Amber Archive Oct 2011: by subject

[AMBER] "Frontiers in Biomolecular Simulation" - Heraeus conference in Germany, Jan. 22.-25. 2012
- steinbrt.rci.rutgers.edu (Mon Oct 10 2011 - 07:34:54 PDT)
[AMBER] 1JFF Antechamber, LEaP problems
- Jason Swails (Sat Oct 29 2011 - 15:52:58 PDT)
- Matthew D Antalek (Sat Oct 29 2011 - 15:12:07 PDT)
- Jason Swails (Sat Oct 29 2011 - 15:03:23 PDT)
- Matthew D Antalek (Sat Oct 29 2011 - 14:51:07 PDT)
[AMBER] 1st DNA Tutorial Pressure
- Ross Walker (Fri Oct 28 2011 - 12:09:15 PDT)
- Yao Yao (Fri Oct 28 2011 - 11:58:34 PDT)
[AMBER] 3D-RISM bugfix for polar/apolar decomposition
- Tyler Luchko (Tue Oct 11 2011 - 11:49:36 PDT)
[AMBER] A Gentle Reminder: Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021)
- Ross Walker (Mon Oct 03 2011 - 19:39:22 PDT)
[AMBER] About defining force direction in SMD simulation
- Jason Swails (Thu Oct 27 2011 - 06:02:09 PDT)
- Mo Chen (Wed Oct 26 2011 - 22:46:36 PDT)
- Mo Chen (Wed Oct 26 2011 - 22:24:01 PDT)
- Jason Swails (Wed Oct 26 2011 - 20:52:17 PDT)
- Mo Chen (Wed Oct 26 2011 - 15:25:02 PDT)
[AMBER] About pmemd and pmemd.MPI
- Ross Walker (Fri Oct 21 2011 - 21:14:50 PDT)
- Mo Chen (Fri Oct 21 2011 - 20:57:31 PDT)
- Mo Chen (Thu Oct 13 2011 - 13:07:05 PDT)
- Ross Walker (Thu Oct 13 2011 - 12:59:25 PDT)
- Mo Chen (Thu Oct 13 2011 - 12:47:30 PDT)
- Jason Swails (Thu Oct 13 2011 - 12:46:03 PDT)
- Mo Chen (Thu Oct 13 2011 - 12:44:39 PDT)
- Ross Walker (Thu Oct 13 2011 - 12:44:27 PDT)
- Jason Swails (Thu Oct 13 2011 - 12:40:37 PDT)
- Mo Chen (Thu Oct 13 2011 - 12:27:34 PDT)
[AMBER] About SMD simulation restart file
- Jason Swails (Mon Oct 17 2011 - 03:56:05 PDT)
- Chinh Su Tran To (Sun Oct 16 2011 - 23:29:44 PDT)
- Jason Swails (Sun Oct 16 2011 - 22:58:43 PDT)
- Chinh Su Tran To (Sun Oct 16 2011 - 22:12:01 PDT)
- Jason Swails (Fri Oct 14 2011 - 21:50:08 PDT)
- Bill Ross (Fri Oct 14 2011 - 21:01:20 PDT)
- Jason Swails (Fri Oct 14 2011 - 20:56:05 PDT)
- Bill Ross (Fri Oct 14 2011 - 17:10:34 PDT)
- Bill Ross (Fri Oct 14 2011 - 17:06:54 PDT)
- Marc van der Kamp (Fri Oct 14 2011 - 06:19:30 PDT)
- Brian Radak (Fri Oct 14 2011 - 06:18:22 PDT)
- Antje Wolf (Fri Oct 14 2011 - 06:09:32 PDT)
- Bill Ross (Thu Oct 13 2011 - 14:49:53 PDT)
- Jason Swails (Thu Oct 13 2011 - 07:29:12 PDT)
- Antje Wolf (Wed Oct 12 2011 - 23:18:14 PDT)
- Mo Chen (Wed Oct 12 2011 - 18:26:59 PDT)
- Bill Ross (Wed Oct 12 2011 - 14:43:31 PDT)
- Adrian Roitberg (Wed Oct 12 2011 - 13:48:10 PDT)
- Mo Chen (Wed Oct 12 2011 - 13:39:12 PDT)
- Adrian Roitberg (Wed Oct 12 2011 - 13:30:09 PDT)
- Mo Chen (Wed Oct 12 2011 - 13:26:29 PDT)
[AMBER] Add extra force in sander.MPI
- case (Sun Oct 02 2011 - 10:49:34 PDT)
- case (Sun Oct 02 2011 - 10:31:58 PDT)
- Chicago Ji (Sun Oct 02 2011 - 02:54:47 PDT)
- Jason Swails (Sat Oct 01 2011 - 12:20:02 PDT)
- Chicago Ji (Sat Oct 01 2011 - 11:23:39 PDT)
[AMBER] Amber 10 compile error
- Kijeong Kwac (Tue Oct 18 2011 - 08:25:11 PDT)
[AMBER] Amber 11, AmberTools 1.5 installation problem
- Tru Huynh (Tue Oct 11 2011 - 23:57:51 PDT)
- David A Case (Fri Oct 07 2011 - 06:56:21 PDT)
- #MAZIAR SOLEYMANI ARDEJANI# (Fri Oct 07 2011 - 03:29:18 PDT)
[AMBER] Amber on IBM Power7 or Opteron 6200 series?
- Ross Walker (Wed Oct 26 2011 - 10:20:58 PDT)
- Gustavo Seabra (Wed Oct 26 2011 - 10:14:24 PDT)
- Carlos Sosa (Wed Oct 26 2011 - 09:24:46 PDT)
- Gustavo Seabra (Wed Oct 26 2011 - 09:17:53 PDT)
[AMBER] AMBER parameters for the acetylated lysine
- Ramu Anandakrishnan (Fri Oct 07 2011 - 04:51:11 PDT)
- FyD (Thu Oct 06 2011 - 22:55:31 PDT)
- Gorka lasso (Wed Oct 05 2011 - 08:19:35 PDT)
[AMBER] Amber Tools 1.5 installation
- Matthew D Antalek (Wed Oct 19 2011 - 05:05:10 PDT)
- Matthew D Antalek (Tue Oct 18 2011 - 20:12:51 PDT)
- David A. Case (Tue Oct 18 2011 - 19:26:50 PDT)
- Matthew D Antalek (Tue Oct 18 2011 - 17:10:50 PDT)
[AMBER] AMBER, haris p has invited you to open a Gmail account
- haris p (Sun Oct 23 2011 - 00:58:40 PDT)
[AMBER] AMBER10
- Shesh Nath (Tue Oct 18 2011 - 23:26:41 PDT)
- Jason Swails (Fri Sep 30 2011 - 23:31:55 PDT)
- Shesh Nath (Fri Sep 30 2011 - 23:09:06 PDT)
[AMBER] ambertool question !!!
- Алексей Раевский (Tue Oct 04 2011 - 00:21:58 PDT)
- Dmitry Nilov (Mon Oct 03 2011 - 20:54:30 PDT)
- David Case (Mon Oct 03 2011 - 16:33:31 PDT)
- Алексей Раевский (Mon Oct 03 2011 - 14:20:43 PDT)
- Алексей Раевский (Mon Oct 03 2011 - 14:20:10 PDT)
[AMBER] AmberTools 1.5 compilation error
- Sasha Buzko (Wed Oct 19 2011 - 17:57:49 PDT)
- Jason Swails (Wed Oct 19 2011 - 17:00:46 PDT)
- Ben Roberts (Wed Oct 19 2011 - 16:45:56 PDT)
- Sasha Buzko (Wed Oct 19 2011 - 16:34:54 PDT)
- Sasha Buzko (Wed Oct 19 2011 - 16:21:55 PDT)
[AMBER] AmberTools-1.5 installation
- Jason Swails (Sun Oct 23 2011 - 21:19:14 PDT)
- Dr. Alaa El-Din A. Abdel-Gawad (Sun Oct 23 2011 - 01:35:57 PDT)
- Jason Swails (Sat Oct 22 2011 - 06:41:02 PDT)
- Dr. Alaa El-Din A. Abdel-Gawad (Sat Oct 22 2011 - 02:38:34 PDT)
- Jan-Philip Gehrcke (Thu Oct 20 2011 - 03:51:26 PDT)
- Dr. Alaa El-Din A. Abdel-Gawad (Thu Oct 20 2011 - 01:40:03 PDT)
- Jason Swails (Tue Oct 18 2011 - 06:42:42 PDT)
- David A Case (Tue Oct 18 2011 - 05:08:15 PDT)
- Dr. Alaa El-Din A. Abdel-Gawad (Tue Oct 18 2011 - 02:05:14 PDT)
- David A. Case (Sun Oct 16 2011 - 13:58:44 PDT)
- Dr. Alaa El-Din A. Gawad (Fri Oct 14 2011 - 13:07:04 PDT)
[AMBER] Ambertools1.5, mmpbsa.py. PB Bomb in pb_atmlist(): maxnba too short
- Qiong Zhang (Tue Oct 25 2011 - 09:56:28 PDT)
- Ray Luo, Ph.D. (Tue Oct 25 2011 - 09:31:25 PDT)
- Qiong Zhang (Tue Oct 25 2011 - 05:13:37 PDT)
- Qiong Zhang (Tue Oct 25 2011 - 02:15:40 PDT)
- Qiong Zhang (Tue Oct 25 2011 - 02:07:55 PDT)
[AMBER] AMOEBA potentials
- David A Case (Fri Oct 07 2011 - 06:43:31 PDT)
- Neha Gandhi (Thu Oct 06 2011 - 19:02:23 PDT)
- David A Case (Thu Oct 06 2011 - 07:06:09 PDT)
- Neha Gandhi (Wed Oct 05 2011 - 00:02:18 PDT)
- case (Tue Oct 04 2011 - 09:05:32 PDT)
- Neha Gandhi (Tue Oct 04 2011 - 02:41:08 PDT)
[AMBER] Antechamber/SQM
- Chidambar Kulkarni (Wed Oct 12 2011 - 07:26:53 PDT)
- David A Case (Wed Oct 12 2011 - 05:17:31 PDT)
- Chidambar Kulkarni (Tue Oct 11 2011 - 21:29:14 PDT)
- David A Case (Tue Oct 11 2011 - 10:18:54 PDT)
- Chidambar Kulkarni (Tue Oct 11 2011 - 09:13:07 PDT)
[AMBER] Applying Bugfixes Amber11
- Matthew D Antalek (Wed Oct 19 2011 - 16:02:40 PDT)
- Niel Henriksen (Wed Oct 19 2011 - 15:51:00 PDT)
- Matthew D Antalek (Wed Oct 19 2011 - 15:46:07 PDT)
[AMBER] Atom ordering after LEAP
- Jason Swails (Mon Oct 31 2011 - 06:46:08 PDT)
- Jason Swails (Mon Oct 31 2011 - 06:45:22 PDT)
- David A Case (Mon Oct 31 2011 - 05:29:11 PDT)
- steinbrt.rci.rutgers.edu (Mon Oct 31 2011 - 01:33:41 PDT)
- Jason Swails (Sun Oct 30 2011 - 14:04:45 PDT)
- Gonzalo Jimenez (Sun Oct 30 2011 - 06:47:58 PDT)
[AMBER] ATP+Mg
- FyD (Wed Oct 26 2011 - 08:50:10 PDT)
- Алексей Раевский (Mon Oct 24 2011 - 06:08:55 PDT)
- filip fratev (Mon Oct 24 2011 - 05:51:55 PDT)
- Gannett, Peter (Mon Oct 24 2011 - 05:34:06 PDT)
- Алексей Раевский (Mon Oct 24 2011 - 05:30:02 PDT)
- Gannett, Peter (Mon Oct 24 2011 - 04:18:04 PDT)
- Алексей Раевский (Mon Oct 24 2011 - 00:59:38 PDT)
[AMBER] bond lengths
- Aparna P (Mon Oct 03 2011 - 21:41:18 PDT)
- David A Case (Mon Oct 03 2011 - 04:40:15 PDT)
- Aparna P (Sun Oct 02 2011 - 22:52:48 PDT)
[AMBER] box information in .inpcrd and .rst files
- Bill Ross (Thu Oct 27 2011 - 15:30:19 PDT)
- Pavan Giovanni (Thu Oct 27 2011 - 08:44:27 PDT)
- David A Case (Thu Oct 27 2011 - 05:10:02 PDT)
- Giovanni Pavan (Wed Oct 26 2011 - 04:35:59 PDT)
[AMBER] Bug in nmode
- David A Case (Fri Oct 28 2011 - 06:51:21 PDT)
- Ake Sandgren (Fri Oct 28 2011 - 01:15:51 PDT)
[AMBER] bug in respgen ?
- thomas.fox.boehringer-ingelheim.com (Fri Oct 07 2011 - 05:15:08 PDT)
[AMBER] Building parallel Amber11 on CRAY XD1
- Dean Cuebas (Fri Oct 28 2011 - 13:13:43 PDT)
- Ross Walker (Tue Oct 25 2011 - 11:57:00 PDT)
- Dean Cuebas (Tue Oct 25 2011 - 11:30:31 PDT)
[AMBER] building topology for a big DNA/protein complex with tleap and sleap
- case (Sun Oct 02 2011 - 10:25:49 PDT)
- Giulia Palermo (Sat Oct 01 2011 - 03:05:49 PDT)
[AMBER] Calculating the force applied to a restrained point
- Jason Swails (Tue Oct 04 2011 - 12:28:38 PDT)
- Ali M. Naserian-Nik (Tue Oct 04 2011 - 12:10:54 PDT)
- Daniel Sindhikara (Tue Oct 04 2011 - 07:29:38 PDT)
- Jason Swails (Tue Oct 04 2011 - 06:51:59 PDT)
- Ali M. Naserian-Nik (Tue Oct 04 2011 - 00:49:01 PDT)
[AMBER] Can we avoid output the distance between closed atoms in the same residue: question for usage of checkoverlap in PTRAJ.
- kurisaki (Wed Oct 12 2011 - 23:31:15 PDT)
[AMBER] changes in secstruct command
- Daniel Roe (Fri Oct 14 2011 - 04:48:08 PDT)
- Antje Wolf (Fri Oct 14 2011 - 03:45:28 PDT)
- Antje Wolf (Fri Oct 14 2011 - 03:42:34 PDT)
[AMBER] chiral restraints
- Jason Swails (Wed Oct 12 2011 - 17:42:08 PDT)
- kirtana S (Wed Oct 12 2011 - 11:05:35 PDT)
[AMBER] compiling amber11 (sander) on Blue Gene/P
- piotr zarzycki (Fri Oct 28 2011 - 01:56:37 PDT)
[AMBER] converting Amber trajectories to Gromacs XTC
- Marc van der Kamp (Sat Oct 15 2011 - 10:03:24 PDT)
- Oliver Grant (Sat Oct 15 2011 - 07:42:55 PDT)
- mish (Sat Oct 15 2011 - 03:52:40 PDT)
[AMBER] crash due to ewald
- Jason Swails (Fri Oct 21 2011 - 07:38:57 PDT)
- Jorgen Simonsen (Fri Oct 21 2011 - 06:59:44 PDT)
- Jason Swails (Fri Oct 21 2011 - 06:37:00 PDT)
- steinbrt.rci.rutgers.edu (Fri Oct 21 2011 - 05:33:37 PDT)
- Jorgen Simonsen (Fri Oct 21 2011 - 05:17:42 PDT)
[AMBER] Creating periodic solvent box
- Dean Cuebas (Tue Oct 04 2011 - 15:21:16 PDT)
- Jason Swails (Tue Oct 04 2011 - 13:43:45 PDT)
- Dean Cuebas (Tue Oct 04 2011 - 13:35:03 PDT)
[AMBER] distribution of selected water
- kirtana S (Thu Oct 27 2011 - 10:10:20 PDT)
[AMBER] does CHECKOVERLAP check image cell?
- kurisaki (Wed Oct 26 2011 - 18:33:41 PDT)
- Thomas Cheatham III (Wed Oct 26 2011 - 13:44:09 PDT)
- kurisaki (Mon Oct 24 2011 - 05:14:44 PDT)
[AMBER] E-mail change
- Jason Swails (Thu Oct 27 2011 - 06:03:32 PDT)
- Maciej Masłyk (Thu Oct 27 2011 - 05:47:39 PDT)
[AMBER] Energetic analysis with MMPBSA.py considering just one molecule ?
- Marek Maly (Fri Sep 30 2011 - 20:13:21 PDT)
[AMBER] Energy calculateion from MD trajectory: can we skip the minimization?
- kurisaki (Mon Oct 17 2011 - 04:32:09 PDT)
- Jason Swails (Mon Oct 17 2011 - 03:59:43 PDT)
- kurisaki (Sun Oct 16 2011 - 23:58:17 PDT)
[AMBER] error "reset fillratio to a larger number 2.000" in mm_pbsa calculation
- Bill Miller III (Tue Oct 18 2011 - 04:01:29 PDT)
- Prajwal Nandekar (Mon Oct 17 2011 - 23:14:54 PDT)
[AMBER] Error using set default PBradii bondi in tleap with pmemd.cuda or sander
- Fabrício Bracht (Thu Oct 20 2011 - 21:51:41 PDT)
- Jason Swails (Thu Oct 20 2011 - 21:12:42 PDT)
- Fabrício Bracht (Thu Oct 20 2011 - 21:05:04 PDT)
[AMBER] Error with 99SBnmr force field
- case (Tue Oct 04 2011 - 05:27:35 PDT)
- Peter Eastman (Mon Oct 03 2011 - 16:18:27 PDT)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
- Ross Walker (Thu Oct 27 2011 - 10:20:14 PDT)
- Ashutosh Shandilya (Thu Oct 27 2011 - 01:39:05 PDT)
- Ashutosh Shandilya (Thu Oct 27 2011 - 01:36:01 PDT)
- Ross Walker (Tue Oct 25 2011 - 09:29:48 PDT)
- Ashutosh Shandilya (Tue Oct 25 2011 - 06:04:20 PDT)
[AMBER] errors when add Zn ions
- Daniel Roe (Fri Oct 21 2011 - 10:35:56 PDT)
- Jason Swails (Fri Oct 21 2011 - 09:59:07 PDT)
- Yunjie Zhao (Fri Oct 21 2011 - 05:37:15 PDT)
[AMBER] extract trajectory and average structure
- Jason Swails (Wed Oct 12 2011 - 10:38:48 PDT)
- najmul arfin (Wed Oct 12 2011 - 07:17:00 PDT)
- najmul arfin (Wed Oct 12 2011 - 07:13:13 PDT)
[AMBER] Failure minimizing pamr7 files from A1 tutorial with NAMD=CUDA
- Francesco Pietra (Thu Oct 20 2011 - 13:29:26 PDT)
- Francesco Pietra (Thu Oct 20 2011 - 13:26:42 PDT)
- Ross Walker (Thu Oct 20 2011 - 09:39:50 PDT)
- Ismail, Mohd F. (Thu Oct 20 2011 - 09:14:37 PDT)
- Francesco Pietra (Thu Oct 20 2011 - 03:24:39 PDT)
- Ross Walker (Thu Oct 20 2011 - 01:17:43 PDT)
- Francesco Pietra (Thu Oct 20 2011 - 01:02:36 PDT)
- Ross Walker (Thu Oct 20 2011 - 00:13:07 PDT)
- Francesco Pietra (Wed Oct 19 2011 - 23:32:13 PDT)
[AMBER] FEP
- steinbrt.rci.rutgers.edu (Mon Oct 10 2011 - 01:32:08 PDT)
- Adrian Roitberg (Sun Oct 09 2011 - 19:26:38 PDT)
- E. Nihal Korkmaz (Sun Oct 09 2011 - 19:15:37 PDT)
- Jason Swails (Sun Oct 09 2011 - 18:14:53 PDT)
- E. Nihal Korkmaz (Sun Oct 09 2011 - 15:35:36 PDT)
[AMBER] ff99-ildn frcmod validation question
- D.G. Sprous, PhD (Tue Oct 11 2011 - 05:12:01 PDT)
[AMBER] Final chance to win a C2070 - Survey ends at midnight PDT tonight Monday Oct 24th 2011. Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f
- Crowley, Michael (Mon Oct 24 2011 - 09:41:31 PDT)
- Ross Walker (Mon Oct 24 2011 - 09:36:35 PDT)
- peker milas (Mon Oct 24 2011 - 09:26:42 PDT)
[AMBER] Final chance to win a C2070 - Survey ends at midnight PDT tonight Monday Oct 24th 2011. Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021)
- Ross Walker (Mon Oct 24 2011 - 09:24:57 PDT)
[AMBER] for mm_pbsa.pl, when MS=0, PB does not work, GB works
- Qiong Zhang (Sun Oct 23 2011 - 08:26:10 PDT)
- Ray Luo, Ph.D. (Sun Oct 23 2011 - 08:23:02 PDT)
- Qiong Zhang (Sat Oct 22 2011 - 22:46:27 PDT)
[AMBER] Force field parameters for polyethene
- 陶晓芳 (Thu Oct 20 2011 - 00:47:07 PDT)
- FyD (Tue Oct 18 2011 - 23:59:22 PDT)
- 陶晓芳 (Tue Oct 18 2011 - 19:31:15 PDT)
- David A Case (Tue Oct 18 2011 - 05:03:08 PDT)
- 陶晓芳 (Mon Oct 17 2011 - 20:18:20 PDT)
[AMBER] From amber to gromacs
- Alan (Fri Oct 14 2011 - 00:56:51 PDT)
- madhumita das (Fri Oct 14 2011 - 00:48:33 PDT)
[AMBER] Fwd: AMBER10
- Shesh Nath (Thu Oct 20 2011 - 08:47:49 PDT)
[AMBER] GB simulation on GPU freezes
- E. Nihal Korkmaz (Tue Oct 18 2011 - 01:08:12 PDT)
- E. Nihal Korkmaz (Mon Oct 17 2011 - 19:08:13 PDT)
- Ross Walker (Mon Oct 17 2011 - 15:24:45 PDT)
- Scott Le Grand (Mon Oct 17 2011 - 14:49:18 PDT)
- E. Nihal Korkmaz (Mon Oct 17 2011 - 13:46:44 PDT)
- E. Nihal Korkmaz (Fri Oct 14 2011 - 16:15:41 PDT)
- Scott Le Grand (Fri Oct 14 2011 - 15:29:39 PDT)
- Ross Walker (Fri Oct 14 2011 - 14:55:30 PDT)
- E. Nihal Korkmaz (Fri Oct 14 2011 - 12:28:12 PDT)
- Ross Walker (Fri Oct 14 2011 - 12:15:59 PDT)
- E. Nihal Korkmaz (Fri Oct 14 2011 - 11:29:20 PDT)
- E. Nihal Korkmaz (Fri Oct 14 2011 - 11:17:00 PDT)
- Scott Le Grand (Fri Oct 14 2011 - 11:05:37 PDT)
- E. Nihal Korkmaz (Fri Oct 14 2011 - 10:55:24 PDT)
[AMBER] GPU Survey link: http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021
- Ross Walker (Mon Oct 24 2011 - 09:55:46 PDT)
[AMBER] Gromacs Make Index in AMBER
- Jason Swails (Fri Oct 07 2011 - 17:00:27 PDT)
- Yao Yao (Fri Oct 07 2011 - 15:56:47 PDT)
[AMBER] Help on self-assembled mono layer
- ros (Mon Oct 17 2011 - 11:58:02 PDT)
[AMBER] HO atom type van der Waals (GLYCAM)
- Matthew Tessier (Wed Oct 05 2011 - 10:44:58 PDT)
[AMBER] How to avoid Zn parametrization?
- FyD (Thu Oct 27 2011 - 01:16:07 PDT)
- Andrew Voronkov (Wed Oct 26 2011 - 05:36:28 PDT)
- Andrew Voronkov (Wed Oct 26 2011 - 05:32:56 PDT)
[AMBER] How to Calculate SASA with Amber?
- Oliver Grant (Tue Oct 11 2011 - 02:13:10 PDT)
- Daniel Roe (Mon Oct 10 2011 - 12:55:39 PDT)
- qiao xue (Sun Oct 09 2011 - 16:53:53 PDT)
- Daniel Roe (Thu Oct 06 2011 - 07:32:59 PDT)
- Jason Swails (Wed Oct 05 2011 - 07:43:04 PDT)
- qiao xue (Wed Oct 05 2011 - 03:53:54 PDT)
[AMBER] how to get tetramer coordinate of Melittin Form PDB ID:2MLT.
- hai wei (Sun Oct 30 2011 - 01:58:16 PDT)
- Hector A. Baldoni (Tue Oct 25 2011 - 15:23:54 PDT)
- hai wei (Sat Oct 22 2011 - 18:36:27 PDT)
[AMBER] how to load atom type for divalent ions in leaprc.ff10?
- Victor Ma (Mon Oct 31 2011 - 08:56:49 PDT)
[AMBER] How to make the library of PNA-DNA duplex
- FyD (Sun Oct 16 2011 - 06:51:10 PDT)
- souvik sur (Sat Oct 15 2011 - 04:57:10 PDT)
[AMBER] How to use "impose" command in ptraj to rotate dihedral angle
- Sai Kumar Ramadugu (Tue Oct 25 2011 - 08:23:24 PDT)
- mish (Mon Oct 24 2011 - 02:49:49 PDT)
[AMBER] Illegal atomic numbers in nucleic10.lib
- Jason Swails (Tue Oct 04 2011 - 13:41:35 PDT)
- Peter Eastman (Tue Oct 04 2011 - 11:13:08 PDT)
- Jason Swails (Tue Oct 04 2011 - 10:47:13 PDT)
- Ross Walker (Tue Oct 04 2011 - 10:44:26 PDT)
- Jason Swails (Tue Oct 04 2011 - 10:34:12 PDT)
- Jason Swails (Tue Oct 04 2011 - 10:31:01 PDT)
- Peter Eastman (Tue Oct 04 2011 - 10:25:44 PDT)
- Ross Walker (Tue Oct 04 2011 - 10:16:54 PDT)
- Peter Eastman (Tue Oct 04 2011 - 09:58:17 PDT)
- Jason Swails (Mon Oct 03 2011 - 19:51:52 PDT)
- Ross Walker (Mon Oct 03 2011 - 19:41:27 PDT)
- Jason Swails (Mon Oct 03 2011 - 19:33:43 PDT)
- Peter Eastman (Mon Oct 03 2011 - 16:57:17 PDT)
[AMBER] input conformations for RESP procedure for modified amino?
- FyD (Thu Oct 27 2011 - 01:52:35 PDT)
- jzintsma.nd.edu (Wed Oct 26 2011 - 10:04:20 PDT)
[AMBER] Inquiry about Amber installation
- Mo Chen (Fri Oct 14 2011 - 16:47:40 PDT)
- Jason Swails (Fri Oct 14 2011 - 15:59:40 PDT)
- Mo Chen (Fri Oct 14 2011 - 13:25:44 PDT)
- Jason Swails (Fri Oct 14 2011 - 12:48:45 PDT)
- Mo Chen (Fri Oct 14 2011 - 11:20:34 PDT)
- Mo Chen (Fri Oct 14 2011 - 11:20:16 PDT)
- Niel Henriksen (Fri Oct 14 2011 - 06:36:03 PDT)
- Jason Swails (Fri Oct 14 2011 - 03:20:20 PDT)
- Mo Chen (Thu Oct 13 2011 - 20:21:09 PDT)
[AMBER] Inquiry about the cutoff (cut, vdw_cutoff, es_cutoff) settings of PMEMD
- Mo Chen (Thu Oct 20 2011 - 09:27:58 PDT)
- Ross Walker (Thu Oct 20 2011 - 00:32:00 PDT)
- Mo Chen (Wed Oct 19 2011 - 19:59:26 PDT)
- Mo Chen (Wed Oct 19 2011 - 19:18:46 PDT)
[AMBER] Installation of AmberTools 1.5 (and Amber 11)
- Ben Ahmady (Tue Oct 18 2011 - 11:08:04 PDT)
- Jason Swails (Tue Oct 18 2011 - 11:02:46 PDT)
- Ben Ahmady (Tue Oct 18 2011 - 10:41:34 PDT)
[AMBER] Interaction Energy in QMMMMD
- Gustavo Seabra (Tue Oct 11 2011 - 11:18:39 PDT)
- Yao Yao (Mon Oct 10 2011 - 12:44:20 PDT)
- Qiantao Wang (Fri Oct 07 2011 - 13:17:10 PDT)
- Yao Yao (Fri Oct 07 2011 - 12:27:30 PDT)
[AMBER] iron sulphur cluster parameters
- francesco oteri (Thu Oct 06 2011 - 06:10:39 PDT)
[AMBER] iron sulphur cluster parametrization
- David Case (Mon Oct 31 2011 - 18:00:09 PDT)
- Francesco Oteri (Sat Oct 29 2011 - 13:35:04 PDT)
- case (Sat Oct 29 2011 - 07:27:04 PDT)
- Francesco Oteri (Sat Oct 29 2011 - 01:39:52 PDT)
[AMBER] Is Amber a 32-bit or 64-bit program?
- Matthew D Antalek (Tue Oct 18 2011 - 17:14:58 PDT)
- Ismail, Mohd F. (Tue Oct 18 2011 - 15:15:11 PDT)
- Jiaqi Jin (Tue Oct 18 2011 - 14:58:57 PDT)
[AMBER] Issue with running sander with SHAKE
- Breuer, Marian (Mon Oct 31 2011 - 11:07:37 PDT)
[AMBER] Judje error
- Алексей Раевский (Sun Oct 16 2011 - 22:49:26 PDT)
- David A. Case (Sun Oct 16 2011 - 18:24:52 PDT)
- Алексей Раевский (Sun Oct 16 2011 - 15:19:37 PDT)
[AMBER] LMOD error and questions
- Daniel Roe (Tue Oct 11 2011 - 13:27:52 PDT)
- Sarah Edwards (Tue Oct 11 2011 - 11:54:41 PDT)
[AMBER] Material including Boron, "ATTN need revision"
- Hoshin Kim (Tue Oct 18 2011 - 16:51:14 PDT)
[AMBER] message during pbsa energy calculation
- JORGE IULEK (Wed Oct 05 2011 - 05:28:09 PDT)
- Jason Swails (Tue Oct 04 2011 - 16:20:43 PDT)
- Jorge Iulek (Tue Oct 04 2011 - 16:17:17 PDT)
[AMBER] Minor RNA bases
- David A Case (Mon Oct 24 2011 - 13:20:27 PDT)
- gunajyoti das (Mon Oct 24 2011 - 05:04:47 PDT)
[AMBER] MMPBSA calculation
- Sangita Kachhap (Tue Oct 04 2011 - 21:13:54 PDT)
- Jason Swails (Tue Oct 04 2011 - 11:29:53 PDT)
- Sangita Kachhap (Tue Oct 04 2011 - 11:06:43 PDT)
- Jason Swails (Tue Oct 04 2011 - 10:42:05 PDT)
- Sangita Kachhap (Tue Oct 04 2011 - 10:14:20 PDT)
[AMBER] MMPBSA error
- Soumya Lipsa Rath (Thu Oct 06 2011 - 03:03:31 PDT)
[AMBER] MMPBSA input error for INP
- Niel Henriksen (Mon Oct 03 2011 - 19:51:18 PDT)
- Jason Swails (Mon Oct 03 2011 - 19:48:33 PDT)
- Niel Henriksen (Mon Oct 03 2011 - 19:33:20 PDT)
[AMBER] MMPBSA on a protein-protein complex when protein contains non-protein
- Jason Swails (Thu Oct 06 2011 - 17:06:33 PDT)
- Irene Newhouse (Thu Oct 06 2011 - 16:09:53 PDT)
[AMBER] MMPBSA.MPI: Entropy
- Jason Swails (Tue Oct 04 2011 - 08:28:14 PDT)
- George Tzotzos (Tue Oct 04 2011 - 07:04:54 PDT)
- Jason Swails (Tue Oct 04 2011 - 06:47:00 PDT)
- George Tzotzos (Tue Oct 04 2011 - 06:35:48 PDT)
- Jason Swails (Mon Oct 03 2011 - 12:47:57 PDT)
- George Tzotzos (Mon Oct 03 2011 - 11:01:10 PDT)
[AMBER] MMPBSA.MPI: IOError: [Errno 9] Bad file descriptor
- Jason Swails (Fri Oct 07 2011 - 08:20:29 PDT)
- George Tzotzos (Fri Oct 07 2011 - 08:07:18 PDT)
- Jan-Philip Gehrcke (Fri Oct 07 2011 - 05:20:23 PDT)
- George Tzotzos (Thu Oct 06 2011 - 15:45:32 PDT)
[AMBER] MMPBSA.py - PB Bomb
- Jesper Soerensen (Tue Oct 18 2011 - 14:06:35 PDT)
- Ray Luo, Ph.D. (Mon Oct 17 2011 - 17:09:25 PDT)
- Jesper Soerensen (Mon Oct 17 2011 - 17:04:13 PDT)
[AMBER] MMPBSA.py -use-mdin. PB Bomb
- Jesper Soerensen (Wed Oct 12 2011 - 12:42:28 PDT)
[AMBER] MMPBSA.py 3DRISM error
- Jesper Soerensen (Thu Oct 06 2011 - 10:47:24 PDT)
- Jason Swails (Thu Oct 06 2011 - 10:08:44 PDT)
- Jesper Soerensen (Wed Oct 05 2011 - 17:18:40 PDT)
[AMBER] MMPBSA.py mask selections
- Jesper Soerensen (Wed Oct 12 2011 - 12:15:45 PDT)
- Jesper Soerensen (Wed Oct 12 2011 - 10:59:12 PDT)
[AMBER] MMPBSA.py.MPI problems: L-J-parameters, bad file descriptors, MMPBSA hangup due to sander failure
- Jan-Philip Gehrcke (Tue Oct 11 2011 - 02:22:40 PDT)
- Jason Swails (Fri Oct 07 2011 - 08:53:12 PDT)
- Jan-Philip Gehrcke (Fri Oct 07 2011 - 02:45:48 PDT)
- Jan-Philip Gehrcke (Wed Oct 05 2011 - 09:16:45 PDT)
- Jason Swails (Wed Oct 05 2011 - 07:40:45 PDT)
- Jan-Philip Gehrcke (Wed Oct 05 2011 - 06:54:15 PDT)
- Jan-Philip Gehrcke (Wed Oct 05 2011 - 03:54:16 PDT)
[AMBER] MMPBSA.py: error during parsing of _MMPBSA_complex_gb.mdout
- Jason Swails (Wed Oct 26 2011 - 07:46:14 PDT)
- Jan-Philip Gehrcke (Wed Oct 26 2011 - 02:00:58 PDT)
- Jason Swails (Tue Oct 25 2011 - 09:04:55 PDT)
- Jan-Philip Gehrcke (Tue Oct 25 2011 - 08:30:40 PDT)
- Jason Swails (Tue Oct 18 2011 - 11:08:31 PDT)
- Jan-Philip Gehrcke (Tue Oct 18 2011 - 10:03:37 PDT)
- Jason Swails (Tue Oct 11 2011 - 06:54:51 PDT)
- Jan-Philip Gehrcke (Tue Oct 11 2011 - 06:20:14 PDT)
[AMBER] MMPBSA.py: no value inserted for "Residues to print": left as "RES EDIT"
- Jan-Philip Gehrcke (Wed Oct 05 2011 - 07:32:45 PDT)
[AMBER] MMPBSA: how to include only some residues
- Victor Ma (Mon Oct 03 2011 - 13:08:49 PDT)
- Jason Swails (Mon Oct 03 2011 - 12:50:38 PDT)
- Victor Ma (Mon Oct 03 2011 - 12:30:22 PDT)
[AMBER] mmtsb problem
- Sel Ercan (Wed Oct 12 2011 - 00:08:46 PDT)
- Sel Ercan (Tue Oct 11 2011 - 06:03:19 PDT)
[AMBER] Molecular velocity from molecular trajectories
- Daniel Roe (Wed Oct 26 2011 - 06:24:13 PDT)
- tommaso.casalini.mail.polimi.it (Wed Oct 26 2011 - 02:51:53 PDT)
[AMBER] molecule out box and correct hbond analysis
- Daniel Roe (Thu Oct 27 2011 - 09:20:23 PDT)
- mirage . (Thu Oct 27 2011 - 08:39:47 PDT)
- Daniel Roe (Thu Oct 27 2011 - 07:15:47 PDT)
- mirage . (Thu Oct 27 2011 - 01:27:54 PDT)
[AMBER] New to AMBER, installation issues
- David A Case (Thu Oct 13 2011 - 07:17:17 PDT)
- peker milas (Wed Oct 12 2011 - 23:36:55 PDT)
- Matthew D Antalek (Wed Oct 12 2011 - 20:31:45 PDT)
- Bill Ross (Wed Oct 12 2011 - 14:29:03 PDT)
- Jason Swails (Wed Oct 12 2011 - 14:16:04 PDT)
- Matthew D Antalek (Wed Oct 12 2011 - 14:07:56 PDT)
- Jason Swails (Wed Oct 12 2011 - 13:50:22 PDT)
- peker milas (Wed Oct 12 2011 - 13:11:06 PDT)
- Matthew D Antalek (Wed Oct 12 2011 - 12:26:36 PDT)
- Carlos Sosa (Wed Oct 12 2011 - 12:17:23 PDT)
- Matthew D Antalek (Wed Oct 12 2011 - 12:06:02 PDT)
[AMBER] non standart residue library creation with tleap (Zn atom)
- FyD (Thu Oct 27 2011 - 00:33:55 PDT)
- Andrew Voronkov (Wed Oct 26 2011 - 05:19:32 PDT)
[AMBER] not too many MD simulations of protein-ligand system?
- ros (Wed Oct 05 2011 - 18:23:09 PDT)
- Yun Shi (Wed Oct 05 2011 - 17:07:13 PDT)
- Carlos Simmerling (Wed Oct 05 2011 - 16:48:14 PDT)
- Yun Shi (Wed Oct 05 2011 - 12:50:54 PDT)
[AMBER] Nudged Elastic Band (NEB) with torque PBS system
- Daniel Roe (Mon Oct 31 2011 - 05:09:57 PDT)
- c00jsw00.nchc.narl.org.tw (Mon Oct 31 2011 - 00:02:26 PDT)
- Carlos Simmerling (Thu Oct 27 2011 - 10:01:36 PDT)
- Jason Swails (Thu Oct 27 2011 - 09:55:03 PDT)
- c00jsw00.nchc.narl.org.tw (Thu Oct 27 2011 - 09:47:48 PDT)
[AMBER] oct or cubic box?
- Bill Ross (Fri Oct 07 2011 - 14:30:39 PDT)
- David A Case (Fri Oct 07 2011 - 12:45:24 PDT)
- Yun Shi (Fri Oct 07 2011 - 11:15:18 PDT)
[AMBER] One more Gentle Reminder: Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021)
- Ross Walker (Thu Oct 13 2011 - 10:33:34 PDT)
[AMBER] Ordering of torsion definitions
- Bill Ross (Tue Oct 04 2011 - 15:52:22 PDT)
- Peter Eastman (Tue Oct 04 2011 - 13:14:36 PDT)
- Bill Ross (Tue Oct 04 2011 - 13:06:53 PDT)
- Ross Walker (Tue Oct 04 2011 - 12:05:51 PDT)
- Peter Eastman (Tue Oct 04 2011 - 11:56:16 PDT)
- Bill Ross (Tue Oct 04 2011 - 11:50:07 PDT)
- Peter Eastman (Tue Oct 04 2011 - 11:17:01 PDT)
- Bill Ross (Tue Oct 04 2011 - 11:05:31 PDT)
- Ross Walker (Tue Oct 04 2011 - 10:41:05 PDT)
- Peter Eastman (Tue Oct 04 2011 - 10:06:20 PDT)
[AMBER] Parallel Amber11 Installation Error
- David Cantu (Sat Oct 08 2011 - 11:28:23 PDT)
- David A Case (Fri Oct 07 2011 - 06:37:17 PDT)
- David Cantu (Thu Oct 06 2011 - 18:25:26 PDT)
- Jason Swails (Thu Oct 06 2011 - 16:40:04 PDT)
- David Cantu (Thu Oct 06 2011 - 15:26:28 PDT)
[AMBER] parameters for anchor-modified glycopeptides
- FyD (Mon Oct 31 2011 - 09:59:29 PDT)
- David A Case (Mon Oct 31 2011 - 05:35:20 PDT)
- Urszula Uciechowska (Sun Oct 30 2011 - 10:10:35 PDT)
[AMBER] PB parameters: SURFTEN/SURFOFF
- Qiong Zhang (Mon Oct 24 2011 - 14:04:30 PDT)
- Jason Swails (Mon Oct 24 2011 - 13:20:34 PDT)
- Qiong Zhang (Mon Oct 24 2011 - 12:50:20 PDT)
- Jason Swails (Sun Oct 23 2011 - 21:21:22 PDT)
- Qiong Zhang (Sat Oct 22 2011 - 22:41:17 PDT)
- Ray Luo, Ph.D. (Sat Oct 22 2011 - 21:19:01 PDT)
- Qiong Zhang (Sat Oct 22 2011 - 13:56:33 PDT)
[AMBER] PBSA grid output using MMPBSA.py
- Jesper Soerensen (Thu Oct 27 2011 - 15:29:10 PDT)
[AMBER] PDB file modification
- David A Case (Mon Oct 03 2011 - 11:31:05 PDT)
- Jason Swails (Mon Oct 03 2011 - 10:53:54 PDT)
- Asmita Gupta (Mon Oct 03 2011 - 10:30:51 PDT)
- David A Case (Mon Oct 03 2011 - 09:03:26 PDT)
- Victor Ma (Mon Oct 03 2011 - 08:05:15 PDT)
- Asmita Gupta (Mon Oct 03 2011 - 07:26:53 PDT)
[AMBER] Periodic Box in igb mode
- David A Case (Mon Oct 31 2011 - 05:25:21 PDT)
- Davood Norouzi (Sun Oct 30 2011 - 05:26:06 PDT)
[AMBER] please help me
- David A Case (Tue Oct 25 2011 - 05:29:06 PDT)
- pancham lal gupta (Mon Oct 24 2011 - 20:08:06 PDT)
- pancham lal gupta (Thu Oct 20 2011 - 02:59:57 PDT)
- Nej Pir (Wed Oct 12 2011 - 06:53:02 PDT)
- Brian Radak (Wed Oct 12 2011 - 06:47:31 PDT)
- steinbrt.rci.rutgers.edu (Wed Oct 12 2011 - 06:39:17 PDT)
- pancham lal gupta (Wed Oct 12 2011 - 06:04:25 PDT)
[AMBER] PLUMED for PATH COLLECTIVE VARIABLES
- Ben Roberts (Sat Oct 01 2011 - 19:32:52 PDT)
- Giulia Palermo (Sat Oct 01 2011 - 11:46:22 PDT)
[AMBER] PMEMD command
- Chinh Su Tran To (Thu Oct 13 2011 - 02:28:43 PDT)
- Chinh Su Tran To (Thu Oct 13 2011 - 00:18:24 PDT)
[AMBER] PMEMD conditions for solvent bulk characterization?
- Dean Cuebas (Mon Oct 17 2011 - 20:22:05 PDT)
- David A. Case (Mon Oct 17 2011 - 18:32:10 PDT)
- Dean Cuebas (Mon Oct 17 2011 - 15:05:31 PDT)
[AMBER] pmemd.cuda and nonzero gbsa
- Scott Le Grand (Tue Oct 04 2011 - 12:52:45 PDT)
- Jason Swails (Tue Oct 04 2011 - 12:38:50 PDT)
- Scott Le Grand (Tue Oct 04 2011 - 12:33:34 PDT)
- E. Nihal Korkmaz (Tue Oct 04 2011 - 12:22:29 PDT)
- Jason Swails (Tue Oct 04 2011 - 12:12:13 PDT)
- Ross Walker (Tue Oct 04 2011 - 11:43:07 PDT)
- E. Nihal Korkmaz (Tue Oct 04 2011 - 11:25:32 PDT)
[AMBER] PNEB on GPUs
- William Cantara (Mon Oct 03 2011 - 17:33:21 PDT)
[AMBER] Poisson-Boltzmann/GB Solvents with FF02
- Neha Gandhi (Thu Oct 13 2011 - 22:50:32 PDT)
[AMBER] Polarization term in Energy
- David A Case (Tue Oct 25 2011 - 05:42:14 PDT)
- Anglea A. (Sun Oct 23 2011 - 06:55:38 PDT)
[AMBER] position restraints on heavy atoms or all?
- Brian Radak (Mon Oct 31 2011 - 06:09:32 PDT)
- Yun Shi (Sat Oct 29 2011 - 17:04:16 PDT)
[AMBER] prmtop details
- Jason Swails (Wed Oct 26 2011 - 19:50:12 PDT)
- Jason Swails (Wed Oct 26 2011 - 18:21:54 PDT)
- Alessandro Nascimento (Wed Oct 26 2011 - 17:13:01 PDT)
- Yao Yao (Wed Oct 26 2011 - 17:10:10 PDT)
[AMBER] Problem in compilng AmberTools1.5 on Mac OSX 10.7.1
- Wei Huang (Sat Oct 01 2011 - 14:02:55 PDT)
[AMBER] problem in interpreting RMSDs
- Jason Swails (Sat Oct 15 2011 - 09:59:49 PDT)
- Sajeewa Pemasinghe (Sat Oct 15 2011 - 09:15:21 PDT)
[AMBER] Problem installing on a mac Lion 10.7 using gcc 4.2
- Jason Swails (Sun Oct 09 2011 - 06:07:28 PDT)
- Gamal Akabani (Thu Oct 06 2011 - 16:01:44 PDT)
[AMBER] problem with sulphur
- Mark Williamson (Wed Oct 26 2011 - 05:20:50 PDT)
- David A Case (Mon Oct 03 2011 - 07:19:50 PDT)
- Jason Swails (Mon Oct 03 2011 - 06:54:08 PDT)
- FyD (Mon Oct 03 2011 - 04:31:34 PDT)
- pancham lal gupta (Mon Oct 03 2011 - 03:39:57 PDT)
[AMBER] Problems with AmberTools compilation under Debian
- James Starlight (Mon Oct 31 2011 - 07:11:51 PDT)
- Jason Swails (Mon Oct 31 2011 - 06:57:44 PDT)
- James Starlight (Mon Oct 31 2011 - 06:23:56 PDT)
- Daniel Roe (Mon Oct 31 2011 - 05:22:31 PDT)
- James Starlight (Mon Oct 31 2011 - 00:42:02 PDT)
- James Starlight (Sun Oct 30 2011 - 08:33:27 PDT)
- Daniel Roe (Sun Oct 30 2011 - 07:00:02 PDT)
- James Starlight (Sun Oct 30 2011 - 06:53:30 PDT)
- James Starlight (Sun Oct 30 2011 - 00:45:33 PDT)
- Daniel Roe (Sat Oct 29 2011 - 13:21:59 PDT)
- James Starlight (Sat Oct 29 2011 - 10:42:29 PDT)
[AMBER] proteins with Ff10 + igb=7
- Abhishek Singh (Wed Oct 12 2011 - 10:41:32 PDT)
- Jason Swails (Wed Oct 12 2011 - 10:37:50 PDT)
- Carlos Simmerling (Wed Oct 12 2011 - 10:36:45 PDT)
- Abhishek Singh (Wed Oct 12 2011 - 10:32:14 PDT)
- David A Case (Wed Oct 12 2011 - 09:23:41 PDT)
- Carlos Simmerling (Wed Oct 12 2011 - 08:55:59 PDT)
- Abhishek Singh (Wed Oct 12 2011 - 08:15:03 PDT)
[AMBER] pseudorotation phase angle for RNA
- David A Case (Thu Oct 27 2011 - 05:05:23 PDT)
- David A Case (Thu Oct 27 2011 - 05:03:40 PDT)
- Ilyas Yildirim (Thu Oct 27 2011 - 01:37:34 PDT)
- Charles Johnson (Wed Oct 26 2011 - 13:57:28 PDT)
- Charles Johnson (Wed Oct 26 2011 - 08:50:56 PDT)
[AMBER] ptraj clustering error
- Rajesh Raju (Fri Oct 07 2011 - 12:47:24 PDT)
- Thomas Cheatham III (Fri Oct 07 2011 - 12:25:16 PDT)
- Rajesh Raju (Fri Oct 07 2011 - 12:08:59 PDT)
[AMBER] QMMMMD blowup
- David A. Case (Fri Oct 14 2011 - 13:22:57 PDT)
- Adrian Roitberg (Fri Oct 14 2011 - 13:13:23 PDT)
- Yao Yao (Fri Oct 14 2011 - 12:58:35 PDT)
[AMBER] QMMMMD blowup STILL
- Ross Walker (Sat Oct 15 2011 - 09:09:31 PDT)
- Yao Yao (Fri Oct 14 2011 - 20:56:07 PDT)
[AMBER] QMMMMD Tutorial Question
- Ross Walker (Wed Oct 05 2011 - 14:59:42 PDT)
- Yao Yao (Wed Oct 05 2011 - 14:52:09 PDT)
[AMBER] quasi-harmonic analysis
- c00jsw00.nchc.narl.org.tw (Wed Oct 26 2011 - 04:00:47 PDT)
- Hannes Loeffler (Wed Oct 26 2011 - 03:25:40 PDT)
- Neha Gandhi (Wed Oct 26 2011 - 02:53:24 PDT)
- Collu, Francesca (DCB) (Wed Oct 26 2011 - 01:56:03 PDT)
- Neha Gandhi (Wed Oct 26 2011 - 01:50:48 PDT)
[AMBER] Query for using Curves+ from Amber trajectories
- Osman, Roman (Fri Oct 28 2011 - 07:11:36 PDT)
- souvik sur (Thu Oct 27 2011 - 23:19:49 PDT)
[AMBER] Question regarding HAS_10_12 flag in PMEMD (LINMIN Failure)
- Ross Walker (Tue Oct 11 2011 - 19:19:21 PDT)
- brian_jo.berkeley.edu (Tue Oct 11 2011 - 18:06:20 PDT)
- Jason Swails (Tue Oct 11 2011 - 18:04:26 PDT)
- Duke, Robert E Jr (Tue Oct 11 2011 - 17:55:46 PDT)
- brian_jo.berkeley.edu (Tue Oct 11 2011 - 17:30:21 PDT)
[AMBER] Radial distribution function
- tommaso.casalini.mail.polimi.it (Thu Oct 06 2011 - 02:31:48 PDT)
[AMBER] Reg:QM region + cutoff larger than box dimension
- Brian Radak (Thu Oct 06 2011 - 10:31:05 PDT)
- Ross Walker (Thu Oct 06 2011 - 10:11:19 PDT)
- Ross Walker (Thu Oct 06 2011 - 09:50:52 PDT)
- Brian Radak (Thu Oct 06 2011 - 09:42:09 PDT)
- Ross Walker (Thu Oct 06 2011 - 09:18:03 PDT)
- Brian Radak (Thu Oct 06 2011 - 08:56:58 PDT)
- kaustubh joshi (Thu Oct 06 2011 - 08:42:58 PDT)
- Brian Radak (Thu Oct 06 2011 - 08:02:44 PDT)
- kaustubh joshi (Thu Oct 06 2011 - 07:46:29 PDT)
[AMBER] regarding qmmm simulation
- Ross Walker (Wed Oct 12 2011 - 09:29:57 PDT)
- jani vinod (Wed Oct 12 2011 - 05:51:45 PDT)
- Ross Walker (Tue Oct 11 2011 - 09:06:09 PDT)
- jani vinod (Tue Oct 11 2011 - 05:30:16 PDT)
[AMBER] reimage method and hbond analysis
- mirage . (Wed Oct 26 2011 - 00:02:47 PDT)
[AMBER] relative binding free energy calculation
- David A. Case (Sat Oct 15 2011 - 08:54:36 PDT)
- leila karami (Sat Oct 15 2011 - 07:00:59 PDT)
[AMBER] REMD: mismatches in potential energy values
- Jason Swails (Tue Oct 25 2011 - 06:28:57 PDT)
- Mariarosaria Ferraro (Tue Oct 25 2011 - 03:24:22 PDT)
[AMBER] residue stripping in ptraj
- Thomas Cheatham III (Tue Oct 11 2011 - 13:11:03 PDT)
- Daniel Roe (Mon Oct 10 2011 - 05:20:50 PDT)
- Praapti Jayaswal (Sun Oct 09 2011 - 22:11:15 PDT)
[AMBER] safemem.o error while compiling Ambertools 1.5
- Josmar R. da Rocha (Thu Oct 13 2011 - 20:34:22 PDT)
- Jason Swails (Thu Oct 13 2011 - 16:07:34 PDT)
- Tyler Luchko (Thu Oct 13 2011 - 16:05:46 PDT)
- Josmar R. da Rocha (Thu Oct 13 2011 - 15:35:25 PDT)
[AMBER] Salt in explicit water
- Daniel Roe (Fri Oct 28 2011 - 04:16:31 PDT)
- Beale, John (Fri Oct 28 2011 - 02:01:20 PDT)
[AMBER] sander bug?
- Jason Swails (Fri Oct 14 2011 - 16:00:41 PDT)
- Adrian Roitberg (Fri Oct 14 2011 - 15:27:29 PDT)
- Yao Yao (Fri Oct 14 2011 - 15:24:16 PDT)
[AMBER] sander mpi error when unfolding the protein
- Chinh Su Tran To (Sun Oct 09 2011 - 19:45:31 PDT)
[AMBER] sander pb focusing error
- Niel Henriksen (Thu Oct 13 2011 - 20:17:06 PDT)
[AMBER] sander pbsa and imin = 5 problem
- Niel Henriksen (Mon Oct 17 2011 - 22:23:35 PDT)
- Niel Henriksen (Mon Oct 17 2011 - 21:26:23 PDT)
- Ray Luo, Ph.D. (Mon Oct 17 2011 - 20:54:29 PDT)
- Niel Henriksen (Mon Oct 17 2011 - 20:27:18 PDT)
[AMBER] sander.MPI
- tsurma.umich.edu (Thu Oct 27 2011 - 07:22:11 PDT)
- David A Case (Thu Oct 27 2011 - 05:15:13 PDT)
- tsurma.umich.edu (Tue Oct 25 2011 - 08:06:42 PDT)
[AMBER] Sander.MPI parallel run
- Ross Walker (Fri Oct 28 2011 - 09:20:36 PDT)
- Lianhu Wei (Fri Oct 28 2011 - 07:33:04 PDT)
- Jason Swails (Thu Oct 27 2011 - 13:21:21 PDT)
- Lianhu Wei (Thu Oct 27 2011 - 13:02:59 PDT)
- Ross Walker (Thu Oct 27 2011 - 12:44:56 PDT)
- Jason Swails (Thu Oct 27 2011 - 12:32:20 PDT)
- Lianhu Wei (Thu Oct 27 2011 - 12:08:11 PDT)
- Ross Walker (Thu Oct 20 2011 - 09:33:14 PDT)
- Lianhu Wei (Thu Oct 20 2011 - 09:04:26 PDT)
[AMBER] SASA calculate
- Ilyas Yildirim (Thu Oct 13 2011 - 06:48:04 PDT)
- Tong Zhu (Thu Oct 13 2011 - 06:36:19 PDT)
[AMBER] SASA calculation: removing water and ion problem.
- Jason Swails (Mon Oct 17 2011 - 04:05:27 PDT)
- David Case (Sun Oct 16 2011 - 09:59:58 PDT)
- Ouaray Z. (Sun Oct 16 2011 - 09:16:58 PDT)
- Sangita Kachhap (Sun Oct 16 2011 - 07:21:53 PDT)
- Ouaray Z. (Sun Oct 16 2011 - 06:14:36 PDT)
[AMBER] Self assembled surface.
- ros (Tue Oct 04 2011 - 15:41:22 PDT)
[AMBER] Self-assembled monolayers
- ros (Sun Oct 16 2011 - 09:19:53 PDT)
[AMBER] Small inquiry regarding MMPBSA.py code
- Jan-Philip Gehrcke (Tue Oct 04 2011 - 11:42:14 PDT)
- Jason Swails (Tue Oct 04 2011 - 10:39:32 PDT)
- Jan-Philip Gehrcke (Tue Oct 04 2011 - 10:00:55 PDT)
[AMBER] Solvent accessible area
- kirtana S (Sun Oct 16 2011 - 09:38:58 PDT)
- Jason Swails (Fri Oct 07 2011 - 09:03:47 PDT)
- kirtana S (Fri Oct 07 2011 - 08:28:35 PDT)
- Daniel Roe (Fri Oct 07 2011 - 05:34:03 PDT)
- kirtana S (Thu Oct 06 2011 - 14:22:52 PDT)
- Jason Swails (Tue Oct 04 2011 - 06:47:48 PDT)
- kirtana S (Mon Oct 03 2011 - 22:36:14 PDT)
- Jason Swails (Mon Oct 03 2011 - 22:09:26 PDT)
- kirtana S (Mon Oct 03 2011 - 21:57:38 PDT)
- Jason Swails (Mon Oct 03 2011 - 18:02:54 PDT)
- kirtana S (Mon Oct 03 2011 - 14:03:50 PDT)
[AMBER] solvents in AMBER
- Yao Yao (Mon Oct 17 2011 - 13:36:02 PDT)
[AMBER] Specifying a gcc compiler for amber tools installation
- Daniel Roe (Fri Oct 28 2011 - 14:27:12 PDT)
- Jason Swails (Fri Oct 28 2011 - 13:01:46 PDT)
- Sai Kumar Ramadugu (Fri Oct 28 2011 - 10:21:50 PDT)
[AMBER] subscription!
- Dr. Alaa El-Din A. Gawad (Fri Oct 14 2011 - 13:09:22 PDT)
[AMBER] The recommended settings for PB analyses reasonably sensitive to istrng parameter and also suitable for charged systems
- Marek Maly (Tue Oct 04 2011 - 17:49:49 PDT)
[AMBER] TMD for a large conformation change
- William Cantara (Mon Oct 03 2011 - 17:52:39 PDT)
[AMBER] Total Energy Autocorrelation Function
- Yao Yao (Thu Oct 06 2011 - 10:30:28 PDT)
- Jason Swails (Thu Oct 06 2011 - 10:09:20 PDT)
- Yao Yao (Thu Oct 06 2011 - 10:06:45 PDT)
- Yao Yao (Wed Oct 05 2011 - 19:40:37 PDT)
[AMBER] Trouble with Installation of AmberTools 1.5
- Tyler Luchko (Mon Oct 17 2011 - 09:19:29 PDT)
- Ben Ahmady (Mon Oct 17 2011 - 09:11:53 PDT)
[AMBER] Turning off non-bonded interactions for specific atomtype pairs
- Marc van der Kamp (Thu Oct 13 2011 - 03:17:28 PDT)
- Jason Swails (Wed Oct 12 2011 - 10:27:28 PDT)
- Qiantao Wang (Wed Oct 12 2011 - 07:21:55 PDT)
- Marc van der Kamp (Wed Oct 12 2011 - 06:21:46 PDT)
- Jason Swails (Tue Oct 11 2011 - 17:59:50 PDT)
- Jason Swails (Tue Oct 11 2011 - 14:46:00 PDT)
- Qiantao Wang (Tue Oct 11 2011 - 08:06:02 PDT)
- Marc van der Kamp (Tue Oct 11 2011 - 01:49:27 PDT)
- Marc van der Kamp (Tue Oct 11 2011 - 01:42:49 PDT)
[AMBER] Turning off non-bonded interactions for specificatomtype pairs
- Jason Swails (Thu Oct 13 2011 - 05:45:03 PDT)
- CHAMI F. (Thu Oct 13 2011 - 04:03:45 PDT)
[AMBER] tutorial A6
- David A Case (Mon Oct 31 2011 - 05:24:19 PDT)
- Jason Swails (Sun Oct 30 2011 - 09:37:13 PDT)
- leila karami (Sun Oct 30 2011 - 03:40:42 PDT)
- leila karami (Sun Oct 30 2011 - 03:21:18 PDT)
[AMBER] umbrella sampling amber11
- Elisa Frezza (Mon Oct 31 2011 - 07:31:56 PDT)
- Jason Swails (Mon Oct 31 2011 - 06:37:43 PDT)
- Elisa Frezza (Mon Oct 31 2011 - 03:55:23 PDT)
- Jason Swails (Sun Oct 30 2011 - 14:55:40 PDT)
- Elisa Frezza (Sun Oct 30 2011 - 14:40:50 PDT)
[AMBER] Using ff10 with ildn or nmr
- David A. Case (Tue Oct 04 2011 - 16:35:35 PDT)
- Jason Swails (Tue Oct 04 2011 - 16:18:35 PDT)
- Peter Eastman (Tue Oct 04 2011 - 15:49:52 PDT)
[AMBER] vmd-l: AMBER prmtop and traj to pqr - radii error
- Jesper Soerensen (Mon Oct 17 2011 - 16:58:53 PDT)
[AMBER] xleap problem
- David A. Case (Sat Oct 15 2011 - 08:50:31 PDT)
- souvik sur (Sat Oct 15 2011 - 04:16:34 PDT)
[AMBER] 回复： oct or cubic box?
- Thomas Cheatham (Sun Oct 09 2011 - 17:55:36 PDT)
- li li (Sun Oct 09 2011 - 17:03:54 PDT)
Gromacs Make Index in AMBER
- Jason Swails (Sat Oct 08 2011 - 09:59:41 PDT)
- Yun Shi (Sat Oct 08 2011 - 08:58:27 PDT)
- Yao Yao (Fri Oct 07 2011 - 17:13:29 PDT)

Amber Archive Oct 2011 by subject