Amber Archive Apr 2006 By Thread
- AMBER: what is the integration scheme for langevin dynamic used in amber8 Li Su (Sat Apr 01 2006 - 05:17:02 PST)
- Re: AMBER: what is the integration scheme for langevin dynamic used in amber8 David A. Case (Sat Apr 01 2006 - 09:18:57 PST)
- Re: AMBER: Announcement: Amber 9 is now available Thomas Patko (CSULB) (Sat Apr 01 2006 - 08:29:26 PST)
- Re: AMBER: Announcement: Amber 9 is now available David A. Case (Sat Apr 01 2006 - 09:21:52 PST)
- Re: AMBER: Announcement: Amber 9 is now available Feng X Zhou (Mon Apr 03 2006 - 08:28:48 PDT)
- Re: AMBER: Announcement: Amber 9 is now available FyD (Mon Apr 03 2006 - 11:00:44 PDT)
- AMBER: Using XML for Amber files David A. Case (Tue Apr 04 2006 - 15:42:35 PDT)
- RE: AMBER: Using XML for Amber files Feng X Zhou (Wed Apr 05 2006 - 08:21:35 PDT)
- Re: AMBER: Using XML for Amber files Xuebin Qiao (Fri Apr 07 2006 - 10:52:08 PDT)
- Re: AMBER: Using XML for Amber files Feng X Zhou (Fri Apr 07 2006 - 11:54:59 PDT)
- AMBER: Umbrella sampling venditti2.unisi.it (Fri Apr 07 2006 - 13:04:55 PDT)
- Re: AMBER: Umbrella sampling David A. Case (Fri Apr 07 2006 - 13:56:48 PDT)
- Re: AMBER: Using XML for Amber files Xuebin Qiao (Mon Apr 24 2006 - 20:57:47 PDT)
- Re: AMBER: Using XML for Amber files Feng X Zhou (Tue Apr 25 2006 - 08:07:39 PDT)
- Re: AMBER: LES error carlos (Sat Apr 01 2006 - 10:04:46 PST)
- AMBER: Different result for serial and parallel sander with IREST=1 (AMBER 8) ! Pradipta Bandyopadhyay (Sun Apr 02 2006 - 22:23:26 PDT)
- Re: AMBER: Different result for serial and parallel sander with IREST=1 (AMBER 8) ! David A. Case (Mon Apr 03 2006 - 07:57:36 PDT)
- AMBER: RMS Wen Li (Mon Apr 03 2006 - 14:03:29 PDT)
- Re: AMBER: RMS carlos (Mon Apr 03 2006 - 14:18:24 PDT)
- Re: AMBER: RMS Wen Li (Tue Apr 04 2006 - 06:59:04 PDT)
- Re: AMBER: RMS carlos (Mon Apr 03 2006 - 14:18:24 PDT)
- AMBER: Semi-empirical parameterization -- van der Waals and H-bonding? Evan Kelly (Mon Apr 03 2006 - 15:28:27 PDT)
- RE: AMBER: Semi-empirical parameterization -- van der Waals and H-bonding? Ross Walker (Mon Apr 03 2006 - 16:53:06 PDT)
- AMBER: Entropy calculations with Nmode and ptraj Daniel Oehme (Tue Apr 04 2006 - 00:24:39 PDT)
- Re: AMBER: Entropy calculations with Nmode and ptraj David A. Case (Tue Apr 04 2006 - 15:50:55 PDT)
- AMBER: POPC parameters xiaoqin huang (Thu Apr 06 2006 - 20:18:10 PDT)
- Re: AMBER: POPC parameters David A. Case (Fri Apr 07 2006 - 09:14:53 PDT)
- AMBER: angle between planes John (Fri Apr 07 2006 - 09:48:38 PDT)
- AMBER: POPC parameters xiaoqin huang (Thu Apr 06 2006 - 20:18:10 PDT)
- Re: AMBER: Entropy calculations with Nmode and ptraj David A. Case (Tue Apr 04 2006 - 15:50:55 PDT)
- AMBER: how to restrain the intramolecular hydrogen bond Ye Mei (Tue Apr 04 2006 - 02:35:42 PDT)
- Re: AMBER: how to restrain the intramolecular hydrogen bond David A. Case (Tue Apr 04 2006 - 15:52:52 PDT)
- AMBER: Obtaining an average structure from a trajectory Alfredo Quevedo (Tue Apr 04 2006 - 16:11:02 PDT)
- RE: AMBER: Obtaining an average structure from a trajectory Ross Walker (Tue Apr 04 2006 - 17:07:18 PDT)
- AMBER: Obtaining an average structure from a trajectory Alfredo Quevedo (Tue Apr 04 2006 - 16:11:02 PDT)
- Re: AMBER: how to restrain the intramolecular hydrogen bond David A. Case (Tue Apr 04 2006 - 15:52:52 PDT)
- AMBER: errors in mm_pbsa.in in AMBER 8 mannul ? tonglei (Tue Apr 04 2006 - 06:10:59 PDT)
- Re: AMBER: errors in mm_pbsa.in in AMBER 8 mannul ? David A. Case (Tue Apr 04 2006 - 15:11:51 PDT)
- Re: AMBER: RMS (fwd) Wen Li (Tue Apr 04 2006 - 08:02:02 PDT)
- Re: AMBER: RMS (fwd) Wen Li (Tue Apr 04 2006 - 08:17:14 PDT)
- AMBER: Any difference about RESP or ESP with Chelpg or MK Jianzhong Liu (Tue Apr 04 2006 - 08:51:36 PDT)
- Re: AMBER: Any difference about RESP or ESP with Chelpg or MK FyD (Tue Apr 04 2006 - 10:01:40 PDT)
- Re: AMBER: Any difference about RESP or ESP with Chelpg or MK David Mobley (Tue Apr 04 2006 - 15:13:30 PDT)
- AMBER: Any difference about RESP or ESP with Chelpg or MK Jianzhong Liu (Tue Apr 04 2006 - 08:51:36 PDT)
- Re: AMBER: RMS (fwd) Wen Li (Tue Apr 04 2006 - 08:17:14 PDT)
- AMBER: molsurf or LCPO method in MM_GB/SA? tonglei (Tue Apr 04 2006 - 18:25:37 PDT)
- AMBER: one question about mm_pbsa ¶ÅÓÀ´º (Tue Apr 04 2006 - 23:47:06 PDT)
- Re: AMBER: one question about mm_pbsa JunJun Liu (Thu Apr 06 2006 - 14:48:20 PDT)
- AMBER: nmode different units cristian obiol (Wed Apr 05 2006 - 03:47:04 PDT)
- AMBER: Claire Zerafa (Wed Apr 05 2006 - 06:33:39 PDT)
- Re: AMBER: David A. Case (Wed Apr 05 2006 - 07:46:18 PDT)
- AMBER: Restarting constant pressure sims with restraints Don.Bashford.stjude.org (Wed Apr 05 2006 - 11:08:41 PDT)
- Re: AMBER: Restarting constant pressure sims with restraints David A. Case (Wed Apr 05 2006 - 11:24:38 PDT)
- Re: AMBER: Restarting constant pressure sims with restraints Robert Duke (Wed Apr 05 2006 - 11:30:05 PDT)
- Re: AMBER: Restarting constant pressure sims with restraints David A. Case (Wed Apr 05 2006 - 11:24:38 PDT)
- AMBER: Question about interpretation of sander.QMMM results Cenk Andac (Thu Apr 06 2006 - 12:10:09 PDT)
- AMBER: MM-GBSA decomposition sishi.tang.utoronto.ca (Thu Apr 06 2006 - 13:20:36 PDT)
- Re: AMBER: MM-GBSA decomposition Holger Gohlke (Sun Apr 09 2006 - 11:13:41 PDT)
- Re: AMBER: MM-GBSA decomposition sishi.tang.utoronto.ca (Sat Apr 15 2006 - 10:54:34 PDT)
- Re: AMBER: MM-GBSA decomposition Holger Gohlke (Sun Apr 09 2006 - 11:13:41 PDT)
- AMBER: PCA venditti2.unisi.it (Thu Apr 06 2006 - 13:27:20 PDT)
- Re: AMBER: PCA Holger Gohlke (Sun Apr 09 2006 - 11:09:06 PDT)
- Re: AMBER: PCA venditti2.unisi.it (Mon Apr 10 2006 - 07:57:41 PDT)
- Re: AMBER: PCA Holger Gohlke (Tue Apr 11 2006 - 05:27:26 PDT)
- Re: AMBER: PCA venditti2.unisi.it (Mon Apr 10 2006 - 07:57:41 PDT)
- Re: AMBER: PCA Holger Gohlke (Sun Apr 09 2006 - 11:09:06 PDT)
- AMBER: organic molecule - from newbie :) Raffaella D'Auria (Thu Apr 06 2006 - 18:55:02 PDT)
- RE: AMBER: organic molecule - from newbie :) Ross Walker (Thu Apr 06 2006 - 19:13:46 PDT)
- RE: AMBER: organic molecule - from newbie :) Raffaella D'Auria (Mon Apr 10 2006 - 15:12:44 PDT)
- RE: AMBER: organic molecule - from newbie :) Ross Walker (Mon Apr 10 2006 - 15:41:56 PDT)
- RE: AMBER: organic molecule - from newbie :) Raffaella D'Auria (Mon Apr 10 2006 - 15:12:44 PDT)
- RE: AMBER: organic molecule - from newbie :) Ross Walker (Thu Apr 06 2006 - 19:13:46 PDT)
- AMBER: NGL error when creating snapshots for MM/PB(GB)SA andy ng (Thu Apr 06 2006 - 23:05:50 PDT)
- Re: AMBER: NGL error when creating snapshots for MM/PB(GB)SA andy ng (Thu Apr 06 2006 - 23:20:16 PDT)
- AMBER: angle between planes John (Fri Apr 07 2006 - 09:55:59 PDT)
- Re: AMBER: angle between planes Chris Moth (Fri Apr 07 2006 - 14:19:26 PDT)
- AMBER: mm-pbsa: distant-dependent dielectric constant lhsong (Sat Apr 08 2006 - 11:30:56 PDT)
- Re: AMBER: mm-pbsa: distant-dependent dielectric constant David A. Case (Sat Apr 08 2006 - 22:23:15 PDT)
- Re: AMBER: mm-pbsa: distant-dependent dielectric constant David A. Case (Sat Apr 08 2006 - 23:11:49 PDT)
- Re: AMBER: mm-pbsa: distant-dependent dielectric constant David A. Case (Sat Apr 08 2006 - 22:23:15 PDT)
- AMBER: "average" command in ptraj Arjen-Joachim Jakobi (Mon Apr 10 2006 - 05:15:16 PDT)
- Re: AMBER: "average" command in ptraj Thomas E. Cheatham, III (Mon Apr 10 2006 - 11:06:20 PDT)
- Re: AMBER: "average" command in ptraj Arjen-Joachim Jakobi (Mon Apr 10 2006 - 11:50:34 PDT)
- AMBER: PB bomb in pb_atmlist(): MAXNEI too short snowyowls (Mon Apr 10 2006 - 05:55:12 PDT)
- Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short Scott Brozell (Mon Apr 10 2006 - 07:59:46 PDT)
- Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short snowyowls (Mon Apr 10 2006 - 20:07:40 PDT)
- Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short Ray Luo (Sun Apr 09 2006 - 19:44:44 PDT)
- Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short snowyowls (Mon Apr 10 2006 - 20:09:35 PDT)
- Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short Scott Brozell (Mon Apr 10 2006 - 07:59:46 PDT)
- AMBER: printing Amber VdW radii as separate column in pdb files Vlad Cojocaru (Mon Apr 10 2006 - 07:41:51 PDT)
- Re: AMBER: printing Amber VdW radii as separate column in pdb files harianto (Mon Apr 10 2006 - 08:12:39 PDT)
- Re: AMBER: printing Amber VdW radii as separate column in pdb files Vlad Cojocaru (Mon Apr 10 2006 - 08:43:18 PDT)
- RE: AMBER: printing Amber VdW radii as separate column in pdb files Ross Walker (Mon Apr 10 2006 - 09:03:18 PDT)
- Re: AMBER: printing Amber VdW radii as separate column in pdb files Vlad Cojocaru (Mon Apr 10 2006 - 08:43:18 PDT)
- Re: AMBER: printing Amber VdW radii as separate column in pdb files harianto (Mon Apr 10 2006 - 08:12:39 PDT)
- AMBER: VdW radii in the topology file Vlad Cojocaru (Mon Apr 10 2006 - 09:14:16 PDT)
- Re: AMBER: VdW radii in the topology file harianto (Mon Apr 10 2006 - 09:51:55 PDT)
- Re: AMBER: VdW radii in the topology file Vlad Cojocaru (Mon Apr 10 2006 - 10:01:33 PDT)
- Re: AMBER: VdW radii in the topology file harianto (Mon Apr 10 2006 - 09:51:55 PDT)
- AMBER: reconstructing PMF Ioana Cozmuta (Mon Apr 10 2006 - 11:15:20 PDT)
- AMBER: "vector" command in ptraj Lishan Yao (Mon Apr 10 2006 - 11:20:56 PDT)
- AMBER: protocols for NMR protein refinement with AMBER ohucke.lav.boehringer-ingelheim.com (Mon Apr 10 2006 - 13:43:44 PDT)
- Re: AMBER: protocols for NMR protein refinement with AMBER David A. Case (Mon Apr 10 2006 - 13:55:43 PDT)
- AMBER: the best force field for DNA Chengwen Chen (Mon Apr 10 2006 - 21:15:25 PDT)
- AMBER: RESP problem Simon Whitehead (Tue Apr 11 2006 - 06:44:00 PDT)
- RE: AMBER: RESP problem Ross Walker (Tue Apr 11 2006 - 08:08:25 PDT)
- AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3 Mathy Froeyen (Tue Apr 11 2006 - 10:44:40 PDT)
- Re: AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3 David A. Case (Tue Apr 11 2006 - 11:19:59 PDT)
- AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3 Mathy Froeyen (Tue Apr 11 2006 - 10:44:40 PDT)
- Re: AMBER: RESP problem FyD (Tue Apr 11 2006 - 09:31:12 PDT)
- AMBER: How to evaluate the binding energy of a ligand? Alfredo Quevedo (Tue Apr 11 2006 - 10:53:50 PDT)
- Re: AMBER: How to evaluate the binding energy of a ligand? David Mobley (Tue Apr 11 2006 - 12:27:13 PDT)
- AMBER: How to evaluate the binding energy of a ligand? Alfredo Quevedo (Tue Apr 11 2006 - 10:53:50 PDT)
- RE: AMBER: RESP problem Ross Walker (Tue Apr 11 2006 - 08:08:25 PDT)
- AMBER: An issue with the "multimolecule and multiconformational" resp fit Jason K (Tue Apr 11 2006 - 11:16:57 PDT)
- Re: AMBER: An issue with the "multimolecule and multiconformational" resp fit FyD (Tue Apr 11 2006 - 12:39:40 PDT)
- AMBER: Nmode memory allocation error ? Junmei Wang (Tue Apr 11 2006 - 11:47:46 PDT)
- Re: AMBER: Nmode memory allocation error ? David A. Case (Tue Apr 11 2006 - 12:09:26 PDT)
- AMBER: Constant P for non-orthorhombic cells Jennie Thomas (Tue Apr 11 2006 - 21:40:00 PDT)
- Re: AMBER: Constant P for non-orthorhombic cells darden (Wed Apr 12 2006 - 05:41:14 PDT)
- Re: AMBER: Constant P for non-orthorhombic cells Michael Crowley (Wed Apr 12 2006 - 11:24:05 PDT)
- Re: AMBER: Constant P for non-orthorhombic cells Jennie Thomas (Wed Apr 12 2006 - 11:36:47 PDT)
- AMBER: Mass wieghted Covariance Matrix Daniel Oehme (Wed Apr 12 2006 - 00:16:32 PDT)
- Re: AMBER: Mass wieghted Covariance Matrix Holger Gohlke (Wed Apr 12 2006 - 00:46:19 PDT)
- AMBER: deviations from idealized geometry Maarit Hellman (Wed Apr 12 2006 - 02:02:33 PDT)
- AMBER: saltcon with explicit water? Kenley Barrett (Wed Apr 12 2006 - 09:36:20 PDT)
- Re: AMBER: saltcon with explicit water? David A. Case (Wed Apr 12 2006 - 12:25:38 PDT)
- Re: AMBER: saltcon with explicit water? Kenley Barrett (Wed Apr 12 2006 - 16:07:44 PDT)
- Re: AMBER: saltcon with explicit water? Bill Ross (Wed Apr 12 2006 - 16:26:05 PDT)
- Re: AMBER: saltcon with explicit water? David A. Case (Wed Apr 12 2006 - 12:25:38 PDT)
- AMBER: Which one is the best force field for DNA? Chengwen Chen (Wed Apr 12 2006 - 20:11:14 PDT)
- Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Thu Apr 13 2006 - 01:11:33 PDT)
- Re: AMBER: Which one is the best force field for DNA? David A. Case (Thu Apr 13 2006 - 14:41:03 PDT)
- Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Fri Apr 14 2006 - 02:57:33 PDT)
- Re: AMBER: Which one is the best force field for DNA? Jiri Sponer (Fri Apr 14 2006 - 03:31:24 PDT)
- Re: AMBER: Which one is the best force field for DNA? David A. Case (Fri Apr 14 2006 - 08:27:52 PDT)
- Re: AMBER: Which one is the best force field for DNA? Jiri Sponer (Fri Apr 14 2006 - 09:59:00 PDT)
- Re: AMBER: Which one is the best force field for DNA? Thomas E. Cheatham, III (Fri Apr 14 2006 - 09:01:50 PDT)
- Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Fri Apr 14 2006 - 09:30:23 PDT)
- Re: AMBER: Which one is the best force field for DNA? Carlos Simmerling (Fri Apr 14 2006 - 09:41:04 PDT)
- Re: AMBER: Which one is the best force field for DNA? Jiri Sponer (Fri Apr 14 2006 - 09:49:58 PDT)
- Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Fri Apr 14 2006 - 10:01:27 PDT)
- Re: AMBER: Which one is the best force field for DNA? Jiri Sponer (Fri Apr 14 2006 - 10:08:34 PDT)
- Re: AMBER: Which one is the best force field for DNA? Thomas Cheatham (Fri Apr 14 2006 - 10:20:14 PDT)
- Re: AMBER: Which one is the best force field for DNA? David A. Case (Fri Apr 14 2006 - 10:53:50 PDT)
- Re: AMBER: Which one is the best force field for DNA? Carlos Simmerling (Fri Apr 14 2006 - 11:28:42 PDT)
- AMBER: Force field for DNA Osmar Norberto de Souza (Mon Apr 17 2006 - 03:50:31 PDT)
- Re: AMBER: Which one is the best force field for DNA? David A. Case (Thu Apr 13 2006 - 14:41:03 PDT)
- Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Thu Apr 13 2006 - 01:11:33 PDT)
- AMBER:a problem in parallel compiler snowyowls (Wed Apr 12 2006 - 21:27:10 PDT)
- AMBER:a problem in parallel compiler snowyowls (Thu Apr 13 2006 - 01:15:09 PDT)
- RE: AMBER:a problem in parallel compiler Ross Walker (Thu Apr 13 2006 - 08:54:43 PDT)
- AMBER:a problem in parallel compiler snowyowls (Thu Apr 13 2006 - 01:15:09 PDT)
- AMBER: Dual Xeon mpich compilation error Simon Whitehead (Thu Apr 13 2006 - 00:56:47 PDT)
- AMBER: one question about mm_pbsa ¶ÅÓÀ´º (Thu Apr 13 2006 - 01:37:50 PDT)
- Re: AMBER: one question about mm_pbsa Ray Luo (Thu Apr 13 2006 - 08:39:53 PDT)
- Re: AMBER: one question about mm_pbsa ¶ÅÓÀ´º (Thu Apr 13 2006 - 19:26:49 PDT)
- AMBER: dual xeon mpich compilation problem: sorted Simon Whitehead (Thu Apr 13 2006 - 05:16:53 PDT)
- AMBER: passwordless ssh stopped working Jan Dohnalek (Thu Apr 13 2006 - 08:51:50 PDT)
- AMBER: Respgen segemtation fault Simon Whitehead (Thu Apr 13 2006 - 09:38:41 PDT)
- Re: AMBER: Respgen segemtation fault David A. Case (Thu Apr 13 2006 - 11:46:55 PDT)
- AMBER: separating LES copies in moil view Amber admin (Thu Apr 13 2006 - 10:28:02 PDT)
- Re: AMBER: separating LES copies in moil view Carlos Simmerling (Thu Apr 13 2006 - 16:45:35 PDT)
- AMBER: Saving single coordinate set from Amber trajectory file as a restrt file. Sergey Krishtal (Thu Apr 13 2006 - 20:05:45 PDT)
- Re: AMBER: Saving single coordinate set from Amber trajectory file as a restrt file. Vlad Cojocaru (Fri Apr 14 2006 - 02:18:41 PDT)
- AMBER: MM-PBSA problem Miguel Ferreira (Fri Apr 14 2006 - 08:27:43 PDT)
- Re: AMBER: MM-PBSA problem Ray Luo (Fri Apr 14 2006 - 09:57:52 PDT)
- Re: AMBER: MM-PBSA problem Miguel Ferreira (Fri Apr 14 2006 - 14:07:20 PDT)
- Re: AMBER: MM-PBSA problem Ray Luo (Fri Apr 14 2006 - 14:40:45 PDT)
- Re: AMBER: MM-PBSA problem Miguel Ferreira (Fri Apr 14 2006 - 14:07:20 PDT)
- Re: AMBER: MM-PBSA problem Miguel Ferreira (Mon Apr 17 2006 - 10:24:05 PDT)
- Re: AMBER: MM-PBSA problem Ray Luo (Fri Apr 14 2006 - 09:57:52 PDT)
- AMBER: DNA tutorial, in vacuo minimization amanda.mccook.gatech.edu (Fri Apr 14 2006 - 12:15:31 PDT)
- RE: AMBER: DNA tutorial, in vacuo minimization Ross Walker (Fri Apr 14 2006 - 12:34:32 PDT)
- AMBER: compile error: can't locate file for: -lcrt1.o xyu3 (Fri Apr 14 2006 - 15:37:50 PDT)
- Re: AMBER: compile error: can't locate file for: -lcrt1.o David A. Case (Fri Apr 14 2006 - 15:58:33 PDT)
- AMBER: amber memory usage Ed Pate (Fri Apr 14 2006 - 15:45:59 PDT)
- Re: AMBER: amber memory usage Robert Duke (Fri Apr 14 2006 - 15:56:12 PDT)
- RE: AMBER: amber memory usage Ross Walker (Fri Apr 14 2006 - 17:28:31 PDT)
- Re: AMBER: amber memory usage David A. Case (Fri Apr 14 2006 - 17:30:44 PDT)
- AMBER: How I wasted a rainy Friday in San Diego David A. Case (Fri Apr 14 2006 - 17:24:00 PDT)
- AMBER: Calculation of g(r) from PTRAJ Ananda Rama Krishnan Selvaraj (Sun Apr 16 2006 - 03:33:25 PDT)
- Re: AMBER: Calculation of g(r) from PTRAJ David A. Case (Mon Apr 17 2006 - 09:45:27 PDT)
- Re: AMBER: Calculation of g(r) from PTRAJ Ananda Rama Krishnan Selvaraj (Mon Apr 17 2006 - 10:45:39 PDT)
- AMBER: amber7 compiling error linfu (Sun Apr 16 2006 - 08:26:17 PDT)
- Re: AMBER: amber7 compiling error Scott Brozell (Sun Apr 16 2006 - 12:30:23 PDT)
- AMBER: Could not find atom type. Sergey Krishtal (Mon Apr 17 2006 - 02:08:19 PDT)
- Re: AMBER: Could not find atom type. David A. Case (Mon Apr 17 2006 - 09:40:05 PDT)
- RE: AMBER: Could not find atom type. Yong Duan (Mon Apr 17 2006 - 09:45:10 PDT)
- Re[2]: AMBER: Could not find atom type. Sergey Krishtal (Tue Apr 18 2006 - 03:48:07 PDT)
- Re: AMBER: Could not find atom type. David A. Case (Tue Apr 18 2006 - 16:06:21 PDT)
- Re[2]: AMBER: Could not find atom type. Sergey Krishtal (Tue Apr 18 2006 - 19:56:30 PDT)
- Re: AMBER: Could not find atom type. David A. Case (Wed Apr 19 2006 - 12:37:33 PDT)
- Re: AMBER: Could not find atom type. David A. Case (Tue Apr 18 2006 - 16:06:21 PDT)
- AMBER: ambpdb and original PDB snoze pa (Mon Apr 17 2006 - 11:20:05 PDT)
- RE: AMBER: ambpdb and original PDB Ross Walker (Mon Apr 17 2006 - 11:28:18 PDT)
- Re: AMBER: ambpdb and original PDB snoze pa (Mon Apr 17 2006 - 11:48:55 PDT)
- Re: AMBER: ambpdb and original PDB Mingfeng Yang (Mon Apr 17 2006 - 13:00:53 PDT)
- Re: AMBER: ambpdb and original PDB Mingfeng Yang (Mon Apr 17 2006 - 13:05:43 PDT)
- Re: AMBER: ambpdb and original PDB snoze pa (Mon Apr 17 2006 - 11:48:55 PDT)
- RE: AMBER: ambpdb and original PDB Ross Walker (Mon Apr 17 2006 - 11:28:18 PDT)
- Re: AMBER: ambpdb and original PDB Bill Ross (Mon Apr 17 2006 - 11:38:17 PDT)
- AMBER: probable bug in antechamber David Mobley (Mon Apr 17 2006 - 16:08:06 PDT)
- Re: AMBER: probable bug in antechamber David A. Case (Mon Apr 17 2006 - 17:33:35 PDT)
- Re: AMBER: probable bug in antechamber David Mobley (Tue Apr 18 2006 - 06:52:13 PDT)
- Re: AMBER: probable bug in antechamber David A. Case (Mon Apr 17 2006 - 17:33:35 PDT)
- AMBER: ibelly & fix atom rdauria.uci.edu (Mon Apr 17 2006 - 20:41:28 PDT)
- Re: AMBER: ibelly & fix atom rdauria.uci.edu (Mon Apr 17 2006 - 20:59:56 PDT)
- RE: AMBER: ibelly & fix atom Ross Walker (Mon Apr 17 2006 - 21:08:42 PDT)
- RE: AMBER: ibelly & fix atom rdauria.uci.edu (Mon Apr 17 2006 - 21:22:16 PDT)
- AMBER: Error in the MD run Ananda Rama Krishnan Selvaraj (Mon Apr 17 2006 - 23:13:04 PDT)
- RE: AMBER: Error in the MD run Ross Walker (Tue Apr 18 2006 - 08:35:41 PDT)
- AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight Ross Walker (Tue Apr 18 2006 - 08:42:41 PDT)
- Re: AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight Shulin Zhuang (Tue Apr 18 2006 - 22:58:06 PDT)
- RE: AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight Ross Walker (Wed Apr 19 2006 - 08:16:51 PDT)
- Re: AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight Shulin Zhuang (Tue Apr 18 2006 - 22:58:06 PDT)
- AMBER: RE: Respgen segemtation fault Simon Whitehead (Wed Apr 19 2006 - 10:10:11 PDT)
- AMBER: Installing Delphi to perform mm_pbsa analysis? Alfredo Quevedo (Wed Apr 19 2006 - 10:39:13 PDT)
- Re: AMBER: Installing Delphi to perform mm_pbsa analysis? David A. Case (Wed Apr 19 2006 - 12:43:46 PDT)
- Re: AMBER: RE: Respgen segemtation fault David A. Case (Thu Apr 20 2006 - 04:49:34 PDT)
- Re: AMBER: RE: Respgen segemtation fault Simon Whitehead (Thu Apr 20 2006 - 05:30:48 PDT)
- AMBER: Antechamber & atom types FyD (Thu Apr 20 2006 - 10:04:17 PDT)
- Re: AMBER: Antechamber & atom types David A. Case (Fri Apr 21 2006 - 08:22:45 PDT)
- AMBER: Installing Delphi to perform mm_pbsa analysis? Alfredo Quevedo (Wed Apr 19 2006 - 10:39:13 PDT)
- AMBER: timing estimates Ed Pate (Wed Apr 19 2006 - 16:10:30 PDT)
- Re: AMBER: timing estimates Robert Duke (Wed Apr 19 2006 - 17:06:59 PDT)
- RE: AMBER: RE: Respgen segemtation fault - debug attempt Simon Whitehead (Thu Apr 20 2006 - 05:48:07 PDT)
- Re: AMBER: RE: Respgen segemtation fault - debug attempt Mark Williamson (Thu Apr 20 2006 - 06:23:55 PDT)
- RE: AMBER: RE: Respgen segemtation fault - debug attempt Simon Whitehead (Thu Apr 20 2006 - 09:30:51 PDT)
- Re: AMBER: RE: Respgen segemtation fault - debug attempt Mark Williamson (Thu Apr 20 2006 - 09:56:55 PDT)
- AMBER: about the decomposition energies using mm/pbsa litong (Thu Apr 20 2006 - 06:34:11 PDT)
- Re: AMBER: about the decomposition energies using mm/pbsa Holger Gohlke (Fri Apr 21 2006 - 00:25:44 PDT)
- AMBER: Non-periodic simulations: How is the system kept together? pascal.baillod.epfl.ch (Thu Apr 20 2006 - 09:13:04 PDT)
- RE: AMBER: Non-periodic simulations: How is the system kept together? Ross Walker (Thu Apr 20 2006 - 09:35:26 PDT)
- AMBER: a question about "solvateoct" in AMBER 8 Chengwen Chen (Thu Apr 20 2006 - 23:48:14 PDT)
- AMBER: Error when compiling amber9 ptraj Thomas Steinbrecher (Fri Apr 21 2006 - 01:19:54 PDT)
- Re: AMBER: Error when compiling amber9 ptraj David A. Case (Fri Apr 21 2006 - 05:08:15 PDT)
- AMBER: a question german (Fri Apr 21 2006 - 04:04:54 PDT)
- RE: AMBER: a question Ross Walker (Fri Apr 21 2006 - 13:35:51 PDT)
- Re: AMBER: a question Robert Duke (Mon Apr 24 2006 - 11:21:34 PDT)
- RE: AMBER: a question Ross Walker (Fri Apr 21 2006 - 13:35:51 PDT)
- AMBER: problems with saveamberprep command JAVIER PEREZ (Fri Apr 21 2006 - 04:33:48 PDT)
- AMBER: mm_pbsa: "Missing values for MM ..." Sam (Fri Apr 21 2006 - 06:39:19 PDT)
- AMBER: Problems compiling amber9 Thomas Steinbrecher (Fri Apr 21 2006 - 07:27:51 PDT)
- Re: AMBER: Problems compiling amber9 David A. Case (Fri Apr 21 2006 - 08:03:37 PDT)
- AMBER: Fujitsu frt compiler Evan Kelly (Fri Apr 21 2006 - 07:53:40 PDT)
- Re: AMBER: a question about "solvateoct" in AMBER 8 Bill Ross (Fri Apr 21 2006 - 11:48:01 PDT)
- Re: AMBER: a question about "solvateoct" in AMBER 8 Michael Crowley (Fri Apr 21 2006 - 12:50:52 PDT)
- Re: AMBER: a question about "solvateoct" in AMBER 8 Chengwen Chen (Sun Apr 23 2006 - 21:13:30 PDT)
- Re: AMBER: a question about "solvateoct" in AMBER 8 Michael Crowley (Fri Apr 21 2006 - 12:50:52 PDT)
- AMBER: amber9 compilation error on SGI altix Lihua Wang (Sat Apr 22 2006 - 10:58:26 PDT)
- RE: AMBER: amber9 compilation error on SGI altix Ross Walker (Sat Apr 22 2006 - 12:21:24 PDT)
- RE: AMBER: amber9 compilation error on SGI altix Lihua Wang (Sat Apr 22 2006 - 15:48:40 PDT)
- RE: AMBER: amber9 compilation error on SGI altix Ross Walker (Sat Apr 22 2006 - 12:21:24 PDT)
- AMBER: increase in computational time with LES Kenley Barrett (Sun Apr 23 2006 - 14:53:29 PDT)
- Re: AMBER: increase in computational time with LES Adrian Roitberg (Sun Apr 23 2006 - 15:26:20 PDT)
- Re: AMBER: increase in computational time with LES Kenley Barrett (Sun Apr 23 2006 - 15:46:56 PDT)
- Re: AMBER: increase in computational time with LES Carlos Simmerling (Sun Apr 23 2006 - 16:00:20 PDT)
- Re: AMBER: increase in computational time with LES Kenley Barrett (Sun Apr 23 2006 - 15:46:56 PDT)
- Re: AMBER: increase in computational time with LES Adrian Roitberg (Sun Apr 23 2006 - 15:26:20 PDT)
- AMBER: LES copies Claudia Steinert (Mon Apr 24 2006 - 01:28:06 PDT)
- Re: AMBER: LES copies Carlos Simmerling (Mon Apr 24 2006 - 04:14:20 PDT)
- AMBER: a quetion german (Mon Apr 24 2006 - 04:17:34 PDT)
- Re: AMBER: a quetion Mingfeng Yang (Mon Apr 24 2006 - 06:07:30 PDT)
- RE: AMBER: a quetion Ross Walker (Mon Apr 24 2006 - 07:52:59 PDT)
- Re: AMBER: a quetion darden (Mon Apr 24 2006 - 07:57:59 PDT)
- AMBER: modeling zinc binding site Jan Kosinski (Mon Apr 24 2006 - 05:28:55 PDT)
- AMBER: MM_PBSA: “Found unknown atflag DELPHI” haixiao jin (Mon Apr 24 2006 - 08:23:23 PDT)
- Re: AMBER: MM_PBSA: “Found unknown atflag DELPHI” Ray Luo (Mon Apr 24 2006 - 11:40:28 PDT)
- Re: AMBER: MM_PBSA: “Found unknown atflag DELPHI” Scott Pendley (Wed Apr 26 2006 - 15:54:53 PDT)
- AMBER: rmsd value for organic molecule Varsha Goyal (Mon Apr 24 2006 - 12:00:20 PDT)
- RE: AMBER: rmsd value for organic molecule Ross Walker (Mon Apr 24 2006 - 12:25:23 PDT)
- RE: AMBER: rmsd value for organic molecule Varsha Goyal (Mon Apr 24 2006 - 13:48:59 PDT)
- RE: AMBER: rmsd value for organic molecule Ross Walker (Mon Apr 24 2006 - 12:25:23 PDT)
- AMBER: compiling errors Alex Tzanov (Mon Apr 24 2006 - 17:17:50 PDT)
- RE: AMBER: compiling errors Ross Walker (Mon Apr 24 2006 - 17:58:52 PDT)
- Re: AMBER: compiling errors Alex Tzanov (Mon Apr 24 2006 - 19:04:10 PDT)
- Re: AMBER: compiling errors Atro Tossavainen (Wed Apr 26 2006 - 00:49:23 PDT)
- RE: AMBER: compiling errors Ross Walker (Mon Apr 24 2006 - 17:58:52 PDT)
- AMBER: Born igb =2 harianto (Mon Apr 24 2006 - 18:27:24 PDT)
- Re: AMBER: Born igb =2 John Mongan (Tue Apr 25 2006 - 10:30:22 PDT)
- AMBER: Test Failure during amber9 serial compilation Thomas Steinbrecher (Tue Apr 25 2006 - 07:17:29 PDT)
- Re: AMBER: Test Failure during amber9 serial compilation Ray Luo (Tue Apr 25 2006 - 11:01:49 PDT)
- RE: AMBER: Test Failure during amber9 serial compilation Ross Walker (Tue Apr 25 2006 - 12:30:19 PDT)
- RE: AMBER: Test Failure during amber9 serial compilation Thomas Steinbrecher (Wed Apr 26 2006 - 02:23:24 PDT)
- Re: AMBER: Test Failure during amber9 serial compilation Ray Luo (Wed Apr 26 2006 - 11:29:11 PDT)
- RE: AMBER: Test Failure during amber9 serial compilation Ross Walker (Wed Apr 26 2006 - 11:49:06 PDT)
- RE: AMBER: Test Failure during amber9 serial compilation Thomas Steinbrecher (Wed Apr 26 2006 - 02:23:24 PDT)
- AMBER: DNA structure Ioana Cozmuta (Tue Apr 25 2006 - 13:17:12 PDT)
- Re: AMBER: DNA structure Ioana Cozmuta (Wed Apr 26 2006 - 12:06:22 PDT)
- AMBER: error propagation in MM-PBSA binding free energy calculation lhsong (Tue Apr 25 2006 - 20:22:41 PDT)
- Re: AMBER: error propagation in MM-PBSA binding free energy calculation Jianyin Shao (Wed Apr 26 2006 - 17:13:48 PDT)
- Re: AMBER: error propagation in MM-PBSA binding free energy calculation lhsong (Fri Apr 28 2006 - 15:37:42 PDT)
- Re: AMBER: error propagation in MM-PBSA binding free energy calculation Jianyin Shao (Wed Apr 26 2006 - 17:13:48 PDT)
- AMBER: two references Ioana Cozmuta (Wed Apr 26 2006 - 13:18:28 PDT)
- AMBER: two references- I got them, thank you! Ioana Cozmuta (Wed Apr 26 2006 - 14:15:11 PDT)
- AMBER: internal coordinates Ioana Cozmuta (Wed Apr 26 2006 - 14:56:20 PDT)
- Re: AMBER: internal coordinates David A. Case (Sun Apr 30 2006 - 09:09:52 PDT)
- AMBER: questions about mm_pbsa Weihua Li (Wed Apr 26 2006 - 20:09:45 PDT)
- Re: AMBER: questions about mm_pbsa Ray Luo (Wed Apr 26 2006 - 18:03:13 PDT)
- AMBER: Force Field Question Ilyas Yildirim (Thu Apr 27 2006 - 14:57:58 PDT)
- AMBER: distance restraints for umbrella sampling mkseo (Thu Apr 27 2006 - 15:21:16 PDT)
- AMBER: heating process r. a. (Thu Apr 27 2006 - 22:56:06 PDT)
- Re: AMBER: heating process Carlos Simmerling (Fri Apr 28 2006 - 04:06:03 PDT)
- AMBER: Langevin mode error?? Cenk Andac (Fri Apr 28 2006 - 04:52:02 PDT)
- Re: AMBER: Langevin mode error?? David A. Case (Fri Apr 28 2006 - 13:13:31 PDT)
- AMBER: Langevin mode error?? Cenk Andac (Fri Apr 28 2006 - 04:52:02 PDT)
- Re: AMBER: heating process Carlos Simmerling (Fri Apr 28 2006 - 04:06:03 PDT)
- AMBER: how to perform parallel MD on a linux cluster with Platform LSF product Yu Zh.H. (Fri Apr 28 2006 - 03:31:08 PDT)
- Re: AMBER: how to perform parallel MD on a linux cluster with Platform LSF product Hector A. Baldoni (Sat Apr 29 2006 - 17:08:30 PDT)
- AMBER: 7-Methylguanine force field parameters Supat Jiranusornkul (Fri Apr 28 2006 - 07:03:22 PDT)
- AMBER: 7-Methylguanine force field parameters Supat Jiranusornkul (Fri Apr 28 2006 - 07:13:55 PDT)
- AMBER: Performing Simulated Annealing? alfredoq.fcq.unc.edu.ar (Fri Apr 28 2006 - 09:58:31 PDT)
- RE: AMBER: Performing Simulated Annealing? Ross Walker (Fri Apr 28 2006 - 10:13:56 PDT)
- Re: AMBER: Performing Simulated Annealing? Carlos Simmerling (Fri Apr 28 2006 - 10:16:43 PDT)
- AMBER: How to build 1,4-dimethyl benzene with amber9 martin peters (Fri Apr 28 2006 - 14:27:09 PDT)
- RE: AMBER: How to build 1,4-dimethyl benzene with amber9 Ross Walker (Fri Apr 28 2006 - 15:10:56 PDT)
- Re: AMBER: How to build 1,4-dimethyl benzene with amber9 martin peters (Fri Apr 28 2006 - 16:00:29 PDT)
- RE: AMBER: How to build 1,4-dimethyl benzene with amber9 Ross Walker (Fri Apr 28 2006 - 16:46:23 PDT)
- Re: AMBER: How to build 1,4-dimethyl benzene with amber9 martin peters (Fri Apr 28 2006 - 16:00:29 PDT)
- RE: AMBER: How to build 1,4-dimethyl benzene with amber9 Ross Walker (Fri Apr 28 2006 - 15:10:56 PDT)
- AMBER: Setting box dimensions in leap Jennie Thomas (Fri Apr 28 2006 - 15:42:38 PDT)
- Re: AMBER: Setting box dimensions in leap David A. Case (Sat Apr 29 2006 - 22:42:48 PDT)
- AMBER: about the execuation of REMD with sander of amber9 pang zhao (Fri Apr 28 2006 - 20:08:41 PDT)
- Re: AMBER: about the execuation of REMD with sander of amber9 pang zhao (Fri Apr 28 2006 - 22:12:22 PDT)
- Re: AMBER: about the execuation of REMD with sander of amber9 Carlos Simmerling (Sat Apr 29 2006 - 06:45:24 PDT)
- Re: AMBER: about the execuation of REMD with sander of amber9 pang zhao (Sun Apr 30 2006 - 01:58:06 PDT)
- Re: AMBER: about the execuation of REMD with sander of amber9 Carlos Simmerling (Sat Apr 29 2006 - 06:45:24 PDT)
- Re: AMBER: about the execuation of REMD with sander of amber9 Carlos Simmerling (Sat Apr 29 2006 - 06:43:46 PDT)
- Re: AMBER: about the execuation of REMD with sander of amber9 pang zhao (Fri Apr 28 2006 - 22:12:22 PDT)
- AMBER: about the shake with self-guide LD pang zhao (Sat Apr 29 2006 - 03:44:39 PDT)
- AMBER: AMBER9: MacG5 parallel sander.MPI In Hee Park (Sat Apr 29 2006 - 13:59:28 PDT)
- Re: AMBER: AMBER9: MacG5 parallel sander.MPI Gert Kiss (Sat Apr 29 2006 - 15:29:51 PDT)
- AMBER: Did these differences come from so-called "different machines" ? Zhihong Yu (Sun Apr 30 2006 - 01:47:28 PDT)
- Re: AMBER: Did these differences come from so-called "different machines" ? David A. Case (Sun Apr 30 2006 - 21:09:35 PDT)
- Re: AMBER: Amber 9, sander imin = 5, -y flag David A. Case (Sun Apr 30 2006 - 21:08:24 PDT)
- Last message date: Wed May 03 2006 - 06:07:07 PDT
- Archived on: Mon Jan 05 2009 - 06:09:26 PST
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