AMBER Archive (2004) - Aug 2004 By Author

Starting: Mon Aug 02 2004 - 04:15:34 CDT
Ending: Tue Aug 31 2004 - 23:53:20 CDT

• Andrew Box
  • RE: AMBER: problem loading pdb in leap. (Tue Aug 24 2004 - 01:30:46 CDT)
• Andy Purkiss
  • AMBER: Bug and Patch in ANAL (Wed Aug 04 2004 - 10:38:30 CDT)
• anita Pachaimuthu
  • Re: AMBER: lib file (Mon Aug 02 2004 - 09:27:51 CDT)
• anshul_at_imtech.res.in
  • AMBER: problem loading molecule in leap (Thu Aug 26 2004 - 15:38:44 CDT)
  • RE: AMBER: problem loading pdb in leap. (Tue Aug 24 2004 - 11:34:58 CDT)
  • AMBER: problem loading pdb in leap. (Tue Aug 24 2004 - 09:52:05 CDT)
  • AMBER: peoblemwith RED II (Tue Aug 17 2004 - 14:15:30 CDT)
  • Re: AMBER: charge not zero (Wed Aug 04 2004 - 22:48:11 CDT)
  • AMBER: charge not zero (Tue Aug 03 2004 - 12:29:12 CDT)
• Asim Okur
  • Re: AMBER: parm94 (Tue Aug 31 2004 - 08:12:58 CDT)
• Atilio Anzellotti
  • Re: AMBER: metal atoms in Xleap (Fri Aug 20 2004 - 15:25:47 CDT)
  • Re: AMBER: metal atoms in Xleap (Fri Aug 20 2004 - 13:43:51 CDT)
  • AMBER: metal atoms in Xleap (Thu Aug 19 2004 - 10:05:23 CDT)
• Bill Ross
  • Re: AMBER: (Mon Aug 30 2004 - 16:33:38 CDT)
  • Re: AMBER: Biotin/streptavidin tutorial. (Fri Aug 27 2004 - 12:57:47 CDT)
  • Re: AMBER: One more question about the tree structure of looping residues (Thu Aug 26 2004 - 13:31:23 CDT)
  • Re: AMBER: About tree structure of TRP residue (Wed Aug 25 2004 - 19:56:13 CDT)
  • Re: AMBER: How to test the used parameters. (Wed Aug 11 2004 - 12:31:28 CDT)
  • Re: AMBER: unknown residue: ABA (Tue Aug 10 2004 - 14:20:36 CDT)
  • Re: AMBER: Adding residues (Mon Aug 09 2004 - 14:23:08 CDT)
  • Re: AMBER: Problems with Carnal coordinate average (Mon Aug 09 2004 - 12:12:04 CDT)
• Bimo Ario Tejo
  • Re: AMBER: How to covalently bind a ligand to a residue? (Fri Aug 06 2004 - 00:06:02 CDT)
• box_twin2_at_hotmail.com
  • AMBER: From Andrew Box: Invitation and new email address (Tue Aug 10 2004 - 19:39:25 CDT)
• bybaker_at_itsa.ucsf.edu
  • Re: AMBER: parm94 (Tue Aug 31 2004 - 20:57:39 CDT)
  • Re: AMBER: parm94 (Tue Aug 31 2004 - 17:15:04 CDT)
  • Re: AMBER: parm94 (Tue Aug 31 2004 - 11:21:00 CDT)
  • AMBER: parm94 (Tue Aug 31 2004 - 01:50:09 CDT)
  • Re: AMBER: MD & net charge (Mon Aug 30 2004 - 17:02:53 CDT)
  • Re: AMBER: MD & net charge (Mon Aug 30 2004 - 15:48:00 CDT)
  • AMBER: MD & net charge (Sun Aug 29 2004 - 01:19:18 CDT)
• cailliez
  • Re: AMBER: restart a MD after replacing molecules (Thu Aug 26 2004 - 03:38:55 CDT)
  • AMBER: restart a MD after replacing molecules (Wed Aug 25 2004 - 09:03:41 CDT)
  • AMBER: questions on mm_pbsa (Fri Aug 20 2004 - 07:13:51 CDT)
• Carlos Simmerling
  • Re: AMBER: MD & net charge (Mon Aug 30 2004 - 15:57:50 CDT)
  • Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) (Mon Aug 30 2004 - 08:51:28 CDT)
  • Re: AMBER: MD & net charge (Mon Aug 30 2004 - 08:41:21 CDT)
  • Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) (Mon Aug 30 2004 - 08:21:36 CDT)
  • Re: AMBER: MD & net charge (Mon Aug 30 2004 - 08:23:20 CDT)
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 14:44:36 CDT)
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 10:36:38 CDT)
  • Re: AMBER: Amber8 - Floating point (Thu Aug 26 2004 - 09:25:31 CDT)
  • Re: AMBER: Amber8 - Floating point (Thu Aug 26 2004 - 09:00:52 CDT)
  • Re: AMBER: Lennard-Jones particle simulation (Wed Aug 25 2004 - 15:06:47 CDT)
  • Re: AMBER: freezing atoms in impliciti solvent (Tue Aug 24 2004 - 12:54:58 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Sat Aug 14 2004 - 07:13:23 CDT)
  • Re: AMBER: simulated annealing (Sat Aug 14 2004 - 07:20:12 CDT)
• Carsten Detering
  • AMBER: mm_pbsa problem (Tue Aug 03 2004 - 15:49:34 CDT)
  • Re: AMBER: recompiling amber8 (Tue Aug 03 2004 - 10:55:04 CDT)
  • AMBER: recompiling amber8 (Mon Aug 02 2004 - 19:57:19 CDT)
• Chen Song
  • AMBER: Using AMBER to simulate carbon nanotubes? (Tue Aug 31 2004 - 05:54:26 CDT)
• Chris Harrison
  • Re: AMBER: MD & net charge (Mon Aug 30 2004 - 08:28:46 CDT)
• Chunhu Tan
  • Re: AMBER: A question about pheTI in AMBER8 test. (Thu Aug 05 2004 - 17:56:56 CDT)
  • AMBER: A question about pheTI in AMBER8 test. (Wed Aug 04 2004 - 16:35:48 CDT)
• CK Sim
  • AMBER: Trajectory file conversion between Amber & Charmm (Tue Aug 24 2004 - 15:42:19 CDT)
• Dalmaris, John
  • AMBER: nonpalar energy contribution-DMSO (Sat Aug 28 2004 - 09:11:43 CDT)
• darden
  • Re: AMBER: Using AMBER to simulate carbon nanotubes? (Tue Aug 31 2004 - 10:43:56 CDT)
  • Re: AMBER: Lennard-Jones particle simulation (Wed Aug 25 2004 - 15:57:15 CDT)
• David A. Case
  • Re: AMBER: Increase lastrst in the &cntrl namelist (Tue Aug 31 2004 - 23:53:20 CDT)
  • Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) (Tue Aug 31 2004 - 23:43:01 CDT)
  • Re: AMBER: Updating Amber 7 (Tue Aug 31 2004 - 23:00:46 CDT)
  • Re: AMBER: (Tue Aug 31 2004 - 22:56:27 CDT)
  • Re: AMBER: PBC in sander (Tue Aug 31 2004 - 22:57:49 CDT)
  • Re: AMBER: ANAL memory problem. (Tue Aug 17 2004 - 11:33:03 CDT)
  • Re: AMBER: Amber: Anal program format (Tue Aug 17 2004 - 11:14:31 CDT)
  • Re: AMBER: About the Amber constraint constant (Tue Aug 17 2004 - 10:08:04 CDT)
  • Re: AMBER: ANAL memory problem. (Mon Aug 16 2004 - 20:34:22 CDT)
  • Re: AMBER: About the Amber constraint constant (Sun Aug 15 2004 - 18:07:11 CDT)
  • Re: AMBER: Angle parameters in phosphate groups (Sun Aug 15 2004 - 17:59:51 CDT)
  • Re: AMBER: Bug: ptraj adds spurious box information (Fri Aug 13 2004 - 17:13:33 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 17:07:42 CDT)
  • Re: AMBER: Temp control (Fri Aug 13 2004 - 15:13:20 CDT)
  • Re: AMBER: Antechamber and dummy atoms (Fri Aug 13 2004 - 09:49:49 CDT)
  • Re: AMBER: opteron 64 bit workstation (Thu Aug 12 2004 - 14:55:13 CDT)
  • Re: AMBER: bending (Thu Aug 12 2004 - 14:48:30 CDT)
  • Re: AMBER: units (Thu Aug 12 2004 - 09:56:09 CDT)
  • Re: AMBER: different cooling schedules for simulated annealing (Thu Aug 12 2004 - 09:55:45 CDT)
  • Re: AMBER: different cooling schedules for simulated annealing (Wed Aug 11 2004 - 09:41:50 CDT)
  • Re: AMBER: Membrane protein simulation (Tue Aug 10 2004 - 20:06:57 CDT)
  • Re: AMBER: how to correct the charge of oligosaccharides (Tue Aug 10 2004 - 09:31:40 CDT)
  • Re: AMBER: Sander (Mon Aug 09 2004 - 17:21:12 CDT)
  • Re: AMBER: Sander (Mon Aug 09 2004 - 11:57:40 CDT)
  • Re: AMBER: antechamber test (Sun Aug 08 2004 - 11:40:34 CDT)
  • Re: AMBER: AMBER7 plastocyanin tutorial problem. (Fri Aug 06 2004 - 14:09:34 CDT)
  • Re: AMBER: another cpinutil.pl error (Fri Aug 06 2004 - 10:58:46 CDT)
  • Re: AMBER: Using TIP4P water in free energy calculation (Fri Aug 06 2004 - 10:56:46 CDT)
  • Re: AMBER: A question about pheTI in AMBER8 test. (Thu Aug 05 2004 - 19:39:06 CDT)
  • Re: AMBER: Using TIP4P water in free energy calculation (Thu Aug 05 2004 - 17:35:22 CDT)
  • Re: AMBER: Bug and Patch in ANAL (Thu Aug 05 2004 - 10:44:38 CDT)
  • Re: AMBER: intense and spectrum (Wed Aug 04 2004 - 18:41:13 CDT)
  • Re: AMBER: A question about pheTI in AMBER8 test. (Wed Aug 04 2004 - 18:38:52 CDT)
  • Re: AMBER: Problem: Installing Amber8 on PC with Windows XP (Tue Aug 03 2004 - 17:28:25 CDT)
  • AMBER: Re: Phosphoserine residue in AMBER (Tue Aug 03 2004 - 16:23:20 CDT)
  • Re: AMBER: Minimum imaging (Tue Aug 03 2004 - 09:25:47 CDT)
  • Re: AMBER: recompiling amber8 (Mon Aug 02 2004 - 20:18:25 CDT)
• David E. Konerding
  • Re: AMBER: pmemd. (Mon Aug 16 2004 - 11:27:02 CDT)
• david.evans_at_ulsop.ac.uk
  • Re: AMBER: How to covalently bind a ligand to a residue? (Fri Aug 06 2004 - 03:22:17 CDT)
  • Re: AMBER: How to covalently bind a ligand to a residue? (Fri Aug 06 2004 - 03:11:39 CDT)
• ding
  • AMBER: Temp control (Fri Aug 13 2004 - 13:46:20 CDT)
• Do Anh Tuan
  • Re: AMBER: Amber 8 Installation - C compiler? (Thu Aug 12 2004 - 00:28:37 CDT)
• Don Bashford
  • AMBER: Bug: ptraj adds spurious box information (Fri Aug 13 2004 - 15:27:54 CDT)
• Dr Gavin Seddon
  • AMBER: installing amber8 (Mon Aug 16 2004 - 04:20:20 CDT)
  • AMBER: installing amber 8 on 64 bit amd opteron (Wed Aug 11 2004 - 00:55:05 CDT)
• Dr. Turgut Bastug
  • AMBER: perturb a water to a dummy water with shake (Mon Aug 09 2004 - 19:24:25 CDT)
• Elijah Gregory
  • Re: AMBER: question about covariance matrix from ptraj (Mon Aug 09 2004 - 15:00:06 CDT)
• fangyu liang
  • Re: AMBER: Amber 8 Installation - C compiler? (Wed Aug 11 2004 - 19:23:03 CDT)
  • Re: AMBER: Problem: Installing Amber8 on PC with Windows XP (Tue Aug 03 2004 - 16:47:08 CDT)
• Florian Barth
  • AMBER: pmemd problems (Fri Aug 13 2004 - 13:52:22 CDT)
• Furse, Kristina Elisabet
  • Re: AMBER: how to deal with the initial structure? (Tue Aug 24 2004 - 14:29:39 CDT)
  • RE: AMBER: Sander : Vrand flag (Tue Aug 24 2004 - 13:47:38 CDT)
• FyD
  • Re: AMBER: peoblemwith RED II (Sat Aug 28 2004 - 04:52:20 CDT)
  • Re: AMBER: peoblemwith RED II (Fri Aug 27 2004 - 05:02:37 CDT)
  • Re: AMBER: RESP charges in Fe+3 heme system (Thu Aug 26 2004 - 13:33:09 CDT)
  • Re: AMBER: RESP calculation with different multiplicities (Thu Aug 26 2004 - 13:09:18 CDT)
  • Re: AMBER: peoblemwith RED II (Thu Aug 26 2004 - 10:44:16 CDT)
  • Re: AMBER: RED fails to read g94 output (Sat Aug 14 2004 - 03:26:33 CDT)
  • Re: AMBER: RED fails to read g94 output (Sat Aug 14 2004 - 00:34:21 CDT)
  • Re: AMBER: Gaussian in RED (Sat Aug 14 2004 - 00:16:30 CDT)
  • Re: AMBER: RESP charge derivation (Wed Aug 11 2004 - 11:55:57 CDT)
  • AMBER: Re: RED II and changepot (Tue Aug 10 2004 - 13:35:05 CDT)
  • Re: AMBER: RESP partial charge calculation (Tue Aug 10 2004 - 12:46:16 CDT)
  • Re: AMBER: charge not zero (Wed Aug 04 2004 - 14:57:51 CDT)
  • Re: AMBER: charge not zero (Wed Aug 04 2004 - 13:23:13 CDT)
  • Re: AMBER: charge not zero (Tue Aug 03 2004 - 09:46:54 CDT)
• Gabbar Daaku
  • AMBER: NTT=0 and TAUTP (Mon Aug 23 2004 - 17:25:26 CDT)
  • AMBER: ptraj -- velocities set to zero? (Thu Aug 12 2004 - 10:53:04 CDT)
  • AMBER: Membrane protein simulation (Tue Aug 10 2004 - 15:37:22 CDT)
• Grace Li
  • AMBER: density calculation in AMBER output (Wed Aug 25 2004 - 08:51:47 CDT)
  • AMBER: error estimates in AMBER (Mon Aug 23 2004 - 15:43:14 CDT)
  • AMBER: how to read in CHARMM or AMBER binary trajectories (Thu Aug 19 2004 - 13:19:48 CDT)
  • AMBER: Minimum imaging (Mon Aug 02 2004 - 22:21:50 CDT)
• Guanglei Cui
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 14:38:44 CDT)
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 10:27:20 CDT)
  • Re: AMBER: Lennard-Jones particle simulation (Wed Aug 25 2004 - 16:11:37 CDT)
  • AMBER: Lennard-Jones particle simulation (Wed Aug 25 2004 - 14:38:57 CDT)
  • Re: AMBER: Increasing MAXATOM in antechamber (Sat Aug 21 2004 - 10:07:10 CDT)
  • Re: AMBER: leap: impose (Tue Aug 17 2004 - 15:15:27 CDT)
  • Re: AMBER: leap: impose (Tue Aug 17 2004 - 14:23:27 CDT)
  • AMBER: leap: impose (Tue Aug 17 2004 - 13:44:04 CDT)
  • Re: AMBER: Angle parameters in phosphate groups (Sun Aug 15 2004 - 09:08:29 CDT)
  • Re: AMBER: Angle parameters in phosphate groups (Thu Aug 12 2004 - 09:18:06 CDT)
  • Re: AMBER: parameter (Wed Aug 11 2004 - 16:07:18 CDT)
  • Re: AMBER: error while loading shared libraries: libcxa.so.5 (Mon Aug 09 2004 - 09:24:06 CDT)
• Guowen Han
  • AMBER: unknown residue: ABA (Tue Aug 10 2004 - 13:31:25 CDT)
• Gustavo Pierdominici Sottile
  • AMBER: angle bending (Thu Aug 19 2004 - 07:31:21 CDT)
  • AMBER: bending (Thu Aug 12 2004 - 15:47:16 CDT)
  • AMBER: bending (Thu Aug 12 2004 - 14:28:42 CDT)
  • AMBER: parameter (Wed Aug 11 2004 - 15:45:02 CDT)
  • AMBER: units (Wed Aug 11 2004 - 10:03:38 CDT)
• Harsh Parikh
  • AMBER: Dr. Herman Von Grafenstein (Tue Aug 17 2004 - 18:43:06 CDT)
• Helios
  • AMBER: Amber: Anal program format (Tue Aug 17 2004 - 01:15:57 CDT)
  • AMBER: Amber: xleap crash (Fri Aug 13 2004 - 07:00:30 CDT)
• hj zou
  • AMBER: how to deal with the initial structure? (Mon Aug 23 2004 - 20:48:22 CDT)
• HL Eastwood
  • AMBER: Problems with Carnal coordinate average (Mon Aug 09 2004 - 06:35:37 CDT)
  • AMBER: xleap problem fixed! (Tue Aug 03 2004 - 12:20:21 CDT)
• Holger Gohlke
  • Re: AMBER: mm_pbsa Abmer8 example (Tue Aug 03 2004 - 01:39:06 CDT)
• James W. Caldwell
  • Re: AMBER: RESP partial charge calculation (Tue Aug 10 2004 - 12:25:55 CDT)
  • Re: AMBER: resp charge calculation for Fe+3 heme (Mon Aug 09 2004 - 15:18:46 CDT)
• Jiri Sponer
  • Re: AMBER: metal atoms in Xleap (Fri Aug 20 2004 - 14:04:32 CDT)
• John Mongan
  • Re: AMBER: cpinutil.pl error (Tue Aug 03 2004 - 13:03:40 CDT)
• Johnson Agbo
  • AMBER: Glycam-04 Parameters in Amber 7 (Mon Aug 30 2004 - 20:12:17 CDT)
  • Re: AMBER: Atomic charges in Lactose (Fri Aug 20 2004 - 14:35:48 CDT)
  • AMBER: Updating Amber 7 (Fri Aug 20 2004 - 13:52:23 CDT)
  • AMBER: Atomic charges in Lactose (Tue Aug 10 2004 - 19:23:53 CDT)
• Joseph Nachman
  • Re: AMBER: Minimum imaging (Wed Aug 04 2004 - 00:01:54 CDT)
• jwcraft_at_uh.edu
  • AMBER: (Mon Aug 30 2004 - 14:54:46 CDT)
• jz7_at_duke.edu
  • AMBER: can MM-PBSA be applied to Charmm format trajectory file? (Thu Aug 19 2004 - 13:55:06 CDT)
  • AMBER: question about covariance matrix from ptraj (Mon Aug 09 2004 - 14:25:10 CDT)
  • AMBER: trival question about format of pev file and covariance matrix (Mon Aug 09 2004 - 10:52:03 CDT)
• Karl N. Kirschner
  • Re: AMBER: Atomic charges in Lactose (Wed Aug 11 2004 - 07:47:46 CDT)
  • Re: AMBER: how to correct the charge of oligosaccharides (Tue Aug 10 2004 - 09:53:29 CDT)
• Lao_3
  • RE: AMBER: unknown residue: ABA (Wed Aug 11 2004 - 10:45:44 CDT)
  • Re: AMBER: unknown residue: ABA (Tue Aug 10 2004 - 16:45:27 CDT)
• Lee SL
  • RE: AMBER: simulated annealing (Sat Aug 14 2004 - 05:40:54 CDT)
  • AMBER: simulated annealing (Sat Aug 14 2004 - 04:51:14 CDT)
• Lihua Wang
  • Re: AMBER: parm94 (Tue Aug 31 2004 - 17:22:29 CDT)
  • Re: AMBER: About tree structure of TRP residue (Wed Aug 25 2004 - 19:16:46 CDT)
  • AMBER: residue database (Sat Aug 14 2004 - 16:55:59 CDT)
  • AMBER: bugfix.all (Tue Aug 10 2004 - 15:48:51 CDT)
• Lijiang Yang
  • AMBER: rdparm problem (Mon Aug 09 2004 - 17:43:10 CDT)
  • Re: AMBER: Using TIP4P water in free energy calculation (Fri Aug 06 2004 - 13:42:06 CDT)
  • Re: AMBER: Using TIP4P water in free energy calculation (Fri Aug 06 2004 - 00:04:07 CDT)
  • AMBER: Using TIP4P water in free energy calculation (Thu Aug 05 2004 - 17:03:36 CDT)
• M. L. Dodson
  • Re: AMBER: Neutral C and N termini. (Sun Aug 29 2004 - 21:14:10 CDT)
  • AMBER: temperature control in coupled potential runs (Mon Aug 16 2004 - 14:05:49 CDT)
  • Re: AMBER: sander.QMMM: CHARGE keyword in divcon.in file (Thu Aug 05 2004 - 17:30:20 CDT)
  • Re: AMBER: sander.QMMM: CHARGE keyword in divcon.in file (Wed Aug 04 2004 - 19:08:07 CDT)
  • AMBER: sander.QMMM: CHARGE keyword in divcon.in file (Wed Aug 04 2004 - 14:23:29 CDT)
• Madalin Giambasu
  • Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) (Mon Aug 30 2004 - 09:47:55 CDT)
  • Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) (Mon Aug 30 2004 - 08:51:35 CDT)
  • AMBER: temperature scaling with ntt=3(Langevin thermostat) (Mon Aug 30 2004 - 03:01:05 CDT)
  • AMBER: pmemd config.h request for athlon (Fri Aug 13 2004 - 12:47:53 CDT)
  • AMBER: question about compilation of AMBER8 on MANDRAKE9.2 (Fri Aug 13 2004 - 05:02:57 CDT)
  • Re: AMBER: different cooling schedules for simulated annealing (Wed Aug 11 2004 - 11:23:08 CDT)
  • AMBER: different cooling schedules for simulated annealing (Wed Aug 11 2004 - 06:51:09 CDT)
  • AMBER: error while loading shared libraries: libcxa.so.5 (Mon Aug 09 2004 - 08:54:00 CDT)
• Marcin Krol
  • Re: AMBER: RMSD result from GB model (Thu Aug 05 2004 - 03:32:36 CDT)
• Mark Williamson
  • Re: AMBER: error while loading shared libraries: libcxa.so.5 (Mon Aug 09 2004 - 09:42:16 CDT)
• Marsita M
  • AMBER: minimization output file format (Thu Aug 12 2004 - 12:51:35 CDT)
• mathew k varghese
  • AMBER: antechamber test (Sun Aug 08 2004 - 07:31:22 CDT)
• MD Tyka, Biochemistry
  • AMBER: Amber 03 Forcefield discrepancy (Mon Aug 30 2004 - 09:36:18 CDT)
• Michael Crowley
  • Re: AMBER: Amber8 - Floating point (Thu Aug 26 2004 - 10:56:06 CDT)
• Mingfeng Yang
  • AMBER: PBC in sander (Tue Aug 31 2004 - 15:27:26 CDT)
• Nelson Fonseca
  • AMBER: ptraj and hbond (Thu Aug 26 2004 - 04:50:39 CDT)
• Nhat-hang Duong
  • AMBER: Pulling versus Distance Restraints (Tue Aug 31 2004 - 16:16:15 CDT)
  • Re: AMBER: Amber8 - Floating point (Thu Aug 26 2004 - 11:51:28 CDT)
  • Re: AMBER: Amber8 - Floating point (Thu Aug 26 2004 - 09:15:00 CDT)
  • AMBER: Amber8 - Floating point (Thu Aug 26 2004 - 08:28:24 CDT)
  • RE: AMBER: Amber 8 - Energy Minimization Parameters (Wed Aug 25 2004 - 15:26:56 CDT)
  • AMBER: Amber 8 - Energy Minimization Parameters (Wed Aug 25 2004 - 10:34:28 CDT)
  • AMBER: Amber 8 Installation - C compiler? (Wed Aug 11 2004 - 16:51:51 CDT)
  • AMBER: Problem: Installing Amber8 on PC with Windows XP (Tue Aug 03 2004 - 15:38:55 CDT)
• Niko Jukarainen
  • Re: AMBER: Increasing MAXATOM in antechamber (Sat Aug 21 2004 - 11:13:56 CDT)
  • AMBER: Increasing MAXATOM in antechamber (Sat Aug 21 2004 - 04:45:08 CDT)
  • RE: AMBER: question about compilation of AMBER8 on MANDRAKE9.2 (Fri Aug 13 2004 - 05:09:10 CDT)
• nurul bahiyah
  • Re: AMBER: simulated annealing (Sun Aug 15 2004 - 07:42:53 CDT)
• Oliver Hucke
  • AMBER: charge perturbation - xleap question (Thu Aug 26 2004 - 13:57:43 CDT)
  • AMBER: mutation of Tyr to Leu with TI (Tue Aug 24 2004 - 18:56:47 CDT)
  • AMBER: born radius and screening parameter for Br (Thu Aug 19 2004 - 17:58:44 CDT)
  • AMBER: intrinsic born radius of Br (Tue Aug 17 2004 - 20:33:18 CDT)
  • AMBER: mm-gbsa (Tue Aug 17 2004 - 18:59:21 CDT)
  • Re: AMBER: Antechamber and dummy atoms (Fri Aug 13 2004 - 12:55:57 CDT)
• opitz_at_che.udel.edu
  • Re: AMBER: Minimization error (Fri Aug 27 2004 - 15:56:46 CDT)
  • Re: AMBER: Minimization error (Wed Aug 25 2004 - 15:55:24 CDT)
  • Re: AMBER: Minimization error (Tue Aug 24 2004 - 16:09:15 CDT)
  • AMBER: Minimization error (Fri Aug 20 2004 - 14:43:31 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Mon Aug 16 2004 - 14:51:30 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Mon Aug 16 2004 - 14:18:50 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Mon Aug 16 2004 - 13:17:35 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 16:08:27 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 15:28:26 CDT)
  • AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 15:08:33 CDT)
• Osman Gani
  • AMBER: Biotin/streptavidin tutorial. (Fri Aug 27 2004 - 04:57:51 CDT)
  • RE: AMBER: ANAL memory problem. (Tue Aug 17 2004 - 05:38:42 CDT)
  • AMBER: ANAL memory problem. (Mon Aug 16 2004 - 08:16:15 CDT)
  • RE: AMBER: pmemd. (Mon Aug 16 2004 - 08:03:15 CDT)
• Ozlem Demir
  • AMBER: How to covalently bind a ligand to a residue? (Thu Aug 05 2004 - 10:54:19 CDT)
• Perdita Barran
  • AMBER: Antechamber and dummy atoms (Fri Aug 13 2004 - 08:03:44 CDT)
• Peter Gannett
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 10:43:33 CDT)
• Piotr Cieplak
  • Re: AMBER: Lennard-Jones particle simulation (Wed Aug 25 2004 - 17:31:37 CDT)
• Raik Grünberg
  • Re: AMBER: ptraj: load crd without hydrogen (i.e. missing parm file) (Mon Aug 02 2004 - 04:30:56 CDT)
  • Re: AMBER: tleap: automatically identify and connect disulfide bonds? (Mon Aug 02 2004 - 04:15:34 CDT)
• RAJA SWAMINATHAN
  • AMBER: thermal ellipsoid-DNA (Thu Aug 19 2004 - 04:29:34 CDT)
  • AMBER: atomic positional fluctuation (Sat Aug 07 2004 - 02:18:32 CDT)
• Ray Luo
  • Re: AMBER: pb_bomb in setgrd() (Tue Aug 10 2004 - 11:29:13 CDT)
  • Re: AMBER: mm_pbsa problem (Tue Aug 03 2004 - 18:18:48 CDT)
• Rhonda Torres
  • Re: AMBER: metal atoms in Xleap (Thu Aug 19 2004 - 11:57:04 CDT)
  • Re: AMBER: Adding residues (Mon Aug 09 2004 - 14:00:50 CDT)
  • Re: AMBER: AMBER7 plastocyanin tutorial problem. (Fri Aug 06 2004 - 12:57:42 CDT)
• Robert Duke
  • AMBER: Improving PMEMD Performance on gigabit ethernet - CORRECTION (Tue Aug 17 2004 - 07:42:33 CDT)
  • AMBER: Improving PMEMD performance on gigabit ethernet Linux clusters (Mon Aug 16 2004 - 16:17:45 CDT)
  • Re: AMBER: pmemd. - OOPS!!! (Mon Aug 16 2004 - 09:45:03 CDT)
  • Re: AMBER: pmemd. (Mon Aug 16 2004 - 09:33:21 CDT)
  • Re: AMBER: pmemd problems (Fri Aug 13 2004 - 14:14:39 CDT)
  • Re: AMBER: pmemd config.h request for athlon (Fri Aug 13 2004 - 13:42:42 CDT)
  • Re: AMBER: pmemd config.h request for athlon (Fri Aug 13 2004 - 13:40:05 CDT)
  • Re: AMBER: recompiling amber8 (Tue Aug 03 2004 - 11:30:41 CDT)
  • Re: AMBER: recompiling amber8 (Mon Aug 02 2004 - 20:12:52 CDT)
• Ross Walker
  • RE: AMBER: Minimization error (Sat Aug 28 2004 - 14:34:31 CDT)
  • RE: AMBER: Minimization error (Wed Aug 25 2004 - 17:35:18 CDT)
  • RE: AMBER: restart a MD after replacing molecules (Wed Aug 25 2004 - 12:29:13 CDT)
  • RE: AMBER: Minimization error (Wed Aug 25 2004 - 12:23:13 CDT)
  • RE: AMBER: density calculation in AMBER output (Wed Aug 25 2004 - 12:11:02 CDT)
  • RE: AMBER: Amber 8 - Energy Minimization Parameters (Wed Aug 25 2004 - 11:02:31 CDT)
  • RE: AMBER: Trajectory file conversion between Amber & Charmm (Tue Aug 24 2004 - 18:51:17 CDT)
  • RE: AMBER: problem loading pdb in leap. (Tue Aug 24 2004 - 12:35:08 CDT)
  • RE: AMBER: problem loading pdb in leap. (Mon Aug 23 2004 - 23:53:49 CDT)
  • RE: AMBER: how to deal with the initial structure? (Mon Aug 23 2004 - 21:19:23 CDT)
  • RE: AMBER: NTT=0 and TAUTP (Mon Aug 23 2004 - 18:03:30 CDT)
  • RE: AMBER: Sander : Vrand flag (Mon Aug 23 2004 - 15:58:15 CDT)
  • RE: AMBER: Sander : Vrand flag (Mon Aug 23 2004 - 14:29:06 CDT)
  • RE: AMBER: Sander : Vrand flag (Mon Aug 23 2004 - 13:20:15 CDT)
  • RE: AMBER: Minimization error (Fri Aug 20 2004 - 17:48:27 CDT)
  • RE: AMBER: can MM-PBSA be applied to Charmm format trajectory file? (Thu Aug 19 2004 - 14:02:50 CDT)
  • RE: AMBER: how to read in CHARMM or AMBER binary trajectories (Thu Aug 19 2004 - 13:30:59 CDT)
  • RE: AMBER: angle bending (Thu Aug 19 2004 - 12:09:52 CDT)
  • RE: AMBER: metal atoms in Xleap (Thu Aug 19 2004 - 11:59:28 CDT)
  • RE: AMBER: question about compilation of AMBER8 on MANDRAKE9.2 (Mon Aug 16 2004 - 13:13:09 CDT)
  • RE: AMBER: pmemd config.h request for athlon (Fri Aug 13 2004 - 13:09:15 CDT)
  • RE: AMBER: Amber: xleap crash (Fri Aug 13 2004 - 11:23:50 CDT)
  • RE: AMBER: minimization output file format (Thu Aug 12 2004 - 14:43:02 CDT)
  • RE: AMBER: Amber 8 Installation - C compiler? (Wed Aug 11 2004 - 19:37:45 CDT)
  • RE: AMBER: How to test the used parameters. (Wed Aug 11 2004 - 12:33:56 CDT)
  • RE: AMBER: bugfix.all (Tue Aug 10 2004 - 19:54:25 CDT)
  • RE: AMBER: unknown residue: ABA (Tue Aug 10 2004 - 13:46:14 CDT)
  • RE: AMBER: Amber8 - LAM MPI Compilation problems (Tue Aug 10 2004 - 11:59:33 CDT)
  • RE: AMBER: Adding residues (Mon Aug 09 2004 - 13:50:59 CDT)
  • AMBER: RE: about PME in Amber6 (Fri Aug 06 2004 - 13:37:06 CDT)
  • RE: AMBER: sander error (Thu Aug 05 2004 - 23:50:09 CDT)
  • RE: AMBER: sander.QMMM: CHARGE keyword in divcon.in file (Wed Aug 04 2004 - 15:48:08 CDT)
  • AMBER: RE: Hello Sir, (Wed Aug 04 2004 - 13:32:28 CDT)
  • RE: AMBER: atoms not in residue templates (Wed Aug 04 2004 - 13:26:55 CDT)
  • RE: AMBER: RMSD result from GB model (Wed Aug 04 2004 - 13:06:50 CDT)
• Rukman Hertadi
  • AMBER: another cpinutil.pl error (Fri Aug 06 2004 - 00:35:09 CDT)
  • AMBER: sander error (Thu Aug 05 2004 - 23:33:41 CDT)
  • AMBER: cpinutil.pl error (Tue Aug 03 2004 - 06:22:59 CDT)
• sachin patil
  • RE: AMBER: Sander : Vrand flag (Tue Aug 31 2004 - 09:15:37 CDT)
  • RE: AMBER: Sander : Vrand flag (Mon Aug 23 2004 - 14:54:52 CDT)
  • RE: AMBER: Sander : Vrand flag (Mon Aug 23 2004 - 14:07:32 CDT)
  • AMBER: Sander : Vrand flag (Mon Aug 23 2004 - 12:59:30 CDT)
  • AMBER: opteron 64 bit workstation (Wed Aug 11 2004 - 13:59:33 CDT)
  • Re: AMBER: Sander (Mon Aug 09 2004 - 13:26:20 CDT)
  • AMBER: Sander (Mon Aug 09 2004 - 11:24:59 CDT)
• Sarah Rankin
  • Re: AMBER: mm_pbsa.pl in Amber8 (Mon Aug 23 2004 - 05:00:21 CDT)
  • Re: AMBER: question about compilation of AMBER8 on MANDRAKE9.2 (Tue Aug 17 2004 - 03:18:30 CDT)
  • Re: AMBER: question about compilation of AMBER8 on MANDRAKE9.2 (Mon Aug 16 2004 - 12:14:38 CDT)
• Sebastian Fernandez Alberti
  • AMBER: RESP charges in Fe+3 heme system (Thu Aug 26 2004 - 12:43:08 CDT)
  • AMBER: RESP calculation with different multiplicities (Tue Aug 17 2004 - 15:44:54 CDT)
  • AMBER: RESP partial charge calculation (Tue Aug 10 2004 - 11:21:06 CDT)
  • AMBER: resp charge calculation for Fe+3 heme (Mon Aug 09 2004 - 14:45:18 CDT)
• Seongeun Yang
  • Re: AMBER: Angle parameters in phosphate groups (Mon Aug 16 2004 - 01:04:16 CDT)
  • Re: AMBER: Angle parameters in phosphate groups (Sat Aug 14 2004 - 04:58:07 CDT)
  • AMBER: Angle parameters in phosphate groups (Thu Aug 12 2004 - 08:29:02 CDT)
  • AMBER: Angle parameters in phosphate groups (Thu Aug 05 2004 - 07:17:44 CDT)
• Sergio E. Wong
  • AMBER: freezing atoms in impliciti solvent (Tue Aug 24 2004 - 12:27:32 CDT)
• Shan, Jufang
  • AMBER: mm_pbsa.pl in Amber8 (Fri Aug 20 2004 - 14:13:54 CDT)
• Sichun Yang
  • AMBER: Increase lastrst in the &cntrl namelist (Tue Aug 31 2004 - 11:06:46 CDT)
• Steve Seibold
  • AMBER: FW: Imaging problem (Mon Aug 02 2004 - 15:32:37 CDT)
• steven.j.enoch_at_gsk.com
  • AMBER: pb_bomb in setgrd() (Tue Aug 10 2004 - 05:34:42 CDT)
• Sébastien Osborne
  • AMBER: mmpbsa question (Thu Aug 19 2004 - 14:58:42 CDT)
• Taner E. Dirama
  • AMBER: turning off HB interactions (Tue Aug 17 2004 - 15:12:34 CDT)
• tang kwa
  • AMBER: error of performing simulation (Fri Aug 27 2004 - 12:07:21 CDT)
  • AMBER: error for performing MD (Fri Aug 27 2004 - 06:51:00 CDT)
• tarek mahfouz
  • AMBER: Neutral C and N termini. (Sun Aug 29 2004 - 18:37:19 CDT)
  • AMBER: Neutral C and N termini. (Fri Aug 27 2004 - 17:58:18 CDT)
  • AMBER: How to test the used parameters. (Wed Aug 11 2004 - 11:56:08 CDT)
  • Re: AMBER: Adding residues (Mon Aug 09 2004 - 13:51:26 CDT)
  • AMBER: AMBER7 plastocyanin tutorial problem. (Fri Aug 06 2004 - 12:40:33 CDT)
• Thomas E. Cheatham, III
  • Re: AMBER: Lennard-Jones particle simulation (Wed Aug 25 2004 - 15:05:58 CDT)
• Thomas Steinbrecher
  • Re: AMBER: charge perturbation - xleap question (Fri Aug 27 2004 - 02:19:25 CDT)
  • Re: AMBER: mutation of Tyr to Leu with TI (Wed Aug 25 2004 - 02:17:34 CDT)
  • Re: AMBER: questions on mm_pbsa (Sat Aug 21 2004 - 06:59:46 CDT)
  • AMBER: Amber8 - LAM MPI Compilation problems (Tue Aug 10 2004 - 11:16:38 CDT)
• Venkata S Koppuravuri
  • AMBER: question on minimization (Thu Aug 26 2004 - 10:41:48 CDT)
• Viktor Hornak
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Mon Aug 16 2004 - 14:26:27 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Mon Aug 16 2004 - 13:45:08 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 16:22:30 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 15:41:27 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 15:20:14 CDT)
  • Re: AMBER: recompiling amber8 (Tue Aug 03 2004 - 15:31:00 CDT)
• Vlad Cojocaru
  • AMBER: Differences in RESP charges for G in RG and DG residues (Mon Aug 30 2004 - 10:59:35 CDT)
  • AMBER: RED BUG!!! (Fri Aug 13 2004 - 07:56:25 CDT)
  • AMBER: RED BUG!!!!...perhaps I fixed it (Fri Aug 13 2004 - 07:34:50 CDT)
  • AMBER: RED fails to read g94 output (Fri Aug 13 2004 - 05:35:20 CDT)
  • AMBER: Gaussian in RED (Thu Aug 12 2004 - 07:37:05 CDT)
  • AMBER: RESP charge derivation (Wed Aug 11 2004 - 11:10:19 CDT)
• Wen-Chi Tseng
  • Re: AMBER: how to correct the charge of oligosaccharides (Thu Aug 12 2004 - 04:16:38 CDT)
  • AMBER: how to correct the charge of oligosaccharides (Mon Aug 09 2004 - 21:28:25 CDT)
• Xiao Jian Tan
  • Re: AMBER: recompiling amber8 (Tue Aug 03 2004 - 13:02:12 CDT)
• Xin Hu
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 16:15:27 CDT)
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 11:36:06 CDT)
  • AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 10:23:08 CDT)
• Yaroslava Yingling
  • AMBER: intense and spectrum (Wed Aug 04 2004 - 13:15:28 CDT)
• yen li
  • AMBER: Adding residues (Mon Aug 09 2004 - 12:47:44 CDT)
• Yong Duan
  • Re: AMBER: Amber 03 Forcefield discrepancy (Mon Aug 30 2004 - 13:16:21 CDT)
• Yongzhi Chen
  • AMBER: atoms not in residue templates (Wed Aug 04 2004 - 12:53:08 CDT)
  • AMBER: RMSD result from GB model (Wed Aug 04 2004 - 12:35:03 CDT)
• Yuhui Cheng
  • AMBER: One more question about the tree structure of looping residues (Wed Aug 25 2004 - 22:11:36 CDT)
  • Re: AMBER: About tree structure of TRP residue (Wed Aug 25 2004 - 19:35:13 CDT)
  • AMBER: About tree structure of TRP residue (Wed Aug 25 2004 - 18:46:36 CDT)
  • Re: AMBER: About the Amber constraint constant (Tue Aug 17 2004 - 01:34:24 CDT)
  • AMBER: About the Amber constraint constant (Sun Aug 15 2004 - 03:12:50 CDT)

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