22 2005 - 11:52:56 PST)
- Ross Walker (Tue Feb 22 2005 - 09:54:37 PST)
- Thomas E. Cheatham, III (Tue Feb 22 2005 - 09:22:18 PST)
- Viktor Hornak (Tue Feb 22 2005 - 09:13:46 PST)
- S. Frank Yan (Tue Feb 22 2005 - 09:04:56 PST)
AMBER: mpirun sander8 problem
- S. Frank Yan (Thu Feb 24 2005 - 08:30:23 PST)
- Guanglei Cui (Thu Feb 24 2005 - 07:46:05 PST)
- S. Frank Yan (Thu Feb 24 2005 - 00:41:14 PST)
- S. Frank Yan (Wed Feb 23 2005 - 08:58:08 PST)
- Carlos Simmerling (Wed Feb 23 2005 - 05:05:01 PST)
- S. Frank Yan (Tue Feb 22 2005 - 23:13:34 PST)
AMBER: Multiple dihedral restraints
- David A. Case (Tue Feb 01 2005 - 14:54:49 PST)
- Joseph Fernandez (Tue Feb 01 2005 - 09:29:40 PST)
AMBER: Multiple dihedral restraints (follow up)
- M. L. Dodson (Thu Feb 03 2005 - 12:07:11 PST)
- David A. Case (Wed Feb 02 2005 - 11:04:47 PST)
- Joseph Fernandez (Wed Feb 02 2005 - 10:11:01 PST)
AMBER: My last posting
- Robert Duke (Thu Feb 24 2005 - 20:15:08 PST)
AMBER: N Metyl amino acids
- Carlos Simmerling (Tue Feb 01 2005 - 04:47:30 PST)
- Andrew Box (Mon Jan 31 2005 - 21:14:47 PST)
AMBER: nmode entropy calculations in MMPBSA
- david.evans.ulsop.ac.uk (Fri Feb 25 2005 - 06:14:55 PST)
- Fabien Cailliez (Fri Feb 25 2005 - 02:20:23 PST)
AMBER: non-periodic condition
- Germán Sciaini (Thu Feb 03 2005 - 12:42:34 PST)
- Ross Walker (Thu Feb 03 2005 - 10:27:30 PST)
- gsciaini (Thu Feb 03 2005 - 08:40:46 PST)
AMBER: nucgen problem
- David A. Case (Fri Feb 11 2005 - 17:37:32 PST)
- Ilyas Yildirim (Fri Feb 11 2005 - 16:56:41 PST)
AMBER: parallel AMBER/pmemd installation problem on Opteron
- Robert Duke (Thu Feb 24 2005 - 20:06:54 PST)
- Lars Packschies (Thu Feb 24 2005 - 15:58:25 PST)
- Robert Duke (Wed Feb 23 2005 - 09:27:13 PST)
- Lars Packschies (Wed Feb 23 2005 - 08:22:59 PST)
- Robert Duke (Wed Feb 23 2005 - 05:17:54 PST)
- Jyh-Shyong Ho (Tue Feb 22 2005 - 21:08:22 PST)
AMBER: PDB conversion to gzmat using antechamber
- David A. Case (Mon Feb 28 2005 - 10:02:58 PST)
- Scott Pendley (Tue Feb 15 2005 - 15:32:21 PST)
AMBER: Phi-Psi-Energy plot
- L Jin (Wed Feb 16 2005 - 07:45:18 PST)
AMBER: pmemd + pgi 5.1 + ntr = 1
- Robert Duke (Thu Feb 24 2005 - 15:22:37 PST)
- Peter Varnai (Thu Feb 24 2005 - 14:59:16 PST)
- Robert Duke (Thu Feb 24 2005 - 14:38:02 PST)
- Peter Varnai (Thu Feb 24 2005 - 14:25:04 PST)
AMBER: Poisson Boltzmann dynamics error
- Rachel Burdge (Thu Feb 10 2005 - 10:51:05 PST)
- Ray Luo (Tue Feb 08 2005 - 04:13:58 PST)
- Ross Walker (Thu Feb 10 2005 - 09:03:46 PST)
- David A. Case (Thu Feb 10 2005 - 08:57:51 PST)
- Rachel Burdge (Thu Feb 10 2005 - 08:04:55 PST)
AMBER: problem in minimization
- David A. Case (Tue Feb 08 2005 - 14:23:51 PST)
- Bill Ross (Tue Feb 08 2005 - 14:16:47 PST)
- Carlos Simmerling (Tue Feb 08 2005 - 13:47:30 PST)
- Bill Ross (Tue Feb 08 2005 - 12:16:18 PST)
- Natasja Brooijmans (Tue Feb 08 2005 - 11:56:22 PST)
- David A. Case (Tue Feb 08 2005 - 11:51:42 PST)
- Gustavo Pierdominici Sottile (Tue Feb 08 2005 - 10:31:17 PST)
AMBER: Problem in ptraj
- Thomas E. Cheatham, III (Wed Feb 02 2005 - 10:34:01 PST)
- Furse, Kristina Elisabet (Wed Feb 02 2005 - 10:16:03 PST)
- anshul.imtech.res.in (Wed Feb 02 2005 - 14:04:28 PST)
- Furse, Kristina Elisabet (Tue Feb 01 2005 - 11:30:53 PST)
- anshul.imtech.res.in (Tue Feb 01 2005 - 14:26:48 PST)
AMBER: problem in writing
- David A. Case (Mon Feb 07 2005 - 15:22:05 PST)
- Gustavo Pierdominici Sottile (Mon Feb 07 2005 - 11:59:49 PST)
AMBER: problem with protein minimization
- Robert Duke (Tue Feb 22 2005 - 09:10:51 PST)
- Ross Walker (Tue Feb 22 2005 - 08:47:56 PST)
- yen li (Tue Feb 22 2005 - 01:26:37 PST)
- David A. Case (Mon Feb 21 2005 - 16:11:37 PST)
- yen li (Mon Feb 21 2005 - 01:12:02 PST)
AMBER: problem with ptraj and randomizeions
- Filip Lankas (Fri Feb 18 2005 - 04:19:10 PST)
- Marie-Pierre Durrieu (Fri Feb 18 2005 - 02:19:06 PST)
- Marie-Pierre Durrieu (Fri Feb 18 2005 - 01:49:16 PST)
- Fabien Cailliez (Fri Feb 18 2005 - 00:50:00 PST)
- Thomas E. Cheatham, III (Thu Feb 17 2005 - 10:57:23 PST)
- Fabien Cailliez (Thu Feb 17 2005 - 09:56:24 PST)
AMBER: problem with solvateBox
- David A. Case (Fri Feb 25 2005 - 13:41:38 PST)
- ReichertD.mir.wustl.edu (Fri Feb 25 2005 - 12:38:51 PST)
AMBER: problems with running sander in parallel on linux
- Scott Brozell (Tue Feb 15 2005 - 14:02:56 PST)
- Piotr Cieplak (Tue Feb 15 2005 - 13:58:09 PST)
- Robert Duke (Tue Feb 15 2005 - 13:25:52 PST)
- Scott Brozell (Tue Feb 15 2005 - 13:01:21 PST)
- Piotr Cieplak (Tue Feb 15 2005 - 12:55:59 PST)
- David E. Konerding DSD staff (Tue Feb 15 2005 - 12:48:50 PST)
- Robert Duke (Tue Feb 15 2005 - 11:43:37 PST)
- Scott Brozell (Tue Feb 15 2005 - 11:42:45 PST)
- Piotr Cieplak (Tue Feb 15 2005 - 11:01:15 PST)
- Ross Walker (Tue Feb 15 2005 - 10:50:53 PST)
- Piotr Cieplak (Tue Feb 15 2005 - 10:28:02 PST)
AMBER: protonate and input conversion error
- David A. Case (Thu Feb 03 2005 - 10:09:31 PST)
- Stern, Julie (Thu Feb 03 2005 - 08:48:20 PST)
AMBER: Protonate state of ARG and LYS.
- Liu, Jingyuan (Thu Feb 10 2005 - 13:56:39 PST)
AMBER: PSC Summer Workshop: Modeling Proteins and Nucleic Acids with AMBER, VMD and the MMTSB Toolkit
- Troy Wymore (Thu Feb 17 2005 - 11:00:36 PST)
AMBER: ptraj
- Gustavo Pierdominici Sottile (Fri Feb 18 2005 - 06:58:37 PST)
AMBER: ptraj error and min problems
- David A. Case (Fri Feb 11 2005 - 08:29:42 PST)
- Gustavo Pierdominici Sottile (Fri Feb 11 2005 - 06:54:23 PST)
AMBER: ptraj for RDF calculations
- Carlos Jaime (Mon Feb 21 2005 - 01:11:22 PST)
- Javier Perez Miron (Mon Feb 21 2005 - 00:42:33 PST)
- Javier Perez Miron (Sat Feb 19 2005 - 08:47:02 PST)
AMBER: ptraj problem
- scopio (Tue Feb 22 2005 - 02:08:28 PST)
- Mayumi Haga (Tue Feb 22 2005 - 01:38:43 PST)
AMBER: ptraj8: trajectory windows
- Anselm Horn (Tue Feb 22 2005 - 09:16:13 PST)
AMBER: Pyranose pucker parameters
- Austin B. Yongye (Sun Feb 27 2005 - 19:08:52 PST)
- Ross Walker (Sun Feb 27 2005 - 11:58:30 PST)
- Austin B. Yongye (Fri Feb 25 2005 - 21:10:06 PST)
AMBER: question about mm_gbsa output file
- michael chen (Wed Feb 09 2005 - 10:10:06 PST)
AMBER: question about surface area to GBsurf calculation
- David A. Case (Thu Feb 10 2005 - 07:55:33 PST)
- michael chen (Wed Feb 09 2005 - 22:20:58 PST)
AMBER: question about tleap load pdb file
- xiaowen (Wed Feb 02 2005 - 19:19:19 PST)
AMBER: Redhat Enterprise Linux
- Beale, John (Wed Feb 02 2005 - 10:01:53 PST)
- Andrew Box (Tue Feb 01 2005 - 15:37:55 PST)
- S. Frank Yan (Tue Feb 01 2005 - 09:57:00 PST)
- Beale, John (Tue Feb 01 2005 - 09:49:20 PST)
AMBER: Restart Problem
- Ross Walker (Mon Feb 14 2005 - 12:01:16 PST)
- opitz.che.udel.edu (Mon Feb 14 2005 - 11:12:54 PST)
AMBER: Restraint of atoms during minimization
- Thomas E. Cheatham, III (Tue Feb 22 2005 - 09:36:42 PST)
- Carlos Simmerling (Tue Feb 22 2005 - 09:28:01 PST)
- David A. Case (Tue Feb 22 2005 - 09:19:17 PST)
- L Jin (Tue Feb 22 2005 - 09:12:13 PST)
- Carlos Simmerling (Tue Feb 22 2005 - 08:34:06 PST)
- L Jin (Tue Feb 22 2005 - 08:17:05 PST)
AMBER: restraint only for Z cartegian coordinate?
- Jaroslav Hanus (Fri Feb 25 2005 - 03:12:48 PST)
- Carlos Simmerling (Tue Feb 22 2005 - 08:02:31 PST)
- Jaroslav Hanus (Tue Feb 22 2005 - 07:40:58 PST)
AMBER: reverse TI charge perturbation
- Eric Hu (Mon Feb 14 2005 - 16:42:14 PST)
- David A. Case (Sat Feb 12 2005 - 16:14:58 PST)
- Eric Hu (Fri Feb 11 2005 - 17:59:10 PST)
AMBER: rms
- Carlos Simmerling (Wed Feb 16 2005 - 05:59:43 PST)
- Gustavo Pierdominici Sottile (Wed Feb 16 2005 - 05:14:50 PST)
AMBER: rotameric populations?
- Cenk Andac (Thu Feb 17 2005 - 07:15:05 PST)
AMBER: running shell scripts in tleap?
- Cenk Andac (Mon Feb 14 2005 - 21:24:44 PST)
- John Bushnell (Mon Feb 14 2005 - 15:32:32 PST)
- Ross Walker (Mon Feb 14 2005 - 15:31:03 PST)
- Lihua Wang (Mon Feb 14 2005 - 15:26:31 PST)
- Cenk Andac (Mon Feb 14 2005 - 14:23:44 PST)
AMBER: sander errors with atom restraints on ia64
- Rachel Burdge (Fri Feb 18 2005 - 08:04:17 PST)
- Viktor Hornak (Thu Feb 17 2005 - 14:46:26 PST)
- Rachel Burdge (Thu Feb 17 2005 - 13:46:04 PST)
AMBER: sander segmentation fault
- Ross Walker (Wed Feb 02 2005 - 18:05:41 PST)
- Thomas E. Cheatham, III (Wed Feb 02 2005 - 15:59:13 PST)
- Furse, Kristina Elisabet (Wed Feb 02 2005 - 15:32:25 PST)
- David A. Case (Wed Feb 02 2005 - 14:39:06 PST)
- Xin Wang (Wed Feb 02 2005 - 13:36:25 PST)
- David A. Case (Wed Feb 02 2005 - 11:28:37 PST)
- Xin Wang (Tue Feb 01 2005 - 14:15:12 PST)
AMBER: separate solvent-solvent and solvent-solute interaction
- Ye MEI (Mon Feb 21 2005 - 19:21:48 PST)
- David A. Case (Mon Feb 21 2005 - 09:07:24 PST)
- Ye MEI (Mon Feb 21 2005 - 04:44:22 PST)
AMBER: setBox buffer in leap
- Stern, Julie (Fri Feb 25 2005 - 10:43:19 PST)
AMBER: simulation with explicit water molecules
- Ye MEI (Sat Feb 19 2005 - 19:24:48 PST)
AMBER: size of solventbox
- Brent Krueger (Wed Feb 23 2005 - 12:54:35 PST)
- Fabien Cailliez (Wed Feb 23 2005 - 03:21:52 PST)
- Germán Sciaini (Wed Feb 23 2005 - 02:50:39 PST)
- Ross Walker (Tue Feb 22 2005 - 21:22:03 PST)
- mathew k varghese (Tue Feb 22 2005 - 20:07:00 PST)
AMBER: soft-cores and Amber
- Carlos Simmerling (Tue Feb 15 2005 - 15:11:14 PST)
- David A. Case (Tue Feb 15 2005 - 14:55:30 PST)
AMBER: solvateOct method
- David A. Case (Fri Feb 25 2005 - 08:53:19 PST)
- Cameron Mura (Wed Feb 23 2005 - 18:26:19 PST)
AMBER: stereo
- Chris Moth (Wed Feb 09 2005 - 12:02:13 PST)
- Vineet Pande (Wed Feb 09 2005 - 10:51:06 PST)
- Filip Lankas (Wed Feb 09 2005 - 09:53:45 PST)
AMBER: tleap load pdb file
- Ross Walker (Wed Feb 09 2005 - 11:18:31 PST)
- xiaowen (Wed Feb 09 2005 - 10:51:44 PST)
- David A. Case (Tue Feb 08 2005 - 11:50:08 PST)
- xiaowen (Mon Feb 07 2005 - 19:52:36 PST)
- xiaowen (Mon Feb 07 2005 - 12:58:39 PST)
- Ross Walker (Sun Feb 06 2005 - 10:50:29 PST)
- xiaowen (Sat Feb 05 2005 - 09:20:12 PST)
- David A. Case (Fri Feb 04 2005 - 14:45:50 PST)
- xiaowen (Fri Feb 04 2005 - 13:18:09 PST)
- David A. Case (Fri Feb 04 2005 - 08:35:49 PST)
- xiaowen (Fri Feb 04 2005 - 07:44:17 PST)
AMBER: too much vacuum in the box created by Leap
- David A. Case (Fri Feb 11 2005 - 08:21:29 PST)
- Carlos Simmerling (Fri Feb 11 2005 - 05:21:23 PST)
- Marie-Pierre Durrieu (Fri Feb 11 2005 - 04:53:35 PST)
AMBER: Topology Format Amber 8
- Ian Withers (Tue Feb 15 2005 - 05:33:15 PST)
- Carlos Simmerling (Tue Feb 15 2005 - 04:42:29 PST)
- Stuart Murdock (Tue Feb 15 2005 - 04:00:56 PST)
AMBER: total energy of solvation
- David A. Case (Tue Feb 22 2005 - 21:40:47 PST)
- Holly Freedman (Tue Feb 22 2005 - 20:05:36 PST)
AMBER: trajectory of minimization
- Ross Walker (Sun Feb 06 2005 - 10:36:29 PST)
- David A. Case (Sat Feb 05 2005 - 10:54:39 PST)
- Stern, Julie (Fri Feb 04 2005 - 15:49:17 PST)
AMBER: Tutorial Request
- David A. Case (Sun Feb 06 2005 - 09:40:28 PST)
- Kara Di Giorgio (Sun Feb 06 2005 - 09:01:15 PST)
AMBER: units describing projection onto modes
- Vlad Cojocaru (Thu Feb 24 2005 - 10:40:18 PST)
AMBER: unnatural ligand
- Eric Hu (Mon Feb 07 2005 - 10:28:14 PST)
- David A. Case (Fri Feb 04 2005 - 14:54:06 PST)
- Eric Hu (Thu Feb 03 2005 - 19:37:41 PST)
AMBER: Use of ibelly with nmode analysis
- David A. Case (Thu Feb 24 2005 - 08:30:31 PST)
- marti (Thu Feb 24 2005 - 03:47:28 PST)
AMBER: vacuum bubbles in system equilibration
- Marie-Pierre Durrieu (Tue Feb 01 2005 - 02:56:21 PST)
AMBER: vlimit
- Gustavo Pierdominici Sottile (Fri Feb 25 2005 - 04:45:35 PST)
- Ross Walker (Mon Feb 14 2005 - 09:14:56 PST)
- Gustavo Pierdominici Sottile (Mon Feb 14 2005 - 04:23:31 PST)
AMBER: vlimit exceeded and temperature blow up
- Carlos Simmerling (Tue Feb 22 2005 - 08:46:21 PST)
- Stern, Julie (Tue Feb 22 2005 - 08:36:05 PST)
AMBER: vlimit problem
- David A. Case (Mon Feb 28 2005 - 09:40:26 PST)
- Ilyas Yildirim (Fri Feb 25 2005 - 17:45:03 PST)
AMBER: Why I couldnt used carnal for analyzed RMSD ?
- Bill Ross (Wed Feb 16 2005 - 10:19:30 PST)
- thanyarat Udom (Wed Feb 16 2005 - 01:28:17 PST)
AMBER: xleap MOVE and .lib file
- Stern, Julie (Wed Feb 02 2005 - 09:01:55 PST)
AMBER: xleap: different distance results from "check" command in xleap
- Woojin Lee (Tue Feb 01 2005 - 21:54:14 PST)
AMBER: XMGR
- Andreas Svrcek-Seiler (Fri Feb 18 2005 - 12:31:15 PST)
- Beale, John (Fri Feb 18 2005 - 10:20:44 PST)
AMBER:how to analyse trajectory files
- S.Sundar Raman (Mon Feb 14 2005 - 20:58:19 PST)
- Vineet Pande (Mon Feb 14 2005 - 03:07:21 PST)
- S.Sundar Raman (Mon Feb 14 2005 - 01:17:39 PST)
pmemd problems
- Robert Duke (Thu Feb 17 2005 - 07:15:33 PST)

Amber Archive Feb 2005 by subject