Amber Archive May 2004 by thread
- Re: AMBER: Amber8 compilation error Arvind (Fri Apr 30 2004 - 12:50:38 PDT)
- Re: AMBER: esp or resp for all_amino94.lib FyD (Fri Apr 30 2004 - 16:28:57 PDT)
- AMBER: problem for compiling amber7 by ifc8 scopio (Sat May 01 2004 - 05:26:57 PDT)
- AMBER: Gibbs and solvent caps Sébastien Osborne (Sat May 01 2004 - 11:59:07 PDT)
- AMBER: ptraj: radius of gyration Sichun Yang (Sat May 01 2004 - 19:50:37 PDT)
- AMBER: xleap problem hj zou (Sun May 02 2004 - 06:49:40 PDT)
- AMBER: nmode analysis sebnem (Sun May 02 2004 - 17:52:12 PDT)
- AMBER: any program or tool Helios Chen (Mon May 03 2004 - 03:16:15 PDT)
- AMBER: some bugfixes David A. Case (Mon May 03 2004 - 11:10:47 PDT)
- AMBER: resp demo files Kristy Mardis (Mon May 03 2004 - 12:29:45 PDT)
- AMBER: why delete water molecule Helios Chen (Mon May 03 2004 - 21:18:49 PDT)
- AMBER: separate the longitudinal and transverse vibrations frequencies xiaowei li (Mon May 03 2004 - 21:33:11 PDT)
- AMBER: Troubles in the NTP simulation: "vlimit exceeded". Ülo Lille (Tue May 04 2004 - 03:16:24 PDT)
- AMBER: PMF correction factor Harvey, David Richard (Tue May 04 2004 - 06:35:13 PDT)
- AMBER: How to choose force constant? tomjas.poczta.onet.pl (Tue May 04 2004 - 06:48:44 PDT)
- AMBER: Normal Mode Analysis possibility myang (Tue May 04 2004 - 08:52:05 PDT)
- Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded". Bill Ross (Tue May 04 2004 - 09:44:16 PDT)
- AMBER: reproduction of RESP charges for Gly Mikyung Seo (Tue May 04 2004 - 10:51:01 PDT)
- AMBER: problem with MM/PBSA Itziar Maestre Asenjo (Tue May 04 2004 - 09:38:32 PDT)
- AMBER: antechamber Guanglei Cui (Tue May 04 2004 - 19:49:28 PDT)
- AMBER: methane box anshul.imtech.res.in (Wed May 05 2004 - 11:57:16 PDT)
- AMBER: ptraj analyze matrix entropy Marcin Krol (Wed May 05 2004 - 02:19:32 PDT)
- AMBER: H Bonds anshul.imtech.res.in (Wed May 05 2004 - 13:07:01 PDT)
- AMBER: Implicit solvents anshul.imtech.res.in (Wed May 05 2004 - 13:10:20 PDT)
- AMBER: reorientation in R.E.D Mikyung Seo (Wed May 05 2004 - 09:38:01 PDT)
- AMBER: antechamber gives GDP 0 charge Raik Grünberg (Wed May 05 2004 - 13:17:53 PDT)
- Re: AMBER: H Bonds Bill Ross (Wed May 05 2004 - 14:18:22 PDT)
- AMBER: Solvent accessible surface area(LCPO) computation Sunil_Koovakkat.berlex.com (Wed May 05 2004 - 14:51:59 PDT)
- AMBER: Sander klambda question Linda Prengaman (Wed May 05 2004 - 15:14:22 PDT)
- AMBER: simulated anealing ...vlimit exceed anshul.imtech.res.in (Thu May 06 2004 - 14:50:35 PDT)
- AMBER: Possible amber8 antechamber PDB parsing bug Mark Williamson (Thu May 06 2004 - 08:16:19 PDT)
- AMBER: ions in mm_pbsa Fang, Jianwen (Thu May 06 2004 - 08:30:12 PDT)
- AMBER: Ligand from CCDC. Osman Gani (Thu May 06 2004 - 08:38:16 PDT)
- AMBER: Possible amber8 antechamber PDB parsing bug Junmei Wang (Thu May 06 2004 - 10:09:30 PDT)
- AMBER: Computing psec/day using Amber 8 Craig TOEPFER (Thu May 06 2004 - 11:21:53 PDT)
- AMBER: Opteron PMEMD Gary Waters (Thu May 06 2004 - 11:29:56 PDT)
- AMBER: cap waters always flexible? Oliver Hucke (Thu May 06 2004 - 13:41:19 PDT)
- AMBER: choosing 3 atoms for reorientaion in R.E.D Mikyung Seo (Thu May 06 2004 - 14:38:19 PDT)
- AMBER: solvent cap and eedmeth Oliver Hucke (Thu May 06 2004 - 16:31:42 PDT)
- AMBER: ntwprt feature in AMBER7 Dave S Walker (Thu May 06 2004 - 19:26:51 PDT)
- AMBER: ptraj analyze matrix entropy Marcin Krol (Fri May 07 2004 - 01:01:23 PDT)
- AMBER: hbond in ptraj Qiang Lu (Fri May 07 2004 - 11:43:33 PDT)
- Re: AMBER: xleap don't recognize formaldehyde? anshul.imtech.res.in (Sat May 08 2004 - 12:44:33 PDT)
- AMBER: Charges and atom type anshul.imtech.res.in (Sat May 08 2004 - 14:06:25 PDT)
- AMBER: what is its file format ? scopio (Sat May 08 2004 - 07:13:21 PDT)
- AMBER: ligand minimization atobak.eden.rutgers.edu (Sat May 08 2004 - 14:13:21 PDT)
- AMBER: MD with NTR + NMROPT Martin Fabani (Mon May 10 2004 - 01:56:28 PDT)
- AMBER: HIS protonation Stefano.Pieraccini.unimi.it (Mon May 10 2004 - 02:50:40 PDT)
- AMBER: ptraj read in matrix Marcin Krol (Mon May 10 2004 - 04:57:25 PDT)
- AMBER: A parm file suit for half beta and half alpha structure Qiang Lu (Mon May 10 2004 - 11:51:57 PDT)
- AMBER: question about mm-pbsa aini.UMDNJ.EDU (Mon May 10 2004 - 17:10:05 PDT)
- AMBER: what does EAMBER stand for? scopio (Mon May 10 2004 - 18:08:35 PDT)
- AMBER: mm-pbsa:- atom charges and radii ? Jeffrey Dyason (Tue May 11 2004 - 01:07:12 PDT)
- AMBER: gaussian03 output in antechamber Stefano.Pieraccini.unimi.it (Tue May 11 2004 - 02:27:46 PDT)
- AMBER: PMEMD Built ? Wont run.. Gary Waters (Tue May 11 2004 - 09:00:33 PDT)
- AMBER: ptraj and LES Guanglei Cui (Tue May 11 2004 - 14:00:12 PDT)
- AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D Mikyung Seo (Tue May 11 2004 - 15:51:01 PDT)
- AMBER: dummy atom other than H Carsten Detering (Tue May 11 2004 - 18:12:22 PDT)
- AMBER: Problem : antechamber produces no output Marc Perea (Tue May 11 2004 - 03:19:52 PDT)
- AMBER: gaussian03 output in antechamber Stefano.Pieraccini.unimi.it (Wed May 12 2004 - 01:46:17 PDT)
- AMBER: shake option in sander Lishan Yao (Wed May 12 2004 - 06:32:48 PDT)
- AMBER: dihedral driver Beale, John (Wed May 12 2004 - 06:58:35 PDT)
- AMBER: performance of periodic vs. non-periodic simulation Oliver Hucke (Wed May 12 2004 - 12:08:18 PDT)
- AMBER: tmd questions hj zou (Wed May 12 2004 - 19:07:36 PDT)
- AMBER: antechamber/Mopac: strange GTP charges Raik Grünberg (Thu May 13 2004 - 10:57:06 PDT)
- AMBER: sander_classic for cap simulations? Oliver Hucke (Thu May 13 2004 - 15:43:36 PDT)
- AMBER: Decomposition in MMPBSA Thomas Steinbrecher (Thu May 13 2004 - 17:15:03 PDT)
- Re: AMBER: mm_pbsa examples; delphi in mm_pbsa Kazuo Koyano (Fri May 14 2004 - 02:35:36 PDT)
- AMBER: FAD cofactor. Osman Gani (Fri May 14 2004 - 02:34:28 PDT)
- AMBER: Converting ORAC's topology file to AMBER's prepi file scopio (Fri May 14 2004 - 05:30:32 PDT)
- AMBER: Simulated annealing ...vlimit problem Venkata S Koppuravuri (Fri May 14 2004 - 07:22:44 PDT)
- AMBER: questions on mm_pbsa Fang, Jianwen (Fri May 14 2004 - 11:49:54 PDT)
- AMBER: solvents reference. Herbert Georg (Fri May 14 2004 - 12:56:38 PDT)
- Five Fingered F'in amber Unreal Photos Fist Action (Fri May 14 2004 - 23:23:15 PDT)
- Five Fingered F'in amber Unreal Photos Fist Action (Fri May 14 2004 - 23:23:18 PDT)
- AMBER: antechamber anshul.imtech.res.in (Sat May 15 2004 - 09:43:48 PDT)
- AMBER: install RESP Gustavo Pierdominici Sottile (Sat May 15 2004 - 04:54:41 PDT)
- AMBER: installing RESP Gustavo Pierdominici Sottile (Sat May 15 2004 - 04:52:59 PDT)
- AMBER: energy conservation with GB !! Pradipta Bandyopadhyay (Sat May 15 2004 - 23:27:01 PDT)
- AMBER: parametrizacion partial charges Gustavo Pierdominici Sottile (Mon May 17 2004 - 06:45:58 PDT)
- AMBER: why EGB = nan Fang, Jianwen (Mon May 17 2004 - 07:54:44 PDT)
- AMBER: Gustavo Pierdominici Sottile (Mon May 17 2004 - 11:38:53 PDT)
- AMBER: Treating atom type LP the same as EP Sarah Wittkopp (Mon May 17 2004 - 12:16:20 PDT)
- AMBER: thermodynamic integration of ring opening Carsten Detering (Mon May 17 2004 - 13:37:42 PDT)
- Re: AMBER: thermodynamic integration of ring opening Bill Ross (Mon May 17 2004 - 15:47:24 PDT)
- AMBER: single amino acid energy Helios Chen (Tue May 18 2004 - 01:15:02 PDT)
- AMBER: PCA prep file Majid moghaddam (Tue May 18 2004 - 01:19:26 PDT)
- AMBER: CAP PROTOCOL SIMULATION Obdulia Rabal (Tue May 18 2004 - 02:32:29 PDT)
- AMBER: Clean in RESP Gustavo Pierdominici Sottile (Tue May 18 2004 - 04:46:38 PDT)
- AMBER: DEBUG and GB Jones, Garth A (Tue May 18 2004 - 05:02:32 PDT)
- AMBER: NTT=4 Joachim Reichelt (Tue May 18 2004 - 07:30:33 PDT)
- AMBER: IGR1/grnam1 problem Marcin Krol (Tue May 18 2004 - 10:40:58 PDT)
- AMBER: PB bomb in pb_saarc S. Frank Yan (Tue May 18 2004 - 13:41:41 PDT)
- AMBER: average structure from traj Holly Freedman (Tue May 18 2004 - 14:30:07 PDT)
- AMBER: Removal of rotation: Flying ice cube koby levy (Tue May 18 2004 - 17:23:54 PDT)
- AMBER: rmsd over residues using ptraj Qiang Lu (Tue May 18 2004 - 17:41:16 PDT)
- Re: AMBER: rmsd over residues using ptraj Bill Ross (Tue May 18 2004 - 17:57:54 PDT)
- AMBER: Does this warning matter? (about improper torsion parameters) J. Zhang, Dr (Tue May 18 2004 - 20:04:32 PDT)
- AMBER: Reproducing the energy during restart in MD! Pradipta Bandyopadhyay (Tue May 18 2004 - 23:33:27 PDT)
- AMBER: problem in antechamber Suwipa saen-oon (Wed May 19 2004 - 01:27:24 PDT)
- AMBER: ptraj bug? Ian Withers (Wed May 19 2004 - 07:33:38 PDT)
- Extreme Privacy Violation 4896 Deanna Yarbro (Wed May 19 2004 - 09:48:11 PDT)
- AMBER: address error Carsten Detering (Wed May 19 2004 - 10:09:12 PDT)
- Re: Re[2]: AMBER: rmsd over residues using ptraj Bill Ross (Wed May 19 2004 - 11:34:08 PDT)
- Re: Re[4]: AMBER: rmsd over residues using ptraj Bill Ross (Wed May 19 2004 - 14:15:01 PDT)
- AMBER: parallel installation problem Oliver Hucke (Wed May 19 2004 - 15:17:08 PDT)
- AMBER: amber7, namelist, xlf and osx Knut Langsetmo (Wed May 19 2004 - 15:47:26 PDT)
- AMBER: Amber8 on Tru64 UNIX on Alpha systems Jiten (Wed May 19 2004 - 18:28:50 PDT)
- AMBER: instalation of RES anshul.imtech.res.in (Thu May 20 2004 - 11:22:08 PDT)
- AMBER: SHAKE in thermodynamic integration by way of riccardo nifosi (Thu May 20 2004 - 03:38:21 PDT)
- AMBER: pbsa calculation on part of the molecule S. Frank Yan (Thu May 20 2004 - 13:25:46 PDT)
- AMBER: Ammonia Lishan Yao (Thu May 20 2004 - 14:11:43 PDT)
- AMBER: PF6- force field parameters Jiten (Thu May 20 2004 - 17:32:29 PDT)
- RE: AMBER: pbsa calculation on part of the molecule & nmode analysis S. Frank Yan (Thu May 20 2004 - 18:06:11 PDT)
- AMBER: Problem compiling amber7 Miguel (Fri May 21 2004 - 02:15:10 PDT)
- Request to mailing list Ahmadis rejected ahmadis-bounces.imperial.ac.uk (Fri May 21 2004 - 05:31:19 PDT)
- AMBER: NHE problem Ryan Ye (Fri May 21 2004 - 22:36:44 PDT)
- AMBER: a question about Van der waals radius Xiao He (Sat May 22 2004 - 05:07:05 PDT)
- AMBER: parallel installation problem Oliver Hucke (Sat May 22 2004 - 17:40:17 PDT)
- AMBER: h bond Ye Mei (Sun May 23 2004 - 23:27:37 PDT)
- AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5.2.0GHz Tru Huynh (Mon May 24 2004 - 00:45:39 PDT)
- Re: AMBER: segmentation fault when running parmchk Chutintorn Punwong (Mon May 24 2004 - 15:34:11 PDT)
- AMBER: Free energies using Sander in Amber8 Jiten (Mon May 24 2004 - 19:52:52 PDT)
- AMBER: IOUTFM and binary/unformatted files error Martin Mucha (Tue May 25 2004 - 00:18:44 PDT)
- AMBER: Installation AMber 8: "cannot find -lU77" A. Hungie (Tue May 25 2004 - 06:21:09 PDT)
- AMBER: mm_pbsa energy decomposition error Fang, Jianwen (Tue May 25 2004 - 07:40:32 PDT)
- AMBER: Compiling AMBER MPI program using GCC/G77 compiler and MPICH on AMD OPTERON 64 Ming Lei (Tue May 25 2004 - 08:27:49 PDT)
- AMBER: Scaling nb between groups Marcin Krol (Tue May 25 2004 - 08:34:00 PDT)
- AMBER: ptraj Holly Freedman (Tue May 25 2004 - 09:16:42 PDT)
- AMBER: A problem for compiling amber8 parallel version Chen Yongzhi (Tue May 25 2004 - 13:58:37 PDT)
- AMBER: protein is out of the water box Feng, Hanqiao (NIH/NCI) (Tue May 25 2004 - 15:35:01 PDT)
- AMBER: Cannot read in sander bybaker.itsa.ucsf.edu (Tue May 25 2004 - 15:51:48 PDT)
- AMBER: Amber 8 compilation A. Hungie (Wed May 26 2004 - 09:23:07 PDT)
- AMBER: types of water atom Gustavo Pierdominici Sottile (Wed May 26 2004 - 10:06:16 PDT)
- Re: AMBER: types of water atom Piotr Cieplak (Wed May 26 2004 - 10:28:17 PDT)
- AMBER: amber 8 under windows XP Adrian E. Roitberg (Wed May 26 2004 - 11:50:02 PDT)
- Re: AMBER: amber 8 under windows XP Piotr Cieplak (Wed May 26 2004 - 15:08:38 PDT)
- AMBER: xleap solvatebox problem Tomas Kubar (Thu May 27 2004 - 05:33:44 PDT)
- AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file Kamp, Marc vander (Thu May 27 2004 - 06:01:13 PDT)
- AMBER: pdb in RED Gustavo Pierdominici Sottile (Thu May 27 2004 - 10:29:44 PDT)
- AMBER: Amber 7 (sander) use of PME Linda Prengaman (Thu May 27 2004 - 12:42:13 PDT)
- Re: AMBER: Cannot read in sander-again bybaker.itsa.ucsf.edu (Thu May 27 2004 - 14:22:00 PDT)
- AMBER: Re: CCL:Helical parameters extraction from trajectory Peter Gannett (Fri May 28 2004 - 04:47:08 PDT)
- AMBER: problems with mpich Amber admin (Fri May 28 2004 - 07:55:25 PDT)
- AMBER: amber on AMD 64 xhu1.memphis.edu (Fri May 28 2004 - 11:56:02 PDT)
- AMBER: Use of RED Gustavo Pierdominici Sottile (Fri May 28 2004 - 11:44:26 PDT)
- AMBER: torsion angles John (Fri May 28 2004 - 16:02:04 PDT)
- AMBER: Sander went through bybaker.itsa.ucsf.edu (Fri May 28 2004 - 17:19:02 PDT)
- AMBER: about amber8, replica exchange J. Zhang, Dr (Fri May 28 2004 - 20:45:49 PDT)
- AMBER: Low frequency in quasi-harmonic analysis!! Pradipta Bandyopadhyay (Sun May 30 2004 - 02:23:50 PDT)
- AMBER: MMPBSA problem Dalmaris, John (Sun May 30 2004 - 06:22:55 PDT)
- AMBER: question about NMODE for RNA xhu1.memphis.edu (Sun May 30 2004 - 15:32:22 PDT)
- AMBER: program compatibility hj zou (Sun May 30 2004 - 19:07:39 PDT)
- AMBER: FEP error/early termination - why? Annette Höglund (Mon May 31 2004 - 06:23:27 PDT)
- AMBER: Install Amber8 under cygwin Seonah Kim (Mon May 31 2004 - 18:35:16 PDT)
- Last message date: Tue Jun 01 2004 - 02:53:00 PDT
- Archived on: Wed Apr 24 2024 - 05:53:20 PDT
