Amber Archive Aug 2004 by subject
359 messages
:
Starting
Mon Aug 02 2004 - 10:53:00 PDT,
Ending
Thu Sep 02 2004 - 01:15:13 PDT
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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)
Last message date
:
Thu Sep 02 2004 - 01:15:13 PDT
Archived on
: Fri Dec 13 2024 - 05:53:24 PST
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