AMBER Archive (2004) - May 2004 By ThreadMost recent messages
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Starting: Sat May 01 2004 - 07:26:57 CDT
Ending: Mon May 31 2004 - 23:42:39 CDT
- AMBER: problem for compiling amber7 by ifc8 scopio (Sat May 01 2004 - 07:26:57 CDT)
- AMBER: Gibbs and solvent caps Sébastien Osborne (Sat May 01 2004 - 13:59:07 CDT)
- AMBER: ptraj: radius of gyration Sichun Yang (Sat May 01 2004 - 21:50:37 CDT)
- AMBER: xleap problem hj zou (Sun May 02 2004 - 08:49:40 CDT)
- AMBER: nmode analysis sebnem (Sun May 02 2004 - 19:52:12 CDT)
- AMBER: any program or tool Helios Chen (Mon May 03 2004 - 05:16:15 CDT)
- AMBER: some bugfixes David A. Case (Mon May 03 2004 - 13:10:47 CDT)
- AMBER: resp demo files Kristy Mardis (Mon May 03 2004 - 14:29:45 CDT)
- AMBER: why delete water molecule Helios Chen (Mon May 03 2004 - 23:18:49 CDT)
- AMBER: separate the longitudinal and transverse vibrations frequencies xiaowei li (Mon May 03 2004 - 23:33:11 CDT)
- AMBER: Troubles in the NTP simulation: "vlimit exceeded". Ülo Lille (Tue May 04 2004 - 05:16:24 CDT)
- AMBER: PMF correction factor Harvey, David Richard (Tue May 04 2004 - 08:35:13 CDT)
- AMBER: How to choose force constant? tomjas_at_poczta.onet.pl (Tue May 04 2004 - 08:48:44 CDT)
- AMBER: Normal Mode Analysis possibility myang (Tue May 04 2004 - 10:52:05 CDT)
- Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded". Bill Ross (Tue May 04 2004 - 11:44:16 CDT)
- AMBER: reproduction of RESP charges for Gly Mikyung Seo (Tue May 04 2004 - 12:51:01 CDT)
- AMBER: problem with MM/PBSA Itziar Maestre Asenjo (Tue May 04 2004 - 11:38:32 CDT)
- AMBER: antechamber Guanglei Cui (Tue May 04 2004 - 21:49:28 CDT)
- AMBER: methane box anshul_at_imtech.res.in (Wed May 05 2004 - 13:57:16 CDT)
- AMBER: ptraj analyze matrix entropy Marcin Krol (Wed May 05 2004 - 04:19:32 CDT)
- AMBER: H Bonds anshul_at_imtech.res.in (Wed May 05 2004 - 15:07:01 CDT)
- AMBER: Implicit solvents anshul_at_imtech.res.in (Wed May 05 2004 - 15:10:20 CDT)
- AMBER: reorientation in R.E.D Mikyung Seo (Wed May 05 2004 - 11:38:01 CDT)
- AMBER: antechamber gives GDP 0 charge Raik Grünberg (Wed May 05 2004 - 15:17:53 CDT)
- Re: AMBER: H Bonds Bill Ross (Wed May 05 2004 - 16:18:22 CDT)
- AMBER: Solvent accessible surface area(LCPO) computation Sunil_Koovakkat_at_berlex.com (Wed May 05 2004 - 16:51:59 CDT)
- AMBER: Sander klambda question Linda Prengaman (Wed May 05 2004 - 17:14:22 CDT)
- AMBER: simulated anealing ...vlimit exceed anshul_at_imtech.res.in (Thu May 06 2004 - 16:50:35 CDT)
- AMBER: Possible amber8 antechamber PDB parsing bug Mark Williamson (Thu May 06 2004 - 10:16:19 CDT)
- AMBER: ions in mm_pbsa Fang, Jianwen (Thu May 06 2004 - 10:30:12 CDT)
- AMBER: Ligand from CCDC. Osman Gani (Thu May 06 2004 - 10:38:16 CDT)
- AMBER: Possible amber8 antechamber PDB parsing bug Junmei Wang (Thu May 06 2004 - 12:09:30 CDT)
- AMBER: Computing psec/day using Amber 8 Craig TOEPFER (Thu May 06 2004 - 13:21:53 CDT)
- AMBER: Opteron PMEMD Gary Waters (Thu May 06 2004 - 13:29:56 CDT)
- AMBER: cap waters always flexible? Oliver Hucke (Thu May 06 2004 - 15:41:19 CDT)
- AMBER: choosing 3 atoms for reorientaion in R.E.D Mikyung Seo (Thu May 06 2004 - 16:38:19 CDT)
- AMBER: solvent cap and eedmeth Oliver Hucke (Thu May 06 2004 - 18:31:42 CDT)
- AMBER: ptraj analyze matrix entropy Marcin Krol (Fri May 07 2004 - 03:01:23 CDT)
- AMBER: hbond in ptraj Qiang Lu (Fri May 07 2004 - 13:43:33 CDT)
- AMBER: Charges and atom type anshul_at_imtech.res.in (Sat May 08 2004 - 16:06:25 CDT)
- AMBER: what is its file format ? scopio (Sat May 08 2004 - 09:13:21 CDT)
- AMBER: ligand minimization atobak_at_eden.rutgers.edu (Sat May 08 2004 - 16:13:21 CDT)
- AMBER: MD with NTR + NMROPT Martin Fabani (Mon May 10 2004 - 03:56:28 CDT)
- AMBER: HIS protonation Stefano.Pieraccini_at_unimi.it (Mon May 10 2004 - 04:50:40 CDT)
- AMBER: ptraj read in matrix Marcin Krol (Mon May 10 2004 - 06:57:25 CDT)
- AMBER: Carnal question opitz_at_che.udel.edu (Mon May 10 2004 - 10:08:18 CDT)
- AMBER: A parm file suit for half beta and half alpha structure Qiang Lu (Mon May 10 2004 - 13:51:57 CDT)
- AMBER: question about mm-pbsa aini_at_UMDNJ.EDU (Mon May 10 2004 - 19:10:05 CDT)
- AMBER: what does EAMBER stand for? scopio (Mon May 10 2004 - 20:08:35 CDT)
- AMBER: mm-pbsa:- atom charges and radii ? Jeffrey Dyason (Tue May 11 2004 - 03:07:12 CDT)
- AMBER: gaussian03 output in antechamber Stefano.Pieraccini_at_unimi.it (Tue May 11 2004 - 04:27:46 CDT)
- AMBER: PMEMD Built ? Wont run.. Gary Waters (Tue May 11 2004 - 11:00:33 CDT)
- AMBER: ptraj and LES Guanglei Cui (Tue May 11 2004 - 16:00:12 CDT)
- AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D Mikyung Seo (Tue May 11 2004 - 17:51:01 CDT)
- AMBER: dummy atom other than H Carsten Detering (Tue May 11 2004 - 20:12:22 CDT)
- AMBER: Problem : antechamber produces no output Marc Perea (Tue May 11 2004 - 05:19:52 CDT)
- AMBER: gaussian03 output in antechamber Stefano.Pieraccini_at_unimi.it (Wed May 12 2004 - 03:46:17 CDT)
- AMBER: shake option in sander Lishan Yao (Wed May 12 2004 - 08:32:48 CDT)
- AMBER: dihedral driver Beale, John (Wed May 12 2004 - 08:58:35 CDT)
- AMBER: performance of periodic vs. non-periodic simulation Oliver Hucke (Wed May 12 2004 - 14:08:18 CDT)
- AMBER: tmd questions hj zou (Wed May 12 2004 - 21:07:36 CDT)
- AMBER: antechamber/Mopac: strange GTP charges Raik Grünberg (Thu May 13 2004 - 12:57:06 CDT)
- AMBER: sander_classic for cap simulations? Oliver Hucke (Thu May 13 2004 - 17:43:36 CDT)
- AMBER: Decomposition in MMPBSA Thomas Steinbrecher (Thu May 13 2004 - 19:15:03 CDT)
- AMBER: FAD cofactor. Osman Gani (Fri May 14 2004 - 04:34:28 CDT)
- AMBER: Converting ORAC's topology file to AMBER's prepi file scopio (Fri May 14 2004 - 07:30:32 CDT)
- AMBER: Simulated annealing ...vlimit problem Venkata S Koppuravuri (Fri May 14 2004 - 09:22:44 CDT)
- AMBER: questions on mm_pbsa Fang, Jianwen (Fri May 14 2004 - 13:49:54 CDT)
- AMBER: solvents reference. Herbert Georg (Fri May 14 2004 - 14:56:38 CDT)
- AMBER: antechamber anshul_at_imtech.res.in (Sat May 15 2004 - 11:43:48 CDT)
- AMBER: install RESP Gustavo Pierdominici Sottile (Sat May 15 2004 - 06:54:41 CDT)
- AMBER: installing RESP Gustavo Pierdominici Sottile (Sat May 15 2004 - 06:52:59 CDT)
- AMBER: energy conservation with GB !! Pradipta Bandyopadhyay (Sun May 16 2004 - 01:27:01 CDT)
- AMBER: parametrizacion partial charges Gustavo Pierdominici Sottile (Mon May 17 2004 - 08:45:58 CDT)
- AMBER: why EGB = nan Fang, Jianwen (Mon May 17 2004 - 09:54:44 CDT)
- AMBER: Gustavo Pierdominici Sottile (Mon May 17 2004 - 13:38:53 CDT)
- AMBER: Treating atom type LP the same as EP Sarah Wittkopp (Mon May 17 2004 - 14:16:20 CDT)
- AMBER: thermodynamic integration of ring opening Carsten Detering (Mon May 17 2004 - 15:37:42 CDT)
- Re: AMBER: thermodynamic integration of ring opening Bill Ross (Mon May 17 2004 - 17:47:24 CDT)
- AMBER: single amino acid energy Helios Chen (Tue May 18 2004 - 03:15:02 CDT)
- AMBER: PCA prep file Majid moghaddam (Tue May 18 2004 - 03:19:26 CDT)
- AMBER: CAP PROTOCOL SIMULATION Obdulia Rabal (Tue May 18 2004 - 04:32:29 CDT)
- AMBER: Clean in RESP Gustavo Pierdominici Sottile (Tue May 18 2004 - 06:46:38 CDT)
- AMBER: DEBUG and GB Jones, Garth A (Tue May 18 2004 - 07:02:32 CDT)
- AMBER: NTT=4 Joachim Reichelt (Tue May 18 2004 - 09:30:33 CDT)
- AMBER: IGR1/grnam1 problem Marcin Krol (Tue May 18 2004 - 12:40:58 CDT)
- AMBER: PB bomb in pb_saarc S. Frank Yan (Tue May 18 2004 - 15:41:41 CDT)
- AMBER: average structure from traj Holly Freedman (Tue May 18 2004 - 16:30:07 CDT)
- AMBER: Removal of rotation: Flying ice cube koby levy (Tue May 18 2004 - 19:23:54 CDT)
- AMBER: rmsd over residues using ptraj Qiang Lu (Tue May 18 2004 - 19:41:16 CDT)
- Re: AMBER: rmsd over residues using ptraj Bill Ross (Tue May 18 2004 - 19:57:54 CDT)
- AMBER: Does this warning matter? (about improper torsion parameters) J. Zhang, Dr (Tue May 18 2004 - 22:04:32 CDT)
- AMBER: Reproducing the energy during restart in MD! Pradipta Bandyopadhyay (Wed May 19 2004 - 01:33:27 CDT)
- AMBER: problem in antechamber Suwipa saen-oon (Wed May 19 2004 - 03:27:24 CDT)
- AMBER: ptraj bug? Ian Withers (Wed May 19 2004 - 09:33:38 CDT)
- AMBER: address error Carsten Detering (Wed May 19 2004 - 12:09:12 CDT)
- Re: Re[2]: AMBER: rmsd over residues using ptraj Bill Ross (Wed May 19 2004 - 13:34:08 CDT)
- Re: Re[4]: AMBER: rmsd over residues using ptraj Bill Ross (Wed May 19 2004 - 16:15:01 CDT)
- AMBER: parallel installation problem Oliver Hucke (Wed May 19 2004 - 17:17:08 CDT)
- AMBER: amber7, namelist, xlf and osx Knut Langsetmo (Wed May 19 2004 - 17:47:26 CDT)
- AMBER: Amber8 on Tru64 UNIX on Alpha systems Jiten (Wed May 19 2004 - 20:28:50 CDT)
- AMBER: instalation of RES anshul_at_imtech.res.in (Thu May 20 2004 - 13:22:08 CDT)
- AMBER: SHAKE in thermodynamic integration by way of riccardo nifosi (Thu May 20 2004 - 05:38:21 CDT)
- AMBER: pbsa calculation on part of the molecule S. Frank Yan (Thu May 20 2004 - 15:25:46 CDT)
- AMBER: Ammonia Lishan Yao (Thu May 20 2004 - 16:11:43 CDT)
- AMBER: PF6- force field parameters Jiten (Thu May 20 2004 - 19:32:29 CDT)
- RE: AMBER: pbsa calculation on part of the molecule & nmode analysis S. Frank Yan (Thu May 20 2004 - 20:06:11 CDT)
- AMBER: Problem compiling amber7 Miguel (Fri May 21 2004 - 04:15:10 CDT)
- AMBER: NHE problem Ryan Ye (Sat May 22 2004 - 00:36:44 CDT)
- AMBER: a question about Van der waals radius Xiao He (Sat May 22 2004 - 07:07:05 CDT)
- AMBER: parallel installation problem Oliver Hucke (Sat May 22 2004 - 19:40:17 CDT)
- AMBER: h bond Ye Mei (Mon May 24 2004 - 01:27:37 CDT)
- AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz Tru Huynh (Mon May 24 2004 - 02:45:39 CDT)
- AMBER: Free energies using Sander in Amber8 Jiten (Mon May 24 2004 - 21:52:52 CDT)
- AMBER: IOUTFM and binary/unformatted files error Martin Mucha (Tue May 25 2004 - 02:18:44 CDT)
- AMBER: Installation AMber 8: "cannot find -lU77" A. Hungie (Tue May 25 2004 - 08:21:09 CDT)
- AMBER: mm_pbsa energy decomposition error Fang, Jianwen (Tue May 25 2004 - 09:40:32 CDT)
- AMBER: Compiling AMBER MPI program using GCC/G77 compiler and MPICH on AMD OPTERON 64 Ming Lei (Tue May 25 2004 - 10:27:49 CDT)
- AMBER: Scaling nb between groups Marcin Krol (Tue May 25 2004 - 10:34:00 CDT)
- AMBER: ptraj Holly Freedman (Tue May 25 2004 - 11:16:42 CDT)
- AMBER: A problem for compiling amber8 parallel version Chen Yongzhi (Tue May 25 2004 - 15:58:37 CDT)
- AMBER: protein is out of the water box Feng, Hanqiao (NIH/NCI) (Tue May 25 2004 - 17:35:01 CDT)
- AMBER: Cannot read in sander bybaker_at_itsa.ucsf.edu (Tue May 25 2004 - 17:51:48 CDT)
- AMBER: Amber 8 compilation A. Hungie (Wed May 26 2004 - 11:23:07 CDT)
- AMBER: types of water atom Gustavo Pierdominici Sottile (Wed May 26 2004 - 12:06:16 CDT)
- Re: AMBER: types of water atom Piotr Cieplak (Wed May 26 2004 - 12:28:17 CDT)
- AMBER: amber 8 under windows XP Adrian E. Roitberg (Wed May 26 2004 - 13:50:02 CDT)
- Re: AMBER: amber 8 under windows XP Piotr Cieplak (Wed May 26 2004 - 17:08:38 CDT)
- AMBER: xleap solvatebox problem Tomas Kubar (Thu May 27 2004 - 07:33:44 CDT)
- AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file Kamp, Marc vander (Thu May 27 2004 - 08:01:13 CDT)
- AMBER: pdb in RED Gustavo Pierdominici Sottile (Thu May 27 2004 - 12:29:44 CDT)
- AMBER: Amber 7 (sander) use of PME Linda Prengaman (Thu May 27 2004 - 14:42:13 CDT)
- Re: AMBER: Cannot read in sander-again bybaker_at_itsa.ucsf.edu (Thu May 27 2004 - 16:22:00 CDT)
- AMBER: Re: CCL:Helical parameters extraction from trajectory Peter Gannett (Fri May 28 2004 - 06:47:08 CDT)
- AMBER: problems with mpich Amber admin (Fri May 28 2004 - 09:55:25 CDT)
- AMBER: amber on AMD 64 xhu1_at_memphis.edu (Fri May 28 2004 - 13:56:02 CDT)
- AMBER: Use of RED Gustavo Pierdominici Sottile (Fri May 28 2004 - 13:44:26 CDT)
- AMBER: torsion angles John (Fri May 28 2004 - 18:02:04 CDT)
- AMBER: Sander went through bybaker_at_itsa.ucsf.edu (Fri May 28 2004 - 19:19:02 CDT)
- AMBER: about amber8, replica exchange J. Zhang, Dr (Fri May 28 2004 - 22:45:49 CDT)
- AMBER: Low frequency in quasi-harmonic analysis!! Pradipta Bandyopadhyay (Sun May 30 2004 - 04:23:50 CDT)
- AMBER: MMPBSA problem Dalmaris, John (Sun May 30 2004 - 08:22:55 CDT)
- AMBER: question about NMODE for RNA xhu1_at_memphis.edu (Sun May 30 2004 - 17:32:22 CDT)
- AMBER: program compatibility hj zou (Sun May 30 2004 - 21:07:39 CDT)
- AMBER: FEP error/early termination - why? Annette Höglund (Mon May 31 2004 - 08:23:27 CDT)
- AMBER: Install Amber8 under cygwin Seonah Kim (Mon May 31 2004 - 20:35:16 CDT)
- AMBER: Software to visualize normal modes! Pradipta Bandyopadhyay (Mon May 31 2004 - 23:42:39 CDT)
Last message date: Thu May 05 2005 - 14:26:38 CDT
Archived on: Thu May 05 2005 - 14:30:00 CDT
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