Amber Archive Aug 2004: By Author

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

Amber Archive Aug 2004 By Author