AMBER Archive (2004) - Aug 2004 By ThreadMost recent messages
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Starting: Mon Aug 02 2004 - 04:15:34 CDT
Ending: Tue Aug 31 2004 - 23:53:20 CDT
- AMBER: FW: Imaging problem Steve Seibold (Mon Aug 02 2004 - 15:32:37 CDT)
- AMBER: recompiling amber8 Carsten Detering (Mon Aug 02 2004 - 19:57:19 CDT)
- AMBER: charge not zero anshul_at_imtech.res.in (Tue Aug 03 2004 - 12:29:12 CDT)
- AMBER: mm_pbsa problem Carsten Detering (Tue Aug 03 2004 - 15:49:34 CDT)
- AMBER: Problem: Installing Amber8 on PC with Windows XP Nhat-hang Duong (Tue Aug 03 2004 - 15:38:55 CDT)
- AMBER: Re: Phosphoserine residue in AMBER David A. Case (Tue Aug 03 2004 - 16:23:20 CDT)
- AMBER: Bug and Patch in ANAL Andy Purkiss (Wed Aug 04 2004 - 10:38:30 CDT)
- AMBER: RMSD result from GB model Yongzhi Chen (Wed Aug 04 2004 - 12:35:03 CDT)
- AMBER: atoms not in residue templates Yongzhi Chen (Wed Aug 04 2004 - 12:53:08 CDT)
- AMBER: intense and spectrum Yaroslava Yingling (Wed Aug 04 2004 - 13:15:28 CDT)
- AMBER: RE: Hello Sir, Ross Walker (Wed Aug 04 2004 - 13:32:28 CDT)
- AMBER: sander.QMMM: CHARGE keyword in divcon.in file M. L. Dodson (Wed Aug 04 2004 - 14:23:29 CDT)
- AMBER: A question about pheTI in AMBER8 test. Chunhu Tan (Wed Aug 04 2004 - 16:35:48 CDT)
- AMBER: Angle parameters in phosphate groups Seongeun Yang (Thu Aug 05 2004 - 07:17:44 CDT)
- AMBER: How to covalently bind a ligand to a residue? Ozlem Demir (Thu Aug 05 2004 - 10:54:19 CDT)
- AMBER: Using TIP4P water in free energy calculation Lijiang Yang (Thu Aug 05 2004 - 17:03:36 CDT)
- AMBER: sander error Rukman Hertadi (Thu Aug 05 2004 - 23:33:41 CDT)
- AMBER: another cpinutil.pl error Rukman Hertadi (Fri Aug 06 2004 - 00:35:09 CDT)
- AMBER: RE: about PME in Amber6 Ross Walker (Fri Aug 06 2004 - 13:37:06 CDT)
- AMBER: atomic positional fluctuation RAJA SWAMINATHAN (Sat Aug 07 2004 - 02:18:32 CDT)
- AMBER: antechamber test mathew k varghese (Sun Aug 08 2004 - 07:31:22 CDT)
- AMBER: Problems with Carnal coordinate average HL Eastwood (Mon Aug 09 2004 - 06:35:37 CDT)
- AMBER: error while loading shared libraries: libcxa.so.5 Madalin Giambasu (Mon Aug 09 2004 - 08:54:00 CDT)
- AMBER: trival question about format of pev file and covariance matrix jz7_at_duke.edu (Mon Aug 09 2004 - 10:52:03 CDT)
- AMBER: Sander sachin patil (Mon Aug 09 2004 - 11:24:59 CDT)
- Re: AMBER: Problems with Carnal coordinate average Bill Ross (Mon Aug 09 2004 - 12:12:04 CDT)
- AMBER: Adding residues yen li (Mon Aug 09 2004 - 12:47:44 CDT)
- AMBER: question about covariance matrix from ptraj jz7_at_duke.edu (Mon Aug 09 2004 - 14:25:10 CDT)
- AMBER: resp charge calculation for Fe+3 heme Sebastian Fernandez Alberti (Mon Aug 09 2004 - 14:45:18 CDT)
- AMBER: rdparm problem Lijiang Yang (Mon Aug 09 2004 - 17:43:10 CDT)
- AMBER: perturb a water to a dummy water with shake Dr. Turgut Bastug (Mon Aug 09 2004 - 19:24:25 CDT)
- AMBER: how to correct the charge of oligosaccharides Wen-Chi Tseng (Mon Aug 09 2004 - 21:28:25 CDT)
- AMBER: pb_bomb in setgrd() steven.j.enoch_at_gsk.com (Tue Aug 10 2004 - 05:34:42 CDT)
- AMBER: Amber8 - LAM MPI Compilation problems Thomas Steinbrecher (Tue Aug 10 2004 - 11:16:38 CDT)
- AMBER: RESP partial charge calculation Sebastian Fernandez Alberti (Tue Aug 10 2004 - 11:21:06 CDT)
- AMBER: unknown residue: ABA Guowen Han (Tue Aug 10 2004 - 13:31:25 CDT)
- AMBER: Re: RED II and changepot FyD (Tue Aug 10 2004 - 13:35:05 CDT)
- Re: AMBER: unknown residue: ABA Bill Ross (Tue Aug 10 2004 - 14:20:36 CDT)
- AMBER: Membrane protein simulation Gabbar Daaku (Tue Aug 10 2004 - 15:37:22 CDT)
- AMBER: bugfix.all Lihua Wang (Tue Aug 10 2004 - 15:48:51 CDT)
- AMBER: Atomic charges in Lactose Johnson Agbo (Tue Aug 10 2004 - 19:23:53 CDT)
- AMBER: From Andrew Box: Invitation and new email address box_twin2_at_hotmail.com (Tue Aug 10 2004 - 19:39:25 CDT)
- AMBER: installing amber 8 on 64 bit amd opteron Dr Gavin Seddon (Wed Aug 11 2004 - 00:55:05 CDT)
- AMBER: units Gustavo Pierdominici Sottile (Wed Aug 11 2004 - 10:03:38 CDT)
- AMBER: RESP charge derivation Vlad Cojocaru (Wed Aug 11 2004 - 11:10:19 CDT)
- Re: AMBER: How to test the used parameters. Bill Ross (Wed Aug 11 2004 - 12:31:28 CDT)
- AMBER: parameter Gustavo Pierdominici Sottile (Wed Aug 11 2004 - 15:45:02 CDT)
- AMBER: Gaussian in RED Vlad Cojocaru (Thu Aug 12 2004 - 07:37:05 CDT)
- AMBER: Angle parameters in phosphate groups Seongeun Yang (Thu Aug 12 2004 - 08:29:02 CDT)
- AMBER: ptraj -- velocities set to zero? Gabbar Daaku (Thu Aug 12 2004 - 10:53:04 CDT)
- AMBER: minimization output file format Marsita M (Thu Aug 12 2004 - 12:51:35 CDT)
- AMBER: bending Gustavo Pierdominici Sottile (Thu Aug 12 2004 - 14:28:42 CDT)
- AMBER: bending Gustavo Pierdominici Sottile (Thu Aug 12 2004 - 15:47:16 CDT)
- AMBER: question about compilation of AMBER8 on MANDRAKE9.2 Madalin Giambasu (Fri Aug 13 2004 - 05:02:57 CDT)
- AMBER: RED fails to read g94 output Vlad Cojocaru (Fri Aug 13 2004 - 05:35:20 CDT)
- AMBER: Amber: xleap crash Helios (Fri Aug 13 2004 - 07:00:30 CDT)
- AMBER: RED BUG!!!!...perhaps I fixed it Vlad Cojocaru (Fri Aug 13 2004 - 07:34:50 CDT)
- AMBER: RED BUG!!! Vlad Cojocaru (Fri Aug 13 2004 - 07:56:25 CDT)
- AMBER: Temp control ding (Fri Aug 13 2004 - 13:46:20 CDT)
- AMBER: pmemd problems Florian Barth (Fri Aug 13 2004 - 13:52:22 CDT)
- AMBER: Moil-view, prmtop, inpcrd question opitz_at_che.udel.edu (Fri Aug 13 2004 - 15:08:33 CDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz_at_che.udel.edu (Fri Aug 13 2004 - 15:28:26 CDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question Viktor Hornak (Fri Aug 13 2004 - 15:20:14 CDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz_at_che.udel.edu (Fri Aug 13 2004 - 16:08:27 CDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question Carlos Simmerling (Sat Aug 14 2004 - 07:13:23 CDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz_at_che.udel.edu (Mon Aug 16 2004 - 13:17:35 CDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz_at_che.udel.edu (Mon Aug 16 2004 - 14:18:50 CDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz_at_che.udel.edu (Mon Aug 16 2004 - 14:51:30 CDT)
- AMBER: Bug: ptraj adds spurious box information Don Bashford (Fri Aug 13 2004 - 15:27:54 CDT)
- AMBER: simulated annealing Lee SL (Sat Aug 14 2004 - 04:51:14 CDT)
- AMBER: residue database Lihua Wang (Sat Aug 14 2004 - 16:55:59 CDT)
- AMBER: About the Amber constraint constant Yuhui Cheng (Sun Aug 15 2004 - 03:12:50 CDT)
- AMBER: installing amber8 Dr Gavin Seddon (Mon Aug 16 2004 - 04:20:20 CDT)
- AMBER: ANAL memory problem. Osman Gani (Mon Aug 16 2004 - 08:16:15 CDT)
- AMBER: temperature control in coupled potential runs M. L. Dodson (Mon Aug 16 2004 - 14:05:49 CDT)
- AMBER: Improving PMEMD performance on gigabit ethernet Linux clusters Robert Duke (Mon Aug 16 2004 - 16:17:45 CDT)
- AMBER: Amber: Anal program format Helios (Tue Aug 17 2004 - 01:15:57 CDT)
- AMBER: peoblemwith RED II anshul_at_imtech.res.in (Tue Aug 17 2004 - 14:15:30 CDT)
- AMBER: Improving PMEMD Performance on gigabit ethernet - CORRECTION Robert Duke (Tue Aug 17 2004 - 07:42:33 CDT)
- AMBER: leap: impose Guanglei Cui (Tue Aug 17 2004 - 13:44:04 CDT)
- AMBER: RESP calculation with different multiplicities Sebastian Fernandez Alberti (Tue Aug 17 2004 - 15:44:54 CDT)
- AMBER: turning off HB interactions Taner E. Dirama (Tue Aug 17 2004 - 15:12:34 CDT)
- AMBER: Dr. Herman Von Grafenstein Harsh Parikh (Tue Aug 17 2004 - 18:43:06 CDT)
- AMBER: mm-gbsa Oliver Hucke (Tue Aug 17 2004 - 18:59:21 CDT)
- AMBER: intrinsic born radius of Br Oliver Hucke (Tue Aug 17 2004 - 20:33:18 CDT)
- AMBER: thermal ellipsoid-DNA RAJA SWAMINATHAN (Thu Aug 19 2004 - 04:29:34 CDT)
- AMBER: angle bending Gustavo Pierdominici Sottile (Thu Aug 19 2004 - 07:31:21 CDT)
- AMBER: metal atoms in Xleap Atilio Anzellotti (Thu Aug 19 2004 - 10:05:23 CDT)
- AMBER: how to read in CHARMM or AMBER binary trajectories Grace Li (Thu Aug 19 2004 - 13:19:48 CDT)
- AMBER: born radius and screening parameter for Br Oliver Hucke (Thu Aug 19 2004 - 17:58:44 CDT)
- AMBER: questions on mm_pbsa cailliez (Fri Aug 20 2004 - 07:13:51 CDT)
- AMBER: Updating Amber 7 Johnson Agbo (Fri Aug 20 2004 - 13:52:23 CDT)
- AMBER: mm_pbsa.pl in Amber8 Shan, Jufang (Fri Aug 20 2004 - 14:13:54 CDT)
- AMBER: Minimization error opitz_at_che.udel.edu (Fri Aug 20 2004 - 14:43:31 CDT)
- AMBER: Increasing MAXATOM in antechamber Niko Jukarainen (Sat Aug 21 2004 - 04:45:08 CDT)
- AMBER: Sander : Vrand flag sachin patil (Mon Aug 23 2004 - 12:59:30 CDT)
- AMBER: error estimates in AMBER Grace Li (Mon Aug 23 2004 - 15:43:14 CDT)
- AMBER: NTT=0 and TAUTP Gabbar Daaku (Mon Aug 23 2004 - 17:25:26 CDT)
- AMBER: how to deal with the initial structure? hj zou (Mon Aug 23 2004 - 20:48:22 CDT)
- AMBER: problem loading pdb in leap. anshul_at_imtech.res.in (Tue Aug 24 2004 - 09:52:05 CDT)
- AMBER: mutation of Tyr to Leu with TI Oliver Hucke (Tue Aug 24 2004 - 18:56:47 CDT)
- AMBER: density calculation in AMBER output Grace Li (Wed Aug 25 2004 - 08:51:47 CDT)
- AMBER: restart a MD after replacing molecules cailliez (Wed Aug 25 2004 - 09:03:41 CDT)
- AMBER: Lennard-Jones particle simulation Guanglei Cui (Wed Aug 25 2004 - 14:38:57 CDT)
- AMBER: About tree structure of TRP residue Yuhui Cheng (Wed Aug 25 2004 - 18:46:36 CDT)
- AMBER: ptraj and hbond Nelson Fonseca (Thu Aug 26 2004 - 04:50:39 CDT)
- AMBER: problem loading molecule in leap anshul_at_imtech.res.in (Thu Aug 26 2004 - 15:38:44 CDT)
- AMBER: question on minimization Venkata S Koppuravuri (Thu Aug 26 2004 - 10:41:48 CDT)
- AMBER: RESP charges in Fe+3 heme system Sebastian Fernandez Alberti (Thu Aug 26 2004 - 12:43:08 CDT)
- Re: AMBER: One more question about the tree structure of looping residues Bill Ross (Thu Aug 26 2004 - 13:31:23 CDT)
- AMBER: charge perturbation - xleap question Oliver Hucke (Thu Aug 26 2004 - 13:57:43 CDT)
- AMBER: Biotin/streptavidin tutorial. Osman Gani (Fri Aug 27 2004 - 04:57:51 CDT)
- AMBER: error for performing MD tang kwa (Fri Aug 27 2004 - 06:51:00 CDT)
- AMBER: snapshots of MD trajectory Xin Hu (Fri Aug 27 2004 - 10:23:08 CDT)
- AMBER: error of performing simulation tang kwa (Fri Aug 27 2004 - 12:07:21 CDT)
- Re: AMBER: Biotin/streptavidin tutorial. Bill Ross (Fri Aug 27 2004 - 12:57:47 CDT)
- AMBER: nonpalar energy contribution-DMSO Dalmaris, John (Sat Aug 28 2004 - 09:11:43 CDT)
- AMBER: MD & net charge bybaker_at_itsa.ucsf.edu (Sun Aug 29 2004 - 01:19:18 CDT)
- AMBER: temperature scaling with ntt=3(Langevin thermostat) Madalin Giambasu (Mon Aug 30 2004 - 03:01:05 CDT)
- AMBER: Amber 03 Forcefield discrepancy MD Tyka, Biochemistry (Mon Aug 30 2004 - 09:36:18 CDT)
- AMBER: Differences in RESP charges for G in RG and DG residues Vlad Cojocaru (Mon Aug 30 2004 - 10:59:35 CDT)
- AMBER: jwcraft_at_uh.edu (Mon Aug 30 2004 - 14:54:46 CDT)
- AMBER: Glycam-04 Parameters in Amber 7 Johnson Agbo (Mon Aug 30 2004 - 20:12:17 CDT)
- AMBER: parm94 bybaker_at_itsa.ucsf.edu (Tue Aug 31 2004 - 01:50:09 CDT)
- AMBER: Using AMBER to simulate carbon nanotubes? Chen Song (Tue Aug 31 2004 - 05:54:26 CDT)
- AMBER: Increase lastrst in the &cntrl namelist Sichun Yang (Tue Aug 31 2004 - 11:06:46 CDT)
- AMBER: PBC in sander Mingfeng Yang (Tue Aug 31 2004 - 15:27:26 CDT)
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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