AMBER Archive (2002) - Dec 2002 By DateMost recent messages
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Starting: Sun Dec 01 2002 - 15:57:13 CST
Ending: Tue Dec 31 2002 - 15:51:31 CST
- RE: solvateOct Kristina Furse (Sun Dec 01 2002 - 15:57:13 CST)
- carnal amber 7.0 Vlad Cojocaru (Mon Dec 02 2002 - 02:35:34 CST)
- combinig two trajectory files. Yongjun Jiang (Mon Dec 02 2002 - 06:18:29 CST)
- Re: combinig two trajectory files. Carlos Simmerling (Mon Dec 02 2002 - 06:49:21 CST)
- Re: combinig two trajectory files. Pascal Bonnet (Mon Dec 02 2002 - 06:50:26 CST)
- Re: solvateOct David A. Case (Mon Dec 02 2002 - 09:40:02 CST)
- err in specifying disulphide bridge using xleap! A.Madhumalar (Mon Dec 02 2002 - 10:25:30 CST)
- LEAP - Introducing dummy atoms Miguel de Federico (Mon Dec 02 2002 - 10:42:49 CST)
- Re: err in specifying disulphide bridge using xleap! David A. Case (Mon Dec 02 2002 - 11:05:01 CST)
- penalty function in NMR refinement Mahadevan Seetharaman (Mon Dec 02 2002 - 11:09:05 CST)
- Re: err in specifying disulphide bridge using xleap! James W. Caldwell (Mon Dec 02 2002 - 13:07:07 CST)
- Re: LEAP - Introducing dummy atoms James W. Caldwell (Mon Dec 02 2002 - 13:11:27 CST)
- Biphasic box (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:13:10 CST)
- test mail Jim Caldwell (Tue Dec 03 2002 - 16:48:07 CST)
- freeware for RNA modeling on Linux (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:10 CST)
- Re: CCL:freeware for RNA modeling on Linux (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:21 CST)
- Constraints in Amber (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:30 CST)
- gB vs. explicit (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:53 CST)
- Amber Trajectories + VMD (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:58:00 CST)
- Energy decomposition with ANAL (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:58:05 CST)
- Reflector problems amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 17:05:02 CST)
- corrupted trajectory Guanglei Cui (Tue Dec 03 2002 - 17:07:46 CST)
- Re: Biphasic box David A. Case (Tue Dec 03 2002 - 17:09:50 CST)
- Re: freeware for RNA modeling on Linux (fwd) David A. Case (Tue Dec 03 2002 - 17:11:48 CST)
- Re: Biphasic box (fwd) James W. Caldwell (Tue Dec 03 2002 - 17:15:50 CST)
- Re: Constraints in Amber David A. Case (Tue Dec 03 2002 - 17:16:02 CST)
- RE: Amber Trajectories + VMD (fwd) Nicholson, James D Mr ARO (Tue Dec 03 2002 - 17:35:09 CST)
- Re: corrupted trajectory Shixiang Yan (Tue Dec 03 2002 - 17:36:37 CST)
- 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)
- Re: corrupted trajectory CUI, Guanglei (Tue Dec 03 2002 - 20:04:13 CST)
- Re: Biphasic box Gemma Kinsella (Wed Dec 04 2002 - 02:15:53 CST)
- Re: gB vs. explicit David A. Case (Wed Dec 04 2002 - 10:28:43 CST)
- Re: Energy decomposition with ANAL (fwd) David A. Case (Wed Dec 04 2002 - 10:31:52 CST)
- restrained MD Vlad Cojocaru (Wed Dec 04 2002 - 12:18:54 CST)
- DIANA like files Vlad Cojocaru (Wed Dec 04 2002 - 14:24:12 CST)
- Amber 7 bugfix 27 !! urgent William Wei (Wed Dec 04 2002 - 14:45:13 CST)
- Re: Amber 7 bugfix 27 !! urgent Holger Gohlke (Wed Dec 04 2002 - 15:18:48 CST)
- MDaemon Warning - Virus Found postmaster_at_bydnet.com.pl (Wed Dec 04 2002 - 21:49:28 CST)
- bug fixes Filip Lankas (Thu Dec 05 2002 - 08:48:00 CST)
- not compiled with -DHAS_10_12!! William Wei (Thu Dec 05 2002 - 10:29:22 CST)
- Re: bug fixes David A. Case (Thu Dec 05 2002 - 10:41:02 CST)
- Re: not compiled with -DHAS_10_12!! Sarah Tschampel (Thu Dec 05 2002 - 10:43:40 CST)
- Re: not compiled with -DHAS_10_12!! Carlos Simmerling (Thu Dec 05 2002 - 11:03:08 CST)
- md failure: deep energetics problem eric hu (Thu Dec 05 2002 - 12:42:42 CST)
- About counterions Andrei Leitão (Thu Dec 05 2002 - 13:10:30 CST)
- Re: Cap-atom-pointer in GIBBS James W. Caldwell (Thu Dec 05 2002 - 13:23:45 CST)
- Re: About counterions David A. Case (Thu Dec 05 2002 - 13:47:04 CST)
- Cap-atom-pointer in GIBBS Jose Ramon Blas (Thu Dec 05 2002 - 13:50:45 CST)
- Re: md failure: deep energetics problem David A. Case (Thu Dec 05 2002 - 13:55:40 CST)
- ptraj rmsd calculation Thomas Steinbrecher (Thu Dec 05 2002 - 14:15:40 CST)
- Overwrite files Joffre Heredia (Thu Dec 05 2002 - 14:25:33 CST)
- Re: Overwrite files Long Hai (Thu Dec 05 2002 - 15:33:53 CST)
- Re: Overwrite files Scott Brozell (Thu Dec 05 2002 - 15:39:23 CST)
- RE: Overwrite files Yong Duan (Thu Dec 05 2002 - 20:41:37 CST)
- timings? Arvid Soederhaell (Fri Dec 06 2002 - 02:51:10 CST)
- positional restraints Vlad Cojocaru (Fri Dec 06 2002 - 06:55:05 CST)
- Re: timings? David A. Case (Fri Dec 06 2002 - 09:46:27 CST)
- Re: positional restraints David A. Case (Fri Dec 06 2002 - 10:05:02 CST)
- Re: Energy decomposition with ANAL Numan Oezguen (Fri Dec 06 2002 - 11:08:20 CST)
- Re: Energy decomposition with ANAL Natasja Brooijmans (Fri Dec 06 2002 - 11:24:21 CST)
- default GB radii Robert G. Endres (Fri Dec 06 2002 - 15:00:31 CST)
- Re: default GB radii David A. Case (Fri Dec 06 2002 - 15:11:13 CST)
- carnal Ioana Cozmuta (Fri Dec 06 2002 - 17:47:56 CST)
- Re: carnal Bill Ross (Fri Dec 06 2002 - 19:16:59 CST)
- Re: default GB radii Andreas Svrcek-Seiler (Sat Dec 07 2002 - 06:02:09 CST)
- (no subject) Jennifer Hawkings (Sat Dec 07 2002 - 16:48:46 CST)
- CHARMm NPT input files Mahadevan Seetharaman (Sat Dec 07 2002 - 17:39:07 CST)
- NMR restrains Marcela Madrid (Mon Dec 09 2002 - 14:33:31 CST)
- running sander_classic for amber6 using different version of mpi Asif Rahaman (Mon Dec 09 2002 - 17:01:35 CST)
- difference in energy in amber6 and amber7 Prabal Maiti (Mon Dec 09 2002 - 20:07:15 CST)
- Question to perturbation charge meiselba (Tue Dec 10 2002 - 07:35:38 CST)
- Re: FEP/Gibbs question Lepsa (Tue Dec 10 2002 - 09:59:39 CST)
- dual H-bonding of bridging waters - CARNAL Michael Ford (Tue Dec 10 2002 - 18:16:24 CST)
- bad protein structure eric hu (Tue Dec 10 2002 - 19:30:52 CST)
- Re: bad protein structure Guanglei Cui (Tue Dec 10 2002 - 23:07:20 CST)
- Re: difference in energy in amber6 and amber7 David A. Case (Wed Dec 11 2002 - 09:40:48 CST)
- Fw: Charges derivation question! Lepsa (Wed Dec 11 2002 - 10:21:23 CST)
- Re: CCL:Amber7 and partial charges David Case (Wed Dec 11 2002 - 12:07:10 CST)
- MM-PBSA: .crg file for Delphi Thomas Steinbrecher (Wed Dec 11 2002 - 12:08:40 CST)
- Re: MM-PBSA: .crg file for Delphi Holger Gohlke (Wed Dec 11 2002 - 12:31:07 CST)
- Question on 2 stage RESP fit Ambarish Nag (Thu Dec 12 2002 - 00:39:08 CST)
- Fw: Fw: Charges derivation question! Lepsa (Thu Dec 12 2002 - 03:55:17 CST)
- Re: Question on 2 stage RESP fit M. L. Dodson (Thu Dec 12 2002 - 07:05:15 CST)
- Business Cooperation (Inheritance Claim) Mr. Daniel Osondu (Thu Dec 12 2002 - 10:10:29 CST)
- MXVAR Guanglei Cui (Thu Dec 12 2002 - 10:34:17 CST)
- Amber 7 MM-PBSA for Amber 6 trajectories Qing Zhang (Thu Dec 12 2002 - 13:52:23 CST)
- ambpdb Vlad Cojocaru (Thu Dec 12 2002 - 16:01:23 CST)
- Re: ambpdb Holger Gohlke (Thu Dec 12 2002 - 18:44:44 CST)
- Business Cooperation (Inheritance Claim) Mr. Daniel Osondu (Fri Dec 13 2002 - 01:50:38 CST)
- GIBBS - end-of-file during read Miguel de Federico (Fri Dec 13 2002 - 04:12:48 CST)
- plotting electrostatic potential surface Ioana Cozmuta (Fri Dec 13 2002 - 17:18:17 CST)
- Re: ambpdb David A. Case (Fri Dec 13 2002 - 22:46:12 CST)
- solvating a protein with large cavity Tom Bishop (Sat Dec 14 2002 - 09:42:38 CST)
- Re: solvating a protein with large cavity M. L. Dodson (Sat Dec 14 2002 - 10:23:15 CST)
- FEP/Gibbs question to valine alanine tutorial meiselba (Sat Dec 14 2002 - 10:58:12 CST)
- Re: Amber 7 MM-PBSA for Amber 6 trajectories David A. Case (Sat Dec 14 2002 - 13:26:01 CST)
- a question about force field in AMBER jzhou (Sat Dec 14 2002 - 19:55:15 CST)
- Re: a question about force field in AMBER sychen (Sat Dec 14 2002 - 23:17:59 CST)
- disulfide bond link between two chains pu xuemei (Mon Dec 16 2002 - 06:50:35 CST)
- Fw: Valine to alanine Gibbs tutorial Lepsa (Mon Dec 16 2002 - 07:20:26 CST)
- Re: disulfide bond link between two chains Natasja Brooijmans (Mon Dec 16 2002 - 07:49:46 CST)
- Re: Energy decomposition with ANAL Numan Oezguen (Mon Dec 16 2002 - 09:49:08 CST)
- Re: a question about force field in AMBER David A. Case (Mon Dec 16 2002 - 19:56:29 CST)
- Re: freeware for RNA modeling on Linux (fwd) Joerg-Gerald Siebers (Mon Dec 16 2002 - 20:43:05 CST)
- sander (CAP) chokes on efc (Itanium2/Linux) Tadashi Takemori (Tue Dec 17 2002 - 01:11:14 CST)
- RST file for nonstandard residue vannajan_at_chiangmai.ac.th (Tue Dec 17 2002 - 03:07:04 CST)
- GIBBS - Routine TORCON (internal constraints) failed Miguel de Federico (Tue Dec 17 2002 - 09:29:04 CST)
- Re: freeware for RNA modeling on Linux (fwd) James W. Caldwell (Tue Dec 17 2002 - 13:09:37 CST)
- Chains, LEaP and ambpdb Luis Gracia (Tue Dec 17 2002 - 13:47:59 CST)
- Re: Chains, LEaP and ambpdb Ioana Cozmuta (Tue Dec 17 2002 - 15:07:24 CST)
- Re: Chains, LEaP and ambpdb David A. Case (Tue Dec 17 2002 - 15:09:48 CST)
- Re: Chains, LEaP and ambpdb Luis Gracia (Tue Dec 17 2002 - 15:23:55 CST)
- RE: sander (CAP) chokes on efc (Itanium2/Linux) Karen Haskell (Tue Dec 17 2002 - 16:05:31 CST)
- water box, Ioana Cozmuta (Tue Dec 17 2002 - 17:18:31 CST)
- solvatebox Luis Gracia (Tue Dec 17 2002 - 18:52:07 CST)
- Re: Chains, LEaP and ambpdb David A. Case (Tue Dec 17 2002 - 21:28:21 CST)
- Studying in Australia John Pritchard (Tue Dec 17 2002 - 22:36:07 CST)
- amber trajectory Ioana Cozmuta (Tue Dec 17 2002 - 23:16:14 CST)
- message during minimization Ioana Cozmuta (Tue Dec 17 2002 - 23:31:52 CST)
- Re: sander (CAP) chokes on efc (Itanium2/Linux) Tadashi Takemori (Wed Dec 18 2002 - 03:38:25 CST)
- Re: Resp Multiconformational charge fitting! Pascal Bonnet (Wed Dec 18 2002 - 04:21:46 CST)
- Re: water box, Carlos Simmerling (Wed Dec 18 2002 - 07:18:18 CST)
- Re: amber trajectory Guanglei Cui (Wed Dec 18 2002 - 09:02:05 CST)
- SUMMARY: solvating a protein with large cavity Tom Bishop (Wed Dec 18 2002 - 09:03:27 CST)
- MPI_BCAST error Nathan A. Baker (Wed Dec 18 2002 - 09:51:02 CST)
- Re: solvatebox Luis Gracia (Wed Dec 18 2002 - 09:58:47 CST)
- Re: message during minimization darden (Wed Dec 18 2002 - 10:24:48 CST)
- Re: water box, darden (Wed Dec 18 2002 - 10:33:07 CST)
- off-to-mol2 Anke Eisenmann (Wed Dec 18 2002 - 10:49:22 CST)
- mm_pbsa error message! William Wei (Wed Dec 18 2002 - 11:17:16 CST)
- Re: mm_pbsa error message! Michael Ford (Wed Dec 18 2002 - 11:37:57 CST)
- Re: off-to-mol2 David A. Case (Wed Dec 18 2002 - 12:03:48 CST)
- About heating... Andrei Leitão (Wed Dec 18 2002 - 12:23:43 CST)
- antechamber Carsten Detering (Wed Dec 18 2002 - 13:38:16 CST)
- Re: About heating... David A. Case (Wed Dec 18 2002 - 13:42:51 CST)
- Re: SUMMARY: solvating a protein with large cavity Richard Henchman (Wed Dec 18 2002 - 13:56:20 CST)
- roar-cp problems M. L. Dodson (Wed Dec 18 2002 - 15:00:37 CST)
- Re: MPI_BCAST error Scott Brozell (Wed Dec 18 2002 - 15:24:55 CST)
- antechamber Carsten Detering (Wed Dec 18 2002 - 16:32:44 CST)
- Re: message during minimization Ioana Cozmuta (Wed Dec 18 2002 - 17:09:05 CST)
- atomicfluct in ptraj Kristina Furse (Wed Dec 18 2002 - 17:16:29 CST)
- Re: water box, Ioana Cozmuta (Wed Dec 18 2002 - 17:37:41 CST)
- Re: water box, David A. Case (Wed Dec 18 2002 - 18:17:31 CST)
- Re: message during minimization darden (Wed Dec 18 2002 - 18:32:21 CST)
- Re: water box, darden (Wed Dec 18 2002 - 18:45:55 CST)
- Re: SUMMARY: solvating a protein with large cavity Ioana Cozmuta (Wed Dec 18 2002 - 19:21:23 CST)
- Re: MPI_BCAST error Nathan A. Baker (Wed Dec 18 2002 - 19:31:47 CST)
- water/nonTIP3P Ioana Cozmuta (Wed Dec 18 2002 - 19:33:23 CST)
- Re: message during minimization Ioana Cozmuta (Wed Dec 18 2002 - 20:02:26 CST)
- Re: water/nonTIP3P Ioana Cozmuta (Wed Dec 18 2002 - 20:17:24 CST)
- ntwv saves v(t) or v(t+dt/2) ? hagop demirdjian (Thu Dec 19 2002 - 10:04:55 CST)
- Re: message during minimization David A. Case (Thu Dec 19 2002 - 10:05:00 CST)
- Re: ntwv saves v(t) or v(t+dt/2) ? David A. Case (Thu Dec 19 2002 - 11:24:33 CST)
- Re: atomicfluct in ptraj David A. Case (Thu Dec 19 2002 - 11:28:43 CST)
- chirality.c failure - diagnosis, but no cure... Michael Ford (Thu Dec 19 2002 - 12:07:07 CST)
- RE: atomicfluct in ptraj Kristina Furse (Thu Dec 19 2002 - 13:28:16 CST)
- RESTARTED DUE TO LINMIN FAILURE William Wei (Thu Dec 19 2002 - 13:33:07 CST)
- Nmode Pratul Agarwal (Thu Dec 19 2002 - 15:07:47 CST)
- Re: RESTARTED DUE TO LINMIN FAILURE Natasja Brooijmans (Thu Dec 19 2002 - 15:16:44 CST)
- Re: Nmode James Caldwell (Thu Dec 19 2002 - 15:17:31 CST)
- Re: chirality.c failure - diagnosis, but no cure... Michael Ford (Thu Dec 19 2002 - 17:25:21 CST)
- selection of residues Ioana Cozmuta (Fri Dec 20 2002 - 18:51:52 CST)
- cap option Ioana Cozmuta (Sun Dec 22 2002 - 19:21:01 CST)
- beginners question dynamic group (Sun Dec 22 2002 - 23:17:52 CST)
- targeted MD sample eric hu (Thu Dec 26 2002 - 14:25:36 CST)
- Molecular dynamic protocol... Andrei Leitão (Fri Dec 27 2002 - 12:40:26 CST)
- Re: Molecular dynamic protocol... David A. Case (Fri Dec 27 2002 - 13:25:51 CST)
- cannot deal with large trajectory? yuann (Sat Dec 28 2002 - 21:17:23 CST)
- Trajectory file converted in pdb file Yongjun Jiang (Sun Dec 29 2002 - 19:13:38 CST)
- Sander rfree error kxg2248_at_njit.edu (Mon Dec 30 2002 - 16:58:19 CST)
- Re: Sander rfree error James Caldwell (Mon Dec 30 2002 - 18:36:45 CST)
- Re: cannot deal with large trajectory? yuann (Mon Dec 30 2002 - 20:55:41 CST)
- new on the Amber web pages... David A. Case (Tue Dec 31 2002 - 15:51:31 CST)
Last message date: Tue Dec 31 2002 - 15:51:31 CST
Archived on: Thu May 05 2005 - 14:17:27 CDT
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