Amber Archive Jun 2004: by subject

[pradipta_b.mail.jnu.ac.in: AMBER: Software to visualize normal modes!]
- David A. Case (Tue Jun 01 2004 - 16:24:54 PDT)
AMBER
- Jiten (Wed Jun 02 2004 - 18:48:37 PDT)
- vidit kumar (Wed Jun 02 2004 - 18:19:08 PDT)
AMBER: "Total vdw box size" information is gone
- Jiten (Mon Jun 28 2004 - 07:45:39 PDT)
- David A. Case (Sun Jun 27 2004 - 14:03:39 PDT)
- Helios Chen (Sun Jun 27 2004 - 00:57:50 PDT)
AMBER: (no subject)
- David A. Case (Sun Jun 27 2004 - 23:12:26 PDT)
- Andrew Box (Sun Jun 27 2004 - 20:29:34 PDT)
AMBER: -p4pg problem
- spookie (Sat Jun 26 2004 - 22:19:33 PDT)
- David A. Case (Sat Jun 26 2004 - 11:54:03 PDT)
- Lubos Vrbka (Sat Jun 26 2004 - 07:42:55 PDT)
- spookie (Sat Jun 26 2004 - 07:00:48 PDT)
- Lubos Vrbka (Sat Jun 26 2004 - 03:59:53 PDT)
- spookie (Sat Jun 26 2004 - 01:34:40 PDT)
AMBER: A problem about a sander parallel run
- Yongzhi Chen (Thu Jun 24 2004 - 11:40:37 PDT)
AMBER: a question on MM-PBSA and Delphi
- Jiayun (Tue Jun 29 2004 - 02:54:46 PDT)
- Thomas Steinbrecher (Wed Jun 23 2004 - 11:09:16 PDT)
- Jiayun (Wed Jun 23 2004 - 11:00:17 PDT)
- Thomas Steinbrecher (Wed Jun 23 2004 - 08:13:48 PDT)
- Jiayun (Wed Jun 23 2004 - 06:34:31 PDT)
AMBER: About DelPhi and GRASP
- Ilyas Yildirim (Wed Jun 02 2004 - 21:10:07 PDT)
AMBER: About Hbond calculations using ptraj
- Thomas E. Cheatham, III (Wed Jun 30 2004 - 11:11:05 PDT)
- javier perez (Mon Jun 28 2004 - 10:43:37 PDT)
AMBER: About TI with sander
- David A. Case (Tue Jun 29 2004 - 09:45:52 PDT)
- Guanglei Cui (Mon Jun 28 2004 - 12:46:52 PDT)
- Chunhu Tan (Mon Jun 28 2004 - 12:35:54 PDT)
AMBER: About umbrella sampling in Amber 8
- David A. Case (Tue Jun 15 2004 - 09:05:59 PDT)
- Yuhui Cheng (Mon Jun 14 2004 - 18:45:44 PDT)
AMBER: Add Hydrogen bond through xLeap?
- Guanglei Cui (Wed Jun 02 2004 - 07:06:47 PDT)
- Nan Lin (Tue Jun 01 2004 - 23:25:18 PDT)
AMBER: all_amino03.in discrepancy
- Dr. Yong Duan (Mon Jun 21 2004 - 09:41:03 PDT)
- Vojtech Klusak (Mon Jun 21 2004 - 02:36:09 PDT)
AMBER: Amber & mutation
- bybaker.itsa.ucsf.edu (Thu Jun 10 2004 - 09:24:24 PDT)
- Tim Meyer (Wed Jun 09 2004 - 22:14:11 PDT)
- bybaker.itsa.ucsf.edu (Wed Jun 09 2004 - 17:53:58 PDT)
AMBER: Amber 8 installation
- David A. Case (Fri Jun 25 2004 - 12:15:50 PDT)
- spookie (Fri Jun 25 2004 - 11:08:21 PDT)
- fangyu liang (Fri Jun 25 2004 - 11:03:06 PDT)
- Ross Walker (Fri Jun 25 2004 - 10:27:23 PDT)
- David A. Case (Fri Jun 25 2004 - 08:33:30 PDT)
- fangyu liang (Fri Jun 25 2004 - 00:34:45 PDT)
- spookie (Thu Jun 24 2004 - 15:42:40 PDT)
- Ross Walker (Thu Jun 24 2004 - 15:38:57 PDT)
- fangyu liang (Thu Jun 24 2004 - 15:24:43 PDT)
AMBER: Amber 8 installation error
- David A. Case (Tue Jun 29 2004 - 16:55:18 PDT)
- Ross Walker (Tue Jun 29 2004 - 16:08:21 PDT)
- fangyu liang (Tue Jun 29 2004 - 15:52:29 PDT)
- fangyu liang (Tue Jun 29 2004 - 15:31:28 PDT)
- David A. Case (Tue Jun 29 2004 - 07:56:53 PDT)
- fangyu liang (Tue Jun 29 2004 - 00:00:32 PDT)
AMBER: Amber force field for protein-DNA system
- David A. Case (Tue Jun 01 2004 - 11:40:15 PDT)
- Bill Ross (Tue Jun 01 2004 - 11:32:52 PDT)
- Ross Walker (Tue Jun 01 2004 - 11:09:37 PDT)
- Rhonda Torres (Tue Jun 01 2004 - 10:24:57 PDT)
- jz7.duke.edu (Tue Jun 01 2004 - 09:14:16 PDT)
AMBER: Amber force field for protein-DNA system (again)
- jz7.duke.edu (Wed Jun 02 2004 - 10:31:56 PDT)
- jz7.duke.edu (Tue Jun 01 2004 - 12:51:59 PDT)
AMBER: Amber Transition State Output
- Johnson Agbo (Thu Jun 10 2004 - 22:28:05 PDT)
- David A. Case (Wed Jun 09 2004 - 18:54:23 PDT)
- Johnson Agbo (Wed Jun 09 2004 - 17:33:58 PDT)
- David A. Case (Wed Jun 09 2004 - 15:55:14 PDT)
- Johnson Agbo (Wed Jun 09 2004 - 12:46:03 PDT)
AMBER: AMBER7 : update force field gaff.dat and parm99.dat
- Guillaume Bollot (Thu Jun 24 2004 - 05:48:39 PDT)
AMBER: AMBER7 update force field
- Guillaume Bollot (Thu Jun 24 2004 - 06:23:44 PDT)
AMBER: Amber7:
- FyD (Thu Jun 03 2004 - 13:11:28 PDT)
- Vidit Kumar (Thu Jun 03 2004 - 12:55:21 PDT)
AMBER: Amber7: pdb format file
- David A. Case (Tue Jun 01 2004 - 12:23:47 PDT)
- Ross Walker (Tue Jun 01 2004 - 11:49:31 PDT)
- Peter Gannett (Tue Jun 01 2004 - 11:22:32 PDT)
- vidit kumar (Tue Jun 01 2004 - 11:13:03 PDT)
AMBER: Amber8 compilation in IBM-AIX
- Jiten (Mon Jun 28 2004 - 17:48:25 PDT)
- David A. Case (Mon Jun 28 2004 - 08:42:20 PDT)
- Nicolas Grima (Mon Jun 28 2004 - 08:13:32 PDT)
- Jiten (Mon Jun 28 2004 - 07:39:02 PDT)
- Nicolas Grima (Mon Jun 28 2004 - 03:55:59 PDT)
- Jiten (Mon Jun 28 2004 - 02:19:42 PDT)
AMBER: Amber8 compilation problems on AIX
- Nicolas Grima (Wed Jun 30 2004 - 00:12:19 PDT)
- Gabbar Daaku (Tue Jun 29 2004 - 19:50:13 PDT)
AMBER: amber8 compile on Lemieux
- Guanglei Cui (Thu Jun 03 2004 - 20:56:13 PDT)
- David A. Case (Thu Jun 03 2004 - 19:39:58 PDT)
- Guanglei Cui (Thu Jun 03 2004 - 08:06:21 PDT)
AMBER: amber8 parallel jobs
- spookie (Fri Jun 25 2004 - 11:05:23 PDT)
- spookie (Fri Jun 25 2004 - 06:42:09 PDT)
- Carlos Simmerling (Thu Jun 24 2004 - 05:17:05 PDT)
- spookie (Wed Jun 23 2004 - 21:50:48 PDT)
AMBER: AMBPDB command requires libcxa.so.5
- Amber admin (Mon Jun 28 2004 - 08:12:45 PDT)
- David A. Case (Sat Jun 26 2004 - 11:56:09 PDT)
- Cenk Andac (Sat Jun 26 2004 - 08:16:52 PDT)
AMBER: antechamber
- Guanglei Cui (Wed Jun 09 2004 - 07:05:02 PDT)
- Matheus Froeyen (Wed Jun 09 2004 - 00:39:26 PDT)
AMBER: antechamber/parmchk ATTN: needs revision
- Nan Lin (Wed Jun 09 2004 - 11:48:55 PDT)
AMBER: Atom Labels
- German Sciaini (Wed Jun 30 2004 - 04:36:14 PDT)
- David A. Case (Tue Jun 29 2004 - 13:54:37 PDT)
- Viktor Hornak (Tue Jun 29 2004 - 13:53:41 PDT)
- Karl N. Kirschner (Tue Jun 29 2004 - 13:36:22 PDT)
AMBER: Bad contacts
- bybaker.itsa.ucsf.edu (Wed Jun 09 2004 - 13:30:38 PDT)
- Carlos Simmerling (Wed Jun 09 2004 - 11:56:09 PDT)
- bybaker.itsa.ucsf.edu (Wed Jun 09 2004 - 10:02:01 PDT)
- bybaker.itsa.ucsf.edu (Mon Jun 07 2004 - 17:44:37 PDT)
- Carlos Simmerling (Mon Jun 07 2004 - 18:26:19 PDT)
- Bill Ross (Mon Jun 07 2004 - 18:37:16 PDT)
AMBER: binary files
- David A. Case (Wed Jun 16 2004 - 07:44:39 PDT)
- richard dimelow (Wed Jun 16 2004 - 06:29:48 PDT)
AMBER: Born radii
- David A. Case (Fri Jun 25 2004 - 08:36:20 PDT)
- Marcin Krol (Fri Jun 25 2004 - 04:24:48 PDT)
AMBER: Box range in vacuum when restart MD
- David A. Case (Wed Jun 23 2004 - 09:06:29 PDT)
- scopio (Wed Jun 23 2004 - 06:22:31 PDT)
AMBER: bug in leap?
- Scott Brozell (Thu Jun 10 2004 - 21:32:24 PDT)
- Tomas Kubar (Tue Jun 08 2004 - 00:27:30 PDT)
- Carsten Detering (Mon Jun 07 2004 - 16:14:30 PDT)
- Ross Walker (Mon Jun 07 2004 - 16:50:10 PDT)
AMBER: Calcium and GB
- David A. Case (Wed Jun 09 2004 - 19:10:26 PDT)
- cailliez (Tue Jun 08 2004 - 04:38:58 PDT)
AMBER: CARNAL RMS
- Wen Li (Mon Jun 07 2004 - 08:25:28 PDT)
AMBER: CARNAL- movement of an axis
- Bill Ross (Thu Jun 03 2004 - 13:53:47 PDT)
- Wen Li (Thu Jun 03 2004 - 13:34:11 PDT)
AMBER: Changing MAXPR in Amber 8?
- David A. Case (Fri Jun 18 2004 - 13:34:43 PDT)
- Robyn Ayscue (Fri Jun 18 2004 - 13:03:06 PDT)
- Ross Walker (Fri Jun 18 2004 - 12:23:33 PDT)
- Robyn Ayscue (Fri Jun 18 2004 - 12:08:13 PDT)
AMBER: Checking Results?
- Linda Prengaman (Thu Jun 10 2004 - 18:49:33 PDT)
AMBER: cluster analysis
- Sue Heavner (Thu Jun 10 2004 - 03:40:56 PDT)
- Tim Meyer (Wed Jun 09 2004 - 06:28:15 PDT)
- Stefano.Pieraccini.unimi.it (Wed Jun 09 2004 - 04:19:40 PDT)
AMBER: cluster MD conformations from sander
- aldo jongejan (Fri Jun 11 2004 - 01:22:40 PDT)
- Wen Li (Thu Jun 10 2004 - 12:13:14 PDT)
AMBER: Compile xleap (amber8) in linux Red Hat 8.0
- Guanglei Cui (Tue Jun 08 2004 - 12:45:56 PDT)
- Viktor Hornak (Tue Jun 08 2004 - 12:30:38 PDT)
- Xiaobing Tian (Tue Jun 08 2004 - 12:21:39 PDT)
- Viktor Hornak (Tue Jun 08 2004 - 11:29:29 PDT)
- Guanglei Cui (Tue Jun 08 2004 - 11:30:05 PDT)
- Xiaobing Tian (Tue Jun 08 2004 - 11:33:43 PDT)
- Scott Brozell (Tue Jun 08 2004 - 11:11:15 PDT)
- Scott Brozell (Tue Jun 08 2004 - 10:53:34 PDT)
- Viktor Hornak (Tue Jun 08 2004 - 10:35:51 PDT)
- Xiaobing Tian (Tue Jun 08 2004 - 09:00:06 PDT)
AMBER: Compiling Amber8 on Mac OS X
- Robyn Ayscue (Mon Jun 14 2004 - 11:41:15 PDT)
- Robyn Ayscue (Mon Jun 14 2004 - 11:39:27 PDT)
- Mengjuei Hsieh (Fri Jun 11 2004 - 15:59:14 PDT)
- Yusuf Abdulghani (Fri Jun 11 2004 - 15:14:12 PDT)
- Mengjuei Hsieh (Thu Jun 10 2004 - 14:11:24 PDT)
- Robyn Ayscue (Thu Jun 10 2004 - 05:25:40 PDT)
AMBER: Config file for installing Amber 8 on PC with Windows XP
- David A. Case (Mon Jun 14 2004 - 18:01:57 PDT)
- fangyu liang (Mon Jun 14 2004 - 16:21:07 PDT)
AMBER: confusion about epsilon=4r for nmode calclation of nucleic acid
- xiaowei li (Thu Jun 03 2004 - 19:52:16 PDT)
- David A. Case (Thu Jun 03 2004 - 19:31:06 PDT)
- xiaowei li (Wed Jun 02 2004 - 20:15:29 PDT)
AMBER: Constant Pressure Problem of MD
- Nan Lin (Mon Jun 07 2004 - 19:04:23 PDT)
- David A. Case (Mon Jun 07 2004 - 19:12:41 PDT)
- SIVA (Mon Jun 07 2004 - 20:53:39 PDT)
AMBER: Core Dump ERROR When Using TIP4P
- David A. Case (Tue Jun 15 2004 - 15:28:36 PDT)
- Dat H. Nguyen (Tue Jun 15 2004 - 14:21:28 PDT)
- David A. Case (Fri Jun 11 2004 - 07:08:18 PDT)
- Dat H. Nguyen (Thu Jun 10 2004 - 18:12:06 PDT)
AMBER: Could not assign parameters
- Sivanesan Dakshanamurthy (Fri Jun 18 2004 - 12:35:32 PDT)
- David A. Case (Fri Jun 18 2004 - 12:04:57 PDT)
- Sivanesan Dakshanamurthy (Fri Jun 18 2004 - 11:52:18 PDT)
AMBER: Deeper problem with the energetics of the system
- David A. Case (Fri Jun 18 2004 - 11:20:20 PDT)
- nlxc (Fri Jun 18 2004 - 10:56:52 PDT)
AMBER: DENSITY in constant pressure MD
- David A. Case (Tue Jun 15 2004 - 15:50:57 PDT)
- nlxc (Tue Jun 15 2004 - 11:17:41 PDT)
AMBER: FEP error/early termination - why?
- Annette Höglund (Tue Jun 01 2004 - 07:34:53 PDT)
AMBER: free energy
- Carlos Simmerling (Mon Jun 28 2004 - 06:06:43 PDT)
- Kazuo Koyano (Mon Jun 28 2004 - 01:45:41 PDT)
- Oliver Hucke (Fri Jun 04 2004 - 12:19:25 PDT)
- A. Hungie (Fri Jun 04 2004 - 10:21:59 PDT)
AMBER: Free energy in Amber8
- David A. Case (Wed Jun 02 2004 - 07:35:24 PDT)
- Jiten (Tue Jun 01 2004 - 18:02:40 PDT)
- David A. Case (Tue Jun 01 2004 - 12:17:34 PDT)
- Miguel (Tue Jun 01 2004 - 04:11:39 PDT)
- Jiten (Tue Jun 01 2004 - 03:11:54 PDT)
AMBER: Gaussian Interface ?
- Jiten (Wed Jun 02 2004 - 08:06:12 PDT)
AMBER: GB parameters for Calcium
- David A. Case (Wed Jun 23 2004 - 11:10:23 PDT)
- cailliez (Wed Jun 23 2004 - 05:39:38 PDT)
AMBER: GB+LES
- Carlos Simmerling (Wed Jun 30 2004 - 04:26:59 PDT)
- Marcin Krol (Wed Jun 30 2004 - 02:43:27 PDT)
AMBER: gibbs in amber8
- David A. Case (Sat Jun 05 2004 - 20:33:37 PDT)
- A. Hungie (Fri Jun 04 2004 - 10:13:12 PDT)
AMBER: Heme parameters
- David A. Case (Tue Jun 01 2004 - 12:20:56 PDT)
- Gustavo Pierdominici Sottile (Tue Jun 01 2004 - 08:32:06 PDT)
AMBER: High B-factor!!
- Bimo Ario Tejo (Tue Jun 22 2004 - 07:25:36 PDT)
- Pradipta Bandyopadhyay (Tue Jun 22 2004 - 05:13:09 PDT)
AMBER: How to neutralize system?
- Guanglei Cui (Wed Jun 09 2004 - 07:58:37 PDT)
- Marcin Krol (Wed Jun 09 2004 - 07:57:11 PDT)
- scopio (Wed Jun 09 2004 - 07:47:44 PDT)
AMBER: ifort -parallel
- Scott Brozell (Fri Jun 11 2004 - 08:36:36 PDT)
- Joachim Reichelt (Fri Jun 11 2004 - 02:15:58 PDT)
AMBER: image and restart problems
- Carlos Simmerling (Tue Jun 29 2004 - 07:57:42 PDT)
- Andy Purkiss (Tue Jun 29 2004 - 06:05:48 PDT)
- Steve Seibold (Tue Jun 29 2004 - 05:56:52 PDT)
AMBER: Improper Torsional Parameters
- Johnson Agbo (Thu Jun 17 2004 - 13:57:08 PDT)
- Carlos Simmerling (Mon Jun 14 2004 - 14:54:57 PDT)
- David A. Case (Mon Jun 14 2004 - 14:20:21 PDT)
- Johnson Agbo (Mon Jun 14 2004 - 13:41:12 PDT)
AMBER: information PROTON_INFO
- Ye Mei (Thu Jun 03 2004 - 20:33:30 PDT)
AMBER: Install Amber8 under cygwin
- Scott Brozell (Tue Jun 01 2004 - 00:22:14 PDT)
AMBER: jump in temperature + problem in trajectory files
- cailliez (Mon Jun 28 2004 - 07:11:14 PDT)
AMBER: leap.log warnings
- scopio (Tue Jun 22 2004 - 17:54:37 PDT)
- German Sciaini (Tue Jun 22 2004 - 03:50:01 PDT)
- Bill Ross (Mon Jun 21 2004 - 12:25:35 PDT)
- Bill Ross (Mon Jun 21 2004 - 10:40:13 PDT)
- David A. Case (Mon Jun 21 2004 - 08:43:07 PDT)
- Bill Ross (Sun Jun 20 2004 - 19:52:17 PDT)
- scopio (Sun Jun 20 2004 - 18:18:40 PDT)
AMBER: LINMIN failure
- Ross Walker (Thu Jun 10 2004 - 23:10:23 PDT)
- Mizuguchi Mineyuki (Thu Jun 10 2004 - 19:58:24 PDT)
- Linda Prengaman (Thu Jun 10 2004 - 14:41:46 PDT)
- Ross Walker (Thu Jun 10 2004 - 10:10:08 PDT)
- Robyn Ayscue (Thu Jun 10 2004 - 04:52:07 PDT)
- Mizuguchi Mineyuki (Wed Jun 09 2004 - 19:40:16 PDT)
AMBER: Loading mol2 Files in XLEaP
- Robyn Ayscue (Fri Jun 04 2004 - 11:24:05 PDT)
- David A. Case (Thu Jun 03 2004 - 15:02:07 PDT)
- Scott Brozell (Thu Jun 03 2004 - 14:49:13 PDT)
- Bill Ross (Thu Jun 03 2004 - 13:44:39 PDT)
- Guanglei Cui (Thu Jun 03 2004 - 12:20:26 PDT)
- FyD (Thu Jun 03 2004 - 12:18:26 PDT)
- Robyn Ayscue (Thu Jun 03 2004 - 11:39:37 PDT)
- FyD (Thu Jun 03 2004 - 09:26:38 PDT)
- Robyn Ayscue (Thu Jun 03 2004 - 09:17:54 PDT)
- Robyn Ayscue (Thu Jun 03 2004 - 09:14:00 PDT)
AMBER: MD & running time
- Robert Duke (Wed Jun 23 2004 - 15:25:27 PDT)
- David A. Case (Wed Jun 23 2004 - 14:02:45 PDT)
- Kristina Furse (Wed Jun 23 2004 - 12:53:13 PDT)
- bybaker.itsa.ucsf.edu (Tue Jun 22 2004 - 21:29:58 PDT)
- Ross Walker (Tue Jun 22 2004 - 20:51:28 PDT)
- Bill Ross (Tue Jun 22 2004 - 18:48:03 PDT)
- Linda Prengaman (Tue Jun 22 2004 - 12:12:00 PDT)
- bybaker.itsa.ucsf.edu (Tue Jun 22 2004 - 16:29:09 PDT)
AMBER: mm_pbsa test problem
- Difei Wang (Wed Jun 02 2004 - 08:54:40 PDT)
AMBER: mm_pbsa.pl question
- Fang, Jianwen (Thu Jun 03 2004 - 10:14:29 PDT)
AMBER: MMPBSA problem
- John (Thu Jun 03 2004 - 09:09:05 PDT)
AMBER: MOIL-View question
- David E. Konerding DSD Staff (Wed Jun 16 2004 - 15:30:47 PDT)
- Joseph Nachman (Wed Jun 16 2004 - 13:22:07 PDT)
- Carlos Simmerling (Wed Jun 16 2004 - 13:25:45 PDT)
- Joseph Nachman (Wed Jun 16 2004 - 12:35:17 PDT)
- Carlos Simmerling (Wed Jun 16 2004 - 04:57:27 PDT)
- Joseph Nachman (Tue Jun 15 2004 - 11:11:30 PDT)
AMBER: N-terminal Arg charges in ff99 not 1.00
- Ross Walker (Wed Jun 30 2004 - 14:26:22 PDT)
- Guanglei Cui (Wed Jun 30 2004 - 14:13:55 PDT)
- Michael Dolan (Wed Jun 30 2004 - 14:08:15 PDT)
AMBER: NEC and Regatta
- Robert Duke (Mon Jun 28 2004 - 05:38:27 PDT)
- Robert Duke (Mon Jun 28 2004 - 05:18:24 PDT)
- Filip Lankas (Mon Jun 28 2004 - 04:47:26 PDT)
AMBER: newer OPLS/AA?
- Sichun Yang (Mon Jun 21 2004 - 16:23:03 PDT)
AMBER: nmanal problem
- Ben Cossins (Mon Jun 21 2004 - 09:40:50 PDT)
- David A. Case (Mon Jun 21 2004 - 08:51:59 PDT)
- Ben Cossins (Mon Jun 21 2004 - 08:45:20 PDT)
AMBER: Nmode
- David A. Case (Thu Jun 17 2004 - 08:14:26 PDT)
- sebnem (Wed Jun 16 2004 - 22:30:54 PDT)
- David A. Case (Wed Jun 16 2004 - 21:20:10 PDT)
- sebnem (Wed Jun 16 2004 - 16:47:18 PDT)
AMBER: nmode with mm/pbsa
- Rhonda Torres (Thu Jun 10 2004 - 11:33:40 PDT)
- Nan Lin (Wed Jun 09 2004 - 18:18:15 PDT)
AMBER: Octahedron Box
- Carlos Simmerling (Mon Jun 28 2004 - 08:43:21 PDT)
- Seonah Kim (Mon Jun 28 2004 - 08:30:34 PDT)
AMBER: octavalent metal
- Brent Krueger (Fri Jun 25 2004 - 14:17:01 PDT)
AMBER: old trajectory file (amber6) to new trajectory file ?
- David A. Case (Wed Jun 09 2004 - 19:16:26 PDT)
- Carlos Simmerling (Tue Jun 08 2004 - 04:37:48 PDT)
- Difei Wang (Mon Jun 07 2004 - 19:55:39 PDT)
AMBER: Opteron-64bit work station
- ian gould (Mon Jun 21 2004 - 09:34:33 PDT)
- sachin patil (Mon Jun 21 2004 - 09:18:16 PDT)
AMBER: parallel Sander (amber8): run-time error under Irix
- Karol Miaskiewicz (Thu Jun 03 2004 - 12:15:05 PDT)
- Viktor Hornak (Thu Jun 03 2004 - 12:01:40 PDT)
- Karol Miaskiewicz (Thu Jun 03 2004 - 08:29:06 PDT)
- Carlos Simmerling (Thu Jun 03 2004 - 08:03:43 PDT)
- Karol Miaskiewicz (Thu Jun 03 2004 - 07:42:25 PDT)
AMBER: paramitrization problem
- lei jia (Tue Jun 08 2004 - 10:45:02 PDT)
- Ross Walker (Tue Jun 08 2004 - 10:31:10 PDT)
- lei jia (Tue Jun 08 2004 - 08:00:11 PDT)
- lei jia (Mon Jun 07 2004 - 15:12:37 PDT)
- Ross Walker (Mon Jun 07 2004 - 15:24:15 PDT)
AMBER: parmcal problem
- David A. Case (Fri Jun 11 2004 - 15:37:53 PDT)
- scopio (Thu Jun 10 2004 - 17:21:30 PDT)
- scopio (Thu Jun 10 2004 - 07:46:11 PDT)
AMBER: PARSE radius for P
- david.evans.ulsop.ac.uk (Thu Jun 10 2004 - 10:59:30 PDT)
AMBER: Partial Charge on ligand for MD & MM/PBSA
- Nan Lin (Mon Jun 07 2004 - 19:11:25 PDT)
AMBER: PBCAL in mm-pbsa calculation
- Kazuo Koyano (Sun Jun 20 2004 - 23:14:56 PDT)
- Thomas Steinbrecher (Fri Jun 11 2004 - 12:53:21 PDT)
- Thomas Steinbrecher (Fri Jun 11 2004 - 11:00:17 PDT)
- nlxc (Fri Jun 11 2004 - 10:26:21 PDT)
AMBER: PBCAL in MM/PBSA
- Thomas Steinbrecher (Fri Jun 25 2004 - 12:37:07 PDT)
- nlxc (Fri Jun 25 2004 - 12:09:19 PDT)
AMBER: PBCAL in mmpbsa
- nlxc (Tue Jun 29 2004 - 17:29:51 PDT)
- Thomas Steinbrecher (Tue Jun 29 2004 - 13:50:43 PDT)
- nlxc (Tue Jun 29 2004 - 11:17:25 PDT)
AMBER: Periodic boundary simulation
- darden (Tue Jun 01 2004 - 06:11:54 PDT)
- Miguel (Tue Jun 01 2004 - 04:14:34 PDT)
- Jiten (Tue Jun 01 2004 - 03:14:59 PDT)
- Soon (Tue Jun 01 2004 - 02:08:31 PDT)
AMBER: POPE membrane, How to obtain prep and parm files?
- Marek Dynowski (Sat Jun 12 2004 - 10:07:08 PDT)
AMBER: problem not with sander, but with mpich
- Viktor Hornak (Mon Jun 28 2004 - 05:48:51 PDT)
- spookie (Mon Jun 28 2004 - 02:08:37 PDT)
AMBER: Problem with menu bar in LEAP
- sachin patil (Sun Jun 27 2004 - 10:01:30 PDT)
- Ross Walker (Fri Jun 25 2004 - 15:12:13 PDT)
- Dat H. Nguyen (Fri Jun 25 2004 - 15:09:00 PDT)
- Cenk Andac (Fri Jun 25 2004 - 14:54:47 PDT)
AMBER: Problems in Amber MPI version (64 bits machine)
- David A. Case (Wed Jun 23 2004 - 10:58:07 PDT)
- Haijun Yang (Wed Jun 23 2004 - 10:33:49 PDT)
- David A. Case (Tue Jun 22 2004 - 17:31:25 PDT)
- Haijun Yang (Tue Jun 22 2004 - 14:57:07 PDT)
AMBER: problems in using glycam
- Karl N. Kirschner (Wed Jun 30 2004 - 08:29:37 PDT)
- David A. Case (Wed Jun 30 2004 - 08:03:07 PDT)
AMBER: problems to run ptraj
- German Sciaini (Tue Jun 22 2004 - 15:29:36 PDT)
AMBER: problems with extra points
- German Sciaini (Fri Jun 18 2004 - 04:08:18 PDT)
- David A. Case (Wed Jun 16 2004 - 11:50:05 PDT)
- German Sciaini (Wed Jun 16 2004 - 09:29:45 PDT)
AMBER: Problems with processing SYBYL-Tripos pdb files in LEAP
- Cenk Andac (Wed Jun 30 2004 - 22:02:17 PDT)
- David A. Case (Wed Jun 30 2004 - 10:50:41 PDT)
- Cenk Andac (Wed Jun 30 2004 - 08:14:18 PDT)
- Cenk Andac (Wed Jun 30 2004 - 08:12:10 PDT)
AMBER: Problems with X.R.E.D.
- FyD (Fri Jun 25 2004 - 10:20:30 PDT)
- Scott (Fri Jun 25 2004 - 08:49:24 PDT)
AMBER: question about building initial structure
- xhu1.memphis.edu (Mon Jun 07 2004 - 10:19:13 PDT)
AMBER: question about building prmtop and inpcrd files in xleap
- David A. Case (Mon Jun 28 2004 - 09:02:37 PDT)
- jz7.duke.edu (Mon Jun 28 2004 - 07:49:39 PDT)
AMBER: Question about dummy atoms
- David A. Case (Tue Jun 29 2004 - 10:24:56 PDT)
- Sébastien Osborne (Tue Jun 29 2004 - 10:16:30 PDT)
AMBER: question about force field
- Carlos Simmerling (Mon Jun 14 2004 - 09:14:18 PDT)
- scopio (Mon Jun 14 2004 - 08:05:57 PDT)
AMBER: question about replica exchange in amber8
- J. Zhang, Dr (Wed Jun 02 2004 - 19:16:19 PDT)
- xiaolin cheng (Wed Jun 02 2004 - 07:23:30 PDT)
- Guanglei Cui (Wed Jun 02 2004 - 06:58:32 PDT)
- apw397.soton.ac.uk (Wed Jun 02 2004 - 02:43:21 PDT)
- J. Zhang, Dr (Wed Jun 02 2004 - 02:24:24 PDT)
AMBER: question about water molecule
- Carlos Simmerling (Mon Jun 28 2004 - 10:48:11 PDT)
- jz7.duke.edu (Mon Jun 28 2004 - 10:34:19 PDT)
AMBER: question about xleap
- jz7.duke.edu (Thu Jun 03 2004 - 12:40:10 PDT)
- Ross Walker (Thu Jun 03 2004 - 12:19:55 PDT)
- jz7.duke.edu (Thu Jun 03 2004 - 11:34:03 PDT)
- Ross Walker (Thu Jun 03 2004 - 11:03:04 PDT)
- Viktor Hornak (Thu Jun 03 2004 - 10:31:23 PDT)
- jz7.duke.edu (Thu Jun 03 2004 - 10:19:27 PDT)
AMBER: Questions about pert.charge and atom type change.
- David A. Case (Wed Jun 30 2004 - 18:10:02 PDT)
- Guanglei Cui (Wed Jun 30 2004 - 17:54:28 PDT)
- Chunhu Tan (Wed Jun 30 2004 - 17:20:38 PDT)
AMBER: questions on mm_pbsa
- Fang, Jianwen (Fri Jun 11 2004 - 07:59:18 PDT)
AMBER: RED
- Xin Hu (Tue Jun 01 2004 - 16:02:37 PDT)
AMBER: Restrain or freeze molecule question?
- Junmei Wang (Thu Jun 24 2004 - 10:44:03 PDT)
- Carlos Simmerling (Thu Jun 24 2004 - 08:39:58 PDT)
- David A. Case (Thu Jun 24 2004 - 08:24:37 PDT)
- Guillaume Bollot (Thu Jun 24 2004 - 03:48:33 PDT)
AMBER: restraints error
- David A. Case (Fri Jun 25 2004 - 12:26:56 PDT)
- Carlos Simmerling (Fri Jun 25 2004 - 11:19:34 PDT)
- Venkata S Koppuravuri (Fri Jun 25 2004 - 11:11:20 PDT)
- David A. Case (Fri Jun 25 2004 - 10:32:48 PDT)
- Carlos Simmerling (Fri Jun 25 2004 - 10:23:26 PDT)
- Venkata S Koppuravuri (Fri Jun 25 2004 - 10:10:35 PDT)
AMBER: RMSD calculations in ptraj and Carnal
- Luis Gracia (Tue Jun 15 2004 - 17:19:53 PDT)
- Joseph Nachman (Mon Jun 21 2004 - 08:07:57 PDT)
- Joseph Nachman (Wed Jun 16 2004 - 13:16:52 PDT)
- Bill Ross (Tue Jun 15 2004 - 13:55:31 PDT)
- Thomas E. Cheatham, III (Tue Jun 15 2004 - 13:06:38 PDT)
- Joseph Nachman (Tue Jun 15 2004 - 12:37:18 PDT)
- Bill Ross (Tue Jun 15 2004 - 12:23:40 PDT)
- Joseph Nachman (Tue Jun 15 2004 - 11:24:38 PDT)
AMBER: Sander & fix atoms
- bybaker.itsa.ucsf.edu (Thu Jun 03 2004 - 15:36:24 PDT)
- bybaker.itsa.ucsf.edu (Thu Jun 03 2004 - 15:32:53 PDT)
- Viktor Hornak (Thu Jun 03 2004 - 14:14:10 PDT)
- Bill Ross (Thu Jun 03 2004 - 14:06:04 PDT)
- bybaker.itsa.ucsf.edu (Thu Jun 03 2004 - 13:59:50 PDT)
- bybaker.itsa.ucsf.edu (Thu Jun 03 2004 - 13:54:55 PDT)
- Viktor Hornak (Thu Jun 03 2004 - 10:22:55 PDT)
- bybaker.itsa.ucsf.edu (Thu Jun 03 2004 - 09:48:40 PDT)
AMBER: sander in parallel, amber8
- spookie (Fri Jun 25 2004 - 11:26:58 PDT)
- Stef (Fri Jun 25 2004 - 11:11:09 PDT)
- spookie (Fri Jun 25 2004 - 01:49:30 PDT)
AMBER: sander of AMBER 8 doesn't work
- David A. Case (Wed Jun 02 2004 - 07:47:20 PDT)
- Feng, Hanqiao (NIH/NCI) (Wed Jun 02 2004 - 05:45:01 PDT)
- Ross Walker (Tue Jun 01 2004 - 11:56:29 PDT)
- Feng, Hanqiao (NIH/NCI) (Tue Jun 01 2004 - 11:39:56 PDT)
AMBER: sander7 on quad opteron
- Tru Huynh (Thu Jun 03 2004 - 11:13:39 PDT)
AMBER: sander8 performance
- David A. Case (Tue Jun 01 2004 - 13:15:50 PDT)
- Oliver Hucke (Tue Jun 01 2004 - 12:46:06 PDT)
- David A. Case (Tue Jun 01 2004 - 12:22:29 PDT)
- Oliver Hucke (Tue Jun 01 2004 - 10:53:46 PDT)
AMBER: savepdb vs ambpdb
- Golebiowski Jerome (Fri Jun 11 2004 - 08:17:40 PDT)
AMBER: segmentation fault when running parmchk
- David A. Case (Fri Jun 11 2004 - 08:00:13 PDT)
- Bill Ross (Tue Jun 08 2004 - 11:16:35 PDT)
- Chutintorn Punwong (Tue Jun 08 2004 - 11:07:45 PDT)
- Chutintorn Punwong (Wed Jun 02 2004 - 12:11:22 PDT)
- David A. Case (Wed Jun 02 2004 - 11:41:56 PDT)
- Chutintorn Punwong (Wed Jun 02 2004 - 10:57:06 PDT)
AMBER: Simulated anealling
- anshul.imtech.res.in (Fri Jun 04 2004 - 13:56:50 PDT)
- anshul.imtech.res.in (Wed Jun 09 2004 - 07:41:56 PDT)
- David A. Case (Thu Jun 03 2004 - 19:34:17 PDT)
- Rhonda Torres (Thu Jun 03 2004 - 11:05:58 PDT)
- anshul.imtech.res.in (Thu Jun 03 2004 - 09:56:58 PDT)
- anshul.imtech.res.in (Thu Jun 03 2004 - 07:30:42 PDT)
- Jiten (Wed Jun 02 2004 - 21:02:00 PDT)
- anshul.imtech.res.in (Thu Jun 03 2004 - 07:12:55 PDT)
AMBER: Software to visualize normal modes!
- John Mongan (Tue Jun 01 2004 - 16:20:38 PDT)
- Pradipta Bandyopadhyay (Mon May 31 2004 - 21:42:39 PDT)
AMBER: solvate proteins in xleap/amber8
- Tomas Kubar (Tue Jun 22 2004 - 00:44:54 PDT)
- David A. Case (Mon Jun 21 2004 - 08:42:47 PDT)
- Ting Wang (Mon Jun 21 2004 - 06:20:03 PDT)
AMBER: Suface area parameter for fluorine in MM/PBSA
- Scott Brozell (Sun Jun 13 2004 - 01:05:02 PDT)
- nlxc (Fri Jun 11 2004 - 16:38:30 PDT)
AMBER: Test run error in amber8 : IBM-AIX
- Jiten (Tue Jun 29 2004 - 18:19:43 PDT)
- David A. Case (Tue Jun 29 2004 - 08:00:58 PDT)
- Jiten (Tue Jun 29 2004 - 05:16:48 PDT)
AMBER: Thank you
- Xiaobing Tian (Thu Jun 10 2004 - 12:37:37 PDT)
AMBER: The first and second derivatives
- Johnson Agbo (Fri Jun 18 2004 - 14:31:15 PDT)
- Bill Ross (Fri Jun 18 2004 - 14:02:22 PDT)
- David A. Case (Fri Jun 18 2004 - 13:25:29 PDT)
- Johnson Agbo (Fri Jun 18 2004 - 12:05:25 PDT)
- David A. Case (Fri Jun 18 2004 - 11:18:34 PDT)
- Johnson Agbo (Fri Jun 18 2004 - 11:08:49 PDT)
AMBER: The parallel problem for umbrella sampling in Amber 8
- David A. Case (Tue Jun 15 2004 - 15:55:20 PDT)
- Yuhui Cheng (Tue Jun 15 2004 - 14:14:07 PDT)
AMBER: TOP file in AMBER7/8
- Carlos Simmerling (Mon Jun 21 2004 - 06:52:38 PDT)
- Ting Wang (Mon Jun 21 2004 - 06:32:25 PDT)
AMBER: traj. analysis
- Joseph Nachman (Wed Jun 30 2004 - 14:44:43 PDT)
- Carlos Simmerling (Wed Jun 30 2004 - 12:08:50 PDT)
- Grace Li (Wed Jun 30 2004 - 12:05:07 PDT)
AMBER: Trajectory file
- Bill Ross (Wed Jun 09 2004 - 14:19:36 PDT)
- Guanglei Cui (Wed Jun 09 2004 - 13:27:16 PDT)
- Joseph Nachman (Wed Jun 09 2004 - 12:22:45 PDT)
AMBER: Trouble running molecular dynamics with an increase in temp in Sander
- Robyn Ayscue (Thu Jun 17 2004 - 08:35:34 PDT)
- Carlos Simmerling (Wed Jun 16 2004 - 08:15:20 PDT)
- Andreas Svrcek-Seiler (Wed Jun 16 2004 - 07:58:33 PDT)
- Carlos Simmerling (Wed Jun 16 2004 - 07:42:33 PDT)
- David A. Case (Wed Jun 16 2004 - 07:40:32 PDT)
- Robyn Ayscue (Wed Jun 16 2004 - 06:43:05 PDT)
AMBER: Units of Charges on Atoms
- Carlos Simmerling (Thu Jun 24 2004 - 12:49:43 PDT)
- Tomas Kubar (Thu Jun 24 2004 - 12:48:36 PDT)
- Johnson Agbo (Thu Jun 24 2004 - 12:22:49 PDT)
AMBER: unnatural base - RESP charges in ANTECHAMBER
- FyD (Tue Jun 08 2004 - 09:23:46 PDT)
- Dr. Rainer Glaser (Mon Jun 07 2004 - 17:12:56 PDT)
- Junmei Wang (Mon Jun 07 2004 - 18:22:31 PDT)
AMBER: Using gibbs to calculate free energy
- David A. Case (Fri Jun 18 2004 - 08:14:55 PDT)
- Xioling Chuang (Fri Jun 18 2004 - 06:15:31 PDT)
AMBER: water BOX
- Xioling Chuang (Mon Jun 07 2004 - 07:09:33 PDT)
AMBER: why the enegy of native state of protein is high in GBSA calculation?
- J. Zhang, Dr (Sat Jun 05 2004 - 18:25:20 PDT)
- Andreas Svrcek-Seiler (Fri Jun 04 2004 - 08:15:03 PDT)
- David A. Case (Fri Jun 04 2004 - 06:00:47 PDT)
- Carlos Simmerling (Fri Jun 04 2004 - 04:52:40 PDT)
- J. Zhang, Dr (Fri Jun 04 2004 - 02:21:20 PDT)
AMBER: Xleap
- Scott Brozell (Thu Jun 10 2004 - 13:36:25 PDT)
- YangPeng (Thu Jun 10 2004 - 01:49:02 PDT)
AMBER: xleap solvatebox problem
- Shan, Jufang (Thu Jun 10 2004 - 07:49:25 PDT)
- Tomas Kubar (Thu Jun 10 2004 - 01:58:51 PDT)
- David A. Case (Wed Jun 09 2004 - 15:51:06 PDT)
- Ross Walker (Wed Jun 09 2004 - 15:48:12 PDT)
- James W. Caldwell (Wed Jun 09 2004 - 15:49:07 PDT)
- Shan, Jufang (Wed Jun 09 2004 - 15:17:59 PDT)
AMBER: Z-DNA
- Bill Ross (Thu Jun 17 2004 - 13:00:55 PDT)
- xiaowei li (Thu Jun 17 2004 - 11:43:13 PDT)
parallel Sander (amber8): run-time error under Irix
- Karol Miaskiewicz (Tue Jun 08 2004 - 13:30:38 PDT)
- Karol Miaskiewicz (Tue Jun 08 2004 - 13:04:14 PDT)

Amber Archive Jun 2004 by subject