Amber Archive Aug 2004 by thread
- Re: AMBER: tleap: automatically identify and connect disulfide bonds? Raik Grünberg (Mon Aug 02 2004 - 02:15:34 PDT)
- Re: AMBER: ptraj: load crd without hydrogen (i.e. missing parm file) Raik Grünberg (Mon Aug 02 2004 - 02:30:56 PDT)
- AMBER: FW: Imaging problem Steve Seibold (Mon Aug 02 2004 - 13:32:37 PDT)
- AMBER: recompiling amber8 Carsten Detering (Mon Aug 02 2004 - 17:57:19 PDT)
- Re: AMBER: mm_pbsa Abmer8 example Holger Gohlke (Mon Aug 02 2004 - 23:39:06 PDT)
- AMBER: charge not zero anshul.imtech.res.in (Tue Aug 03 2004 - 10:29:12 PDT)
- AMBER: xleap problem fixed! HL Eastwood (Tue Aug 03 2004 - 10:20:21 PDT)
- AMBER: mm_pbsa problem Carsten Detering (Tue Aug 03 2004 - 13:49:34 PDT)
- AMBER: Problem: Installing Amber8 on PC with Windows XP Nhat-hang Duong (Tue Aug 03 2004 - 13:38:55 PDT)
- AMBER: Re: Phosphoserine residue in AMBER David A. Case (Tue Aug 03 2004 - 14:23:20 PDT)
- AMBER: Bug and Patch in ANAL Andy Purkiss (Wed Aug 04 2004 - 08:38:30 PDT)
- AMBER: RMSD result from GB model Yongzhi Chen (Wed Aug 04 2004 - 10:35:03 PDT)
- AMBER: atoms not in residue templates Yongzhi Chen (Wed Aug 04 2004 - 10:53:08 PDT)
- AMBER: intense and spectrum Yaroslava Yingling (Wed Aug 04 2004 - 11:15:28 PDT)
- AMBER: RE: Hello Sir, Ross Walker (Wed Aug 04 2004 - 11:32:28 PDT)
- AMBER: sander.QMMM: CHARGE keyword in divcon.in file M. L. Dodson (Wed Aug 04 2004 - 12:23:29 PDT)
- AMBER: A question about pheTI in AMBER8 test. Chunhu Tan (Wed Aug 04 2004 - 14:35:48 PDT)
- AMBER: Angle parameters in phosphate groups Seongeun Yang (Thu Aug 05 2004 - 05:17:44 PDT)
- AMBER: How to covalently bind a ligand to a residue? Ozlem Demir (Thu Aug 05 2004 - 08:54:19 PDT)
- AMBER: Using TIP4P water in free energy calculation Lijiang Yang (Thu Aug 05 2004 - 15:03:36 PDT)
- AMBER: sander error Rukman Hertadi (Thu Aug 05 2004 - 21:33:41 PDT)
- AMBER: another cpinutil.pl error Rukman Hertadi (Thu Aug 05 2004 - 22:35:09 PDT)
- AMBER: RE: about PME in Amber6 Ross Walker (Fri Aug 06 2004 - 11:37:06 PDT)
- AMBER: atomic positional fluctuation RAJA SWAMINATHAN (Sat Aug 07 2004 - 00:18:32 PDT)
- AMBER: antechamber test mathew k varghese (Sun Aug 08 2004 - 05:31:22 PDT)
- AMBER: Problems with Carnal coordinate average HL Eastwood (Mon Aug 09 2004 - 04:35:37 PDT)
- AMBER: error while loading shared libraries: libcxa.so.5 Madalin Giambasu (Mon Aug 09 2004 - 06:54:00 PDT)
- AMBER: trival question about format of pev file and covariance matrix jz7.duke.edu (Mon Aug 09 2004 - 08:52:03 PDT)
- AMBER: Sander sachin patil (Mon Aug 09 2004 - 09:24:59 PDT)
- Re: AMBER: Problems with Carnal coordinate average Bill Ross (Mon Aug 09 2004 - 10:12:04 PDT)
- Re: AMBER: Adding residues tarek mahfouz (Mon Aug 09 2004 - 11:51:26 PDT)
- RE: AMBER: Adding residues Ross Walker (Mon Aug 09 2004 - 11:50:59 PDT)
- AMBER: question about covariance matrix from ptraj jz7.duke.edu (Mon Aug 09 2004 - 12:25:10 PDT)
- AMBER: resp charge calculation for Fe+3 heme Sebastian Fernandez Alberti (Mon Aug 09 2004 - 12:45:18 PDT)
- AMBER: rdparm problem Lijiang Yang (Mon Aug 09 2004 - 15:43:10 PDT)
- AMBER: perturb a water to a dummy water with shake Dr. Turgut Bastug (Mon Aug 09 2004 - 17:24:25 PDT)
- AMBER: how to correct the charge of oligosaccharides Wen-Chi Tseng (Mon Aug 09 2004 - 19:28:25 PDT)
- AMBER: pb_bomb in setgrd() steven.j.enoch.gsk.com (Tue Aug 10 2004 - 03:34:42 PDT)
- AMBER: Amber8 - LAM MPI Compilation problems Thomas Steinbrecher (Tue Aug 10 2004 - 09:16:38 PDT)
- AMBER: RESP partial charge calculation Sebastian Fernandez Alberti (Tue Aug 10 2004 - 09:21:06 PDT)
- AMBER: unknown residue: ABA Guowen Han (Tue Aug 10 2004 - 11:31:25 PDT)
- AMBER: Re: RED II and changepot FyD (Tue Aug 10 2004 - 11:35:05 PDT)
- Re: AMBER: unknown residue: ABA Bill Ross (Tue Aug 10 2004 - 12:20:36 PDT)
- AMBER: Membrane protein simulation Gabbar Daaku (Tue Aug 10 2004 - 13:37:22 PDT)
- AMBER: bugfix.all Lihua Wang (Tue Aug 10 2004 - 13:48:51 PDT)
- AMBER: Atomic charges in Lactose Johnson Agbo (Tue Aug 10 2004 - 17:23:53 PDT)
- AMBER: installing amber 8 on 64 bit amd opteron Dr Gavin Seddon (Tue Aug 10 2004 - 22:55:05 PDT)
- AMBER: units Gustavo Pierdominici Sottile (Wed Aug 11 2004 - 08:03:38 PDT)
- AMBER: RESP charge derivation Vlad Cojocaru (Wed Aug 11 2004 - 09:10:19 PDT)
- Re: AMBER: How to test the used parameters. Bill Ross (Wed Aug 11 2004 - 10:31:28 PDT)
- AMBER: opteron 64 bit workstation sachin patil (Wed Aug 11 2004 - 11:59:33 PDT)
- AMBER: parameter Gustavo Pierdominici Sottile (Wed Aug 11 2004 - 13:45:02 PDT)
- AMBER: Gaussian in RED Vlad Cojocaru (Thu Aug 12 2004 - 05:37:05 PDT)
- AMBER: Angle parameters in phosphate groups Seongeun Yang (Thu Aug 12 2004 - 06:29:02 PDT)
- AMBER: ptraj -- velocities set to zero? Gabbar Daaku (Thu Aug 12 2004 - 08:53:04 PDT)
- AMBER: minimization output file format Marsita M (Thu Aug 12 2004 - 10:51:35 PDT)
- AMBER: bending Gustavo Pierdominici Sottile (Thu Aug 12 2004 - 12:28:42 PDT)
- AMBER: bending Gustavo Pierdominici Sottile (Thu Aug 12 2004 - 13:47:16 PDT)
- AMBER: question about compilation of AMBER8 on MANDRAKE9.2 Madalin Giambasu (Fri Aug 13 2004 - 03:02:57 PDT)
- AMBER: RED fails to read g94 output Vlad Cojocaru (Fri Aug 13 2004 - 03:35:20 PDT)
- AMBER: Amber: xleap crash Helios (Fri Aug 13 2004 - 05:00:30 PDT)
- AMBER: RED BUG!!!!...perhaps I fixed it Vlad Cojocaru (Fri Aug 13 2004 - 05:34:50 PDT)
- AMBER: RED BUG!!! Vlad Cojocaru (Fri Aug 13 2004 - 05:56:25 PDT)
- AMBER: Temp control ding (Fri Aug 13 2004 - 11:46:20 PDT)
- AMBER: pmemd problems Florian Barth (Fri Aug 13 2004 - 11:52:22 PDT)
- AMBER: Moil-view, prmtop, inpcrd question opitz.che.udel.edu (Fri Aug 13 2004 - 13:08:33 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question Viktor Hornak (Fri Aug 13 2004 - 13:20:14 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz.che.udel.edu (Fri Aug 13 2004 - 13:28:26 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz.che.udel.edu (Fri Aug 13 2004 - 14:08:27 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question Carlos Simmerling (Sat Aug 14 2004 - 05:13:23 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz.che.udel.edu (Mon Aug 16 2004 - 11:17:35 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz.che.udel.edu (Mon Aug 16 2004 - 12:18:50 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz.che.udel.edu (Mon Aug 16 2004 - 12:51:30 PDT)
- AMBER: Bug: ptraj adds spurious box information Don Bashford (Fri Aug 13 2004 - 13:27:54 PDT)
- AMBER: simulated annealing Lee SL (Sat Aug 14 2004 - 02:51:14 PDT)
- AMBER: residue database Lihua Wang (Sat Aug 14 2004 - 14:55:59 PDT)
- AMBER: About the Amber constraint constant Yuhui Cheng (Sun Aug 15 2004 - 01:12:50 PDT)
- AMBER: installing amber8 Dr Gavin Seddon (Mon Aug 16 2004 - 02:20:20 PDT)
- RE: AMBER: pmemd. Osman Gani (Mon Aug 16 2004 - 06:03:15 PDT)
- AMBER: ANAL memory problem. Osman Gani (Mon Aug 16 2004 - 06:16:15 PDT)
- AMBER: temperature control in coupled potential runs M. L. Dodson (Mon Aug 16 2004 - 12:05:49 PDT)
- AMBER: Improving PMEMD performance on gigabit ethernet Linux clusters Robert Duke (Mon Aug 16 2004 - 14:17:45 PDT)
- AMBER: Amber: Anal program format Helios (Mon Aug 16 2004 - 23:15:57 PDT)
- AMBER: peoblemwith RED II anshul.imtech.res.in (Tue Aug 17 2004 - 12:15:30 PDT)
- AMBER: Improving PMEMD Performance on gigabit ethernet - CORRECTION Robert Duke (Tue Aug 17 2004 - 05:42:33 PDT)
- AMBER: leap: impose Guanglei Cui (Tue Aug 17 2004 - 11:44:04 PDT)
- AMBER: RESP calculation with different multiplicities Sebastian Fernandez Alberti (Tue Aug 17 2004 - 13:44:54 PDT)
- AMBER: turning off HB interactions Taner E. Dirama (Tue Aug 17 2004 - 13:12:34 PDT)
- AMBER: Dr. Herman Von Grafenstein Harsh Parikh (Tue Aug 17 2004 - 16:43:06 PDT)
- AMBER: mm-gbsa Oliver Hucke (Tue Aug 17 2004 - 16:59:21 PDT)
- AMBER: intrinsic born radius of Br Oliver Hucke (Tue Aug 17 2004 - 18:33:18 PDT)
- AMBER: thermal ellipsoid-DNA RAJA SWAMINATHAN (Thu Aug 19 2004 - 02:29:34 PDT)
- AMBER: angle bending Gustavo Pierdominici Sottile (Thu Aug 19 2004 - 05:31:21 PDT)
- AMBER: metal atoms in Xleap Atilio Anzellotti (Thu Aug 19 2004 - 08:05:23 PDT)
- AMBER: how to read in CHARMM or AMBER binary trajectories Grace Li (Thu Aug 19 2004 - 11:19:48 PDT)
- AMBER: mmpbsa question Sébastien Osborne (Thu Aug 19 2004 - 12:58:42 PDT)
- AMBER: born radius and screening parameter for Br Oliver Hucke (Thu Aug 19 2004 - 15:58:44 PDT)
- AMBER: questions on mm_pbsa cailliez (Fri Aug 20 2004 - 05:13:51 PDT)
- AMBER: Updating Amber 7 Johnson Agbo (Fri Aug 20 2004 - 11:52:23 PDT)
- AMBER: mm_pbsa.pl in Amber8 Shan, Jufang (Fri Aug 20 2004 - 12:13:54 PDT)
- AMBER: Minimization error opitz.che.udel.edu (Fri Aug 20 2004 - 12:43:31 PDT)
- AMBER: Increasing MAXATOM in antechamber Niko Jukarainen (Sat Aug 21 2004 - 02:45:08 PDT)
- AMBER: Sander : Vrand flag sachin patil (Mon Aug 23 2004 - 10:59:30 PDT)
- AMBER: error estimates in AMBER Grace Li (Mon Aug 23 2004 - 13:43:14 PDT)
- AMBER: NTT=0 and TAUTP Gabbar Daaku (Mon Aug 23 2004 - 15:25:26 PDT)
- AMBER: how to deal with the initial structure? hj zou (Mon Aug 23 2004 - 18:48:22 PDT)
- AMBER: problem loading pdb in leap. anshul.imtech.res.in (Tue Aug 24 2004 - 07:52:05 PDT)
- AMBER: mutation of Tyr to Leu with TI Oliver Hucke (Tue Aug 24 2004 - 16:56:47 PDT)
- AMBER: density calculation in AMBER output Grace Li (Wed Aug 25 2004 - 06:51:47 PDT)
- AMBER: restart a MD after replacing molecules cailliez (Wed Aug 25 2004 - 07:03:41 PDT)
- AMBER: Lennard-Jones particle simulation Guanglei Cui (Wed Aug 25 2004 - 12:38:57 PDT)
- AMBER: About tree structure of TRP residue Yuhui Cheng (Wed Aug 25 2004 - 16:46:36 PDT)
- AMBER: ptraj and hbond Nelson Fonseca (Thu Aug 26 2004 - 02:50:39 PDT)
- AMBER: problem loading molecule in leap anshul.imtech.res.in (Thu Aug 26 2004 - 13:38:44 PDT)
- AMBER: question on minimization Venkata S Koppuravuri (Thu Aug 26 2004 - 08:41:48 PDT)
- AMBER: RESP charges in Fe+3 heme system Sebastian Fernandez Alberti (Thu Aug 26 2004 - 10:43:08 PDT)
- Re: AMBER: One more question about the tree structure of looping residues Bill Ross (Thu Aug 26 2004 - 11:31:23 PDT)
- AMBER: charge perturbation - xleap question Oliver Hucke (Thu Aug 26 2004 - 11:57:43 PDT)
- AMBER: Biotin/streptavidin tutorial. Osman Gani (Fri Aug 27 2004 - 02:57:51 PDT)
- AMBER: error for performing MD tang kwa (Fri Aug 27 2004 - 04:51:00 PDT)
- AMBER: snapshots of MD trajectory Xin Hu (Fri Aug 27 2004 - 08:23:08 PDT)
- AMBER: error of performing simulation tang kwa (Fri Aug 27 2004 - 10:07:21 PDT)
- Re: AMBER: Biotin/streptavidin tutorial. Bill Ross (Fri Aug 27 2004 - 10:57:47 PDT)
- AMBER: nonpalar energy contribution-DMSO Dalmaris, John (Sat Aug 28 2004 - 07:11:43 PDT)
- AMBER: MD & net charge bybaker.itsa.ucsf.edu (Sat Aug 28 2004 - 23:19:18 PDT)
- AMBER: temperature scaling with ntt=3(Langevin thermostat) Madalin Giambasu (Mon Aug 30 2004 - 01:01:05 PDT)
- AMBER: Amber 03 Forcefield discrepancy MD Tyka, Biochemistry (Mon Aug 30 2004 - 07:36:18 PDT)
- AMBER: Differences in RESP charges for G in RG and DG residues Vlad Cojocaru (Mon Aug 30 2004 - 08:59:35 PDT)
- AMBER: jwcraft.uh.edu (Mon Aug 30 2004 - 12:54:46 PDT)
- Re: AMBER: Bill Ross (Mon Aug 30 2004 - 14:33:38 PDT)
- AMBER: Glycam-04 Parameters in Amber 7 Johnson Agbo (Mon Aug 30 2004 - 18:12:17 PDT)
- AMBER: parm94 bybaker.itsa.ucsf.edu (Mon Aug 30 2004 - 23:50:09 PDT)
- AMBER: Using AMBER to simulate carbon nanotubes? Chen Song (Tue Aug 31 2004 - 03:54:26 PDT)
- AMBER: Increase lastrst in the &cntrl namelist Sichun Yang (Tue Aug 31 2004 - 09:06:46 PDT)
- AMBER: PBC in sander Mingfeng Yang (Tue Aug 31 2004 - 13:27:26 PDT)
- Last message date: Thu Sep 02 2004 - 01:15:13 PDT
- Archived on: Sun Dec 22 2024 - 05:53:22 PST
