Amber Archive Jul 2012: by subject

[AMBER] "Error: unknown flag: -rismmpi"
- Daniel Sindhikara (Wed Jul 25 2012 - 19:10:25 PDT)
- Tyler Luchko (Wed Jul 25 2012 - 06:16:55 PDT)
- Daniel Sindhikara (Wed Jul 25 2012 - 00:07:09 PDT)
[AMBER] After autoimage, rms jump
- Daniel Roe (Tue Jul 31 2012 - 09:22:31 PDT)
- Daniel Roe (Tue Jul 31 2012 - 06:53:53 PDT)
- Catein Catherine (Tue Jul 31 2012 - 00:17:12 PDT)
[AMBER] all_prot_nucleic10.lib file in amber12
- FyD (Wed Jul 04 2012 - 01:16:10 PDT)
[AMBER] Amber 11: iwrap=1 separates two RNA chains
- Jason Swails (Tue Jul 17 2012 - 08:02:06 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Tue Jul 17 2012 - 07:30:44 PDT)
[AMBER] AMBER 12 benchmarks
- Hannes Loeffler (Wed Jul 11 2012 - 01:27:14 PDT)
- Hannes Loeffler (Wed Jul 11 2012 - 01:25:38 PDT)
- Jason Swails (Thu Jul 05 2012 - 10:02:42 PDT)
- Albert (Thu Jul 05 2012 - 09:56:00 PDT)
- Ross Walker (Thu Jul 05 2012 - 09:28:02 PDT)
- Ross Walker (Thu Jul 05 2012 - 09:23:14 PDT)
- Hannes Loeffler (Thu Jul 05 2012 - 08:56:20 PDT)
- Hannes Loeffler (Thu Jul 05 2012 - 08:49:38 PDT)
- Albert (Thu Jul 05 2012 - 06:54:23 PDT)
- Jan-Philip Gehrcke (Thu Jul 05 2012 - 06:06:09 PDT)
- Hannes Loeffler (Thu Jul 05 2012 - 05:54:37 PDT)
[AMBER] Amber Error
- David A Case (Mon Jul 23 2012 - 04:48:48 PDT)
- hclengineer niper (Mon Jul 23 2012 - 00:38:14 PDT)
- David A Case (Fri Jul 20 2012 - 05:37:03 PDT)
- hclengineer niper (Fri Jul 20 2012 - 04:26:37 PDT)
[AMBER] AMBER GPU Bench mark procedure
- Ross Walker (Mon Jul 16 2012 - 09:30:05 PDT)
- Ravi Teja (Mon Jul 16 2012 - 04:41:52 PDT)
[AMBER] Amber10 and AmberTools12 compatibility
- Jason Swails (Sat Jul 14 2012 - 15:08:26 PDT)
- vaibhav dixit (Sat Jul 14 2012 - 08:17:45 PDT)
- David Case (Sat Jul 14 2012 - 05:31:15 PDT)
- vaibhav dixit (Fri Jul 13 2012 - 22:32:23 PDT)
[AMBER] AMBER11_CUDA issue with binary restart
- Ross Walker (Fri Jul 13 2012 - 06:53:08 PDT)
- HIMANSHU JOSHI (Thu Jul 12 2012 - 22:47:03 PDT)
[AMBER] AMBER12 - ninterface for double bilayer system
- Benjamin D Madej (Tue Jul 24 2012 - 07:36:51 PDT)
- Albert (Tue Jul 17 2012 - 22:52:45 PDT)
- Benjamin Madej (Tue Jul 17 2012 - 16:30:57 PDT)
- Albert (Mon Jul 16 2012 - 22:09:37 PDT)
- Benjamin Madej (Mon Jul 16 2012 - 16:26:32 PDT)
- Ross Walker (Mon Jul 16 2012 - 10:58:33 PDT)
- James Murdock (Mon Jul 16 2012 - 03:30:52 PDT)
[AMBER] Amber12 issue with SMD protocol
- Jason Swails (Thu Jul 26 2012 - 12:02:41 PDT)
- Niel Henriksen (Thu Jul 26 2012 - 09:14:24 PDT)
- David Case (Thu Jul 26 2012 - 09:02:30 PDT)
- Jan-Philip Gehrcke (Thu Jul 26 2012 - 06:14:08 PDT)
- Jason Swails (Thu Jul 26 2012 - 05:12:09 PDT)
- Jan-Philip Gehrcke (Thu Jul 26 2012 - 03:18:33 PDT)
- Agostino Bruno (Thu Jul 26 2012 - 03:05:25 PDT)
[AMBER] Amber12 qm_ewald
- Brian Radak (Fri Jul 13 2012 - 09:17:32 PDT)
- DJH71.pitt.edu (Fri Jul 13 2012 - 09:01:39 PDT)
[AMBER] Amber: mm_pbsa.pl
- Ray Luo, Ph.D. (Tue Jul 10 2012 - 08:05:20 PDT)
- rajeevy.iitk.ac.in (Mon Jul 09 2012 - 21:40:00 PDT)
- Qin Cai (Mon Jul 09 2012 - 17:40:45 PDT)
- Ray Luo (Mon Jul 09 2012 - 16:09:14 PDT)
- Jason Swails (Mon Jul 09 2012 - 08:43:40 PDT)
- rajeevy.iitk.ac.in (Mon Jul 09 2012 - 05:25:45 PDT)
- Jason Swails (Wed Jul 04 2012 - 12:41:53 PDT)
- rajeevy.iitk.ac.in (Wed Jul 04 2012 - 07:54:10 PDT)
- case (Wed Jul 04 2012 - 05:54:58 PDT)
- rajeevy.iitk.ac.in (Tue Jul 03 2012 - 23:24:42 PDT)
- Jason Swails (Tue Jul 03 2012 - 07:36:21 PDT)
- rajeevy.iitk.ac.in (Tue Jul 03 2012 - 07:03:00 PDT)
- Jason Swails (Mon Jul 02 2012 - 07:41:56 PDT)
- rajeevy.iitk.ac.in (Mon Jul 02 2012 - 07:36:42 PDT)
- Ray Luo, Ph.D. (Sun Jul 01 2012 - 07:41:58 PDT)
- rajeevy.iitk.ac.in (Sun Jul 01 2012 - 00:10:01 PDT)
[AMBER] ambertool12 installation in Cygwin
- Jason Swails (Sun Jul 15 2012 - 15:32:31 PDT)
- case (Sun Jul 15 2012 - 06:04:43 PDT)
- 钟舜 (Sat Jul 14 2012 - 19:22:33 PDT)
[AMBER] aMD issues: sander vs. pmemd vs. pmemd.cuda
- Romelia Salomon (Thu Jul 26 2012 - 17:39:02 PDT)
- Romelia Salomon (Thu Jul 26 2012 - 17:02:24 PDT)
- Niel Henriksen (Thu Jul 26 2012 - 13:24:36 PDT)
[AMBER] amd.log file
- Milo Westler (Mon Jul 09 2012 - 17:32:31 PDT)
- Nadeem A. Vellore (Mon Jul 09 2012 - 14:03:26 PDT)
- Milo Westler (Mon Jul 09 2012 - 12:48:06 PDT)
[AMBER] Any AMBER's reference article on modeling transmembrane proteins?
- Catein Catherine (Sat Jul 21 2012 - 09:20:51 PDT)
[AMBER] Any parameters can be used to model a transmembrane protein?
- Benjamin D Madej (Tue Jul 24 2012 - 08:02:45 PDT)
- Catein Catherine (Thu Jul 19 2012 - 06:24:09 PDT)
[AMBER] Aqueous Ionic Grouping Problems
- David A. Case (Tue Jul 10 2012 - 15:01:04 PDT)
- Eckler, Logan, H (Tue Jul 10 2012 - 14:23:59 PDT)
[AMBER] atoms on phosphonic acid groups collapse during minimization
- Jason Swails (Mon Jul 30 2012 - 15:25:15 PDT)
- Maria Minakova (Mon Jul 30 2012 - 14:16:03 PDT)
- Dr. Vitaly V. G. Chaban (Thu Jul 12 2012 - 17:26:28 PDT)
- Bill Ross (Thu Jul 12 2012 - 17:24:47 PDT)
- Bill Ross (Thu Jul 12 2012 - 17:15:40 PDT)
- Maria Minakova (Thu Jul 12 2012 - 16:30:03 PDT)
- Bill Ross (Thu Jul 12 2012 - 16:20:21 PDT)
- Dr. Vitaly V. G. Chaban (Thu Jul 12 2012 - 16:05:42 PDT)
- Maria Minakova (Thu Jul 12 2012 - 15:23:28 PDT)
[AMBER] Bending force constant in kcal/mol/rad2 from bending frequency(cm-1)
- arup pathak (Wed Jul 25 2012 - 04:56:19 PDT)
[AMBER] benzene-sulfonate (atom type for Sulfur)
- Jio M (Sat Jul 14 2012 - 03:30:51 PDT)
- FyD (Sat Jul 14 2012 - 03:11:33 PDT)
- Jio M (Sat Jul 14 2012 - 02:25:28 PDT)
- FyD (Sat Jul 14 2012 - 02:15:46 PDT)
- Jio M (Fri Jul 13 2012 - 23:31:53 PDT)
- FyD (Fri Jul 13 2012 - 09:01:43 PDT)
- Jio M (Fri Jul 13 2012 - 05:37:56 PDT)
[AMBER] Bfactor for binding site waters
- Senthil Natesan (Thu Jul 26 2012 - 07:40:05 PDT)
- Thomas Cheatham III (Wed Jul 25 2012 - 14:36:58 PDT)
- Senthil Natesan (Wed Jul 25 2012 - 09:26:36 PDT)
[AMBER] Bug in AmberTools12 cpptraj? 'trajout onlyframes' doesn't work
- Marc van der Kamp (Tue Jul 31 2012 - 09:24:32 PDT)
- Jason Swails (Tue Jul 31 2012 - 09:16:45 PDT)
- Daniel Roe (Tue Jul 31 2012 - 08:52:42 PDT)
- Marc van der Kamp (Tue Jul 31 2012 - 08:38:18 PDT)
- Daniel Roe (Tue Jul 31 2012 - 07:18:37 PDT)
- Marc van der Kamp (Tue Jul 31 2012 - 07:08:49 PDT)
- Daniel Roe (Tue Jul 31 2012 - 06:49:50 PDT)
- Marc van der Kamp (Tue Jul 31 2012 - 06:46:12 PDT)
- Marc van der Kamp (Tue Jul 31 2012 - 06:24:01 PDT)
[AMBER] Bug in PM6: Halogens (?)
- DJH71.pitt.edu (Tue Jul 31 2012 - 10:15:40 PDT)
- Andreas Goetz (Fri Jul 27 2012 - 20:29:32 PDT)
- Qiantao Wang (Fri Jul 27 2012 - 10:31:38 PDT)
- DJH71.pitt.edu (Wed Jul 25 2012 - 12:31:09 PDT)
[AMBER] Bug? tleap of AmberTools12 cannot deal with branch carbohydrates contain sialic acid
- Tomoshi Kameda (Fri Jul 13 2012 - 23:54:44 PDT)
- Jodi Ann Hadden (Thu Jul 12 2012 - 05:19:07 PDT)
- Tomoshi Kameda (Wed Jul 11 2012 - 23:58:49 PDT)
- Tomoshi Kameda (Wed Jul 11 2012 - 16:21:46 PDT)
[AMBER] Bugfix 16: New cpptraj action, AutoImage
- Daniel Roe (Thu Jul 26 2012 - 07:36:42 PDT)
[AMBER] can Amber run in Anton?
- Dr. Vitaly V. G. Chaban (Fri Jul 13 2012 - 19:02:53 PDT)
- case (Fri Jul 13 2012 - 17:59:08 PDT)
- Albert (Fri Jul 13 2012 - 11:01:10 PDT)
[AMBER] compilation aborted for pme_setup.f90 (code 1)
- David A Case (Fri Jul 27 2012 - 08:34:23 PDT)
- Jorgen Simonsen (Thu Jul 26 2012 - 20:11:17 PDT)
[AMBER] compiling amber on Ranger/Teragrid
- Ross Walker (Mon Jul 30 2012 - 14:03:56 PDT)
- Pawel (Mon Jul 30 2012 - 13:36:09 PDT)
[AMBER] Compiling Amber12 on the Cray XK6 (Jaguar)
- Gustavo Seabra (Mon Jul 09 2012 - 13:03:12 PDT)
- Jason Swails (Mon Jul 09 2012 - 12:52:43 PDT)
- Gustavo Seabra (Mon Jul 09 2012 - 12:43:37 PDT)
[AMBER] complex of protein dimer and two ligands simulated MMPBSA.py error
- kamlesh sahu (Mon Jul 23 2012 - 17:58:20 PDT)
- Jason Swails (Mon Jul 23 2012 - 04:51:22 PDT)
- kamlesh sahu (Mon Jul 23 2012 - 00:51:47 PDT)
- kamlesh sahu (Tue Jul 03 2012 - 00:48:34 PDT)
- Jason Swails (Mon Jul 02 2012 - 06:43:54 PDT)
- kamlesh sahu (Mon Jul 02 2012 - 01:19:28 PDT)
[AMBER] Constraint simulations
- Jason Swails (Wed Jul 04 2012 - 09:21:11 PDT)
- Rajendra Sharma (Wed Jul 04 2012 - 00:21:24 PDT)
[AMBER] Continuation of thread regarding problems with Zinc parameterization with MCPB (Apparently solved)
- Fabrício Bracht (Mon Jul 16 2012 - 13:24:48 PDT)
[AMBER] cpptraj-secstruct N-terminal proline
- colvin (Tue Jul 10 2012 - 18:36:44 PDT)
- David A. Case (Tue Jul 10 2012 - 14:55:22 PDT)
- Daniel Roe (Tue Jul 10 2012 - 07:15:39 PDT)
- colvin (Tue Jul 10 2012 - 01:06:16 PDT)
[AMBER] Creating AMBER files from implicit solvent CHARMM19 force field
- David A. Case (Tue Jul 31 2012 - 14:40:19 PDT)
- Anna Tarakanova (Tue Jul 31 2012 - 08:52:41 PDT)
[AMBER] CUDA MPI failed in Ubuntu
- Albert (Thu Jul 05 2012 - 08:38:26 PDT)
[AMBER] Defining bonds between calcium and protein
- Zalikha Ibrahim (Tue Jul 17 2012 - 19:08:17 PDT)
- David A Case (Tue Jul 17 2012 - 05:02:22 PDT)
- Zalikha Ibrahim (Tue Jul 17 2012 - 01:02:16 PDT)
[AMBER] Difference between "jar=1" and "ncsu_smd" when running SMD simulations
- 崔颖璐 (Thu Jul 19 2012 - 00:21:15 PDT)
- Jason Swails (Wed Jul 18 2012 - 19:39:29 PDT)
- Jason Swails (Wed Jul 18 2012 - 19:37:58 PDT)
- 崔颖璐 (Wed Jul 18 2012 - 19:11:55 PDT)
[AMBER] different RMSF between CPU and GPU
- Ross Walker (Sat Jul 07 2012 - 21:21:57 PDT)
- Massimiliano Porrini (Sat Jul 07 2012 - 11:57:19 PDT)
- Ross Walker (Fri Jul 06 2012 - 14:51:14 PDT)
- Massimiliano Porrini (Fri Jul 06 2012 - 12:37:17 PDT)
[AMBER] Difficult Problem: iwrap=1 and ptraj for a protein complex.
- Daniel Roe (Mon Jul 23 2012 - 09:08:34 PDT)
- Catein Catherine (Sun Jul 22 2012 - 19:36:59 PDT)
[AMBER] Difficulty using ptraj to generate pdb frames from .mdcrd trajectory
- Daniel Roe (Fri Jul 13 2012 - 06:59:46 PDT)
- Thomas Cheatham (Thu Jul 12 2012 - 12:34:37 PDT)
- Jason Swails (Thu Jul 12 2012 - 12:27:19 PDT)
- Gordon S Freeman (Tue Jul 10 2012 - 15:15:14 PDT)
- Daniel Roe (Tue Jul 10 2012 - 07:24:40 PDT)
- Gordon S Freeman (Thu Jul 05 2012 - 12:23:42 PDT)
[AMBER] Dihedral parameters assignment by tleap
- Jason Swails (Mon Jul 16 2012 - 13:59:02 PDT)
- Yun Shi (Mon Jul 16 2012 - 13:03:21 PDT)
- David A Case (Mon Jul 16 2012 - 11:31:48 PDT)
- Yun Shi (Mon Jul 16 2012 - 09:59:48 PDT)
[AMBER] Diverging sander.MPI results according to core allocation
- Bashford, Donald (Thu Jul 26 2012 - 15:25:11 PDT)
[AMBER] entropy calculations
- Jason Swails (Fri Jul 06 2012 - 11:05:09 PDT)
- bmartini (Fri Jul 06 2012 - 09:48:39 PDT)
- Jason Swails (Thu Jul 05 2012 - 12:29:24 PDT)
- bmartini (Thu Jul 05 2012 - 12:05:26 PDT)
- Jason Swails (Thu Jul 05 2012 - 10:05:16 PDT)
- bmartini (Thu Jul 05 2012 - 09:50:49 PDT)
[AMBER] Error in post-processing REMD trajectory
- Jason Swails (Mon Jul 02 2012 - 08:52:49 PDT)
- Dilraj LAMA (Mon Jul 02 2012 - 05:13:00 PDT)
[AMBER] Error in ptraj after using iwrap=1, even using center and image origin
- Marc van der Kamp (Wed Jul 18 2012 - 08:36:10 PDT)
- Catein Catherine (Wed Jul 18 2012 - 08:14:32 PDT)
- Daniel Roe (Wed Jul 18 2012 - 07:02:33 PDT)
- Catein Catherine (Tue Jul 17 2012 - 20:18:42 PDT)
[AMBER] Error in ptraj analysis after using iwrap=1
- Jason Swails (Fri Jul 27 2012 - 10:35:53 PDT)
- Catein Catherine (Fri Jul 27 2012 - 10:10:30 PDT)
- Daniel Roe (Thu Jul 26 2012 - 19:02:50 PDT)
- Catein Catherine (Mon Jul 16 2012 - 06:25:55 PDT)
[AMBER] Error in writing of coordinate file after simulation
- Daniel Roe (Fri Jul 13 2012 - 11:08:21 PDT)
- Ashutosh Shandilya (Thu Jul 12 2012 - 11:17:08 PDT)
[AMBER] Error on REMD trajectory analysis
- Dilraj LAMA (Mon Jul 02 2012 - 05:11:17 PDT)
[AMBER] error to run pmemd.MPI on Opteron CPU
- Yubo Fan (Thu Jul 05 2012 - 08:05:09 PDT)
- Jason Swails (Tue Jul 03 2012 - 05:02:16 PDT)
- David A Case (Tue Jul 03 2012 - 04:54:59 PDT)
- Yubo Fan (Mon Jul 02 2012 - 22:52:30 PDT)
[AMBER] error with ambertools12 and amber10 installation
- David A. Case (Wed Jul 25 2012 - 04:34:50 PDT)
- vaibhav dixit (Wed Jul 25 2012 - 02:24:11 PDT)
- David A Case (Fri Jul 20 2012 - 05:29:29 PDT)
- vaibhav dixit (Fri Jul 20 2012 - 04:13:33 PDT)
- David A Case (Thu Jul 19 2012 - 08:33:00 PDT)
- vaibhav dixit (Thu Jul 19 2012 - 04:39:06 PDT)
[AMBER] Error: Error in box coord line of trajectory (AMBER 12.0) - MM/PBSA per residue decomposition
- Ashley Ferraro (Wed Jul 11 2012 - 17:25:56 PDT)
[AMBER] Error: periodicity of dihedral is zero
- Francesco Pietra (Wed Jul 25 2012 - 22:58:19 PDT)
- Jason Swails (Wed Jul 25 2012 - 12:06:24 PDT)
- Lorenzo Gontrani (Wed Jul 25 2012 - 09:56:38 PDT)
- David A. Case (Tue Jul 24 2012 - 14:43:41 PDT)
- Francesco Pietra (Tue Jul 24 2012 - 08:44:22 PDT)
- Jason Swails (Tue Jul 24 2012 - 05:16:20 PDT)
- Francesco Pietra (Tue Jul 24 2012 - 01:26:01 PDT)
[AMBER] failure about pmemd.cuda
- case (Sun Jul 01 2012 - 05:21:38 PDT)
- caobb0214 (Sat Jun 30 2012 - 20:27:10 PDT)
[AMBER] ff12SB
- Carlos Simmerling (Wed Jul 04 2012 - 12:09:07 PDT)
- manikanthan bhavaraju (Wed Jul 04 2012 - 12:04:44 PDT)
[AMBER] Force field for bend DNA
- sudipta (Thu Jul 05 2012 - 17:07:00 PDT)
[AMBER] frcmod file to include Urey Bradley angle terms
- Jason Swails (Thu Jul 12 2012 - 12:03:29 PDT)
- Scott Pendley (Thu Jul 12 2012 - 11:44:49 PDT)
[AMBER] Fwd: AmberTools 12 pbsa: missing newline character in OpenDX output (patched gen_dx_file.F90 attached)
- Ray Luo, Ph.D. (Tue Jul 10 2012 - 08:15:09 PDT)
- Jan-Philip Gehrcke (Tue Jul 10 2012 - 00:20:21 PDT)
- Ray Luo (Mon Jul 09 2012 - 13:19:01 PDT)
- Jason Swails (Mon Jul 09 2012 - 13:04:10 PDT)
- Jan-Philip Gehrcke (Mon Jul 09 2012 - 11:57:21 PDT)
[AMBER] Fwd: complex of protein dimer and two ligands simulated MMPBSA.py error
- Jason Swails (Mon Jul 23 2012 - 20:39:03 PDT)
- kamlesh sahu (Mon Jul 23 2012 - 19:42:44 PDT)
- Jason Swails (Mon Jul 23 2012 - 19:27:49 PDT)
- kamlesh sahu (Mon Jul 23 2012 - 18:41:17 PDT)
[AMBER] Fwd: GAFF c2-c data lacking?
- Francesco Pietra (Sun Jul 29 2012 - 08:02:49 PDT)
[AMBER] Fwd: pbsa: unit of the electrostatic potential values written to DX file
- Ray Luo, Ph.D. (Tue Jul 24 2012 - 11:09:44 PDT)
- Jan-Philip Gehrcke (Tue Jul 24 2012 - 01:55:15 PDT)
- Ray Luo, Ph.D. (Mon Jul 23 2012 - 09:59:21 PDT)
[AMBER] Fwd: Protein aggregation energy calculation
- Jason Swails (Sat Jul 07 2012 - 18:50:25 PDT)
- Binwu Zhao (Sat Jul 07 2012 - 14:54:32 PDT)
[AMBER] GAFF c2-c data lacking?
- Francesco Pietra (Sun Jul 29 2012 - 07:31:26 PDT)
[AMBER] GBIS and SASA
- Aron Broom (Thu Jul 19 2012 - 21:31:21 PDT)
- case (Thu Jul 19 2012 - 18:43:41 PDT)
- Aron Broom (Thu Jul 19 2012 - 15:03:29 PDT)
[AMBER] Global Minimum?
- Dr. Vitaly V. G. Chaban (Sun Jul 15 2012 - 21:44:03 PDT)
- jit mukherjee (Sun Jul 15 2012 - 21:21:51 PDT)
- Dr. Vitaly V. G. Chaban (Sun Jul 15 2012 - 10:44:49 PDT)
- jit mukherjee (Sun Jul 15 2012 - 09:45:13 PDT)
- jit mukherjee (Sun Jul 15 2012 - 08:47:48 PDT)
- Dr. Vitaly V. G. Chaban (Sun Jul 15 2012 - 08:44:14 PDT)
- jit mukherjee (Sun Jul 15 2012 - 08:38:36 PDT)
- Carlos Simmerling (Sun Jul 15 2012 - 06:03:37 PDT)
- steinbrt.rci.rutgers.edu (Sun Jul 15 2012 - 05:38:00 PDT)
- jit mukherjee (Sun Jul 15 2012 - 02:56:29 PDT)
[AMBER] GPU bugs for Amber 12?
- Albert (Mon Jul 16 2012 - 11:53:44 PDT)
- Albert (Mon Jul 16 2012 - 11:17:17 PDT)
- Scott Le Grand (Mon Jul 16 2012 - 10:56:35 PDT)
- Ross Walker (Mon Jul 16 2012 - 10:54:48 PDT)
- Albert (Mon Jul 16 2012 - 09:42:42 PDT)
[AMBER] Help with amber12 at ORNL
- David A Case (Wed Jul 18 2012 - 13:08:58 PDT)
- Foertter, Fernanda S. (Wed Jul 18 2012 - 10:37:24 PDT)
- David A Case (Wed Jul 18 2012 - 10:02:38 PDT)
- Foertter, Fernanda S. (Wed Jul 18 2012 - 08:31:19 PDT)
[AMBER] How to Calculate SASA with Amber?
- Daniel Roe (Tue Jul 24 2012 - 15:47:54 PDT)
- Daniel Roe (Tue Jul 24 2012 - 15:46:47 PDT)
- Shafinaz Chowdhury (Tue Jul 24 2012 - 13:40:56 PDT)
[AMBER] How to call up ptraj in supercomputer facilities? should I use mpi?
- Catein Catherine (Sun Jul 01 2012 - 23:41:59 PDT)
- Jason Swails (Sun Jul 01 2012 - 08:23:24 PDT)
- Ben Roberts (Sat Jun 30 2012 - 22:43:03 PDT)
[AMBER] How to combine mdcrd and netcdf files to one single netcdf file?
- case (Thu Jul 05 2012 - 16:26:47 PDT)
- Catein Catherine (Thu Jul 05 2012 - 15:47:03 PDT)
[AMBER] How to convert AMBER atom type to CYANA
- Hector A. Baldoni (Thu Jul 19 2012 - 07:52:53 PDT)
- David A Case (Wed Jul 18 2012 - 09:38:50 PDT)
- Rahul Banerjee (Wed Jul 18 2012 - 07:23:33 PDT)
- case (Tue Jul 17 2012 - 17:38:18 PDT)
- Rahul Banerjee (Tue Jul 17 2012 - 15:18:19 PDT)
[AMBER] How to install bugfix.16 specifically?
- Catein Catherine (Mon Jul 30 2012 - 07:16:47 PDT)
- Jason Swails (Mon Jul 30 2012 - 06:14:31 PDT)
- Catein Catherine (Mon Jul 30 2012 - 04:31:24 PDT)
- Jason Swails (Mon Jul 30 2012 - 03:32:32 PDT)
- Catein Catherine (Sun Jul 29 2012 - 23:37:53 PDT)
- Catein Catherine (Sun Jul 29 2012 - 21:29:10 PDT)
[AMBER] how to make statistics of solvent molecules?
- Albert (Fri Jul 20 2012 - 22:07:52 PDT)
- Daniel Roe (Fri Jul 20 2012 - 09:33:06 PDT)
- Albert (Fri Jul 20 2012 - 00:52:31 PDT)
[AMBER] How to read netcdf files to ptraj?
- Daniel Roe (Fri Jul 13 2012 - 07:09:56 PDT)
- Catein Catherine (Thu Jul 12 2012 - 22:39:43 PDT)
- Daniel Roe (Thu Jul 12 2012 - 22:05:24 PDT)
- Catein Catherine (Thu Jul 12 2012 - 21:54:57 PDT)
[AMBER] http://archive.ambermd.org/201206/0014.html
- Osman, Roman (Fri Jul 13 2012 - 09:42:35 PDT)
[AMBER] I can prepare Na+ parameter files under LEAPRC.CONSTPH.
- kurisaki (Sun Jul 08 2012 - 19:08:38 PDT)
- Jason Swails (Sun Jul 08 2012 - 18:58:22 PDT)
- kurisaki (Sun Jul 08 2012 - 18:07:38 PDT)
- Jason Swails (Sun Jul 08 2012 - 09:09:02 PDT)
- kurisaki (Sun Jul 08 2012 - 01:22:39 PDT)
[AMBER] iAPBS
- David A Case (Fri Jul 27 2012 - 08:37:59 PDT)
- Robert Konecny (Fri Jul 27 2012 - 08:19:49 PDT)
- huseyin istanbullu (Fri Jul 27 2012 - 05:53:53 PDT)
[AMBER] Installation Amber 12 using cygwin on windows 7 64 bit
- Daniel Roe (Tue Jul 10 2012 - 08:44:43 PDT)
- Mohammad Jane Alam (Tue Jul 10 2012 - 07:54:36 PDT)
[AMBER] Installation of Amber in Cygwin
- Daniel Roe (Thu Jul 19 2012 - 17:55:45 PDT)
- 钟舜 (Thu Jul 19 2012 - 17:48:40 PDT)
- Jason Swails (Thu Jul 19 2012 - 05:36:20 PDT)
- Jason Swails (Wed Jul 18 2012 - 19:42:02 PDT)
- 钟舜 (Wed Jul 18 2012 - 19:38:46 PDT)
- Daniel Roe (Wed Jul 18 2012 - 12:37:40 PDT)
- Jason Swails (Wed Jul 18 2012 - 12:35:04 PDT)
[AMBER] installation of amber10
- Jorgen Simonsen (Thu Jul 26 2012 - 18:34:46 PDT)
- Jason Swails (Wed Jul 25 2012 - 20:27:40 PDT)
- Jorgen Simonsen (Wed Jul 25 2012 - 20:00:58 PDT)
- Jason Swails (Wed Jul 25 2012 - 12:09:10 PDT)
- Jorgen Simonsen (Wed Jul 25 2012 - 10:35:41 PDT)
- Jorgen Simonsen (Wed Jul 25 2012 - 10:15:46 PDT)
- Daniel Roe (Wed Jul 25 2012 - 09:30:19 PDT)
- Jorgen Simonsen (Wed Jul 25 2012 - 09:18:18 PDT)
[AMBER] installing Amber12
- Jason Swails (Thu Jul 12 2012 - 05:03:30 PDT)
- Jason Swails (Wed Jul 11 2012 - 05:07:42 PDT)
- huseyin istanbullu (Wed Jul 11 2012 - 02:17:00 PDT)
- huseyin istanbullu (Wed Jul 11 2012 - 01:57:42 PDT)
[AMBER] installing on ubuntu 12.04 LTS 64 bit
- Catein Catherine (Mon Jul 16 2012 - 06:19:38 PDT)
- Jason Swails (Mon Jul 16 2012 - 04:47:43 PDT)
- huseyin istanbullu (Mon Jul 16 2012 - 01:31:53 PDT)
[AMBER] Interaction energy between residue pairs
- Jason Swails (Thu Jul 19 2012 - 20:06:04 PDT)
- Fabrício Bracht (Thu Jul 19 2012 - 19:58:46 PDT)
- Jason Swails (Thu Jul 19 2012 - 19:37:43 PDT)
- Carlos Simmerling (Thu Jul 19 2012 - 19:02:14 PDT)
- Jason Swails (Thu Jul 19 2012 - 18:57:11 PDT)
- Carlos Simmerling (Thu Jul 19 2012 - 16:25:12 PDT)
- Irene Newhouse (Thu Jul 19 2012 - 15:21:06 PDT)
- Fabrício Bracht (Thu Jul 19 2012 - 14:47:25 PDT)
[AMBER] internal dielectric constant in MMPBSA
- Qiong Zhang (Wed Jul 25 2012 - 09:58:22 PDT)
- Ray Luo, Ph.D. (Wed Jul 25 2012 - 09:44:35 PDT)
- Qiong Zhang (Wed Jul 25 2012 - 07:36:40 PDT)
- Jason Swails (Wed Jul 25 2012 - 07:11:16 PDT)
- Qiong Zhang (Wed Jul 25 2012 - 06:15:21 PDT)
- Qiong Zhang (Tue Jul 24 2012 - 18:12:11 PDT)
[AMBER] Ion clumping in large protein-RNA systems
- Kamali Sripathi (Fri Jul 06 2012 - 07:06:35 PDT)
- Kevin Hauser (Thu Jul 05 2012 - 08:16:06 PDT)
- Kamali Sripathi (Thu Jul 05 2012 - 07:41:49 PDT)
[AMBER] Iwrap=1 and imaging revisited
- Daniel Roe (Mon Jul 23 2012 - 08:16:21 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Fri Jul 20 2012 - 08:05:01 PDT)
[AMBER] KeyError: 'Total' at parsing MMPBSA results
- Jason Swails (Mon Jul 23 2012 - 09:17:02 PDT)
- Miguel Ortiz Lombardía (Mon Jul 23 2012 - 09:08:15 PDT)
- Jason Swails (Mon Jul 23 2012 - 08:43:07 PDT)
- Miguel Ortiz Lombardía (Mon Jul 23 2012 - 05:56:25 PDT)
- Jason Swails (Mon Jul 23 2012 - 04:41:41 PDT)
- Miguel Ortiz Lombardía (Mon Jul 23 2012 - 01:01:45 PDT)
[AMBER] Langevin Dynamics
- Qian Wang (Tue Jul 17 2012 - 08:05:13 PDT)
- David A Case (Tue Jul 17 2012 - 04:50:18 PDT)
- Jason Swails (Mon Jul 16 2012 - 18:29:10 PDT)
- Qian Wang (Mon Jul 16 2012 - 15:55:53 PDT)
[AMBER] LEaP problems with non-standard residue
- Francesco Pietra (Fri Jul 20 2012 - 06:57:25 PDT)
[AMBER] lipid params
- Jio M (Tue Jul 17 2012 - 03:14:35 PDT)
- Benjamin Madej (Mon Jul 16 2012 - 14:54:29 PDT)
- Jio M (Sat Jul 14 2012 - 00:57:58 PDT)
- Benjamin Madej (Fri Jul 13 2012 - 12:14:46 PDT)
- Jio M (Fri Jul 13 2012 - 07:00:56 PDT)
- Ross Walker (Fri Jul 13 2012 - 06:43:00 PDT)
- Jio M (Fri Jul 13 2012 - 02:42:39 PDT)
- Gould, Ian R (Fri Jul 13 2012 - 02:17:54 PDT)
- Jio M (Fri Jul 13 2012 - 02:10:01 PDT)
- Vlad Cojocaru (Fri Jul 13 2012 - 01:53:23 PDT)
- Jio M (Fri Jul 13 2012 - 01:35:31 PDT)
[AMBER] Looping over a trajectory
- Lee-Ping Wang (Wed Jul 04 2012 - 12:48:01 PDT)
[AMBER] Met92 not bound to Cu atom in TUTORIAL-A1(simple version)
- Mahendra B Thapa (Wed Jul 11 2012 - 13:50:55 PDT)
[AMBER] mm_pbsa (.pl) calculations for a complex composed of 11 chains and 6 ligand molecules
- Anselm Horn (Tue Jul 31 2012 - 04:46:36 PDT)
- Naeem Attari (Mon Jul 30 2012 - 04:58:31 PDT)
[AMBER] MMPBSA calculation problem
- 刘金峰 (Wed Jul 04 2012 - 22:17:46 PDT)
[AMBER] MMPBSA Entropies: N-mode and Quasi Harmonic calculations
- Jason Swails (Tue Jul 17 2012 - 05:58:46 PDT)
- George Tzotzos (Tue Jul 17 2012 - 04:38:16 PDT)
[AMBER] MMPBSA per-residue decomposition: how is the polar solvation contribution calculated?
- Jan-Philip Gehrcke (Thu Jul 26 2012 - 03:51:58 PDT)
- Ray Luo, Ph.D. (Wed Jul 25 2012 - 10:30:36 PDT)
- Jan-Philip Gehrcke (Wed Jul 25 2012 - 03:07:12 PDT)
[AMBER] MMPBSA results and huge SD
- Jason Swails (Mon Jul 09 2012 - 09:06:01 PDT)
- Massimiliano Porrini (Mon Jul 09 2012 - 06:35:51 PDT)
[AMBER] MMPBSA.py
- Bill Miller III (Tue Jul 17 2012 - 03:48:52 PDT)
- Delwar Hossain (Mon Jul 16 2012 - 19:55:46 PDT)
[AMBER] MMPBSA.py decomposition option
- Hannes Kopitz (Tue Jul 10 2012 - 20:45:05 PDT)
- Damodaran, Komath (Tue Jul 10 2012 - 09:06:31 PDT)
[AMBER] MMPBSA: dubious results
- Jason Swails (Fri Jul 13 2012 - 19:04:46 PDT)
- George Tzotzos (Fri Jul 13 2012 - 11:34:21 PDT)
- George Tzotzos (Mon Jul 09 2012 - 13:34:31 PDT)
- Damodaran, Komath (Mon Jul 09 2012 - 13:24:52 PDT)
- Jason Swails (Mon Jul 09 2012 - 13:03:13 PDT)
- George Tzotzos (Mon Jul 09 2012 - 10:37:04 PDT)
- Jason Swails (Mon Jul 09 2012 - 08:50:07 PDT)
- George Tzotzos (Mon Jul 09 2012 - 04:18:49 PDT)
[AMBER] mobility of protein from MD trajectories
- kamlesh sahu (Mon Jul 30 2012 - 19:42:32 PDT)
[AMBER] Molecular Surface from MMPBSA
- Ray Luo, Ph.D. (Thu Jul 26 2012 - 09:40:50 PDT)
- David A. Case (Thu Jul 26 2012 - 05:00:05 PDT)
- Damodaran, Komath (Wed Jul 25 2012 - 10:58:41 PDT)
[AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1
- Jason Swails (Wed Jul 11 2012 - 21:00:07 PDT)
- Fabrício Bracht (Wed Jul 11 2012 - 17:22:47 PDT)
- Jason Swails (Wed Jul 11 2012 - 12:54:40 PDT)
- Fabrício Bracht (Wed Jul 11 2012 - 12:44:39 PDT)
- Jason Swails (Wed Jul 11 2012 - 12:03:29 PDT)
- Fabrício Bracht (Wed Jul 11 2012 - 11:28:57 PDT)
- Jason Swails (Sun Jul 08 2012 - 10:46:53 PDT)
- Fabrício Bracht (Sat Jul 07 2012 - 23:41:35 PDT)
- Ben Roberts (Sat Jul 07 2012 - 02:28:30 PDT)
- Fabrício Bracht (Fri Jul 06 2012 - 10:56:20 PDT)
- Jason Swails (Thu Jul 05 2012 - 15:19:29 PDT)
- Ben Roberts (Thu Jul 05 2012 - 14:48:27 PDT)
- Fabrício Bracht (Thu Jul 05 2012 - 13:42:09 PDT)
- Ben Roberts (Wed Jul 04 2012 - 17:04:46 PDT)
- Fabrício Bracht (Wed Jul 04 2012 - 11:20:16 PDT)
[AMBER] no restart file from pmemd.cuda in Amber 11
- Seren Soner (Fri Jul 13 2012 - 07:03:53 PDT)
- Ross Walker (Fri Jul 13 2012 - 06:57:53 PDT)
- Seren Soner (Fri Jul 13 2012 - 06:44:02 PDT)
[AMBER] NPT equilibration error: ASSERTion 'e' failed in nonbond_list.F90 at line 849
- Dr. Vitaly V. G. Chaban (Mon Jul 30 2012 - 14:53:44 PDT)
- Dr. Vitaly V. G. Chaban (Mon Jul 30 2012 - 14:39:51 PDT)
- Maria Minakova (Mon Jul 30 2012 - 12:32:34 PDT)
[AMBER] npt stacked with CUDA running
- Albert (Fri Jul 13 2012 - 22:58:13 PDT)
- Albert (Fri Jul 13 2012 - 22:48:15 PDT)
- case (Fri Jul 13 2012 - 18:10:12 PDT)
- Albert (Fri Jul 13 2012 - 13:15:03 PDT)
[AMBER] parameters reading
- Jason Swails (Sun Jul 15 2012 - 17:02:51 PDT)
- Yun Shi (Sun Jul 15 2012 - 15:42:38 PDT)
[AMBER] Parmtop files for TI Softcore Potentials
- steinbrt.rci.rutgers.edu (Mon Jul 16 2012 - 23:48:49 PDT)
- Marek Maly (Mon Jul 16 2012 - 12:18:45 PDT)
- Kepa K. Burusco (Mon Jul 16 2012 - 11:30:24 PDT)
[AMBER] PB with inp=2 doesn't recognize ff10 atom types? (Amber Archive Mar 2012)
- Miguel Ortiz Lombardia (Fri Jul 13 2012 - 05:21:40 PDT)
[AMBER] pbsa: how to increase the sampling volume (grid dimensions)?
- Jan-Philip Gehrcke (Tue Jul 24 2012 - 10:13:00 PDT)
[AMBER] pbsa: unit of the electrostatic potential values written to DX file
- Jan-Philip Gehrcke (Mon Jul 23 2012 - 08:43:20 PDT)
[AMBER] pi-pi stacking interaction and hydrogen bonding with amber
- Jason Swails (Thu Jul 19 2012 - 20:09:42 PDT)
- jit mukherjee (Wed Jul 18 2012 - 22:14:02 PDT)
- Jiri Sponer (Wed Jul 18 2012 - 02:53:32 PDT)
- Alessandro Contini (Wed Jul 18 2012 - 01:00:52 PDT)
- steinbrt.rci.rutgers.edu (Wed Jul 18 2012 - 00:47:54 PDT)
- jit mukherjee (Tue Jul 17 2012 - 21:32:34 PDT)
- Jiri Sponer (Tue Jul 17 2012 - 07:49:13 PDT)
- Jiri Sponer (Tue Jul 17 2012 - 07:44:38 PDT)
- jit mukherjee (Tue Jul 17 2012 - 07:43:27 PDT)
- Gustavo Seabra (Tue Jul 17 2012 - 07:38:49 PDT)
- Jiri Sponer (Tue Jul 17 2012 - 07:33:05 PDT)
- Gustavo Seabra (Tue Jul 17 2012 - 07:08:15 PDT)
- jit mukherjee (Tue Jul 17 2012 - 01:42:37 PDT)
- Bill Ross (Mon Jul 16 2012 - 22:17:37 PDT)
- jit mukherjee (Mon Jul 16 2012 - 21:25:07 PDT)
- jit mukherjee (Mon Jul 16 2012 - 12:13:21 PDT)
- Dean Cuebas (Mon Jul 16 2012 - 11:23:18 PDT)
- Dr. Vitaly V. G. Chaban (Mon Jul 16 2012 - 11:21:48 PDT)
- jit mukherjee (Mon Jul 16 2012 - 10:59:22 PDT)
- Jiri Sponer (Mon Jul 16 2012 - 09:47:58 PDT)
- jit mukherjee (Mon Jul 16 2012 - 09:37:31 PDT)
[AMBER] PMF of a salt bridge.
- Kevin Hauser (Sun Jul 22 2012 - 16:28:38 PDT)
- Aron Broom (Sun Jul 22 2012 - 13:14:38 PDT)
- Rajendra Sharma (Sun Jul 22 2012 - 12:03:08 PDT)
[AMBER] Polarizable vs Fixed Charge FF
- Nikolay Igorovich Rodionov (Fri Jul 06 2012 - 07:11:28 PDT)
[AMBER] Polarization
- David A Case (Tue Jul 17 2012 - 04:52:46 PDT)
- Nikolay Igorovich Rodionov (Mon Jul 16 2012 - 17:10:09 PDT)
[AMBER] problem in converting rst-file to pdb using cpptraj
- Daniel Roe (Mon Jul 30 2012 - 10:43:04 PDT)
- Mahendra B Thapa (Mon Jul 30 2012 - 09:32:24 PDT)
[AMBER] problem in installing sander.MPI
- David A Case (Mon Jul 23 2012 - 04:51:25 PDT)
- Miguel Ortiz Lombardía (Mon Jul 23 2012 - 02:28:08 PDT)
- devawati dutta (Mon Jul 23 2012 - 02:12:50 PDT)
[AMBER] problem in minimization
- jit mukherjee (Mon Jul 16 2012 - 09:35:00 PDT)
- steinbrt.rci.rutgers.edu (Mon Jul 16 2012 - 09:23:13 PDT)
- Jason Swails (Mon Jul 16 2012 - 09:16:07 PDT)
- Dr. Vitaly V. G. Chaban (Mon Jul 16 2012 - 08:30:34 PDT)
- jit mukherjee (Mon Jul 16 2012 - 08:23:21 PDT)
[AMBER] problem in parallel testing
- David A. Case (Tue Jul 24 2012 - 05:41:33 PDT)
- steinbrt.rci.rutgers.edu (Tue Jul 24 2012 - 03:57:33 PDT)
- devawati dutta (Tue Jul 24 2012 - 03:51:30 PDT)
[AMBER] problem to attach n terminal residue to protein
- Sanjib Paul (Mon Jul 16 2012 - 03:38:52 PDT)
- Sanjib Paul (Mon Jul 16 2012 - 03:36:38 PDT)
- case (Sun Jul 15 2012 - 06:08:45 PDT)
- Sanjib Paul (Sun Jul 15 2012 - 00:21:38 PDT)
[AMBER] Problem while running MMPBSA
- Jan-Philip Gehrcke (Tue Jul 10 2012 - 07:16:35 PDT)
- qiqi (Tue Jul 10 2012 - 06:26:54 PDT)
- Ray Luo (Mon Jul 09 2012 - 15:58:16 PDT)
- qiqi (Mon Jul 09 2012 - 14:05:00 PDT)
- Jason Swails (Thu Jul 05 2012 - 08:28:50 PDT)
- qiqi (Thu Jul 05 2012 - 07:32:58 PDT)
- Jason Swails (Tue Jul 03 2012 - 20:31:01 PDT)
- qiqi (Mon Jul 02 2012 - 12:37:15 PDT)
- Jason Swails (Sun Jul 01 2012 - 19:18:11 PDT)
[AMBER] Problem with MMPBSA using a solvated structure topology
- Jason Swails (Tue Jul 17 2012 - 06:03:15 PDT)
- Osman, Roman (Tue Jul 17 2012 - 05:53:03 PDT)
- Jason Swails (Mon Jul 16 2012 - 19:21:18 PDT)
- Osman, Roman (Mon Jul 16 2012 - 18:57:12 PDT)
[AMBER] Problem with MMPBSA.py.MPI
- sudipta (Mon Jul 23 2012 - 17:35:32 PDT)
- Ray Luo, Ph.D. (Mon Jul 23 2012 - 16:42:38 PDT)
- Jason Swails (Mon Jul 23 2012 - 16:21:37 PDT)
- sudipta (Mon Jul 23 2012 - 16:09:00 PDT)
- Ray Luo, Ph.D. (Mon Jul 23 2012 - 15:09:45 PDT)
- sudipta (Mon Jul 23 2012 - 15:01:00 PDT)
- Ray Luo, Ph.D. (Mon Jul 23 2012 - 14:54:44 PDT)
- sudipta (Mon Jul 23 2012 - 14:38:59 PDT)
- Jason Swails (Mon Jul 23 2012 - 14:32:01 PDT)
- sudipta (Mon Jul 23 2012 - 14:11:15 PDT)
- Miguel Ortiz Lombardia (Mon Jul 23 2012 - 14:03:15 PDT)
- sudipta (Mon Jul 23 2012 - 13:03:06 PDT)
[AMBER] problem with testing water movement during md simulation
- Joshua Adelman (Sun Jul 22 2012 - 11:27:23 PDT)
- Danny Blue (Sun Jul 22 2012 - 09:44:27 PDT)
[AMBER] Problems parameterizing water/ZN active site with MKT++
- Fabrício Bracht (Tue Jul 31 2012 - 12:36:56 PDT)
[AMBER] Protein aggregation energy calculation(Binwu Zhao)
- Binwu Zhao (Thu Jul 12 2012 - 11:28:21 PDT)
[AMBER] protonated nucleic acid residues
- Jason Swails (Fri Jul 06 2012 - 15:40:32 PDT)
- Timothy Robbins (trobbins) (Fri Jul 06 2012 - 14:13:32 PDT)
[AMBER] Ptraj discrepancy
- C.M.Sampson (Thu Jul 12 2012 - 06:01:48 PDT)
- David A. Case (Thu Jul 12 2012 - 04:48:28 PDT)
- C.M.Sampson (Thu Jul 12 2012 - 02:56:49 PDT)
[AMBER] qmmm_EXTERN/ tests failing
- Andreas Goetz (Sun Jul 22 2012 - 14:18:50 PDT)
[AMBER] Quantification of fraction of Helicity.
- Rajendra Sharma (Mon Jul 16 2012 - 04:08:51 PDT)
[AMBER] Question about corrections to the quasi-harmonic approximation
- David A Case (Mon Jul 23 2012 - 06:31:47 PDT)
- zhouhaibin2008.ok (Sun Jul 22 2012 - 08:39:26 PDT)
[AMBER] Question concerning TI using soft core potential
- David A Case (Mon Jul 23 2012 - 06:31:09 PDT)
- Wook Lee (Mon Jul 23 2012 - 06:31:49 PDT)
- Wook Lee (Mon Jul 23 2012 - 06:18:46 PDT)
- steinbrt.rci.rutgers.edu (Mon Jul 23 2012 - 06:00:02 PDT)
- Wook Lee (Mon Jul 23 2012 - 05:30:29 PDT)
- steinbrt.rci.rutgers.edu (Sat Jul 21 2012 - 10:16:54 PDT)
- Wook Lee (Sat Jul 21 2012 - 06:35:08 PDT)
- Wook Lee (Sat Jul 21 2012 - 06:33:16 PDT)
- David A Case (Thu Jul 19 2012 - 12:07:57 PDT)
- steinbrt.rci.rutgers.edu (Thu Jul 19 2012 - 08:36:52 PDT)
- Wook Lee (Thu Jul 19 2012 - 08:19:49 PDT)
- steinbrt.rci.rutgers.edu (Thu Jul 19 2012 - 07:19:05 PDT)
- Wook Lee (Thu Jul 19 2012 - 07:04:21 PDT)
[AMBER] radgyr command ?
- Marek Maly (Fri Jul 27 2012 - 05:50:24 PDT)
- Daniel Roe (Thu Jul 26 2012 - 20:45:06 PDT)
- Marek Maly (Thu Jul 26 2012 - 09:30:13 PDT)
[AMBER] RDF calculation
- Bhanita Sharma (Tue Jul 24 2012 - 23:40:27 PDT)
[AMBER] RDF considering center of mass
- Bhanita Sharma (Wed Jul 25 2012 - 21:47:31 PDT)
[AMBER] Regarding creating a leap input file
- David A Case (Mon Jul 23 2012 - 06:26:27 PDT)
- aneesh cna (Mon Jul 23 2012 - 05:25:32 PDT)
[AMBER] Restrained minimization
- Jason Swails (Sun Jul 22 2012 - 11:17:31 PDT)
- Hirdesh Kumar (Sun Jul 22 2012 - 01:30:43 PDT)
- pancham lal gupta (Sat Jul 21 2012 - 23:10:47 PDT)
- Jason Swails (Sat Jul 21 2012 - 14:52:01 PDT)
- pancham lal gupta (Sat Jul 21 2012 - 10:31:00 PDT)
[AMBER] RNA chi torsion corrections
- Ilyas Yildirim (Wed Jul 18 2012 - 08:41:45 PDT)
- Jiri Sponer (Wed Jul 18 2012 - 03:40:14 PDT)
- Asmita Gupta (Wed Jul 18 2012 - 03:06:21 PDT)
[AMBER] Script to restore resid numbering
- Francesco Pietra (Tue Jul 03 2012 - 00:49:03 PDT)
[AMBER] Simple question about Amber version
- Daniel Roe (Mon Jul 30 2012 - 06:34:18 PDT)
- scanya.interia.eu (Mon Jul 30 2012 - 05:41:46 PDT)
[AMBER] stripping number of residues (>20K) problem
- Daniel Roe (Thu Jul 26 2012 - 07:10:20 PDT)
- Jio M (Wed Jul 25 2012 - 22:51:38 PDT)
- Jio M (Wed Jul 25 2012 - 03:57:26 PDT)
- Daniel Roe (Mon Jul 23 2012 - 07:32:34 PDT)
- Jio M (Mon Jul 23 2012 - 01:54:11 PDT)
- Jason Swails (Sun Jul 22 2012 - 11:12:35 PDT)
- Jio M (Sun Jul 22 2012 - 06:46:10 PDT)
- case (Sun Jul 22 2012 - 05:16:32 PDT)
- Jio M (Sun Jul 22 2012 - 02:48:44 PDT)
[AMBER] Sulfotyrosine force field
- Jio M (Fri Jul 13 2012 - 00:15:25 PDT)
- FyD (Fri Jul 13 2012 - 00:03:07 PDT)
- David Case (Thu Jul 12 2012 - 13:19:33 PDT)
- Pedro Swagger (Thu Jul 12 2012 - 12:56:45 PDT)
[AMBER] system out of pbc box
- Albert (Fri Jul 13 2012 - 00:57:42 PDT)
[AMBER] the meaning of variables used in source file force.f
- Jason Swails (Mon Jul 23 2012 - 16:03:28 PDT)
- Xin Geng (Mon Jul 23 2012 - 15:22:24 PDT)
[AMBER] Thermodynamic integration with polarizable force field
- case (Wed Jul 04 2012 - 09:24:01 PDT)
- VAN DAMME Steven (Wed Jul 04 2012 - 05:56:27 PDT)
[AMBER] TI calculation Amber 12
- Anna Bauß (Mon Jul 02 2012 - 05:07:34 PDT)
- steinbrt.rci.rutgers.edu (Mon Jul 02 2012 - 04:58:33 PDT)
- Anna Bauß (Mon Jul 02 2012 - 04:47:43 PDT)
- David A Case (Mon Jul 02 2012 - 04:40:02 PDT)
- steinbrt.rci.rutgers.edu (Mon Jul 02 2012 - 02:54:39 PDT)
- Anna Bauß (Mon Jul 02 2012 - 02:36:30 PDT)
[AMBER] TI calculation with amber and finite size correction for PME
- case (Sat Jul 21 2012 - 06:22:54 PDT)
- manikanthan bhavaraju (Fri Jul 20 2012 - 22:17:06 PDT)
- manikanthan bhavaraju (Fri Jul 20 2012 - 14:02:54 PDT)
[AMBER] TI with softcore at lambda=0 or 1?
- Liu Denis (Thu Jul 26 2012 - 01:11:40 PDT)
- steinbrt.rci.rutgers.edu (Thu Jul 26 2012 - 00:31:37 PDT)
- Liu Denis (Wed Jul 25 2012 - 19:58:18 PDT)
[AMBER] trajectory imaging results in structural clashes in protein-ligand complexes
- Daniel Roe (Fri Jul 13 2012 - 09:50:51 PDT)
- Harald Lanig (Mon Jul 02 2012 - 05:11:30 PDT)
- Harald Lanig (Mon Jul 02 2012 - 09:40:38 PDT)
- Jason Swails (Mon Jul 02 2012 - 06:48:50 PDT)
- Fredrick Devadoss (Mon Jul 02 2012 - 06:40:22 PDT)
[AMBER] trajin lastframe keyword problem
- Marek Maly (Fri Jul 27 2012 - 09:51:55 PDT)
- Daniel Roe (Fri Jul 27 2012 - 09:45:41 PDT)
- Marek Maly (Fri Jul 27 2012 - 09:01:19 PDT)
[AMBER] Two md.in files in manual and tutorials when running SMD
- 崔颖璐 (Tue Jul 17 2012 - 00:35:51 PDT)
[AMBER] Updated free GPU test drives for AMBER
- Ross Walker (Mon Jul 09 2012 - 21:56:17 PDT)
[AMBER] Using CHAMBER with implicit solvent CHARMM force field
- Marc van der Kamp (Tue Jul 31 2012 - 00:54:35 PDT)
- Anna Tarakanova (Mon Jul 30 2012 - 14:36:05 PDT)
[AMBER] velocities and irest=0 in Amber 11/12
- Jan-Philip Gehrcke (Thu Jul 05 2012 - 05:13:25 PDT)
- Jason Swails (Wed Jul 04 2012 - 11:52:42 PDT)
- Jan-Philip Gehrcke (Wed Jul 04 2012 - 09:55:58 PDT)
- Jan-Philip Gehrcke (Wed Jul 04 2012 - 09:46:59 PDT)
- Jason Swails (Wed Jul 04 2012 - 09:28:38 PDT)
- Jan-Philip Gehrcke (Wed Jul 04 2012 - 08:33:46 PDT)
[AMBER] what do the preceding "E" and "B" mean in rdparm dihedral prints
- Jason Swails (Sun Jul 15 2012 - 20:23:06 PDT)
- Yun Shi (Sun Jul 15 2012 - 19:38:51 PDT)
[AMBER] What is the typical stimulation time?
- Ross Walker (Sat Jul 07 2012 - 21:19:40 PDT)
- Ilyas Yildirim (Sat Jul 07 2012 - 10:34:33 PDT)
- George Tzotzos (Sat Jul 07 2012 - 04:37:39 PDT)
- Ilyas Yildirim (Fri Jul 06 2012 - 12:04:16 PDT)
- Carlos Simmerling (Fri Jul 06 2012 - 11:21:55 PDT)
- George Tzotzos (Fri Jul 06 2012 - 11:18:34 PDT)
- Carlos Simmerling (Fri Jul 06 2012 - 10:48:20 PDT)
- Ross Walker (Fri Jul 06 2012 - 09:23:09 PDT)
- steinbrt.rci.rutgers.edu (Fri Jul 06 2012 - 02:51:28 PDT)
- Dr. Vitaly V. G. Chaban (Thu Jul 05 2012 - 19:25:24 PDT)
- Ganesh Kamath (Thu Jul 05 2012 - 19:06:46 PDT)
- Dr. Vitaly V. G. Chaban (Thu Jul 05 2012 - 18:55:18 PDT)
- Baldoni Hector Armando (Thu Jul 05 2012 - 18:45:22 PDT)
- Carlos Simmerling (Thu Jul 05 2012 - 17:49:17 PDT)
- Catein Catherine (Thu Jul 05 2012 - 17:44:23 PDT)
[AMBER] xLeap and Windows questions
- Mickey Richards (Wed Jul 25 2012 - 08:21:20 PDT)
- Jason Swails (Wed Jul 25 2012 - 06:39:20 PDT)
- Mickey Richards (Tue Jul 24 2012 - 17:19:57 PDT)
- Daniel Roe (Tue Jul 24 2012 - 15:59:30 PDT)
- Mickey Richards (Tue Jul 24 2012 - 11:56:33 PDT)
[AMBER] ZAFF parameters
- Jason Swails (Tue Jul 31 2012 - 08:13:48 PDT)
- Tong Zhu (Tue Jul 31 2012 - 00:44:13 PDT)
- Siavoush Dastmalchi (Sun Jul 29 2012 - 05:15:39 PDT)
- Siavoush Dastmalchi (Wed Jul 18 2012 - 22:33:26 PDT)
all_prot_nucleic10.lib file in amber12
- FyD (Fri Jul 06 2012 - 23:12:37 PDT)
- Jason Swails (Wed Jul 04 2012 - 09:26:46 PDT)
How to Calculate SASA with Amber?
- Daniel Roe (Wed Jul 25 2012 - 09:18:28 PDT)
- Shafinaz Chowdhury (Wed Jul 25 2012 - 09:09:40 PDT)
line 22350: type: mpic++: not found NETCDF configure succeeded.
- Jorgen Simonsen (Tue Jul 24 2012 - 23:00:04 PDT)
- Jorgen Simonsen (Tue Jul 24 2012 - 17:50:52 PDT)
- Daniel Roe (Tue Jul 24 2012 - 15:44:00 PDT)
- Jorgen Simonsen (Tue Jul 24 2012 - 14:34:32 PDT)

Amber Archive Jul 2012 by subject