Amber Archive Dec 2002: by subject

(no subject)
- Jennifer Hawkings (Sat Dec 07 2002 - 14:48:46 PST)
a question about force field in AMBER
- David A. Case (Mon Dec 16 2002 - 17:56:29 PST)
- sychen (Sat Dec 14 2002 - 21:17:59 PST)
- jzhou (Sat Dec 14 2002 - 17:55:15 PST)
About counterions
- David A. Case (Thu Dec 05 2002 - 11:47:04 PST)
- Andrei Leit�o (Thu Dec 05 2002 - 11:10:30 PST)
About heating...
- David A. Case (Wed Dec 18 2002 - 11:42:51 PST)
- Andrei Leit�o (Wed Dec 18 2002 - 10:23:43 PST)
Amber 7 bugfix 27 !! urgent
- Holger Gohlke (Wed Dec 04 2002 - 13:18:48 PST)
- William Wei (Wed Dec 04 2002 - 12:45:13 PST)
Amber 7 MM-PBSA for Amber 6 trajectories
- David A. Case (Sat Dec 14 2002 - 11:26:01 PST)
- Qing Zhang (Thu Dec 12 2002 - 11:52:23 PST)
Amber Trajectories + VMD (fwd)
- Nicholson, James D Mr ARO (Tue Dec 03 2002 - 15:35:09 PST)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:58:00 PST)
amber trajectory
- Ioana Cozmuta (Tue Dec 17 2002 - 21:16:14 PST)
ambpdb
- David A. Case (Fri Dec 13 2002 - 20:46:12 PST)
- Holger Gohlke (Thu Dec 12 2002 - 16:44:44 PST)
- Vlad Cojocaru (Thu Dec 12 2002 - 14:01:23 PST)
antechamber
- Carsten Detering (Wed Dec 18 2002 - 14:32:44 PST)
- Carsten Detering (Wed Dec 18 2002 - 11:38:16 PST)
atomicfluct in ptraj
- Kristina Furse (Thu Dec 19 2002 - 11:28:16 PST)
- David A. Case (Thu Dec 19 2002 - 09:28:43 PST)
- Kristina Furse (Wed Dec 18 2002 - 15:16:29 PST)
bad protein structure
- eric hu (Tue Dec 10 2002 - 17:30:52 PST)
beginners question
- dynamic group (Sun Dec 22 2002 - 21:17:52 PST)
Biphasic box
- Gemma Kinsella (Wed Dec 04 2002 - 00:15:53 PST)
- David A. Case (Tue Dec 03 2002 - 15:09:50 PST)
Biphasic box (fwd)
- James W. Caldwell (Tue Dec 03 2002 - 15:15:50 PST)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:13:10 PST)
bug fixes
- David A. Case (Thu Dec 05 2002 - 08:41:02 PST)
- Filip Lankas (Thu Dec 05 2002 - 06:48:00 PST)
Business Cooperation (Inheritance Claim)
- Mr. Daniel Osondu (Fri Dec 13 2002 - 01:50:38 PST)
- Mr. Daniel Osondu (Thu Dec 12 2002 - 10:10:29 PST)
cannot deal with large trajectory?
- yuann (Mon Dec 30 2002 - 18:55:41 PST)
- yuann (Sat Dec 28 2002 - 19:17:23 PST)
cap option
- Ioana Cozmuta (Sun Dec 22 2002 - 17:21:01 PST)
Cap-atom-pointer in GIBBS
- Jose Ramon Blas (Thu Dec 05 2002 - 11:50:45 PST)
- James W. Caldwell (Thu Dec 05 2002 - 11:23:45 PST)
carnal
- Bill Ross (Fri Dec 06 2002 - 17:16:59 PST)
- Ioana Cozmuta (Fri Dec 06 2002 - 15:47:56 PST)
carnal amber 7.0
- Vlad Cojocaru (Mon Dec 02 2002 - 00:35:34 PST)
CCL:Amber7 and partial charges
- David Case (Wed Dec 11 2002 - 10:07:10 PST)
CCL:freeware for RNA modeling on Linux (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:57:21 PST)
Chains, LEaP and ambpdb
- David A. Case (Tue Dec 17 2002 - 19:28:21 PST)
- Luis Gracia (Tue Dec 17 2002 - 13:23:55 PST)
- David A. Case (Tue Dec 17 2002 - 13:09:48 PST)
- Ioana Cozmuta (Tue Dec 17 2002 - 13:07:24 PST)
- Luis Gracia (Tue Dec 17 2002 - 11:47:59 PST)
Charges derivation question!
- Lepsa (Thu Dec 12 2002 - 01:55:17 PST)
- Lepsa (Wed Dec 11 2002 - 08:21:23 PST)
CHARMm NPT input files
- Mahadevan Seetharaman (Sat Dec 07 2002 - 15:39:07 PST)
chirality.c failure - diagnosis, but no cure...
- Michael Ford (Thu Dec 19 2002 - 15:25:21 PST)
- Michael Ford (Thu Dec 19 2002 - 10:07:07 PST)
combinig two trajectory files.
- Pascal Bonnet (Mon Dec 02 2002 - 04:50:26 PST)
- Carlos Simmerling (Mon Dec 02 2002 - 04:49:21 PST)
- Yongjun Jiang (Mon Dec 02 2002 - 04:18:29 PST)
Constraints in Amber
- David A. Case (Tue Dec 03 2002 - 15:16:02 PST)
Constraints in Amber (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:57:30 PST)
corrupted trajectory
- CUI, Guanglei (Tue Dec 03 2002 - 18:04:13 PST)
- Shixiang Yan (Tue Dec 03 2002 - 15:36:37 PST)
deep energetics problem
- David A. Case (Thu Dec 05 2002 - 11:55:40 PST)
- eric hu (Thu Dec 05 2002 - 10:42:42 PST)
default GB radii
- Andreas Svrcek-Seiler (Sat Dec 07 2002 - 04:02:09 PST)
- David A. Case (Fri Dec 06 2002 - 13:11:13 PST)
- Robert G. Endres (Fri Dec 06 2002 - 13:00:31 PST)
DIANA like files
- Vlad Cojocaru (Wed Dec 04 2002 - 12:24:12 PST)
difference in energy in amber6 and amber7
- David A. Case (Wed Dec 11 2002 - 07:40:48 PST)
- Prabal Maiti (Mon Dec 09 2002 - 18:07:15 PST)
disulfide bond link between two chains
- Natasja Brooijmans (Mon Dec 16 2002 - 05:49:46 PST)
- pu xuemei (Mon Dec 16 2002 - 04:50:35 PST)
dual H-bonding of bridging waters - CARNAL
- Michael Ford (Tue Dec 10 2002 - 16:16:24 PST)
Energy decomposition with ANAL
- Numan Oezguen (Mon Dec 16 2002 - 07:49:08 PST)
- Natasja Brooijmans (Fri Dec 06 2002 - 09:24:21 PST)
- Numan Oezguen (Fri Dec 06 2002 - 09:08:20 PST)
Energy decomposition with ANAL (fwd)
- David A. Case (Wed Dec 04 2002 - 08:31:52 PST)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:58:05 PST)
err in specifying disulphide bridge using xleap!
- James W. Caldwell (Mon Dec 02 2002 - 11:07:07 PST)
- David A. Case (Mon Dec 02 2002 - 09:05:01 PST)
- A.Madhumalar (Mon Dec 02 2002 - 08:25:30 PST)
FEP/Gibbs question
- Lepsa (Tue Dec 10 2002 - 07:59:39 PST)
FEP/Gibbs question to valine alanine tutorial
- meiselba (Sat Dec 14 2002 - 08:58:12 PST)
freeware for RNA modeling on Linux (fwd)
- James W. Caldwell (Tue Dec 17 2002 - 11:09:37 PST)
- Joerg-Gerald Siebers (Mon Dec 16 2002 - 18:43:05 PST)
- David A. Case (Tue Dec 03 2002 - 15:11:48 PST)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:57:10 PST)
gB vs. explicit
- David A. Case (Wed Dec 04 2002 - 08:28:43 PST)
gB vs. explicit (fwd)
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:57:53 PST)
GIBBS - end-of-file during read
- Miguel de Federico (Fri Dec 13 2002 - 02:12:48 PST)
GIBBS - Routine TORCON (internal constraints) failed
- Miguel de Federico (Tue Dec 17 2002 - 07:29:04 PST)
increasing the number of processors
- Ioana Cozmuta (Tue Dec 03 2002 - 16:17:58 PST)
increasing the number of processors (fwd)
- Ioana Cozmuta (Tue Dec 03 2002 - 16:19:24 PST)
LEAP - Introducing dummy atoms
- James W. Caldwell (Mon Dec 02 2002 - 11:11:27 PST)
- Miguel de Federico (Mon Dec 02 2002 - 08:42:49 PST)
MDaemon Warning - Virus Found
- postmaster_at_bydnet.com.pl (Wed Dec 04 2002 - 19:49:28 PST)
message during minimization
- David A. Case (Thu Dec 19 2002 - 08:05:00 PST)
- Ioana Cozmuta (Wed Dec 18 2002 - 18:02:26 PST)
- darden (Wed Dec 18 2002 - 16:32:21 PST)
- Ioana Cozmuta (Wed Dec 18 2002 - 15:09:05 PST)
- darden (Wed Dec 18 2002 - 08:24:48 PST)
- Ioana Cozmuta (Tue Dec 17 2002 - 21:31:52 PST)
MM-PBSA: .crg file for Delphi
- Holger Gohlke (Wed Dec 11 2002 - 10:31:07 PST)
- Thomas Steinbrecher (Wed Dec 11 2002 - 10:08:40 PST)
mm_pbsa error message!
- Michael Ford (Wed Dec 18 2002 - 09:37:57 PST)
- William Wei (Wed Dec 18 2002 - 09:17:16 PST)
Molecular dynamic protocol...
- David A. Case (Fri Dec 27 2002 - 11:25:51 PST)
- Andrei Leit�o (Fri Dec 27 2002 - 10:40:26 PST)
MPI_BCAST error
- Nathan A. Baker (Wed Dec 18 2002 - 17:31:47 PST)
- Scott Brozell (Wed Dec 18 2002 - 13:24:55 PST)
- Nathan A. Baker (Wed Dec 18 2002 - 07:51:02 PST)
new on the Amber web pages...
- David A. Case (Tue Dec 31 2002 - 13:51:31 PST)
Nmode
- James Caldwell (Thu Dec 19 2002 - 13:17:31 PST)
- Pratul Agarwal (Thu Dec 19 2002 - 13:07:47 PST)
NMR restrains
- Marcela Madrid (Mon Dec 09 2002 - 12:33:31 PST)
not compiled with -DHAS_10_12!!
- Carlos Simmerling (Thu Dec 05 2002 - 09:03:08 PST)
- Sarah Tschampel (Thu Dec 05 2002 - 08:43:40 PST)
- William Wei (Thu Dec 05 2002 - 08:29:22 PST)
ntwv saves v(t) or v(t+dt/2) ?
- David A. Case (Thu Dec 19 2002 - 09:24:33 PST)
- hagop demirdjian (Thu Dec 19 2002 - 08:04:55 PST)
off-to-mol2
- David A. Case (Wed Dec 18 2002 - 10:03:48 PST)
- Anke Eisenmann (Wed Dec 18 2002 - 08:49:22 PST)
Overwrite files
- Yong Duan (Thu Dec 05 2002 - 18:41:37 PST)
- Scott Brozell (Thu Dec 05 2002 - 13:39:23 PST)
- Long Hai (Thu Dec 05 2002 - 13:33:53 PST)
- Joffre Heredia (Thu Dec 05 2002 - 12:25:33 PST)
penalty function in NMR refinement
- Mahadevan Seetharaman (Mon Dec 02 2002 - 09:09:05 PST)
plotting electrostatic potential surface
- Ioana Cozmuta (Fri Dec 13 2002 - 15:18:17 PST)
positional restraints
- David A. Case (Fri Dec 06 2002 - 08:05:02 PST)
- Vlad Cojocaru (Fri Dec 06 2002 - 04:55:05 PST)
ptraj rmsd calculation
- Thomas Steinbrecher (Thu Dec 05 2002 - 12:15:40 PST)
Question on 2 stage RESP fit
- M. L. Dodson (Thu Dec 12 2002 - 05:05:15 PST)
- Ambarish Nag (Wed Dec 11 2002 - 22:39:08 PST)
Question to perturbation charge
- meiselba (Tue Dec 10 2002 - 05:35:38 PST)
Reflector problems
- amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 15:05:02 PST)
Resp Multiconformational charge fitting!
- Pascal Bonnet (Wed Dec 18 2002 - 02:21:46 PST)
RESTARTED DUE TO LINMIN FAILURE
- Natasja Brooijmans (Thu Dec 19 2002 - 13:16:44 PST)
- William Wei (Thu Dec 19 2002 - 11:33:07 PST)
restrained MD
- Vlad Cojocaru (Wed Dec 04 2002 - 10:18:54 PST)
roar-cp problems
- M. L. Dodson (Wed Dec 18 2002 - 13:00:37 PST)
RST file for nonstandard residue
- vannajan_at_chiangmai.ac.th (Tue Dec 17 2002 - 01:07:04 PST)
running sander_classic for amber6 using different version of mpi
- Asif Rahaman (Mon Dec 09 2002 - 15:01:35 PST)
sander (CAP) chokes on efc (Itanium2/Linux)
- Tadashi Takemori (Wed Dec 18 2002 - 01:38:25 PST)
- Karen Haskell (Tue Dec 17 2002 - 14:05:31 PST)
- Tadashi Takemori (Mon Dec 16 2002 - 23:11:14 PST)
Sander rfree error
- James Caldwell (Mon Dec 30 2002 - 16:36:45 PST)
- kxg2248_at_njit.edu (Mon Dec 30 2002 - 14:58:19 PST)
selection of residues
- Ioana Cozmuta (Fri Dec 20 2002 - 16:51:52 PST)
solvatebox
- Luis Gracia (Wed Dec 18 2002 - 07:58:47 PST)
- Luis Gracia (Tue Dec 17 2002 - 16:52:07 PST)
solvateOct
- David A. Case (Mon Dec 02 2002 - 07:40:02 PST)
- Kristina Furse (Sun Dec 01 2002 - 13:57:13 PST)
solvating a protein with large cavity
- M. L. Dodson (Sat Dec 14 2002 - 08:23:15 PST)
- Tom Bishop (Sat Dec 14 2002 - 07:42:38 PST)
Studying in Australia
- John Pritchard (Tue Dec 17 2002 - 22:36:07 PST)
SUMMARY: solvating a protein with large cavity
- Ioana Cozmuta (Wed Dec 18 2002 - 17:21:23 PST)
- Richard Henchman (Wed Dec 18 2002 - 11:56:20 PST)
- Tom Bishop (Wed Dec 18 2002 - 07:03:27 PST)
targeted MD sample
- eric hu (Thu Dec 26 2002 - 12:25:36 PST)
test mail
- Jim Caldwell (Tue Dec 03 2002 - 14:48:07 PST)
timings?
- David A. Case (Fri Dec 06 2002 - 07:46:27 PST)
- Arvid Soederhaell (Fri Dec 06 2002 - 00:51:10 PST)
Trajectory file converted in pdb file
- Yongjun Jiang (Sun Dec 29 2002 - 17:13:38 PST)
Valine to alanine Gibbs tutorial
- Lepsa (Mon Dec 16 2002 - 05:20:26 PST)
water box,
- darden (Wed Dec 18 2002 - 16:45:55 PST)
- David A. Case (Wed Dec 18 2002 - 16:17:31 PST)
- Ioana Cozmuta (Wed Dec 18 2002 - 15:37:41 PST)
- darden (Wed Dec 18 2002 - 08:33:07 PST)
- Carlos Simmerling (Wed Dec 18 2002 - 05:18:18 PST)
- Ioana Cozmuta (Tue Dec 17 2002 - 15:18:31 PST)
water/nonTIP3P
- Ioana Cozmuta (Wed Dec 18 2002 - 18:17:24 PST)
- Ioana Cozmuta (Wed Dec 18 2002 - 17:33:23 PST)

Amber Archive Dec 2002 by subject