Amber Archive Aug 2004: By Subject

about PME in Amber6
- Ross Walker (Fri Aug 06 2004 - 11:37:06 PDT)
AMBER:
- David A. Case (Tue Aug 31 2004 - 20:56:27 PDT)
- Bill Ross (Mon Aug 30 2004 - 14:33:38 PDT)
- jwcraft.uh.edu (Mon Aug 30 2004 - 12:54:46 PDT)
AMBER: A question about pheTI in AMBER8 test.
- David A. Case (Thu Aug 05 2004 - 17:39:06 PDT)
- Chunhu Tan (Thu Aug 05 2004 - 15:56:56 PDT)
- David A. Case (Wed Aug 04 2004 - 16:38:52 PDT)
- Chunhu Tan (Wed Aug 04 2004 - 14:35:48 PDT)
AMBER: About the Amber constraint constant
- David A. Case (Tue Aug 17 2004 - 08:08:04 PDT)
- Yuhui Cheng (Mon Aug 16 2004 - 23:34:24 PDT)
- David A. Case (Sun Aug 15 2004 - 16:07:11 PDT)
- Yuhui Cheng (Sun Aug 15 2004 - 01:12:50 PDT)
AMBER: About tree structure of TRP residue
- Bill Ross (Wed Aug 25 2004 - 17:56:13 PDT)
- Yuhui Cheng (Wed Aug 25 2004 - 17:35:13 PDT)
- Lihua Wang (Wed Aug 25 2004 - 17:16:46 PDT)
- Yuhui Cheng (Wed Aug 25 2004 - 16:46:36 PDT)
AMBER: Adding residues
- Bill Ross (Mon Aug 09 2004 - 12:23:08 PDT)
- Rhonda Torres (Mon Aug 09 2004 - 12:00:50 PDT)
- Ross Walker (Mon Aug 09 2004 - 11:50:59 PDT)
- tarek mahfouz (Mon Aug 09 2004 - 11:51:26 PDT)
AMBER: Amber 03 Forcefield discrepancy
- Yong Duan (Mon Aug 30 2004 - 11:16:21 PDT)
- MD Tyka, Biochemistry (Mon Aug 30 2004 - 07:36:18 PDT)
AMBER: Amber 8 - Energy Minimization Parameters
- Nhat-hang Duong (Wed Aug 25 2004 - 13:26:56 PDT)
- Ross Walker (Wed Aug 25 2004 - 09:02:31 PDT)
- Nhat-hang Duong (Wed Aug 25 2004 - 08:34:28 PDT)
AMBER: Amber 8 Installation - C compiler?
- Do Anh Tuan (Wed Aug 11 2004 - 22:28:37 PDT)
- Ross Walker (Wed Aug 11 2004 - 17:37:45 PDT)
- fangyu liang (Wed Aug 11 2004 - 17:23:03 PDT)
- Nhat-hang Duong (Wed Aug 11 2004 - 14:51:51 PDT)
AMBER: AMBER7 plastocyanin tutorial problem.
- David A. Case (Fri Aug 06 2004 - 12:09:34 PDT)
- Rhonda Torres (Fri Aug 06 2004 - 10:57:42 PDT)
- tarek mahfouz (Fri Aug 06 2004 - 10:40:33 PDT)
AMBER: Amber8 - Floating point
- Nhat-hang Duong (Thu Aug 26 2004 - 09:51:28 PDT)
- Michael Crowley (Thu Aug 26 2004 - 08:56:06 PDT)
- Carlos Simmerling (Thu Aug 26 2004 - 07:25:31 PDT)
- Nhat-hang Duong (Thu Aug 26 2004 - 07:15:00 PDT)
- Carlos Simmerling (Thu Aug 26 2004 - 07:00:52 PDT)
- Nhat-hang Duong (Thu Aug 26 2004 - 06:28:24 PDT)
AMBER: Amber8 - LAM MPI Compilation problems
- Ross Walker (Tue Aug 10 2004 - 09:59:33 PDT)
- Thomas Steinbrecher (Tue Aug 10 2004 - 09:16:38 PDT)
AMBER: Amber: Anal program format
- David A. Case (Tue Aug 17 2004 - 09:14:31 PDT)
- Helios (Mon Aug 16 2004 - 23:15:57 PDT)
AMBER: Amber: xleap crash
- Ross Walker (Fri Aug 13 2004 - 09:23:50 PDT)
- Helios (Fri Aug 13 2004 - 05:00:30 PDT)
AMBER: ANAL memory problem.
- David A. Case (Tue Aug 17 2004 - 09:33:03 PDT)
- Osman Gani (Tue Aug 17 2004 - 03:38:42 PDT)
- David A. Case (Mon Aug 16 2004 - 18:34:22 PDT)
- Osman Gani (Mon Aug 16 2004 - 06:16:15 PDT)
AMBER: angle bending
- Ross Walker (Thu Aug 19 2004 - 10:09:52 PDT)
- Gustavo Pierdominici Sottile (Thu Aug 19 2004 - 05:31:21 PDT)
AMBER: Angle parameters in phosphate groups
- Seongeun Yang (Sun Aug 15 2004 - 23:04:16 PDT)
- David A. Case (Sun Aug 15 2004 - 15:59:51 PDT)
- Guanglei Cui (Sun Aug 15 2004 - 07:08:29 PDT)
- Seongeun Yang (Sat Aug 14 2004 - 02:58:07 PDT)
- Guanglei Cui (Thu Aug 12 2004 - 07:18:06 PDT)
- Seongeun Yang (Thu Aug 12 2004 - 06:29:02 PDT)
- Seongeun Yang (Thu Aug 05 2004 - 05:17:44 PDT)
AMBER: another cpinutil.pl error
- David A. Case (Fri Aug 06 2004 - 08:58:46 PDT)
- Rukman Hertadi (Thu Aug 05 2004 - 22:35:09 PDT)
AMBER: Antechamber and dummy atoms
- Oliver Hucke (Fri Aug 13 2004 - 10:55:57 PDT)
- David A. Case (Fri Aug 13 2004 - 07:49:49 PDT)
- Perdita Barran (Fri Aug 13 2004 - 06:03:44 PDT)
AMBER: antechamber test
- David A. Case (Sun Aug 08 2004 - 09:40:34 PDT)
- mathew k varghese (Sun Aug 08 2004 - 05:31:22 PDT)
AMBER: Atomic charges in Lactose
- Johnson Agbo (Fri Aug 20 2004 - 12:35:48 PDT)
- Karl N. Kirschner (Wed Aug 11 2004 - 05:47:46 PDT)
- Johnson Agbo (Tue Aug 10 2004 - 17:23:53 PDT)
AMBER: atomic positional fluctuation
- RAJA SWAMINATHAN (Sat Aug 07 2004 - 00:18:32 PDT)
AMBER: atoms not in residue templates
- Ross Walker (Wed Aug 04 2004 - 11:26:55 PDT)
- Yongzhi Chen (Wed Aug 04 2004 - 10:53:08 PDT)
AMBER: bending
- Gustavo Pierdominici Sottile (Thu Aug 12 2004 - 13:47:16 PDT)
- David A. Case (Thu Aug 12 2004 - 12:48:30 PDT)
- Gustavo Pierdominici Sottile (Thu Aug 12 2004 - 12:28:42 PDT)
AMBER: Biotin/streptavidin tutorial.
- Bill Ross (Fri Aug 27 2004 - 10:57:47 PDT)
- Osman Gani (Fri Aug 27 2004 - 02:57:51 PDT)
AMBER: born radius and screening parameter for Br
- Oliver Hucke (Thu Aug 19 2004 - 15:58:44 PDT)
AMBER: Bug and Patch in ANAL
- David A. Case (Thu Aug 05 2004 - 08:44:38 PDT)
- Andy Purkiss (Wed Aug 04 2004 - 08:38:30 PDT)
AMBER: Bug: ptraj adds spurious box information
- David A. Case (Fri Aug 13 2004 - 15:13:33 PDT)
- Don Bashford (Fri Aug 13 2004 - 13:27:54 PDT)
AMBER: bugfix.all
- Ross Walker (Tue Aug 10 2004 - 17:54:25 PDT)
- Lihua Wang (Tue Aug 10 2004 - 13:48:51 PDT)
AMBER: can MM-PBSA be applied to Charmm format trajectory file?
- Ross Walker (Thu Aug 19 2004 - 12:02:50 PDT)
- jz7.duke.edu (Thu Aug 19 2004 - 11:55:06 PDT)
AMBER: charge not zero
- FyD (Wed Aug 04 2004 - 12:57:51 PDT)
- FyD (Wed Aug 04 2004 - 11:23:13 PDT)
- anshul.imtech.res.in (Wed Aug 04 2004 - 20:48:11 PDT)
- FyD (Tue Aug 03 2004 - 07:46:54 PDT)
- anshul.imtech.res.in (Tue Aug 03 2004 - 10:29:12 PDT)
AMBER: charge perturbation - xleap question
- Thomas Steinbrecher (Fri Aug 27 2004 - 00:19:25 PDT)
- Oliver Hucke (Thu Aug 26 2004 - 11:57:43 PDT)
AMBER: cpinutil.pl error
- John Mongan (Tue Aug 03 2004 - 11:03:40 PDT)
- Rukman Hertadi (Tue Aug 03 2004 - 04:22:59 PDT)
AMBER: density calculation in AMBER output
- Ross Walker (Wed Aug 25 2004 - 10:11:02 PDT)
- Grace Li (Wed Aug 25 2004 - 06:51:47 PDT)
AMBER: Differences in RESP charges for G in RG and DG residues
- Vlad Cojocaru (Mon Aug 30 2004 - 08:59:35 PDT)
AMBER: different cooling schedules for simulated annealing
- David A. Case (Thu Aug 12 2004 - 07:55:45 PDT)
- Madalin Giambasu (Wed Aug 11 2004 - 09:23:08 PDT)
- David A. Case (Wed Aug 11 2004 - 07:41:50 PDT)
- Madalin Giambasu (Wed Aug 11 2004 - 04:51:09 PDT)
AMBER: Dr. Herman Von Grafenstein
- Harsh Parikh (Tue Aug 17 2004 - 16:43:06 PDT)
AMBER: error estimates in AMBER
- Grace Li (Mon Aug 23 2004 - 13:43:14 PDT)
AMBER: error for performing MD
- tang kwa (Fri Aug 27 2004 - 04:51:00 PDT)
AMBER: error of performing simulation
- tang kwa (Fri Aug 27 2004 - 10:07:21 PDT)
AMBER: error while loading shared libraries: libcxa.so.5
- Mark Williamson (Mon Aug 09 2004 - 07:42:16 PDT)
- Guanglei Cui (Mon Aug 09 2004 - 07:24:06 PDT)
- Madalin Giambasu (Mon Aug 09 2004 - 06:54:00 PDT)
AMBER: freezing atoms in impliciti solvent
- Carlos Simmerling (Tue Aug 24 2004 - 10:54:58 PDT)
- Sergio E. Wong (Tue Aug 24 2004 - 10:27:32 PDT)
AMBER: Gaussian in RED
- FyD (Fri Aug 13 2004 - 22:16:30 PDT)
- Vlad Cojocaru (Thu Aug 12 2004 - 05:37:05 PDT)
AMBER: Glycam-04 Parameters in Amber 7
- Johnson Agbo (Mon Aug 30 2004 - 18:12:17 PDT)
AMBER: how to correct the charge of oligosaccharides
- Wen-Chi Tseng (Thu Aug 12 2004 - 02:16:38 PDT)
- Karl N. Kirschner (Tue Aug 10 2004 - 07:53:29 PDT)
- David A. Case (Tue Aug 10 2004 - 07:31:40 PDT)
- Wen-Chi Tseng (Mon Aug 09 2004 - 19:28:25 PDT)
AMBER: How to covalently bind a ligand to a residue?
- david.evans.ulsop.ac.uk (Fri Aug 06 2004 - 01:22:17 PDT)
- david.evans.ulsop.ac.uk (Fri Aug 06 2004 - 01:11:39 PDT)
- Bimo Ario Tejo (Thu Aug 05 2004 - 22:06:02 PDT)
- Ozlem Demir (Thu Aug 05 2004 - 08:54:19 PDT)
AMBER: how to deal with the initial structure?
- Furse, Kristina Elisabet (Tue Aug 24 2004 - 12:29:39 PDT)
- Ross Walker (Mon Aug 23 2004 - 19:19:23 PDT)
- hj zou (Mon Aug 23 2004 - 18:48:22 PDT)
AMBER: how to read in CHARMM or AMBER binary trajectories
- Ross Walker (Thu Aug 19 2004 - 11:30:59 PDT)
- Grace Li (Thu Aug 19 2004 - 11:19:48 PDT)
AMBER: How to test the used parameters.
- Ross Walker (Wed Aug 11 2004 - 10:33:56 PDT)
- Bill Ross (Wed Aug 11 2004 - 10:31:28 PDT)
- tarek mahfouz (Wed Aug 11 2004 - 09:56:08 PDT)
AMBER: Improving PMEMD Performance on gigabit ethernet - CORRECTION
- Robert Duke (Tue Aug 17 2004 - 05:42:33 PDT)
AMBER: Improving PMEMD performance on gigabit ethernet Linux clusters
- Robert Duke (Mon Aug 16 2004 - 14:17:45 PDT)
AMBER: Increase lastrst in the &cntrl namelist
- Sichun Yang (Tue Aug 31 2004 - 23:29:27 PDT)
- David A. Case (Tue Aug 31 2004 - 21:53:20 PDT)
- Sichun Yang (Tue Aug 31 2004 - 09:06:46 PDT)
AMBER: Increasing MAXATOM in antechamber
- Niko Jukarainen (Sat Aug 21 2004 - 09:13:56 PDT)
- Guanglei Cui (Sat Aug 21 2004 - 08:07:10 PDT)
- Niko Jukarainen (Sat Aug 21 2004 - 02:45:08 PDT)
AMBER: installing amber 8 on 64 bit amd opteron
- Dr Gavin Seddon (Tue Aug 10 2004 - 22:55:05 PDT)
AMBER: installing amber8
- Dr Gavin Seddon (Mon Aug 16 2004 - 02:20:20 PDT)
AMBER: intense and spectrum
- David A. Case (Wed Aug 04 2004 - 16:41:13 PDT)
- Yaroslava Yingling (Wed Aug 04 2004 - 11:15:28 PDT)
AMBER: intrinsic born radius of Br
- Oliver Hucke (Tue Aug 17 2004 - 18:33:18 PDT)
AMBER: leap: impose
- Guanglei Cui (Tue Aug 17 2004 - 13:15:27 PDT)
- Guanglei Cui (Tue Aug 17 2004 - 12:23:27 PDT)
- Guanglei Cui (Tue Aug 17 2004 - 11:44:04 PDT)
AMBER: Lennard-Jones particle simulation
- Piotr Cieplak (Wed Aug 25 2004 - 15:31:37 PDT)
- Guanglei Cui (Wed Aug 25 2004 - 14:11:37 PDT)
- darden (Wed Aug 25 2004 - 13:57:15 PDT)
- Carlos Simmerling (Wed Aug 25 2004 - 13:06:47 PDT)
- Thomas E. Cheatham, III (Wed Aug 25 2004 - 13:05:58 PDT)
- Guanglei Cui (Wed Aug 25 2004 - 12:38:57 PDT)
AMBER: MD & net charge
- bybaker.itsa.ucsf.edu (Mon Aug 30 2004 - 15:02:53 PDT)
- Carlos Simmerling (Mon Aug 30 2004 - 13:57:50 PDT)
- bybaker.itsa.ucsf.edu (Mon Aug 30 2004 - 13:48:00 PDT)
- Carlos Simmerling (Mon Aug 30 2004 - 06:41:21 PDT)
- Chris Harrison (Mon Aug 30 2004 - 06:28:46 PDT)
- Carlos Simmerling (Mon Aug 30 2004 - 06:23:20 PDT)
- bybaker.itsa.ucsf.edu (Sat Aug 28 2004 - 23:19:18 PDT)
AMBER: Membrane protein simulation
- David A. Case (Tue Aug 10 2004 - 18:06:57 PDT)
- Gabbar Daaku (Tue Aug 10 2004 - 13:37:22 PDT)
AMBER: metal atoms in Xleap
- Atilio Anzellotti (Fri Aug 20 2004 - 13:25:47 PDT)
- Jiri Sponer (Fri Aug 20 2004 - 12:04:32 PDT)
- Atilio Anzellotti (Fri Aug 20 2004 - 11:43:51 PDT)
- Ross Walker (Thu Aug 19 2004 - 09:59:28 PDT)
- Rhonda Torres (Thu Aug 19 2004 - 09:57:04 PDT)
- Atilio Anzellotti (Thu Aug 19 2004 - 08:05:23 PDT)
AMBER: Minimization error
- Ross Walker (Sat Aug 28 2004 - 12:34:31 PDT)
- opitz.che.udel.edu (Fri Aug 27 2004 - 13:56:46 PDT)
- Ross Walker (Wed Aug 25 2004 - 15:35:18 PDT)
- opitz.che.udel.edu (Wed Aug 25 2004 - 13:55:24 PDT)
- Ross Walker (Wed Aug 25 2004 - 10:23:13 PDT)
- opitz.che.udel.edu (Tue Aug 24 2004 - 14:09:15 PDT)
- Ross Walker (Fri Aug 20 2004 - 15:48:27 PDT)
- opitz.che.udel.edu (Fri Aug 20 2004 - 12:43:31 PDT)
AMBER: minimization output file format
- Ross Walker (Thu Aug 12 2004 - 12:43:02 PDT)
- Marsita M (Thu Aug 12 2004 - 10:51:35 PDT)
AMBER: Minimum imaging
- Joseph Nachman (Tue Aug 03 2004 - 22:01:54 PDT)
- David A. Case (Tue Aug 03 2004 - 07:25:47 PDT)
- Grace Li (Mon Aug 02 2004 - 20:21:50 PDT)
AMBER: mm-gbsa
- Oliver Hucke (Tue Aug 17 2004 - 16:59:21 PDT)
AMBER: mm_pbsa Abmer8 example
- Holger Gohlke (Mon Aug 02 2004 - 23:39:06 PDT)
AMBER: mm_pbsa problem
- Ray Luo (Tue Aug 03 2004 - 16:18:48 PDT)
- Carsten Detering (Tue Aug 03 2004 - 13:49:34 PDT)
AMBER: mm_pbsa.pl in Amber8
- Sarah Rankin (Mon Aug 23 2004 - 03:00:21 PDT)
- Shan, Jufang (Fri Aug 20 2004 - 12:13:54 PDT)
AMBER: mmpbsa question
- Sébastien Osborne (Thu Aug 19 2004 - 12:58:42 PDT)
AMBER: Moil-view, prmtop, inpcrd question
- opitz.che.udel.edu (Mon Aug 16 2004 - 12:51:30 PDT)
- Viktor Hornak (Mon Aug 16 2004 - 12:26:27 PDT)
- opitz.che.udel.edu (Mon Aug 16 2004 - 12:18:50 PDT)
- Viktor Hornak (Mon Aug 16 2004 - 11:45:08 PDT)
- opitz.che.udel.edu (Mon Aug 16 2004 - 11:17:35 PDT)
- Carlos Simmerling (Sat Aug 14 2004 - 05:13:23 PDT)
- David A. Case (Fri Aug 13 2004 - 15:07:42 PDT)
- Viktor Hornak (Fri Aug 13 2004 - 14:22:30 PDT)
- opitz.che.udel.edu (Fri Aug 13 2004 - 14:08:27 PDT)
- Viktor Hornak (Fri Aug 13 2004 - 13:41:27 PDT)
- opitz.che.udel.edu (Fri Aug 13 2004 - 13:28:26 PDT)
- Viktor Hornak (Fri Aug 13 2004 - 13:20:14 PDT)
- opitz.che.udel.edu (Fri Aug 13 2004 - 13:08:33 PDT)
AMBER: mutation of Tyr to Leu with TI
- Thomas Steinbrecher (Wed Aug 25 2004 - 00:17:34 PDT)
- Oliver Hucke (Tue Aug 24 2004 - 16:56:47 PDT)
AMBER: Neutral C and N termini.
- M. L. Dodson (Sun Aug 29 2004 - 19:14:10 PDT)
- tarek mahfouz (Sun Aug 29 2004 - 16:37:19 PDT)
- tarek mahfouz (Fri Aug 27 2004 - 15:58:18 PDT)
AMBER: nonpalar energy contribution-DMSO
- Dalmaris, John (Sat Aug 28 2004 - 07:11:43 PDT)
AMBER: NTT=0 and TAUTP
- Ross Walker (Mon Aug 23 2004 - 16:03:30 PDT)
- Gabbar Daaku (Mon Aug 23 2004 - 15:25:26 PDT)
AMBER: One more question about the tree structure of looping residues
- Bill Ross (Thu Aug 26 2004 - 11:31:23 PDT)
- Yuhui Cheng (Wed Aug 25 2004 - 20:11:36 PDT)
AMBER: opteron 64 bit workstation
- David A. Case (Thu Aug 12 2004 - 12:55:13 PDT)
- sachin patil (Wed Aug 11 2004 - 11:59:33 PDT)
AMBER: parameter
- Guanglei Cui (Wed Aug 11 2004 - 14:07:18 PDT)
- Gustavo Pierdominici Sottile (Wed Aug 11 2004 - 13:45:02 PDT)
AMBER: parm94
- bybaker.itsa.ucsf.edu (Tue Aug 31 2004 - 18:57:39 PDT)
- Lihua Wang (Tue Aug 31 2004 - 15:22:29 PDT)
- bybaker.itsa.ucsf.edu (Tue Aug 31 2004 - 15:15:04 PDT)
- bybaker.itsa.ucsf.edu (Tue Aug 31 2004 - 09:21:00 PDT)
- Asim Okur (Tue Aug 31 2004 - 06:12:58 PDT)
- bybaker.itsa.ucsf.edu (Mon Aug 30 2004 - 23:50:09 PDT)
AMBER: pb_bomb in setgrd()
- Ray Luo (Tue Aug 10 2004 - 09:29:13 PDT)
- steven.j.enoch.gsk.com (Tue Aug 10 2004 - 03:34:42 PDT)
AMBER: PBC in sander
- David A. Case (Tue Aug 31 2004 - 20:57:49 PDT)
- Mingfeng Yang (Tue Aug 31 2004 - 13:27:26 PDT)
AMBER: peoblemwith RED II
- FyD (Sat Aug 28 2004 - 02:52:20 PDT)
- FyD (Fri Aug 27 2004 - 03:02:37 PDT)
- FyD (Thu Aug 26 2004 - 08:44:16 PDT)
- anshul.imtech.res.in (Tue Aug 17 2004 - 12:15:30 PDT)
AMBER: perturb a water to a dummy water with shake
- Dr. Turgut Bastug (Mon Aug 09 2004 - 17:24:25 PDT)
AMBER: pmemd config.h request for athlon
- Robert Duke (Fri Aug 13 2004 - 11:42:42 PDT)
- Robert Duke (Fri Aug 13 2004 - 11:40:05 PDT)
- Ross Walker (Fri Aug 13 2004 - 11:09:15 PDT)
- Madalin Giambasu (Fri Aug 13 2004 - 10:47:53 PDT)
AMBER: pmemd problems
- Robert Duke (Fri Aug 13 2004 - 12:14:39 PDT)
- Florian Barth (Fri Aug 13 2004 - 11:52:22 PDT)
AMBER: pmemd.
- David E. Konerding (Mon Aug 16 2004 - 09:27:02 PDT)
- Robert Duke (Mon Aug 16 2004 - 07:33:21 PDT)
- Osman Gani (Mon Aug 16 2004 - 06:03:15 PDT)
AMBER: pmemd. - OOPS!!!
- Robert Duke (Mon Aug 16 2004 - 07:45:03 PDT)
AMBER: problem loading molecule in leap
- anshul.imtech.res.in (Thu Aug 26 2004 - 13:38:44 PDT)
AMBER: problem loading pdb in leap.
- Ross Walker (Tue Aug 24 2004 - 10:35:08 PDT)
- Andrew Box (Mon Aug 23 2004 - 23:30:46 PDT)
- anshul.imtech.res.in (Tue Aug 24 2004 - 09:34:58 PDT)
- Ross Walker (Mon Aug 23 2004 - 21:53:49 PDT)
- anshul.imtech.res.in (Tue Aug 24 2004 - 07:52:05 PDT)
AMBER: Problem: Installing Amber8 on PC with Windows XP
- David A. Case (Tue Aug 03 2004 - 15:28:25 PDT)
- fangyu liang (Tue Aug 03 2004 - 14:47:08 PDT)
- Nhat-hang Duong (Tue Aug 03 2004 - 13:38:55 PDT)
AMBER: Problems with Carnal coordinate average
- Bill Ross (Mon Aug 09 2004 - 10:12:04 PDT)
- HL Eastwood (Mon Aug 09 2004 - 04:35:37 PDT)
AMBER: ptraj -- velocities set to zero?
- Gabbar Daaku (Thu Aug 12 2004 - 08:53:04 PDT)
AMBER: ptraj and hbond
- Nelson Fonseca (Thu Aug 26 2004 - 02:50:39 PDT)
AMBER: ptraj: load crd without hydrogen (i.e. missing parm file)
- Raik Grünberg (Mon Aug 02 2004 - 02:30:56 PDT)
AMBER: Pulling versus Distance Restraints
- Nhat-hang Duong (Tue Aug 31 2004 - 14:16:15 PDT)
AMBER: question about compilation of AMBER8 on MANDRAKE9.2
- Sarah Rankin (Tue Aug 17 2004 - 01:18:30 PDT)
- Ross Walker (Mon Aug 16 2004 - 11:13:09 PDT)
- Sarah Rankin (Mon Aug 16 2004 - 10:14:38 PDT)
- Niko Jukarainen (Fri Aug 13 2004 - 03:09:10 PDT)
- Madalin Giambasu (Fri Aug 13 2004 - 03:02:57 PDT)
AMBER: question about covariance matrix from ptraj
- Elijah Gregory (Mon Aug 09 2004 - 13:00:06 PDT)
- jz7.duke.edu (Mon Aug 09 2004 - 12:25:10 PDT)
AMBER: question on minimization
- Venkata S Koppuravuri (Thu Aug 26 2004 - 08:41:48 PDT)
AMBER: questions on mm_pbsa
- Thomas Steinbrecher (Sat Aug 21 2004 - 04:59:46 PDT)
- cailliez (Fri Aug 20 2004 - 05:13:51 PDT)
AMBER: rdparm problem
- Lijiang Yang (Mon Aug 09 2004 - 15:43:10 PDT)
AMBER: recompiling amber8
- Viktor Hornak (Tue Aug 03 2004 - 13:31:00 PDT)
- Xiao Jian Tan (Tue Aug 03 2004 - 11:02:12 PDT)
- Robert Duke (Tue Aug 03 2004 - 09:30:41 PDT)
- Carsten Detering (Tue Aug 03 2004 - 08:55:04 PDT)
- David A. Case (Mon Aug 02 2004 - 18:18:25 PDT)
- Robert Duke (Mon Aug 02 2004 - 18:12:52 PDT)
- Carsten Detering (Mon Aug 02 2004 - 17:57:19 PDT)
AMBER: RED BUG!!!
- Vlad Cojocaru (Fri Aug 13 2004 - 05:56:25 PDT)
AMBER: RED BUG!!!!...perhaps I fixed it
- Vlad Cojocaru (Fri Aug 13 2004 - 05:34:50 PDT)
AMBER: RED fails to read g94 output
- FyD (Sat Aug 14 2004 - 01:26:33 PDT)
- FyD (Fri Aug 13 2004 - 22:34:21 PDT)
- Vlad Cojocaru (Fri Aug 13 2004 - 03:35:20 PDT)
AMBER: residue database
- Lihua Wang (Sat Aug 14 2004 - 14:55:59 PDT)
AMBER: RESP calculation with different multiplicities
- FyD (Thu Aug 26 2004 - 11:09:18 PDT)
- Sebastian Fernandez Alberti (Tue Aug 17 2004 - 13:44:54 PDT)
AMBER: resp charge calculation for Fe+3 heme
- James W. Caldwell (Mon Aug 09 2004 - 13:18:46 PDT)
- Sebastian Fernandez Alberti (Mon Aug 09 2004 - 12:45:18 PDT)
AMBER: RESP charge derivation
- FyD (Wed Aug 11 2004 - 09:55:57 PDT)
- Vlad Cojocaru (Wed Aug 11 2004 - 09:10:19 PDT)
AMBER: RESP charges in Fe+3 heme system
- FyD (Thu Aug 26 2004 - 11:33:09 PDT)
- Sebastian Fernandez Alberti (Thu Aug 26 2004 - 10:43:08 PDT)
AMBER: RESP partial charge calculation
- FyD (Tue Aug 10 2004 - 10:46:16 PDT)
- James W. Caldwell (Tue Aug 10 2004 - 10:25:55 PDT)
- Sebastian Fernandez Alberti (Tue Aug 10 2004 - 09:21:06 PDT)
AMBER: restart a MD after replacing molecules
- cailliez (Thu Aug 26 2004 - 01:38:55 PDT)
- Ross Walker (Wed Aug 25 2004 - 10:29:13 PDT)
- cailliez (Wed Aug 25 2004 - 07:03:41 PDT)
AMBER: RMSD result from GB model
- Marcin Krol (Thu Aug 05 2004 - 01:32:36 PDT)
- Ross Walker (Wed Aug 04 2004 - 11:06:50 PDT)
- Yongzhi Chen (Wed Aug 04 2004 - 10:35:03 PDT)
AMBER: Sander
- David A. Case (Mon Aug 09 2004 - 15:21:12 PDT)
- sachin patil (Mon Aug 09 2004 - 11:26:20 PDT)
- David A. Case (Mon Aug 09 2004 - 09:57:40 PDT)
- sachin patil (Mon Aug 09 2004 - 09:24:59 PDT)
AMBER: Sander : Vrand flag
- sachin patil (Tue Aug 31 2004 - 07:15:37 PDT)
- Furse, Kristina Elisabet (Tue Aug 24 2004 - 11:47:38 PDT)
- Ross Walker (Mon Aug 23 2004 - 13:58:15 PDT)
- sachin patil (Mon Aug 23 2004 - 12:54:52 PDT)
- Ross Walker (Mon Aug 23 2004 - 12:29:06 PDT)
- sachin patil (Mon Aug 23 2004 - 12:07:32 PDT)
- Ross Walker (Mon Aug 23 2004 - 11:20:15 PDT)
- sachin patil (Mon Aug 23 2004 - 10:59:30 PDT)
AMBER: sander error
- Ross Walker (Thu Aug 05 2004 - 21:50:09 PDT)
- Rukman Hertadi (Thu Aug 05 2004 - 21:33:41 PDT)
AMBER: sander.QMMM: CHARGE keyword in divcon.in file
- M. L. Dodson (Thu Aug 05 2004 - 15:30:20 PDT)
- M. L. Dodson (Wed Aug 04 2004 - 17:08:07 PDT)
- Ross Walker (Wed Aug 04 2004 - 13:48:08 PDT)
- M. L. Dodson (Wed Aug 04 2004 - 12:23:29 PDT)
AMBER: simulated annealing
- nurul bahiyah (Sun Aug 15 2004 - 05:42:53 PDT)
- Carlos Simmerling (Sat Aug 14 2004 - 05:20:12 PDT)
- Lee SL (Sat Aug 14 2004 - 03:40:54 PDT)
- Lee SL (Sat Aug 14 2004 - 02:51:14 PDT)
AMBER: snapshots of MD trajectory
- Xin Hu (Fri Aug 27 2004 - 14:15:27 PDT)
- Carlos Simmerling (Fri Aug 27 2004 - 12:44:36 PDT)
- Guanglei Cui (Fri Aug 27 2004 - 12:38:44 PDT)
- Xin Hu (Fri Aug 27 2004 - 09:36:06 PDT)
- Peter Gannett (Fri Aug 27 2004 - 08:43:33 PDT)
- Carlos Simmerling (Fri Aug 27 2004 - 08:36:38 PDT)
- Guanglei Cui (Fri Aug 27 2004 - 08:27:20 PDT)
- Xin Hu (Fri Aug 27 2004 - 08:23:08 PDT)
AMBER: Temp control
- David A. Case (Fri Aug 13 2004 - 13:13:20 PDT)
- ding (Fri Aug 13 2004 - 11:46:20 PDT)
AMBER: temperature control in coupled potential runs
- M. L. Dodson (Mon Aug 16 2004 - 12:05:49 PDT)
AMBER: temperature scaling with ntt=3(Langevin thermostat)
- David A. Case (Tue Aug 31 2004 - 21:43:01 PDT)
- Madalin Giambasu (Mon Aug 30 2004 - 07:47:55 PDT)
- Carlos Simmerling (Mon Aug 30 2004 - 06:51:28 PDT)
- Madalin Giambasu (Mon Aug 30 2004 - 06:51:35 PDT)
- Carlos Simmerling (Mon Aug 30 2004 - 06:21:36 PDT)
- Madalin Giambasu (Mon Aug 30 2004 - 01:01:05 PDT)
AMBER: thermal ellipsoid-DNA
- RAJA SWAMINATHAN (Thu Aug 19 2004 - 02:29:34 PDT)
AMBER: tleap: automatically identify and connect disulfide bonds?
- Raik Grünberg (Mon Aug 02 2004 - 02:15:34 PDT)
AMBER: Trajectory file conversion between Amber & Charmm
- Ross Walker (Tue Aug 24 2004 - 16:51:17 PDT)
- CK Sim (Tue Aug 24 2004 - 13:42:19 PDT)
AMBER: trival question about format of pev file and covariance matrix
- jz7.duke.edu (Mon Aug 09 2004 - 08:52:03 PDT)
AMBER: turning off HB interactions
- Taner E. Dirama (Tue Aug 17 2004 - 13:12:34 PDT)
AMBER: units
- David A. Case (Thu Aug 12 2004 - 07:56:09 PDT)
- Gustavo Pierdominici Sottile (Wed Aug 11 2004 - 08:03:38 PDT)
AMBER: unknown residue: ABA
- Lao_3 (Wed Aug 11 2004 - 08:45:44 PDT)
- Lao_3 (Tue Aug 10 2004 - 14:45:27 PDT)
- Bill Ross (Tue Aug 10 2004 - 12:20:36 PDT)
- Ross Walker (Tue Aug 10 2004 - 11:46:14 PDT)
- Guowen Han (Tue Aug 10 2004 - 11:31:25 PDT)
AMBER: Updating Amber 7
- David A. Case (Tue Aug 31 2004 - 21:00:46 PDT)
- Johnson Agbo (Fri Aug 20 2004 - 11:52:23 PDT)
AMBER: Using AMBER to simulate carbon nanotubes?
- darden (Tue Aug 31 2004 - 08:43:56 PDT)
- Chen Song (Tue Aug 31 2004 - 03:54:26 PDT)
AMBER: Using TIP4P water in free energy calculation
- Lijiang Yang (Fri Aug 06 2004 - 11:42:06 PDT)
- David A. Case (Fri Aug 06 2004 - 08:56:46 PDT)
- Lijiang Yang (Thu Aug 05 2004 - 22:04:07 PDT)
- David A. Case (Thu Aug 05 2004 - 15:35:22 PDT)
- Lijiang Yang (Thu Aug 05 2004 - 15:03:36 PDT)
AMBER: xleap problem fixed!
- HL Eastwood (Tue Aug 03 2004 - 10:20:21 PDT)
Hello Sir,
- Ross Walker (Wed Aug 04 2004 - 11:32:28 PDT)
Imaging problem
- Steve Seibold (Mon Aug 02 2004 - 13:32:37 PDT)
Phosphoserine residue in AMBER
- David A. Case (Tue Aug 03 2004 - 14:23:20 PDT)
RED II and changepot
- FyD (Tue Aug 10 2004 - 11:35:05 PDT)

Amber Archive Aug 2004 By Subject