Amber Archive Jun 2004 by thread
- AMBER: Software to visualize normal modes! Pradipta Bandyopadhyay (Mon May 31 2004 - 21:42:39 PDT)
- Re: AMBER: Install Amber8 under cygwin Scott Brozell (Tue Jun 01 2004 - 00:22:14 PDT)
- AMBER: Periodic boundary simulation Soon (Tue Jun 01 2004 - 02:08:31 PDT)
- AMBER: Free energy in Amber8 Jiten (Tue Jun 01 2004 - 03:11:54 PDT)
- Re: AMBER: FEP error/early termination - why? Annette Höglund (Tue Jun 01 2004 - 07:34:53 PDT)
- AMBER: Heme parameters Gustavo Pierdominici Sottile (Tue Jun 01 2004 - 08:32:06 PDT)
- AMBER: Amber force field for protein-DNA system jz7.duke.edu (Tue Jun 01 2004 - 09:14:16 PDT)
- AMBER: sander8 performance Oliver Hucke (Tue Jun 01 2004 - 10:53:46 PDT)
- AMBER: Amber7: pdb format file vidit kumar (Tue Jun 01 2004 - 11:13:03 PDT)
- AMBER: sander of AMBER 8 doesn't work Feng, Hanqiao (NIH/NCI) (Tue Jun 01 2004 - 11:39:56 PDT)
- AMBER: RED Xin Hu (Tue Jun 01 2004 - 16:02:37 PDT)
- Re: [pradipta_b.mail.jnu.ac.in: AMBER: Software to visualize normal modes!] David A. Case (Tue Jun 01 2004 - 16:24:54 PDT)
- AMBER: Add Hydrogen bond through xLeap? Nan Lin (Tue Jun 01 2004 - 23:25:18 PDT)
- AMBER: question about replica exchange in amber8 J. Zhang, Dr (Wed Jun 02 2004 - 02:24:24 PDT)
- AMBER: Gaussian Interface ? Jiten (Wed Jun 02 2004 - 08:06:12 PDT)
- AMBER: Amber force field for protein-DNA system (again) jz7.duke.edu (Wed Jun 02 2004 - 10:31:56 PDT)
- Re: AMBER: segmentation fault when running parmchk Chutintorn Punwong (Wed Jun 02 2004 - 10:57:06 PDT)
- AMBER: confusion about epsilon=4r for nmode calclation of nucleic acid xiaowei li (Wed Jun 02 2004 - 20:15:29 PDT)
- AMBER: simulated anealling anshul.imtech.res.in (Thu Jun 03 2004 - 07:12:55 PDT)
- AMBER: Simulated anealling anshul.imtech.res.in (Thu Jun 03 2004 - 07:30:42 PDT)
- AMBER: parallel Sander (amber8): run-time error under Irix Karol Miaskiewicz (Thu Jun 03 2004 - 07:42:25 PDT)
- AMBER: amber8 compile on Lemieux Guanglei Cui (Thu Jun 03 2004 - 08:06:21 PDT)
- AMBER: MMPBSA problem John (Thu Jun 03 2004 - 09:09:05 PDT)
- AMBER: Loading mol2 Files in XLEaP Robyn Ayscue (Thu Jun 03 2004 - 09:14:00 PDT)
- AMBER: Loading mol2 files in XLEaP Robyn Ayscue (Thu Jun 03 2004 - 09:17:54 PDT)
- AMBER: Sander & fix atoms bybaker.itsa.ucsf.edu (Thu Jun 03 2004 - 09:48:40 PDT)
- AMBER: mm_pbsa.pl question Fang, Jianwen (Thu Jun 03 2004 - 10:14:29 PDT)
- AMBER: sander7 on quad opteron Tru Huynh (Thu Jun 03 2004 - 11:13:39 PDT)
- Re: AMBER: CARNAL- movement of an axis Bill Ross (Thu Jun 03 2004 - 13:53:47 PDT)
- AMBER: information PROTON_INFO Ye Mei (Thu Jun 03 2004 - 20:33:30 PDT)
- AMBER: why the enegy of native state of protein is high in GBSA calculation? J. Zhang, Dr (Fri Jun 04 2004 - 02:21:20 PDT)
- AMBER: gibbs in amber8 A. Hungie (Fri Jun 04 2004 - 10:13:12 PDT)
- AMBER: free energy A. Hungie (Fri Jun 04 2004 - 10:21:59 PDT)
- AMBER: water BOX Xioling Chuang (Mon Jun 07 2004 - 07:09:33 PDT)
- AMBER: CARNAL RMS Wen Li (Mon Jun 07 2004 - 08:25:28 PDT)
- AMBER: question about building initial structure xhu1.memphis.edu (Mon Jun 07 2004 - 10:19:13 PDT)
- Re: AMBER: Bad contacts Bill Ross (Mon Jun 07 2004 - 18:37:16 PDT)
- AMBER: Partial Charge on ligand for MD & MM/PBSA Nan Lin (Mon Jun 07 2004 - 19:11:25 PDT)
- AMBER: bug in leap? Carsten Detering (Mon Jun 07 2004 - 16:14:30 PDT)
- AMBER: Bad contacts bybaker.itsa.ucsf.edu (Mon Jun 07 2004 - 17:44:37 PDT)
- AMBER: paramitrization problem lei jia (Mon Jun 07 2004 - 15:12:37 PDT)
- AMBER: unnatural base - RESP charges in ANTECHAMBER Dr. Rainer Glaser (Mon Jun 07 2004 - 17:12:56 PDT)
- AMBER: Constant Pressure Problem of MD Nan Lin (Mon Jun 07 2004 - 19:04:23 PDT)
- AMBER: Calcium and GB cailliez (Tue Jun 08 2004 - 04:38:58 PDT)
- AMBER: Compile xleap (amber8) in linux Red Hat 8.0 Xiaobing Tian (Tue Jun 08 2004 - 09:00:06 PDT)
- AMBER: antechamber Matheus Froeyen (Wed Jun 09 2004 - 00:39:26 PDT)
- AMBER: cluster analysis Stefano.Pieraccini.unimi.it (Wed Jun 09 2004 - 04:19:40 PDT)
- AMBER: How to neutralize system? scopio (Wed Jun 09 2004 - 07:47:44 PDT)
- AMBER: Amber Transition State Output Johnson Agbo (Wed Jun 09 2004 - 12:46:03 PDT)
- Re: AMBER: Trajectory file Bill Ross (Wed Jun 09 2004 - 14:19:36 PDT)
- AMBER: xleap solvatebox problem Shan, Jufang (Wed Jun 09 2004 - 15:17:59 PDT)
- AMBER: antechamber/parmchk ATTN: needs revision Nan Lin (Wed Jun 09 2004 - 11:48:55 PDT)
- AMBER: Amber & mutation bybaker.itsa.ucsf.edu (Wed Jun 09 2004 - 17:53:58 PDT)
- AMBER: nmode with mm/pbsa Nan Lin (Wed Jun 09 2004 - 18:18:15 PDT)
- AMBER: Xleap YangPeng (Thu Jun 10 2004 - 01:49:02 PDT)
- AMBER: Compiling Amber8 on Mac OS X Robyn Ayscue (Thu Jun 10 2004 - 05:25:40 PDT)
- AMBER: parmcal problem scopio (Thu Jun 10 2004 - 07:46:11 PDT)
- AMBER: xleap solvatebox problem Shan, Jufang (Thu Jun 10 2004 - 07:49:25 PDT)
- AMBER: PARSE radius for P david.evans.ulsop.ac.uk (Thu Jun 10 2004 - 10:59:30 PDT)
- AMBER: Core Dump ERROR When Using TIP4P Dat H. Nguyen (Thu Jun 10 2004 - 18:12:06 PDT)
- AMBER: Checking Results? Linda Prengaman (Thu Jun 10 2004 - 18:49:33 PDT)
- AMBER: ifort -parallel Joachim Reichelt (Fri Jun 11 2004 - 02:15:58 PDT)
- RE: AMBER: questions on mm_pbsa Fang, Jianwen (Fri Jun 11 2004 - 07:59:18 PDT)
- AMBER: savepdb vs ambpdb Golebiowski Jerome (Fri Jun 11 2004 - 08:17:40 PDT)
- AMBER: PBCAL in mm-pbsa calculation nlxc (Fri Jun 11 2004 - 10:26:21 PDT)
- AMBER: Suface area parameter for fluorine in MM/PBSA nlxc (Fri Jun 11 2004 - 16:38:30 PDT)
- AMBER: POPE membrane, How to obtain prep and parm files? Marek Dynowski (Sat Jun 12 2004 - 10:07:08 PDT)
- AMBER: question about force field scopio (Mon Jun 14 2004 - 08:05:57 PDT)
- AMBER: Improper Torsional Parameters Johnson Agbo (Mon Jun 14 2004 - 13:41:12 PDT)
- AMBER: Config file for installing Amber 8 on PC with Windows XP fangyu liang (Mon Jun 14 2004 - 16:21:07 PDT)
- AMBER: About umbrella sampling in Amber 8 Yuhui Cheng (Mon Jun 14 2004 - 18:45:44 PDT)
- AMBER: DENSITY in constant pressure MD nlxc (Tue Jun 15 2004 - 11:17:41 PDT)
- Re: AMBER: RMSD calculations in ptraj and Carnal Bill Ross (Tue Jun 15 2004 - 12:23:40 PDT)
- AMBER: binary files richard dimelow (Wed Jun 16 2004 - 06:29:48 PDT)
- AMBER: Trouble running molecular dynamics with an increase in temp in Sander Robyn Ayscue (Wed Jun 16 2004 - 06:43:05 PDT)
- AMBER: problems with extra points German Sciaini (Wed Jun 16 2004 - 09:29:45 PDT)
- AMBER: Nmode sebnem (Wed Jun 16 2004 - 16:47:18 PDT)
- AMBER: Z-DNA xiaowei li (Thu Jun 17 2004 - 11:43:13 PDT)
- Re: AMBER: Z-DNA Bill Ross (Thu Jun 17 2004 - 13:00:55 PDT)
- AMBER: Using gibbs to calculate free energy Xioling Chuang (Fri Jun 18 2004 - 06:15:31 PDT)
- AMBER: Deeper problem with the energetics of the system nlxc (Fri Jun 18 2004 - 10:56:52 PDT)
- AMBER: The first and second derivatives Johnson Agbo (Fri Jun 18 2004 - 11:08:49 PDT)
- AMBER: Could not assign parameters Sivanesan Dakshanamurthy (Fri Jun 18 2004 - 11:52:18 PDT)
- AMBER: Changing MAXPR in Amber 8? Robyn Ayscue (Fri Jun 18 2004 - 12:08:13 PDT)
- AMBER: leap.log warnings scopio (Sun Jun 20 2004 - 18:18:40 PDT)
- Re: AMBER: leap.log warnings Bill Ross (Sun Jun 20 2004 - 19:52:17 PDT)
- AMBER: solvate proteins in xleap/amber8 Ting Wang (Mon Jun 21 2004 - 06:20:03 PDT)
- AMBER: TOP file in AMBER7/8 Ting Wang (Mon Jun 21 2004 - 06:32:25 PDT)
- AMBER: nmanal problem Ben Cossins (Mon Jun 21 2004 - 08:45:20 PDT)
- AMBER: Opteron-64bit work station sachin patil (Mon Jun 21 2004 - 09:18:16 PDT)
- AMBER: High B-factor!! Pradipta Bandyopadhyay (Tue Jun 22 2004 - 05:13:09 PDT)
- Re: AMBER: MD & running time Linda Prengaman (Tue Jun 22 2004 - 12:12:00 PDT)
- AMBER: problems to run ptraj German Sciaini (Tue Jun 22 2004 - 15:29:36 PDT)
- AMBER: Problems in Amber MPI version (64 bits machine) Haijun Yang (Tue Jun 22 2004 - 14:57:07 PDT)
- Thanks - Re: AMBER: MD & running time bybaker.itsa.ucsf.edu (Tue Jun 22 2004 - 16:29:09 PDT)
- Re: AMBER: MD & running time Bill Ross (Tue Jun 22 2004 - 18:48:03 PDT)
- AMBER: GB parameters for Calcium cailliez (Wed Jun 23 2004 - 05:39:38 PDT)
- AMBER: Box range in vacuum when restart MD scopio (Wed Jun 23 2004 - 06:22:31 PDT)
- AMBER: a question on MM-PBSA and Delphi Jiayun (Wed Jun 23 2004 - 06:34:31 PDT)
- AMBER: amber8 parallel jobs spookie (Wed Jun 23 2004 - 21:50:48 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: Restrain or freeze molecule question? Guillaume Bollot (Thu Jun 24 2004 - 03:48:33 PDT)
- AMBER: A problem about a sander parallel run Yongzhi Chen (Thu Jun 24 2004 - 11:40:37 PDT)
- AMBER: Units of Charges on Atoms Johnson Agbo (Thu Jun 24 2004 - 12:22:49 PDT)
- AMBER: Amber 8 installation fangyu liang (Thu Jun 24 2004 - 15:24:43 PDT)
- AMBER: Born radii Marcin Krol (Fri Jun 25 2004 - 04:24:48 PDT)
- AMBER: sander in parallel, amber8 spookie (Fri Jun 25 2004 - 01:49:30 PDT)
- AMBER: Problems with X.R.E.D. Scott (Fri Jun 25 2004 - 08:49:24 PDT)
- AMBER: restraints error Venkata S Koppuravuri (Fri Jun 25 2004 - 10:10:35 PDT)
- AMBER: PBCAL in MM/PBSA nlxc (Fri Jun 25 2004 - 12:09:19 PDT)
- AMBER: octavalent metal Brent Krueger (Fri Jun 25 2004 - 14:17:01 PDT)
- AMBER: Problem with menu bar in LEAP Cenk Andac (Fri Jun 25 2004 - 14:54:47 PDT)
- AMBER: -p4pg problem spookie (Sat Jun 26 2004 - 01:34:40 PDT)
- AMBER: "Total vdw box size" information is gone Helios Chen (Sun Jun 27 2004 - 00:57:50 PDT)
- AMBER: (no subject) Andrew Box (Sun Jun 27 2004 - 20:29:34 PDT)
- AMBER: problem not with sander, but with mpich spookie (Mon Jun 28 2004 - 02:08:37 PDT)
- AMBER: Amber8 compilation in IBM-AIX Jiten (Mon Jun 28 2004 - 02:19:42 PDT)
- AMBER: jump in temperature + problem in trajectory files cailliez (Mon Jun 28 2004 - 07:11:14 PDT)
- AMBER: question about building prmtop and inpcrd files in xleap jz7.duke.edu (Mon Jun 28 2004 - 07:49:39 PDT)
- AMBER: Octahedron Box Seonah Kim (Mon Jun 28 2004 - 08:30:34 PDT)
- AMBER: About TI with sander Chunhu Tan (Mon Jun 28 2004 - 12:35:54 PDT)
- AMBER: Amber 8 installation error fangyu liang (Tue Jun 29 2004 - 00:00:32 PDT)
- AMBER: Test run error in amber8 : IBM-AIX Jiten (Tue Jun 29 2004 - 05:16:48 PDT)
- AMBER: image and restart problems Steve Seibold (Tue Jun 29 2004 - 05:56:52 PDT)
- AMBER: PBCAL in mmpbsa nlxc (Tue Jun 29 2004 - 11:17:25 PDT)
- AMBER: Atom Labels Karl N. Kirschner (Tue Jun 29 2004 - 13:36:22 PDT)
- AMBER: Amber8 compilation problems on AIX Gabbar Daaku (Tue Jun 29 2004 - 19:50:13 PDT)
- AMBER: GB+LES Marcin Krol (Wed Jun 30 2004 - 02:43:27 PDT)
- AMBER: About Hbond calculations using ptraj javier perez (Mon Jun 28 2004 - 10:43:37 PDT)
- Re: AMBER: problems in using glycam David A. Case (Wed Jun 30 2004 - 08:03:07 PDT)
- AMBER: traj. analysis Grace Li (Wed Jun 30 2004 - 12:05:07 PDT)
- AMBER: N-terminal Arg charges in ff99 not 1.00 Michael Dolan (Wed Jun 30 2004 - 14:08:15 PDT)
- Last message date: Thu Jul 01 2004 - 06:53:00 PDT
- Archived on: Mon Dec 02 2024 - 05:53:22 PST
