AMBER Archive (2004) - Oct 2004 By Date

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Starting: Fri Oct 01 2004 - 09:30:53 CDT
Ending: Sun Oct 31 2004 - 13:39:48 CST

AMBER: (no subject) Rasha Radwan (Fri Oct 01 2004 - 09:30:53 CDT)
AMBER: hydrogen bonds Jessica Koplin (Fri Oct 01 2004 - 11:24:29 CDT)
AMBER: frcmod_dmso Vincent Bisetty (Fri Oct 01 2004 - 16:21:42 CDT)
RE: AMBER: frcmod_dmso Ross Walker (Fri Oct 01 2004 - 17:05:05 CDT)
AMBER: amber 8 error Abd Ghani Bin Abd Aziz (Sat Oct 02 2004 - 02:25:30 CDT)
Re: AMBER: amber 8 error Tomas Linhart (Sat Oct 02 2004 - 03:04:43 CDT)
Re: AMBER: amber 8 error Abd Ghani Bin Abd Aziz (Sat Oct 02 2004 - 04:26:10 CDT)
AMBER: small molecule simulation hj zou (Sun Oct 03 2004 - 00:59:55 CDT)
Re: AMBER: small molecule simulation Carlos Simmerling (Sun Oct 03 2004 - 07:54:40 CDT)
AMBER: antechamber, mopac RESTART opitz_at_che.udel.edu (Sun Oct 03 2004 - 13:41:24 CDT)
AMBER: Running on MPI wish_71 (Sun Oct 03 2004 - 20:59:58 CDT)
Re: AMBER: Running on MPI Jiten (Sun Oct 03 2004 - 22:08:54 CDT)
AMBER: mdinfo on amber6 Abd Ghani Bin Abd Aziz (Mon Oct 04 2004 - 00:26:41 CDT)
AMBER: neutral Arg, charged Tyr ?? Peter Trodler (Mon Oct 04 2004 - 02:25:49 CDT)
Re: AMBER: mdinfo on amber6 Tomas Linhart (Mon Oct 04 2004 - 02:49:29 CDT)
Re: AMBER: mdinfo on amber6 Carlos Simmerling (Mon Oct 04 2004 - 06:40:03 CDT)
Re: AMBER: Running on MPI Carlos Simmerling (Mon Oct 04 2004 - 06:37:18 CDT)
AMBER: amber with MPI Stefano.Pieraccini_at_unimi.it (Mon Oct 04 2004 - 09:40:16 CDT)
AMBER: Phosphoserine Venkata S Koppuravuri (Mon Oct 04 2004 - 14:26:28 CDT)
AMBER: Is AME equal to NME? myang_at_vitamin.uni.cc (Mon Oct 04 2004 - 14:15:46 CDT)
Re: AMBER: Is AME equal to NME? myang_at_vitamin.uni.cc (Mon Oct 04 2004 - 15:07:12 CDT)
AMBER: building a small molecule mathew k varghese (Tue Oct 05 2004 - 04:01:09 CDT)
Re: AMBER: Running on MPI wish_71 (Tue Oct 05 2004 - 05:17:55 CDT)
Re: AMBER: hydrogen bonds Tim Meyer (Tue Oct 05 2004 - 06:11:09 CDT)
Re: AMBER: Running on MPI Carlos Simmerling (Tue Oct 05 2004 - 07:16:59 CDT)
AMBER: Parameters for phosphorylated aminoacids Nadine Homeyer (Tue Oct 05 2004 - 10:21:31 CDT)
Re: AMBER: Parameters for phosphorylated aminoacids Carlos Simmerling (Tue Oct 05 2004 - 10:58:07 CDT)
AMBER: parameter error for a ligand Sivanesan Dakshanamurthy (Tue Oct 05 2004 - 11:59:54 CDT)
Re: AMBER: building a small molecule Oliver Hucke (Tue Oct 05 2004 - 12:15:00 CDT)
AMBER: problem with protonate Richard Stefl (Tue Oct 05 2004 - 12:44:05 CDT)
AMBER: question about nmode xiaowei li (Tue Oct 05 2004 - 13:09:15 CDT)
Re: AMBER: question about nmode David A. Case (Tue Oct 05 2004 - 14:03:52 CDT)
AMBER: Note to all concerning filtering of messages posted to the amber list. Ross Walker (Tue Oct 05 2004 - 14:51:34 CDT)
RE: AMBER: frcmod_dmso Ross Walker (Tue Oct 05 2004 - 15:10:41 CDT)
Re: AMBER: parameter error for a ligand David A. Case (Tue Oct 05 2004 - 15:23:01 CDT)
Re: AMBER: problem with protonate myang_at_vitamin.uni.cc (Tue Oct 05 2004 - 15:36:36 CDT)
Re: AMBER: problem with protonate David A. Case (Tue Oct 05 2004 - 16:31:12 CDT)
Re: AMBER: parameter error for a ligand Sivanesan Dakshanamurthy (Tue Oct 05 2004 - 16:45:51 CDT)
AMBER: Compiling using pgf90 David Lomelin (Tue Oct 05 2004 - 20:33:22 CDT)
Re: AMBER: Running on MPI wish_71 (Tue Oct 05 2004 - 21:43:16 CDT)
Re: AMBER: Note to all concerning filtering of messages posted to the amber list. Stef (Wed Oct 06 2004 - 03:33:17 CDT)
AMBER: Comparison of simulation results on amber7 and amber 8 anshul_at_imtech.res.in (Wed Oct 06 2004 - 15:28:04 CDT)
AMBER: ptraj and PCA J Pang (Wed Oct 06 2004 - 05:54:17 CDT)
Re: AMBER: Parameters for phosphorylated aminoacids Nadine Homeyer (Wed Oct 06 2004 - 05:57:14 CDT)
Re: AMBER: Comparison of simulation results on amber7 and amber 8 Carlos Simmerling (Wed Oct 06 2004 - 08:36:03 CDT)
Re: AMBER: Running on MPI Carlos Simmerling (Wed Oct 06 2004 - 09:33:19 CDT)
AMBER: Antechamber on cluster with queue? opitz_at_che.udel.edu (Wed Oct 06 2004 - 10:08:25 CDT)
Re: AMBER: Antechamber on cluster with queue? David A. Case (Wed Oct 06 2004 - 10:24:17 CDT)
Re: AMBER: Antechamber on cluster with queue? opitz_at_che.udel.edu (Wed Oct 06 2004 - 11:06:43 CDT)
Re: AMBER: Antechamber on cluster with queue? David A. Case (Wed Oct 06 2004 - 11:31:53 CDT)
Re: AMBER: Comparison of simulation results on amber7 and amber 8 Sergio E. Wong (Wed Oct 06 2004 - 11:54:44 CDT)
Re: AMBER: Compiling using pgf90 Craig TOEPFER (Wed Oct 06 2004 - 11:52:06 CDT)
Re: AMBER: Comparison of simulation results on amber7 and amber 8 Carlos Simmerling (Wed Oct 06 2004 - 12:21:54 CDT)
AMBER: GIbbs : failure to start sachin patil (Wed Oct 06 2004 - 13:01:23 CDT)
Re: AMBER: Compiling using pgf90 David Lomelin (Wed Oct 06 2004 - 15:30:34 CDT)
AMBER: atoms out of bounds Balvinder Singh (Thu Oct 07 2004 - 16:27:45 CDT)
Re: AMBER: atoms out of bounds Carlos Simmerling (Thu Oct 07 2004 - 07:17:15 CDT)
AMBER: AddIons Vincent Bisetty (Thu Oct 07 2004 - 07:15:03 CDT)
AMBER: ptraj analyze modes question Vlad Cojocaru (Thu Oct 07 2004 - 08:17:02 CDT)
AMBER: rms fluctuation units from ptraj Vlad Cojocaru (Thu Oct 07 2004 - 08:36:03 CDT)
Re: AMBER: AddIons Bill Ross (Thu Oct 07 2004 - 14:36:24 CDT)
AMBER: solute leaving PBC box opitz_at_che.udel.edu (Thu Oct 07 2004 - 16:24:47 CDT)
Re: AMBER: solute leaving PBC box Carlos Simmerling (Thu Oct 07 2004 - 16:48:12 CDT)
Re: AMBER: solute leaving PBC box opitz_at_che.udel.edu (Thu Oct 07 2004 - 17:01:19 CDT)
Re: AMBER: solute leaving PBC box myang_at_vitamin.uni.cc (Thu Oct 07 2004 - 17:00:09 CDT)
Re: AMBER: solute leaving PBC box Carlos Simmerling (Thu Oct 07 2004 - 17:43:49 CDT)
AMBER: Problem with AMBER/ANAL Daniel Wetzler (Fri Oct 08 2004 - 03:31:29 CDT)
AMBER: MAXATOM failure in ANTECHAMBER Cenk Andac (Fri Oct 08 2004 - 04:31:18 CDT)
Re: AMBER: MAXATOM failure in ANTECHAMBER david.evans_at_ulsop.ac.uk (Fri Oct 08 2004 - 05:09:18 CDT)
AMBER: problems with dihedrals Petr Kulhanek (Fri Oct 08 2004 - 07:53:03 CDT)
Re: AMBER: problems with dihedrals Carlos Simmerling (Fri Oct 08 2004 - 08:27:44 CDT)
Re: AMBER: solute leaving PBC box opitz_at_che.udel.edu (Fri Oct 08 2004 - 08:43:06 CDT)
Re: AMBER: solute leaving PBC box Carlos Simmerling (Fri Oct 08 2004 - 09:02:42 CDT)
AMBER: generalized Born parameters Peter Varnai (Fri Oct 08 2004 - 09:16:08 CDT)
AMBER: sander8 Vincent Bisetty (Fri Oct 08 2004 - 09:59:01 CDT)
Re: AMBER: sander8 Carlos Simmerling (Fri Oct 08 2004 - 10:07:23 CDT)
Re: AMBER: generalized Born parameters David A. Case (Fri Oct 08 2004 - 11:08:02 CDT)
Re: AMBER: Problem with AMBER/ANAL David A. Case (Fri Oct 08 2004 - 11:15:12 CDT)
AMBER: A torsion parameter in AMBER2003 force field Scott E. Boesch (Fri Oct 08 2004 - 11:23:41 CDT)
Re: AMBER: A torsion parameter in AMBER2003 force field David A. Case (Fri Oct 08 2004 - 11:53:21 CDT)
RE: AMBER: A torsion parameter in AMBER2003 force field Yong Duan (Fri Oct 08 2004 - 12:41:41 CDT)
AMBER: restrain one tosion angle Yaroslava Yingling (Fri Oct 08 2004 - 14:02:01 CDT)
Re: AMBER: restrain one tosion angle Carlos Simmerling (Fri Oct 08 2004 - 14:10:16 CDT)
Re: AMBER: restrain one tosion angle Yaroslava Yingling (Fri Oct 08 2004 - 14:20:09 CDT)
Re: AMBER: restrain one tosion angle Carlos Simmerling (Fri Oct 08 2004 - 15:50:34 CDT)
AMBER: Box information from Amber Priti Hansia (Sat Oct 09 2004 - 06:19:46 CDT)
Re: AMBER: Box information from Amber Carlos Simmerling (Sat Oct 09 2004 - 07:10:56 CDT)
Re: AMBER: sander8 Vincent Bisetty (Sat Oct 09 2004 - 11:13:55 CDT)
Re: AMBER: sander8 Carlos Simmerling (Sat Oct 09 2004 - 12:39:34 CDT)
Re: AMBER: Box information from Amber Priti Hansia (Sat Oct 09 2004 - 12:51:16 CDT)
Re: AMBER: Box information from Amber Carlos Simmerling (Sat Oct 09 2004 - 13:00:43 CDT)
AMBER: about antechamber MURAT CETINKAYA (Sat Oct 09 2004 - 20:48:52 CDT)
AMBER: Amber8 compilation in Dec-Alpha Jiten (Sun Oct 10 2004 - 11:22:01 CDT)
AMBER: exclusion list Guanglei Cui (Sun Oct 10 2004 - 11:34:38 CDT)
AMBER: nmode error Xiao He (Mon Oct 11 2004 - 02:10:22 CDT)
AMBER: question about mm_pbsa and nmode Xiao He (Mon Oct 11 2004 - 02:43:53 CDT)
AMBER: AMBER 8 installation trouble Atro Tossavainen (Mon Oct 11 2004 - 03:36:44 CDT)
AMBER: AMBER 8 installation - continued Atro Tossavainen (Mon Oct 11 2004 - 03:57:45 CDT)
AMBER: Hot solvent/cold solute reference Stef (Mon Oct 11 2004 - 05:56:30 CDT)
Re: AMBER: Hot solvent/cold solute reference Andreas Svrcek-Seiler (Mon Oct 11 2004 - 08:16:18 CDT)
AMBER: Distance Restraints Nelson Fonseca (Mon Oct 11 2004 - 07:56:23 CDT)
Re: AMBER: nmode error David A. Case (Mon Oct 11 2004 - 10:09:18 CDT)
Re: AMBER: Distance Restraints David A. Case (Mon Oct 11 2004 - 10:17:39 CDT)
Re: AMBER: exclusion list Guanglei Cui (Mon Oct 11 2004 - 10:26:20 CDT)
Re: AMBER: AMBER 8 installation trouble David A. Case (Mon Oct 11 2004 - 10:43:44 CDT)
Re: AMBER: about antechamber David A. Case (Mon Oct 11 2004 - 11:13:05 CDT)
Re: AMBER: Hot solvent/cold solute reference Stef (Mon Oct 11 2004 - 11:41:10 CDT)
RE: AMBER: Amber8 compilation in Dec-Alpha Ross Walker (Mon Oct 11 2004 - 12:09:40 CDT)
RE: AMBER: AMBER 8 installation - continued Ross Walker (Mon Oct 11 2004 - 12:17:50 CDT)
AMBER: how to set up more than 3 groups constrain Â¬Ç¿ (Mon Oct 11 2004 - 13:33:51 CDT)
AMBER: Question about restart MD Xin Hu (Mon Oct 11 2004 - 13:38:38 CDT)
Re: AMBER: Question about restart MD Carlos Simmerling (Mon Oct 11 2004 - 13:55:39 CDT)
Re: AMBER: Question about restart MD myang_at_vitamin.uni.cc (Mon Oct 11 2004 - 14:05:04 CDT)
RE: AMBER: Question about restart MD Ross Walker (Mon Oct 11 2004 - 14:06:09 CDT)
AMBER: About missing residues Xiao He (Mon Oct 11 2004 - 22:21:47 CDT)
Re: AMBER: About missing residues FyD (Tue Oct 12 2004 - 00:27:58 CDT)
AMBER: process_mdout.perl bybaker_at_itsa.ucsf.edu (Tue Oct 12 2004 - 01:08:06 CDT)
Re: AMBER: process_mdout.perl Donald Thomas (Tue Oct 12 2004 - 01:23:13 CDT)
Re: AMBER: AMBER 8 installation trouble Atro Tossavainen (Tue Oct 12 2004 - 02:29:23 CDT)
AMBER: RE:sander8 Vincent Bisetty (Tue Oct 12 2004 - 02:19:35 CDT)
Re: AMBER: AMBER 8 installation - continued Atro Tossavainen (Tue Oct 12 2004 - 02:37:24 CDT)
AMBER: More installation problems on Solaris 8 Atro Tossavainen (Tue Oct 12 2004 - 02:44:01 CDT)
Re: AMBER: process_mdout.perl Tomas Linhart (Tue Oct 12 2004 - 02:43:28 CDT)
AMBER: Parameter for chlorophyll Fajar Rakhman Wibowo (Tue Oct 12 2004 - 05:46:27 CDT)
AMBER: rms fluct and displacement in modes analysis Vlad Cojocaru (Tue Oct 12 2004 - 05:47:34 CDT)
Re: AMBER: RE:sander8 Carlos Simmerling (Tue Oct 12 2004 - 06:21:02 CDT)
AMBER: Questions about MD sampling Xin Hu (Tue Oct 12 2004 - 10:03:06 CDT)
Re: AMBER: Questions about MD sampling Thomas E. Cheatham, III (Tue Oct 12 2004 - 11:12:18 CDT)
Re: AMBER: rms fluct and displacement in modes analysis David A. Case (Tue Oct 12 2004 - 11:19:48 CDT)
AMBER: klambdas and Weights for Gaussian Quadrature Nelson Fonseca (Tue Oct 12 2004 - 12:01:33 CDT)
Re: AMBER: AMBER 8 installation trouble David A. Case (Tue Oct 12 2004 - 12:28:14 CDT)
RE: AMBER: Questions about MD sampling Ross Walker (Tue Oct 12 2004 - 12:25:30 CDT)
RE: AMBER: Questions about MD sampling Ross Walker (Tue Oct 12 2004 - 12:31:12 CDT)
AMBER: Re: rms fluct and displacement in modes analysis Vlad Cojocaru (Tue Oct 12 2004 - 12:39:33 CDT)
AMBER: Carnal & Radius of gyration opitz_at_che.udel.edu (Tue Oct 12 2004 - 16:29:26 CDT)
Re: AMBER: Carnal & Radius of gyration Bill Ross (Tue Oct 12 2004 - 16:51:30 CDT)
Re: AMBER: klambdas and Weights for Gaussian Quadrature David A. Case (Tue Oct 12 2004 - 18:37:11 CDT)
AMBER: PBSA parameter question (Radii and Charges) Marc Baaden (Tue Oct 12 2004 - 19:01:19 CDT)
AMBER: process_mdout.perl: work now bybaker_at_itsa.ucsf.edu (Tue Oct 12 2004 - 20:32:49 CDT)
AMBER: Re: process_mdout.perl bybaker_at_itsa.ucsf.edu (Tue Oct 12 2004 - 20:36:45 CDT)
AMBER: A question on AMBER8 installation Hwankyu Lee (Tue Oct 12 2004 - 23:39:33 CDT)
RE: AMBER: A question on AMBER8 installation Ross Walker (Wed Oct 13 2004 - 00:43:49 CDT)
Re: AMBER: AMBER 8 installation trouble Atro Tossavainen (Wed Oct 13 2004 - 01:56:19 CDT)
Re: AMBER: Running on MPI Carlos Simmerling (Wed Oct 13 2004 - 08:59:38 CDT)
AMBER: Plot B-factor extracted from PDB file Xin Hu (Wed Oct 13 2004 - 09:41:29 CDT)
Re: AMBER: A question on AMBER8 installation David A. Case (Wed Oct 13 2004 - 09:58:58 CDT)
Re: Re: AMBER: Running on MPI Wu Yingliang (Wed Oct 13 2004 - 08:49:48 CDT)
Re: Re: AMBER: Running on MPI David A. Case (Wed Oct 13 2004 - 10:57:24 CDT)
Re: AMBER: PBSA parameter question (Radii and Charges) Ray Luo (Wed Oct 13 2004 - 11:38:38 CDT)
RE: Re: AMBER: Running on MPI Ross Walker (Wed Oct 13 2004 - 11:51:23 CDT)
Re: Re: AMBER: Running on MPI Bill Ross (Wed Oct 13 2004 - 12:02:42 CDT)
RE: AMBER: A question on AMBER8 installation Bill Ross (Wed Oct 13 2004 - 12:13:48 CDT)
Re: AMBER: A question on AMBER8 installation Scott Brozell (Wed Oct 13 2004 - 12:24:51 CDT)
AMBER: MMPBSA PB parameters - PARSE implementation in Amber Marc Baaden (Wed Oct 13 2004 - 12:42:34 CDT)
Re: AMBER: A question on AMBER8 installation Hwankyu Lee (Wed Oct 13 2004 - 12:53:30 CDT)
RE: AMBER: A question on AMBER8 installation Ross Walker (Wed Oct 13 2004 - 15:21:27 CDT)
AMBER: Question about Amino acid mutations sachin patil (Wed Oct 13 2004 - 18:03:22 CDT)
AMBER: errors in SGI Xiao He (Thu Oct 14 2004 - 02:08:42 CDT)
AMBER: Problem with EDIT (AMBER 5) Daniel Wetzler (Thu Oct 14 2004 - 06:53:45 CDT)
AMBER: modes analysis in ptraj Vlad Cojocaru (Thu Oct 14 2004 - 07:13:14 CDT)
Re: AMBER: Problem with EDIT (AMBER 5) Daniel Wetzler (Thu Oct 14 2004 - 07:23:32 CDT)
AMBER: distance between images riccardo nifosi (Thu Oct 14 2004 - 09:56:40 CDT)
AMBER: mm-pbsa problem Dawei Zhang (Thu Oct 14 2004 - 09:36:03 CDT)
AMBER: amber8 compilation on AIX (regatta) SEKIJIMA Masakazu (Thu Oct 14 2004 - 08:41:40 CDT)
Re: AMBER: errors in SGI David A. Case (Thu Oct 14 2004 - 10:04:24 CDT)
Re: AMBER: distance between images Bill Ross (Thu Oct 14 2004 - 10:09:11 CDT)
Re: AMBER: distance between images Thomas E. Cheatham, III (Thu Oct 14 2004 - 10:51:33 CDT)
AMBER: Amber8 - Energy Calculations Nhat-hang Duong (Thu Oct 14 2004 - 10:53:29 CDT)
RE: AMBER: A question on AMBER8 installation Hwankyu Lee (Thu Oct 14 2004 - 11:04:18 CDT)
Re: Re: AMBER: errors in SGI Xiao He (Thu Oct 14 2004 - 11:09:40 CDT)
AMBER: (no subject) HL Eastwood (Thu Oct 14 2004 - 11:33:34 CDT)
RE: Re: AMBER: errors in SGI Ross Walker (Thu Oct 14 2004 - 11:34:46 CDT)
Re: Re: AMBER: errors in SGI David A. Case (Thu Oct 14 2004 - 11:33:32 CDT)
AMBER: Problem with installing Amber8: Where are the MK libraries? HL Eastwood (Thu Oct 14 2004 - 11:34:54 CDT)
Re: AMBER: A question on AMBER8 installation David A. Case (Thu Oct 14 2004 - 11:45:30 CDT)
RE: AMBER: A question on AMBER8 installation Ross Walker (Thu Oct 14 2004 - 11:50:25 CDT)
RE: AMBER: Problem with installing Amber8: Where are the MK libraries? Ross Walker (Thu Oct 14 2004 - 12:00:02 CDT)
Re: AMBER: amber8 compilation on AIX (regatta) David A. Case (Thu Oct 14 2004 - 12:36:28 CDT)
Re: AMBER: Problem with installing Amber8: Where are the MK libraries? Andreas Svrcek-Seiler (Thu Oct 14 2004 - 12:42:35 CDT)
RE: AMBER: Problem with installing Amber8: Where are the MK libraries? HL Eastwood (Thu Oct 14 2004 - 12:42:54 CDT)
Re: AMBER: Amber8 - Energy Calculations David A. Case (Thu Oct 14 2004 - 12:55:38 CDT)
RE: AMBER: A question on AMBER8 installation Hwankyu Lee (Thu Oct 14 2004 - 12:57:45 CDT)
RE: AMBER: Problem with installing Amber8: Where are the MK libraries? Ross Walker (Thu Oct 14 2004 - 13:06:52 CDT)
AMBER: Use of intel compilers v8.1 for Amber 8. Ross Walker (Thu Oct 14 2004 - 13:13:15 CDT)
RE: AMBER: A question on AMBER8 installation Hwankyu Lee (Thu Oct 14 2004 - 13:13:33 CDT)
Re: AMBER: A question on AMBER8 installation David A. Case (Thu Oct 14 2004 - 13:22:14 CDT)
Re: AMBER: A question on AMBER8 installation M. L. Dodson (Thu Oct 14 2004 - 13:41:15 CDT)
AMBER: normal mode analysis after energy minimizaiton using sander xiaowei li (Thu Oct 14 2004 - 16:57:30 CDT)
Re: AMBER: normal mode analysis after energy minimizaiton using sander David A. Case (Thu Oct 14 2004 - 18:35:01 CDT)
Re: AMBER: A question on AMBER8 installation Hwankyu Lee (Thu Oct 14 2004 - 22:01:05 CDT)
AMBER: Curves 5.3 Mu Yuguang \(Dr\) (Thu Oct 14 2004 - 21:57:57 CDT)
AMBER: Amber 8 - OS support. Poh-Guan Khoo (Fri Oct 15 2004 - 00:54:27 CDT)
Re: AMBER: Problem with installing Amber8: Where are the MK libraries? Atro Tossavainen (Fri Oct 15 2004 - 01:24:13 CDT)
Re: AMBER: Problem with installing Amber8: Where are the MK libraries? Atro Tossavainen (Fri Oct 15 2004 - 02:13:55 CDT)
RE: AMBER: Problem with installing Amber8: Where are the MK libraries? Ross Walker (Fri Oct 15 2004 - 02:26:32 CDT)
Re: AMBER: AMBER 8 installation trouble Atro Tossavainen (Fri Oct 15 2004 - 02:20:54 CDT)
RE: AMBER: Problem with installing Amber8: Where are the MK libraries? Ross Walker (Fri Oct 15 2004 - 02:29:47 CDT)
AMBER: question about molsurf Xiao He (Fri Oct 15 2004 - 03:13:05 CDT)
AMBER: ptraj and clustering Fabian Boes (Fri Oct 15 2004 - 03:15:51 CDT)
Re: AMBER: Problem with installing Amber8: Where are the MK libraries? Atro Tossavainen (Fri Oct 15 2004 - 04:59:29 CDT)
Re: AMBER: Amber8: ifort 8.0.046 Woo hoo! HL Eastwood (Fri Oct 15 2004 - 05:36:57 CDT)
Re: AMBER: Amber8: ifort 8.0.046 Woo hoo! Atro Tossavainen (Fri Oct 15 2004 - 05:55:27 CDT)
AMBER: difference in GBSOL in amber7 and amber8 Xiao He (Fri Oct 15 2004 - 06:11:11 CDT)
Re: AMBER: Amber8: ifort 8.0.046 Woo hoo! Atro Tossavainen (Fri Oct 15 2004 - 07:38:59 CDT)
AMBER: Trajectory corruption Steve Seibold (Fri Oct 15 2004 - 08:48:50 CDT)
Re: AMBER: AMBER 8 installation trouble David A. Case (Fri Oct 15 2004 - 09:51:59 CDT)
Re: AMBER: Trajectory corruption Carlos Simmerling (Fri Oct 15 2004 - 09:54:14 CDT)
Re: AMBER: A question on AMBER8 installation David A. Case (Fri Oct 15 2004 - 09:58:29 CDT)
Re: AMBER: difference in GBSOL in amber7 and amber8 David A. Case (Fri Oct 15 2004 - 10:07:04 CDT)
Re: AMBER: modes analysis in ptraj David A. Case (Fri Oct 15 2004 - 10:18:50 CDT)
Re: AMBER: question about molsurf David A. Case (Fri Oct 15 2004 - 10:28:10 CDT)
AMBER: pmemd and ifort 8.1 Niko Jukarainen (Fri Oct 15 2004 - 08:14:03 CDT)
Re: AMBER: pmemd and ifort 8.1 Robert Duke (Fri Oct 15 2004 - 12:10:08 CDT)
Re: AMBER: Trajectory corruption Adrian E. Roitberg (Fri Oct 15 2004 - 12:06:23 CDT)
Re: AMBER: Trajectory corruption Bill Ross (Fri Oct 15 2004 - 13:00:59 CDT)
AMBER: from gaussian to antechamber Cai, Yufeng (Fri Oct 15 2004 - 13:14:48 CDT)
AMBER: changepot Cai, Yufeng (Fri Oct 15 2004 - 13:33:08 CDT)
AMBER: H bond calculation of CHARMM trajactory using PTRAJ anshul_at_imtech.res.in (Fri Oct 15 2004 - 23:59:33 CDT)
Re: AMBER: from gaussian to antechamber Robyn Ayscue (Fri Oct 15 2004 - 13:41:56 CDT)
Re: AMBER: changepot & mol2 file FyD (Fri Oct 15 2004 - 13:59:46 CDT)
AMBER: error in mm_pbsa Xiao He (Sat Oct 16 2004 - 04:12:41 CDT)
AMBER: amber 8 error Abd Ghani Abd Aziz (Sat Oct 16 2004 - 04:19:38 CDT)
Re: AMBER: error in mm_pbsa Wu Yingliang (Sat Oct 16 2004 - 04:52:47 CDT)
AMBER: amber 8 parallel problem Abd Ghani Abd Aziz (Sat Oct 16 2004 - 05:47:44 CDT)
Re: AMBER: error in mm_pbsa Holger Gohlke (Sat Oct 16 2004 - 08:53:36 CDT)
Re: Re: AMBER: error in mm_pbsa Xiao He (Sat Oct 16 2004 - 10:40:17 CDT)
RE: AMBER: amber 8 error Ross Walker (Sun Oct 17 2004 - 00:20:34 CDT)
RE: AMBER: amber 8 parallel problem Ross Walker (Sun Oct 17 2004 - 00:28:51 CDT)
AMBER: order parameter Jessica Koplin (Sun Oct 17 2004 - 05:30:44 CDT)
Re: AMBER: order parameter Carlos Simmerling (Sun Oct 17 2004 - 08:14:43 CDT)
Re: AMBER: problems with dihedrals - extended information Petr Kulhanek (Sun Oct 17 2004 - 10:39:31 CDT)
RE: AMBER: amber 8 parallel problem Ross Walker (Sun Oct 17 2004 - 13:05:33 CDT)
AMBER: problem with antechamber Cai, Yufeng (Sun Oct 17 2004 - 21:04:28 CDT)
AMBER: More AMBER 8 compilation problems on OSF1 4.0F Atro Tossavainen (Mon Oct 18 2004 - 03:08:30 CDT)
AMBER: about AM1-BCC charge method Xiao He (Mon Oct 18 2004 - 08:21:34 CDT)
Re: AMBER: about AM1-BCC charge method Natasja Brooijmans (Mon Oct 18 2004 - 08:38:11 CDT)
Re: Re: AMBER: about AM1-BCC charge method Xiao He (Mon Oct 18 2004 - 08:59:43 CDT)
AMBER: Calculating H-Bond networks using ptraj Thomas Steinbrecher (Mon Oct 18 2004 - 09:12:05 CDT)
AMBER: file corruption with ptraj Steve Seibold (Mon Oct 18 2004 - 10:10:51 CDT)
AMBER: const-P MD at high T MURAT CETINKAYA (Mon Oct 18 2004 - 10:27:49 CDT)
Re: AMBER: file corruption with ptraj Thomas E. Cheatham, III (Mon Oct 18 2004 - 10:42:02 CDT)
Re: AMBER: file corruption with ptraj cailliez (Mon Oct 18 2004 - 10:32:32 CDT)
Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F David A. Case (Mon Oct 18 2004 - 10:59:58 CDT)
Re: AMBER: const-P MD at high T Carlos Simmerling (Mon Oct 18 2004 - 11:25:52 CDT)
Re: AMBER: const-P MD at high T MURAT CETINKAYA (Mon Oct 18 2004 - 11:52:11 CDT)
Re: AMBER: const-P MD at high T Carlos Simmerling (Mon Oct 18 2004 - 12:22:48 CDT)
Re: AMBER: problems with dihedrals - extended information David A. Case (Mon Oct 18 2004 - 12:42:50 CDT)
Re: AMBER: const-P MD at high T Bill Ross (Mon Oct 18 2004 - 12:47:58 CDT)
Re: AMBER: problems with dihedrals - extended information Bill Ross (Mon Oct 18 2004 - 13:04:33 CDT)
Re: AMBER: const-P MD at high T MURAT CETINKAYA (Mon Oct 18 2004 - 13:13:07 CDT)
Re: AMBER: const-P MD at high T Bill Ross (Mon Oct 18 2004 - 13:26:26 CDT)
Re: AMBER: const-P MD at high T Carlos Simmerling (Mon Oct 18 2004 - 13:29:35 CDT)
Re: AMBER: const-P MD at high T Bill Ross (Mon Oct 18 2004 - 14:16:26 CDT)
Re: AMBER: problem with antechamber David A. Case (Mon Oct 18 2004 - 15:14:29 CDT)
AMBER: question on NAB ioana_at_pegasus.arc.nasa.gov (Mon Oct 18 2004 - 16:18:19 CDT)
AMBER: question on NMR restrain Â¬Ç¿ (Mon Oct 18 2004 - 17:55:54 CDT)
Re: AMBER: question on NMR restrain David A. Case (Mon Oct 18 2004 - 20:30:30 CDT)
AMBER: error in using AM1-BCC charge by antechamber Xiao He (Mon Oct 18 2004 - 23:22:04 CDT)
Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F Atro Tossavainen (Tue Oct 19 2004 - 01:21:57 CDT)
AMBER: BOND energy during minimisation cailliez (Tue Oct 19 2004 - 02:53:47 CDT)
AMBER: amber 8 error Abd Ghani Abd Aziz (Tue Oct 19 2004 - 03:14:24 CDT)
Re: AMBER: BOND energy during minimisation Stef (Tue Oct 19 2004 - 03:35:05 CDT)
Re: AMBER: amber 8 error Andreas Svrcek-Seiler (Tue Oct 19 2004 - 04:00:59 CDT)
Re: AMBER: amber 8 error Atro Tossavainen (Tue Oct 19 2004 - 05:23:23 CDT)
Re: AMBER: amber 8 error Carlos Simmerling (Tue Oct 19 2004 - 06:22:37 CDT)
Re: AMBER: BOND energy during minimisation Carlos Simmerling (Tue Oct 19 2004 - 06:21:28 CDT)
Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F M. L. Dodson (Tue Oct 19 2004 - 07:22:32 CDT)
Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F Atro Tossavainen (Tue Oct 19 2004 - 07:39:21 CDT)
Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F David A. Case (Tue Oct 19 2004 - 09:48:52 CDT)
Re: AMBER: BOND energy during minimisation David A. Case (Tue Oct 19 2004 - 09:59:46 CDT)
Re: AMBER: question on NAB David A. Case (Tue Oct 19 2004 - 10:06:50 CDT)
Re: AMBER: BOND energy during minimisation cailliez (Tue Oct 19 2004 - 11:12:55 CDT)
Re: AMBER: BOND energy during minimisation Carlos Simmerling (Tue Oct 19 2004 - 12:33:52 CDT)
AMBER: MAXMASK problem Qiang Lu (Tue Oct 19 2004 - 12:19:54 CDT)
Re: AMBER: recovering total force array Dave S Walker (Tue Oct 19 2004 - 14:04:16 CDT)
Re: AMBER: A question on AMBER8 installation Hwankyu Lee (Tue Oct 19 2004 - 15:43:48 CDT)
Re: AMBER: MAXMASK problem David A. Case (Tue Oct 19 2004 - 16:10:29 CDT)
Re: AMBER: recovering total force array David A. Case (Tue Oct 19 2004 - 16:26:31 CDT)
Re: AMBER: MAXMASK problem Qiang Lu (Tue Oct 19 2004 - 17:25:03 CDT)
AMBER: Sander-7 for Win32 Vlad (Tue Oct 19 2004 - 18:11:38 CDT)
Re: AMBER: A question on AMBER8 installation David A. Case (Tue Oct 19 2004 - 18:27:08 CDT)
Re: AMBER: recovering total force array Dave S Walker (Tue Oct 19 2004 - 18:59:00 CDT)
Re: AMBER: A question on AMBER8 installation Hwankyu Lee (Tue Oct 19 2004 - 23:12:20 CDT)
Re: AMBER: A question on AMBER8 installation David A. Case (Wed Oct 20 2004 - 00:04:36 CDT)
Re: AMBER: BOND energy during minimisation cailliez (Wed Oct 20 2004 - 02:16:26 CDT)
Re: AMBER: A question on AMBER8 installation Robert Duke (Wed Oct 20 2004 - 07:35:00 CDT)
Re: AMBER: H bond calculation of CHARMM trajactory using PTRAJ Thomas E. Cheatham, III (Wed Oct 20 2004 - 09:16:50 CDT)
AMBER: About STD in NMODE Xiao He (Wed Oct 20 2004 - 11:06:15 CDT)
AMBER: International PhD Symppozium "DECODING NATURE: HIERARCHY OF INTERACTIONS" Vlad Cojocaru (Wed Oct 20 2004 - 11:10:43 CDT)
AMBER: Question about Xleap David LeBard (Wed Oct 20 2004 - 17:28:28 CDT)
Re: AMBER: Sander-7 for Win32 David A. Case (Wed Oct 20 2004 - 18:03:49 CDT)
AMBER: bugfix.17 Helios Chen (Thu Oct 21 2004 - 11:26:23 CDT)
AMBER: Wich CPU? Joachim Reichelt (Thu Oct 21 2004 - 04:34:26 CDT)
AMBER: Amber: what different? Helios Chen (Thu Oct 21 2004 - 20:58:42 CDT)
Re: AMBER: Wich CPU? Robert Duke (Thu Oct 21 2004 - 08:23:48 CDT)
AMBER: add charge error message: Number of electrons is odd berry1027 Eric (Fri Oct 22 2004 - 03:45:30 CDT)
RE: AMBER: Question about Xleap Ross Walker (Fri Oct 22 2004 - 08:31:58 CDT)
AMBER: Jiten (Fri Oct 22 2004 - 10:17:15 CDT)
Re: AMBER: add charge error message: Number of electrons is odd David A. Case (Fri Oct 22 2004 - 16:12:00 CDT)
AMBER: MD problem (very long parhabs endless runtime) Daniel Wetzler (Sat Oct 23 2004 - 08:05:49 CDT)
RE: AMBER: MD problem (very long parhabs endless runtime) Ross Walker (Sat Oct 23 2004 - 11:57:39 CDT)
Re: AMBER: MD problem (very long parhabs endless runtime) Daniel Wetzler (Sat Oct 23 2004 - 13:16:12 CDT)
Re: AMBER: MD problem (very long parhabs endless runtime) myang_at_vitamin.uni.cc (Sat Oct 23 2004 - 13:35:59 CDT)
RE: AMBER: MD problem (very long parhabs endless runtime) Ross Walker (Sat Oct 23 2004 - 13:53:22 CDT)
Re: AMBER: MD problem (very long parhabs endless runtime) Daniel Wetzler (Sun Oct 24 2004 - 04:40:09 CDT)
AMBER: No radius for F atom in MM_PBSA Xiao He (Sun Oct 24 2004 - 08:30:48 CDT)
Re: AMBER: Amber: what different? David A. Case (Sun Oct 24 2004 - 09:17:47 CDT)
AMBER: continue for No radius for F atom in MM_PBSA Xiao He (Sun Oct 24 2004 - 09:40:21 CDT)
Re: AMBER: continue for No radius for F atom in MM_PBSA Holger Gohlke (Sun Oct 24 2004 - 15:06:15 CDT)
AMBER: parallel of sander_classic Xioling Chuang (Mon Oct 25 2004 - 00:57:16 CDT)
AMBER: PMF tang kwa (Mon Oct 25 2004 - 06:59:22 CDT)
Re: AMBER: PMF Carlos Simmerling (Mon Oct 25 2004 - 07:14:19 CDT)
Re: AMBER: parallel of sander_classic David A. Case (Mon Oct 25 2004 - 08:17:44 CDT)
RE: AMBER: parallel of sander_classic Ross Walker (Mon Oct 25 2004 - 08:15:58 CDT)
AMBER: long minimization in sander MURAT CETINKAYA (Mon Oct 25 2004 - 09:53:14 CDT)
Re: AMBER: long minimization in sander Bill Ross (Mon Oct 25 2004 - 10:09:49 CDT)
RE: AMBER: long minimization in sander Ross Walker (Mon Oct 25 2004 - 10:11:29 CDT)
Re: AMBER: long minimization in sander MURAT CETINKAYA (Mon Oct 25 2004 - 10:32:10 CDT)
AMBER: MM_PBSA reproduction of literature values and accuracy Karl N. Kirschner (Mon Oct 25 2004 - 12:41:34 CDT)
Re: AMBER: MM_PBSA reproduction of literature values and accuracy Carlos Simmerling (Mon Oct 25 2004 - 12:53:50 CDT)
Re: AMBER: long minimization in sander Bill Ross (Mon Oct 25 2004 - 15:30:32 CDT)
AMBER: pure aromatic? Cai, Yufeng (Mon Oct 25 2004 - 16:16:06 CDT)
RE: AMBER: long minimization in sander Ross Walker (Mon Oct 25 2004 - 19:03:19 CDT)
AMBER: No skew or curtosis when zero variance in moment Xiao He (Mon Oct 25 2004 - 23:55:08 CDT)
AMBER: Continued:No skew or curtosis when zero variance in moment Xiao He (Tue Oct 26 2004 - 00:02:31 CDT)
Re: AMBER: MM_PBSA reproduction of literature values and accuracy Thomas Steinbrecher (Tue Oct 26 2004 - 02:05:51 CDT)
Re: AMBER: Continued:No skew or curtosis when zero variance in moment Elijah Gregory (Tue Oct 26 2004 - 08:48:55 CDT)
Re: AMBER: parallel of sander_classic Michael Crowley (Tue Oct 26 2004 - 15:03:36 CDT)
AMBER 8 default is now HIS->HIE and not HIS->HID - typo? Chris Moth (Tue Oct 26 2004 - 15:24:05 CDT)
Re: AMBER: MM_PBSA reproduction of literature values and accuracy Karl N. Kirschner (Tue Oct 26 2004 - 17:35:19 CDT)
Re: AMBER: MM_PBSA reproduction of literature values and accuracy Carlos Simmerling (Tue Oct 26 2004 - 17:51:16 CDT)
AMBER: AM1-BCC charges Xin Hu (Tue Oct 26 2004 - 19:19:04 CDT)
Re: AMBER: AM1-BCC charges Oliver Hucke (Tue Oct 26 2004 - 20:29:02 CDT)
AMBER: how to neutralize the peptide Ye Mei (Tue Oct 26 2004 - 21:10:23 CDT)
AMBER: questions regarding JTREE Annette Höglund (Wed Oct 27 2004 - 10:37:06 CDT)
Re: AMBER: how to neutralize the peptide Joseph Nachman (Wed Oct 27 2004 - 12:04:50 CDT)
Re: AMBER: how to neutralize the peptide Chris Moth (Wed Oct 27 2004 - 11:57:23 CDT)
Re: AMBER: questions regarding JTREE Bill Ross (Wed Oct 27 2004 - 12:53:39 CDT)
AMBER: getting new box info Vincent Bisetty (Thu Oct 28 2004 - 09:25:51 CDT)
Re: AMBER: getting new box info David A. Case (Thu Oct 28 2004 - 09:39:07 CDT)
AMBER: a question on ntwx and ntwr scopio (Thu Oct 28 2004 - 09:42:14 CDT)
Re: AMBER: a question on ntwx and ntwr Carlos Simmerling (Thu Oct 28 2004 - 10:50:10 CDT)
Re: AMBER: getting new box info Melinda Layten (Thu Oct 28 2004 - 10:46:57 CDT)
Re: AMBER: AMBER 8 default is now HIS->HIE and not HIS->HID - typo? David A. Case (Thu Oct 28 2004 - 11:50:34 CDT)
AMBER: solvation free energies using mmpbsa Karl N. Kirschner (Thu Oct 28 2004 - 12:15:38 CDT)
AMBER: icc 8.0 built antechamber Scott Brozell (Thu Oct 28 2004 - 12:24:02 CDT)
Re: AMBER: solvation free energies using mmpbsa FyD (Thu Oct 28 2004 - 12:33:34 CDT)
Re: AMBER: solvation free energies using mmpbsa Ray Luo (Wed Oct 27 2004 - 23:06:07 CDT)
AMBER: trajectory file question? opitz_at_che.udel.edu (Thu Oct 28 2004 - 13:15:12 CDT)
Re: AMBER: trajectory file question? Melinda Layten (Thu Oct 28 2004 - 14:35:17 CDT)
AMBER: question about ptraj's Mask Kun Song (Thu Oct 28 2004 - 15:52:08 CDT)
Re: AMBER: question about ptraj's Mask Viktor Hornak (Thu Oct 28 2004 - 16:03:45 CDT)
Re: AMBER: question about ptraj's Mask Kun Song (Thu Oct 28 2004 - 16:10:34 CDT)
AMBER: sander gets stuck MURAT CETINKAYA (Fri Oct 29 2004 - 09:32:22 CDT)
RE: AMBER: sander gets stuck Ross Walker (Fri Oct 29 2004 - 09:52:43 CDT)
RE: AMBER: sander gets stuck MURAT CETINKAYA (Fri Oct 29 2004 - 10:11:15 CDT)
AMBER: Settings about frozen atoms in sander Xiao He (Fri Oct 29 2004 - 10:17:07 CDT)
Re: AMBER: Settings about frozen atoms in sander Jiten (Fri Oct 29 2004 - 11:05:36 CDT)
AMBER: amber7 test on osx Knut Langsetmo (Fri Oct 29 2004 - 13:03:25 CDT)
Re: AMBER: amber7 test on osx Michael Crowley (Fri Oct 29 2004 - 13:31:09 CDT)
RE: AMBER: amber7 test on osx Ross Walker (Fri Oct 29 2004 - 13:38:31 CDT)
Re: AMBER: Settings about frozen atoms in sander Bill Ross (Fri Oct 29 2004 - 13:44:41 CDT)
AMBER: RSM fluctuation & residues bybaker_at_itsa.ucsf.edu (Fri Oct 29 2004 - 15:21:42 CDT)
AMBER: sander error Xiao He (Sat Oct 30 2004 - 01:49:17 CDT)
Re: AMBER: sander error Jiten (Sat Oct 30 2004 - 02:58:33 CDT)
Re: Re: AMBER: sander error Xiao He (Sat Oct 30 2004 - 03:19:15 CDT)
AMBER: MD after partially solvated Xiao He (Sat Oct 30 2004 - 21:52:51 CDT)
Re: AMBER: MD after partially solvated Carlos Simmerling (Sat Oct 30 2004 - 22:11:27 CDT)
AMBER: RSM & ptraj bybaker_at_itsa.ucsf.edu (Sun Oct 31 2004 - 01:13:10 CDT)
Re: AMBER: RSM & ptraj Carlos Simmerling (Sun Oct 31 2004 - 01:25:14 CDT)
Re: AMBER: RSM & ptraj Elijah Gregory (Sun Oct 31 2004 - 01:29:23 CDT)
AMBER: RSM fluctuation by residues bybaker_at_itsa.ucsf.edu (Sun Oct 31 2004 - 01:22:53 CDT)
AMBER: ptraj questions Amber admin (Sun Oct 31 2004 - 08:59:51 CST)
Re: AMBER: ptraj questions Carlos Simmerling (Sun Oct 31 2004 - 09:45:21 CST)
Re: AMBER: ptraj questions Carlos Simmerling (Sun Oct 31 2004 - 11:06:54 CST)
Re: AMBER: ptraj questions Viktor Hornak (Sun Oct 31 2004 - 13:39:48 CST)
AMBER: Re: RSM & ptraj bybaker_at_itsa.ucsf.edu (Sun Oct 31 2004 - 12:43:41 CST)

Last message date: Thu May 05 2005 - 14:26:38 CDT
Archived on: Thu May 05 2005 - 14:30:04 CDT

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