AMBER Archive (2002) - Sep 2002 By ThreadMost recent messages
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Starting: Sun Sep 01 2002 - 13:32:08 CDT
Ending: Mon Sep 30 2002 - 19:34:28 CDT
- mpirun Ioana Cozmuta (Sun Sep 01 2002 - 13:32:08 CDT)
- additional info Ioana Cozmuta (Sun Sep 01 2002 - 13:44:32 CDT)
- mm_pbsa positive binding energies Mathy Froeyen (Mon Sep 02 2002 - 04:11:34 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Mon Sep 02 2002 - 05:12:42 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Mon Sep 02 2002 - 06:25:18 CDT)
- carnal averaging Vlad Cojocaru (Mon Sep 02 2002 - 06:43:33 CDT)
- atoms coming too close during MD (with SHAKE on) Pratul Agarwal (Mon Sep 02 2002 - 20:01:18 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Tue Sep 03 2002 - 06:57:12 CDT)
- compile Moil-View, GL header files Jianhui Wu (Tue Sep 03 2002 - 10:20:09 CDT)
- protein minimization m.elizabeth sophia (Tue Sep 03 2002 - 11:01:35 CDT)
- question Ioana Cozmuta (Tue Sep 03 2002 - 12:46:04 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Wed Sep 04 2002 - 05:40:26 CDT)
- Escaping Atoms ch cureton (Wed Sep 04 2002 - 05:43:03 CDT)
- old prmtop Thomas Steinbrecher (Wed Sep 04 2002 - 10:56:47 CDT)
- how to detect bad contact? X. Tan (Wed Sep 04 2002 - 14:14:40 CDT)
- cut-off question Ioana Cozmuta (Wed Sep 04 2002 - 14:43:38 CDT)
- DNA Tutorial Script Joel Konkle-Parker (Wed Sep 04 2002 - 18:18:16 CDT)
- average structure Raja Swaminathan (Thu Sep 05 2002 - 12:16:03 CDT)
- bondbydistance eric hu (Thu Sep 05 2002 - 18:20:43 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Sep 06 2002 - 06:13:47 CDT)
- group selection for all heavy atoms ? Raik Grunberg (Fri Sep 06 2002 - 11:23:33 CDT)
- compiling amber on a linux box using DMEM-ALLOC ramon kleber da rocha (Fri Sep 06 2002 - 15:46:43 CDT)
- cut-off question Cozmuta (Fri Sep 06 2002 - 17:49:21 CDT)
- about amber and charmm, thanks Zhang Jian (Sun Sep 08 2002 - 04:10:57 CDT)
- who to address this to?... Jessica Swanson (Sun Sep 08 2002 - 17:59:23 CDT)
- Distace dependent dielectric constant Lorenzo Gontrani (Mon Sep 09 2002 - 03:33:43 CDT)
- parameterization of a new class of compounds (nucleic acid base analogues) Vlad Cojocaru (Mon Sep 09 2002 - 04:40:05 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Mon Sep 09 2002 - 06:04:45 CDT)
- amber7 compilation on irix6.4 mp K.Seshadri (Mon Sep 09 2002 - 12:44:13 CDT)
- How to check whether the trajectory file matches the coordinates file or not? Ling Zhang (Mon Sep 09 2002 - 13:31:13 CDT)
- why are the results so large difference calculating by mm_pbsa and mm_gbsa? Yongjun Jiang (Tue Sep 10 2002 - 02:18:46 CDT)
- Strange MD simulation results with GB solvation at high temp. Soonmin Jang (Tue Sep 10 2002 - 05:09:06 CDT)
- nmode compile question? Yongjun Jiang (Tue Sep 10 2002 - 07:46:18 CDT)
- GBSA and surface crystal waters Raik Grunberg (Tue Sep 10 2002 - 09:44:20 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Tue Sep 10 2002 - 10:57:00 CDT)
- rdparm Joffre Heredia (Tue Sep 10 2002 - 13:07:26 CDT)
- loadpdb error messages Joel Konkle-Parker (Tue Sep 10 2002 - 17:58:07 CDT)
- Polarizability, a general question Michal Otyepka (Wed Sep 11 2002 - 03:56:32 CDT)
- memory allocation in mm_pbsa Giulio Rastelli (Wed Sep 11 2002 - 05:41:04 CDT)
- just a test Vlad Cojocaru (Wed Sep 11 2002 - 08:39:59 CDT)
- Problems during equilibration Pratul Agarwal (Wed Sep 11 2002 - 14:38:36 CDT)
- Dual Processor AMD vs. Single Processor DeLano, Warren (Wed Sep 11 2002 - 19:34:47 CDT)
- why are the results so large difference calculating by mm_pbsaandmm_gbsa? Yongjun Jiang (Thu Sep 12 2002 - 02:25:32 CDT)
- Qustion about calculation of pressure Nikolai Smolin (Thu Sep 12 2002 - 05:01:44 CDT)
- sorry this is just a test Vlad Cojocaru (Thu Sep 12 2002 - 10:23:24 CDT)
- leap and topology file Marcela Madrid (Thu Sep 12 2002 - 11:12:20 CDT)
- sander.LES questions Peter Varnai (Thu Sep 12 2002 - 11:27:12 CDT)
- large energy fluctration eric hu (Thu Sep 12 2002 - 13:05:10 CDT)
- the amino group of 2amino purine has strange behaviour Vlad Cojocaru (Thu Sep 12 2002 - 13:42:10 CDT)
- Changing MAXINT Joel Konkle-Parker (Thu Sep 12 2002 - 18:21:13 CDT)
- binding site volume Shixiang Yan (Thu Sep 12 2002 - 18:38:41 CDT)
- problems on IBM AIX Giovanni Fossati (Thu Sep 12 2002 - 20:43:52 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Sep 13 2002 - 08:10:40 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Sep 13 2002 - 08:13:22 CDT)
- Beowulf killing jobs Peter Gannett (Fri Sep 13 2002 - 16:03:19 CDT)
- Help using moilview to make animations of trajectories Nicholson, James D Mr ARO (Fri Sep 13 2002 - 17:15:33 CDT)
- D-tryptophan Perdita Barran (Sat Sep 14 2002 - 09:16:45 CDT)
- amber K.Veluraja (Mon Sep 16 2002 - 00:14:04 CDT)
- amber question yao yong (Mon Sep 16 2002 - 06:03:16 CDT)
- example 1 problems Alicia Hopkins (Mon Sep 16 2002 - 10:57:23 CDT)
- assistance required amit kumar (Mon Sep 16 2002 - 11:25:05 CDT)
- SETVEL, incorrect number of arguments? Giovanni Fossati (Mon Sep 16 2002 - 17:43:30 CDT)
- non-bonded metal ion in complex yuann (Tue Sep 17 2002 - 01:28:45 CDT)
- question about nmode again. Yongjun Jiang (Tue Sep 17 2002 - 02:15:54 CDT)
- mm_pbsa question. wentaofu (Tue Sep 17 2002 - 10:35:59 CDT)
- Density during equilibration (sander) Pratul Agarwal (Tue Sep 17 2002 - 11:56:10 CDT)
- Z DNA Sue Heavner (Tue Sep 17 2002 - 14:55:04 CDT)
- Carnal+HBond confusion Sanjeev B.S. (Wed Sep 18 2002 - 23:18:36 CDT)
- bug in New2oldparm Pascal Bonnet (Thu Sep 19 2002 - 05:35:46 CDT)
- new2oldparm format (2) Pascal Bonnet (Thu Sep 19 2002 - 05:43:39 CDT)
- a freeware to display RMSD matrices Vlad Cojocaru (Thu Sep 19 2002 - 07:44:53 CDT)
- offset of temperature when running MD with CAP and no periodic conditions Therese Malliavin (Thu Sep 19 2002 - 10:44:24 CDT)
- compiling without ISTAR2 Prem Raj (Thu Sep 19 2002 - 12:27:48 CDT)
- image X. Tan (Thu Sep 19 2002 - 12:32:15 CDT)
- Question about Counterions Markus Drumm (Thu Sep 19 2002 - 12:38:24 CDT)
- BLOWUP after 100 ns??? Randy M. Wadkins (Thu Sep 19 2002 - 15:51:28 CDT)
- npairs Prem Raj (Thu Sep 19 2002 - 17:22:42 CDT)
- Dynamic Movement of Molecule Yuuki Komata (Fri Sep 20 2002 - 03:03:48 CDT)
- Re: Parameters for AMBER David A. Case (Fri Sep 20 2002 - 08:53:18 CDT)
- mol2 file format in the future of amber M. L. Dodson (Fri Sep 20 2002 - 09:41:02 CDT)
- (no subject) Prem Raj (Fri Sep 20 2002 - 11:42:14 CDT)
- vlimit and vmax Prem Raj (Fri Sep 20 2002 - 12:27:07 CDT)
- mm_pbsa Sue Heavner (Fri Sep 20 2002 - 15:00:36 CDT)
- Periodicity Question DeLano, Warren (Fri Sep 20 2002 - 19:29:49 CDT)
- Re: Do I have to rerun 1ns MD?? Holger Gohlke (Sun Sep 22 2002 - 14:30:40 CDT)
- Re: betaP,SURFOFF inconsistency Holger Gohlke (Sun Sep 22 2002 - 15:20:03 CDT)
- ptraj-6.4/LES Peter Varnai (Mon Sep 23 2002 - 04:18:25 CDT)
- Fw: Do I have to rerun 1ns MD?? Lepsa (Mon Sep 23 2002 - 10:50:26 CDT)
- mm_pbsa output error Michael Murray (Mon Sep 23 2002 - 12:26:11 CDT)
- antechamber best practices/charge equivalence w/ AM1-BCC Tom Bishop (Mon Sep 23 2002 - 16:28:57 CDT)
- watershell in ptraj Michael Trieb (Tue Sep 24 2002 - 04:03:49 CDT)
- Mopac509mn/linux James W. Caldwell (Tue Sep 24 2002 - 10:00:20 CDT)
- ambpdb? Arvid Soederhaell (Wed Sep 25 2002 - 02:38:34 CDT)
- ptraj - BONDS_WITHOUT_HYDROGEN Sophia Kondratova (Wed Sep 25 2002 - 11:54:48 CDT)
- (no subject) Apostoluk, Wlodzimierz K (Wed Sep 25 2002 - 14:09:53 CDT)
- compiling amber 7 with Intel Fortran Compiler 6.0 ramon kleber da rocha (Wed Sep 25 2002 - 14:23:21 CDT)
- sander_classic: Recompile without ISTAR2 Mahadevan Seetharaman (Wed Sep 25 2002 - 14:53:59 CDT)
- ISTAR2 - oops, just found the answer... Mahadevan Seetharaman (Wed Sep 25 2002 - 14:55:46 CDT)
- compiling amber 7 with Intel Fortran Compiler 6.0 (fwd) John Bushnell (Wed Sep 25 2002 - 15:10:50 CDT)
- RMSD for heavy atoms only Pratul Agarwal (Wed Sep 25 2002 - 15:54:45 CDT)
- Question about Antechamber Masaki Tomimoto (Wed Sep 25 2002 - 16:37:55 CDT)
- mm_pbsa and statistic program Pascal Bonnet (Thu Sep 26 2002 - 05:50:52 CDT)
- different counterions for special type of DNA Vlad Cojocaru (Thu Sep 26 2002 - 07:59:31 CDT)
- Re: GB tutorial David A. Case (Thu Sep 26 2002 - 10:31:19 CDT)
- Torsion driving ch cureton (Thu Sep 26 2002 - 11:00:34 CDT)
- Question on Antechamber paper Nicholson, James D Mr ARO (Thu Sep 26 2002 - 12:18:17 CDT)
- Amber Reflector James W. Caldwell (Thu Sep 26 2002 - 12:47:58 CDT)
- Constant pressure equilibration in a system with a solvent cap dianah_at_unm.edu (Thu Sep 26 2002 - 20:04:38 CDT)
- nmanal help request Peter Fojan (Fri Sep 27 2002 - 08:59:11 CDT)
- MM-PBSA basics Michael Ford (Fri Sep 27 2002 - 14:53:01 CDT)
- MD Primers Joel Konkle-Parker (Fri Sep 27 2002 - 14:54:03 CDT)
- Is H-bonding really there? suvendu lomash (Fri Sep 27 2002 - 14:59:48 CDT)
- Anal Error : Group Lifeng Tian (Fri Sep 27 2002 - 17:35:23 CDT)
- Request for help with Antechamber Nicholson, James D Mr ARO (Fri Sep 27 2002 - 18:58:58 CDT)
- question about using 10-12 in amber7/sander. Margaret Cheung (Sat Sep 28 2002 - 14:53:56 CDT)
- parameters for sugars A.Madhumalar (Sun Sep 29 2002 - 11:30:36 CDT)
- groups in targeted md Christoph Brockmann (Mon Sep 30 2002 - 08:15:10 CDT)
- Amber 7 and 6 topology files. Miguel de Federico (Mon Sep 30 2002 - 10:08:36 CDT)
- BondEn shoots in solvent minimization suvendu lomash (Mon Sep 30 2002 - 10:50:39 CDT)
- write problem on IBM-AIX Giovanni Fossati (Mon Sep 30 2002 - 10:51:54 CDT)
- Image charges with the solvate cap command dkeller_at_unm.edu (Mon Sep 30 2002 - 10:52:11 CDT)
- Problems with poly(A)-poly(T) tutorial... Andrei Leitão (Mon Sep 30 2002 - 14:55:53 CDT)
- Partial charge generation RESP/antechamber James W. Caldwell (Mon Sep 30 2002 - 17:27:37 CDT)
- divalent cations parameters Apostoluk, Wlodzimierz K (Mon Sep 30 2002 - 17:38:11 CDT)
Last message date: Tue Dec 31 2002 - 15:51:31 CST
Archived on: Thu May 05 2005 - 14:17:26 CDT
244 messages sorted by:
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