AMBER Archive (2002) - Aug 2002 By ThreadMost recent messages
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About this archive
Starting: Thu Aug 01 2002 - 05:50:32 CDT
Ending: Sat Aug 31 2002 - 12:58:35 CDT
- problem with amber7 mpi Bimo Ario Tejo (Thu Aug 01 2002 - 05:50:32 CDT)
- Potential Energy and RMS-Deviation Issues mdk7p_at_cms.mail.virginia.edu (Thu Aug 01 2002 - 10:01:07 CDT)
- distance restraint stuff Layi Adekoya (Thu Aug 01 2002 - 10:24:50 CDT)
- file Cozmuta (Thu Aug 01 2002 - 12:24:13 CDT)
- proton_info/PS Cozmuta (Thu Aug 01 2002 - 12:29:02 CDT)
- Using the new2oldparm command dianah_at_unm.edu (Thu Aug 01 2002 - 15:18:32 CDT)
- MD on cytochrome Mahadevan Seetharaman (Thu Aug 01 2002 - 16:15:52 CDT)
- Solvated DNA using Amber 7 Nicholson, James D Mr ARO (Thu Aug 01 2002 - 16:32:13 CDT)
- reorder water with nmropt Peter Varnai (Fri Aug 02 2002 - 07:24:59 CDT)
- look for benchmark with myrinet vs. 100-BT Jianhui Wu (Fri Aug 02 2002 - 12:15:29 CDT)
- FWD: RE: Including explicit waters in GB dynamics Kristina Furse (Fri Aug 02 2002 - 15:32:52 CDT)
- igb=2 in amber7 Randy M. Wadkins (Fri Aug 02 2002 - 17:28:48 CDT)
- water box-nonperiodic Cozmuta (Fri Aug 02 2002 - 22:14:35 CDT)
- PROTON_INFO Cozmuta (Fri Aug 02 2002 - 22:25:37 CDT)
- Benchmarks Sanjeev B.S. (Sat Aug 03 2002 - 00:48:09 CDT)
- Please give me a hand on understanding AMBER/MPI and locmem. Margaret Cheung (Sat Aug 03 2002 - 01:49:46 CDT)
- Generalized Born and OPLS potential Soonmin Jang (Sat Aug 03 2002 - 03:05:27 CDT)
- problems with parallel sander on linux clusters? David Case (Sun Aug 04 2002 - 13:34:20 CDT)
- (no subject) sepideh ameli (Sun Aug 04 2002 - 14:01:20 CDT)
- Import of CHARMM force field and GB potential parameters into Amber7 Soonmin Jang (Sun Aug 04 2002 - 21:19:20 CDT)
- MD in alcohol Marc DOBLER (Sun Aug 04 2002 - 21:33:52 CDT)
- Information request - where to buy software Claire Edmonds (Mon Aug 05 2002 - 08:23:59 CDT)
- Amber 7 timings? Jim (Mon Aug 05 2002 - 09:53:25 CDT)
- "number of processors must be a power of two" Jim (Tue Aug 06 2002 - 09:50:53 CDT)
- Amber trajectory movies in Powerpoint mdk7p_at_cms.mail.virginia.edu (Tue Aug 06 2002 - 10:53:39 CDT)
- creating a solvent box Bimo Ario Tejo (Tue Aug 06 2002 - 12:23:13 CDT)
- am1-bcc charges Sophia Kondratova (Tue Aug 06 2002 - 13:26:22 CDT)
- check-up question Cozmuta (Tue Aug 06 2002 - 14:13:31 CDT)
- charges Cozmuta (Tue Aug 06 2002 - 18:24:14 CDT)
- (no subject) Giulio Rastelli (Wed Aug 07 2002 - 04:07:21 CDT)
- SHAKE problem Rosalia Pascual (Wed Aug 07 2002 - 10:13:12 CDT)
- Amber+Mosix Jianhui Wu (Wed Aug 07 2002 - 15:40:15 CDT)
- mpich, I/O, Master node, filesystem Jianhui Wu (Wed Aug 07 2002 - 23:24:13 CDT)
- Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system. jeff dyason (Wed Aug 07 2002 - 23:45:49 CDT)
- nmode segmentation fault zhongh_at_umich.edu (Thu Aug 08 2002 - 08:56:08 CDT)
- Gentoo vs. Redhat Linux, shared/distributed filesystem Jianhui Wu (Thu Aug 08 2002 - 14:44:53 CDT)
- protonation pH dependent Cozmuta (Thu Aug 08 2002 - 16:14:46 CDT)
- LINMIN failure during minimization Giulio Rastelli (Fri Aug 09 2002 - 03:46:18 CDT)
- namelist error with sander Andreas Kerzmann (Fri Aug 09 2002 - 03:47:53 CDT)
- problems runing gibbs on a IBM SP2 machine ramon kleber da rocha (Fri Aug 09 2002 - 09:48:11 CDT)
- FW: Compiling on HP-UX 11.00 Hagedorn, Dan N (Fri Aug 09 2002 - 13:45:00 CDT)
- Amber/Gentoo linux Jianhui Wu (Fri Aug 09 2002 - 14:53:16 CDT)
- Nanotubes with AMBER Stefan Andreev Andreev (Sun Aug 11 2002 - 18:59:26 CDT)
- literature for NVE Khatcharin Siriwong (Mon Aug 12 2002 - 04:07:05 CDT)
- Constant pressure MD problems (sander) Pratul Agarwal (Mon Aug 12 2002 - 09:45:15 CDT)
- Memory and swap in sander William Wei (Mon Aug 12 2002 - 10:11:35 CDT)
- chesey@panther.gsu.edu Michael G Cooney (Mon Aug 12 2002 - 14:03:37 CDT)
- misdirected message Michael G Cooney (Mon Aug 12 2002 - 14:35:35 CDT)
- Format of prep input files dianah_at_unm.edu (Tue Aug 13 2002 - 12:42:11 CDT)
- sander minimizations failing John Bushnell (Tue Aug 13 2002 - 19:03:12 CDT)
- minimization in amber7 for nonperiodic systems David Case (Wed Aug 14 2002 - 00:47:43 CDT)
- dihedral parameter for conjugated double bonds in GAFF Giulio Rastelli (Wed Aug 14 2002 - 03:37:50 CDT)
- GB in Amber7 Jithesh (Wed Aug 14 2002 - 03:37:54 CDT)
- problem reading rstrnt file with pgf77 compiled sander Michael Petersen (Wed Aug 14 2002 - 05:13:24 CDT)
- Carnal stream problem Vlad Cojocaru (Wed Aug 14 2002 - 09:45:04 CDT)
- Running amber7 on Param10000 Sanjeev B.S. (Wed Aug 14 2002 - 10:38:34 CDT)
- Q: waters in NPT & periodic boundary condition Masaki Tomimoto (Wed Aug 14 2002 - 11:06:15 CDT)
- a question about carnal Vlad Cojocaru (Wed Aug 14 2002 - 11:39:36 CDT)
- E going up and down??? Jiyoung Heo (Wed Aug 14 2002 - 16:13:44 CDT)
- Can we get trajectories coordinates after FIT in Carnal? William Wei (Wed Aug 14 2002 - 16:52:34 CDT)
- mpi version of sander in Amber 6.0 with constraints Stefan Andreev Andreev (Wed Aug 14 2002 - 17:13:26 CDT)
- PMF with sander module mer_at_gordon.chem.wayne.edu (Wed Aug 14 2002 - 18:23:25 CDT)
- problem with amber7 compiling on SGI Chris Switzer (Wed Aug 14 2002 - 20:26:54 CDT)
- force field name A. Hungie (Thu Aug 15 2002 - 08:50:48 CDT)
- sander on NEC-SX5 C. Klein (Thu Aug 15 2002 - 11:12:24 CDT)
- trajectory file limit??? Vlad Cojocaru (Thu Aug 15 2002 - 11:43:54 CDT)
- Re: Help needed about mm_pbsa Holger Gohlke (Thu Aug 15 2002 - 12:04:03 CDT)
- Order of a protein, bound waters and ligand in saveamberparm Masaki Tomimoto (Thu Aug 15 2002 - 15:25:45 CDT)
- GB in amber6 Prabal Maiti (Thu Aug 15 2002 - 19:26:22 CDT)
- add DUMMY atom into coordinate file yuann (Fri Aug 16 2002 - 04:12:04 CDT)
- Re: problem reading rstrnt file with pgf77 Michael Petersen (Fri Aug 16 2002 - 08:23:48 CDT)
- dihedral parameter for conjugated double bonds in GAFF Giulio Rastelli (Fri Aug 16 2002 - 11:37:03 CDT)
- Etot drops after restarting MD in sander Pratul Agarwal (Fri Aug 16 2002 - 13:18:58 CDT)
- antechamber's prepc option Matthew Lee (Fri Aug 16 2002 - 14:20:59 CDT)
- a couple missing gaff angle terms Matthew Lee (Fri Aug 16 2002 - 16:55:44 CDT)
- average of LES copies mer_at_chem.wayne.edu (Sun Aug 18 2002 - 20:00:22 CDT)
- Antibody residue numbering Mark Hsieh (Mon Aug 19 2002 - 15:56:00 CDT)
- mail host switchover jim caldwell (Mon Aug 19 2002 - 16:58:11 CDT)
- Im lost Sankha Subhra Som (Tue Aug 20 2002 - 00:16:00 CDT)
- PC (principal component) analysis Soonmin Jang (Tue Aug 20 2002 - 03:02:24 CDT)
- segmentation fault Vlad Cojocaru (Tue Aug 20 2002 - 16:21:30 CDT)
- Nitro parameters Jerry Matthew Parks (Wed Aug 21 2002 - 16:28:48 CDT)
- RMSD by residue (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:49:39 CDT)
- Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:02 CDT)
- adding_hydrogens_to_pdb (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:07 CDT)
- ewald bomb in md equilibration (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:14 CDT)
- why is mm_pbsa broken ? (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:27 CDT)
- ambpdb problem (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:32 CDT)
- Gibbs (FEP) (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:36 CDT)
- QUICK HELP! Parameters for neutral amino acids (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:43 CDT)
- amber7, gaff and minimization (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:50 CDT)
- regarding RESP run from gamess output (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:55 CDT)
- why is mm_pbsa broken ? (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:59 CDT)
- Re: Can we get trajectories coordinates after FIT in Carnal? (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:03 CDT)
- How to make mpeg files from amber trajectories (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:07 CDT)
- Carnal RMSDs (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:12 CDT)
- Re: Etot drops after restarting MD in sander (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:16 CDT)
- turning off ewald (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:21 CDT)
- a more general question about ff (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:25 CDT)
- leaprc file (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:29 CDT)
- Torsion restraint between center of mass groups Pratul Agarwal (Mon Aug 26 2002 - 16:51:33 CDT)
- a more general question (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:41 CDT)
- leaprc file (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:44 CDT)
- Re: Extra points (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:49 CDT)
- Scaling of Sander on Linux Clusters (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:57 CDT)
- Re: "number of processors must be a power of two" (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:52:01 CDT)
- Using GBSA for a DNA-PROTEIN complex (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:52:06 CDT)
- test James W. Caldwell (Mon Aug 26 2002 - 17:04:35 CDT)
- mail reflector James W. Caldwell (Mon Aug 26 2002 - 17:35:53 CDT)
- ewald bomb in md equilibration Sophia Kondratova (Mon Aug 26 2002 - 17:54:37 CDT)
- Re: Carnal RMSDs Bill Ross (Mon Aug 26 2002 - 18:56:50 CDT)
- Interface and Amber 7.0 Nigel D Priestley (Mon Aug 26 2002 - 21:45:55 CDT)
- question Sankha Subhra Som (Tue Aug 27 2002 - 01:24:32 CDT)
- amber7: ES40s Sanjeev B.S. (Tue Aug 27 2002 - 08:08:49 CDT)
- difference 94 99 force field Vlad Cojocaru (Tue Aug 27 2002 - 08:34:11 CDT)
- Re: how to make mpeg files from amber trajectories Anke Eisenmann (Tue Aug 27 2002 - 09:41:01 CDT)
- problem in MD Xiang Mao (Tue Aug 27 2002 - 19:05:11 CDT)
- What's this "interface" the tutorial talks about? Andreas Kerzmann (Wed Aug 28 2002 - 07:41:01 CDT)
- iwrap and image Sophia Kondratova (Wed Aug 28 2002 - 07:55:36 CDT)
- Fw: amber problem Carlos Simmerling (Wed Aug 28 2002 - 12:10:26 CDT)
- [Re: can carnal do the job as anal to break down the energy?] Holger Gohlke (Wed Aug 28 2002 - 13:36:51 CDT)
- gibbs sara nunez (Wed Aug 28 2002 - 14:52:56 CDT)
- [Re: can carnal do the job as anal to break down the energy?] Bill Ross (Wed Aug 28 2002 - 15:35:40 CDT)
- a missing variable Vlad Cojocaru (Wed Aug 28 2002 - 15:43:04 CDT)
- sorry!!!!maybe another stupid question Vlad Cojocaru (Wed Aug 28 2002 - 17:48:03 CDT)
- Tutorial Error Message Joel Konkle-Parker (Wed Aug 28 2002 - 18:19:48 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Thu Aug 29 2002 - 05:14:06 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Thu Aug 29 2002 - 07:20:52 CDT)
- pbc in amber Xiang Mao (Thu Aug 29 2002 - 08:00:04 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Thu Aug 29 2002 - 12:02:23 CDT)
- image command Sophia Kondratova (Thu Aug 29 2002 - 12:46:01 CDT)
- PyMOL + AMBER Trajectories DeLano, Warren (Thu Aug 29 2002 - 13:27:01 CDT)
- ES40 hangs amber7 jobs. Sanjeev B.S. (Thu Aug 29 2002 - 22:09:13 CDT)
- dump coordinate into mdcrd A. Hungie (Fri Aug 30 2002 - 03:03:17 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Aug 30 2002 - 05:08:15 CDT)
- example gibbs file for the methane tutorial Andreas Kerzmann (Fri Aug 30 2002 - 05:18:06 CDT)
- NTX value giudice (Fri Aug 30 2002 - 05:31:19 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Aug 30 2002 - 05:59:25 CDT)
- sander7 on IBM 7040-681 under AIX 5.1 Peter Varnai (Fri Aug 30 2002 - 08:01:07 CDT)
- ewald bomb Vlad Cojocaru (Fri Aug 30 2002 - 08:38:49 CDT)
- Vanderbilt Biomolecular Modeling Symposium Jarrod Smith (Fri Aug 30 2002 - 13:00:40 CDT)
- Binding site volume/Sander MD Jianhui Wu (Fri Aug 30 2002 - 16:20:09 CDT)
- GBSA with IGB=2, setting the PBradii bondi Sarangan Ravichandran (Fri Aug 30 2002 - 16:55:28 CDT)
Last message date: Tue Dec 31 2002 - 15:51:31 CST
Archived on: Thu May 05 2005 - 14:17:26 CDT
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