AMBER Archive (2002) - Dec 2002 By Author

174 messages sorted by: [ date ] [ thread ] [ subject ]
About this archive

Starting: Sun Dec 01 2002 - 15:57:13 CST
Ending: Tue Dec 31 2002 - 15:51:31 CST

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

Last message date: Tue Dec 31 2002 - 15:51:31 CST
Archived on: Thu May 05 2005 - 14:17:27 CDT

174 messages sorted by: [ date ] [ thread ] [ subject ]
About this archive