Amber Archive Mar 2012: by subject

[AMBER-Developers] [AMBER] Alkali and Halide Monovalent Ion : paper
- David A Case (Tue Mar 06 2012 - 09:42:15 PST)
[AMBER] ./nab -c dna3.nab,nab2c failed!
- David A Case (Mon Mar 05 2012 - 06:54:20 PST)
- Yudong Sun (Mon Mar 05 2012 - 06:40:03 PST)
[AMBER] [q4md-fft] how to keep atom restrained in R.E.D?
- FyD (Wed Mar 07 2012 - 01:01:44 PST)
[AMBER] ABMD in pmemd.cuda in AMBER 12
- Aron Broom (Mon Mar 26 2012 - 10:39:36 PDT)
- Ross Walker (Thu Mar 01 2012 - 13:33:38 PST)
- Jason Swails (Thu Mar 01 2012 - 12:35:47 PST)
- Aron Broom (Thu Mar 01 2012 - 10:45:37 PST)
- M. L. Dodson (Thu Mar 01 2012 - 10:43:37 PST)
- Jason Swails (Thu Mar 01 2012 - 10:18:17 PST)
- Aron Broom (Thu Mar 01 2012 - 10:08:52 PST)
[AMBER] About ANAL
- David A. Case (Sun Mar 25 2012 - 07:47:38 PDT)
- wei wang (Sun Mar 25 2012 - 02:33:33 PDT)
[AMBER] About ANAL problem: Amber
- 王伟 (Sat Mar 24 2012 - 00:41:00 PDT)
- 王伟 (Fri Mar 23 2012 - 07:37:32 PDT)
- 王伟 (Thu Mar 22 2012 - 06:14:43 PDT)
- David A Case (Thu Mar 22 2012 - 05:14:10 PDT)
- Soumya Lipsa Rath (Wed Mar 21 2012 - 23:25:36 PDT)
- David A Case (Wed Mar 21 2012 - 04:55:01 PDT)
- 王伟 (Wed Mar 21 2012 - 04:16:23 PDT)
[AMBER] Alkali and Halide Monovalent Ion : paper
- CHAMI F. (Tue Mar 06 2012 - 07:27:17 PST)
- Brian Radak (Mon Mar 05 2012 - 09:28:40 PST)
- CHAMI F. (Mon Mar 05 2012 - 09:18:17 PST)
[AMBER] AM1
- Jacopo Sgrignani (Wed Mar 07 2012 - 23:23:57 PST)
- Brian Radak (Wed Mar 07 2012 - 07:33:33 PST)
- Jacopo Sgrignani (Wed Mar 07 2012 - 03:17:51 PST)
[AMBER] Amber 10 parallel installation error
- David A Case (Fri Mar 16 2012 - 05:20:17 PDT)
- Shaandar Nyamtulga (Wed Mar 14 2012 - 00:19:03 PDT)
[AMBER] Amber 11 Compilation Error (again!)
- Jason Swails (Wed Mar 21 2012 - 05:16:25 PDT)
- Adam Jion (Wed Mar 21 2012 - 04:57:37 PDT)
[AMBER] Amber and Short Bonds
- Jason Swails (Tue Mar 27 2012 - 05:59:12 PDT)
- Aronica, Pietro (Tue Mar 27 2012 - 05:24:43 PDT)
- Adrian Roitberg (Mon Mar 26 2012 - 17:08:47 PDT)
- Aronica, Pietro (Mon Mar 26 2012 - 17:02:02 PDT)
- Jason Swails (Mon Mar 26 2012 - 16:47:36 PDT)
- Aronica, Pietro (Mon Mar 26 2012 - 16:18:35 PDT)
- Thomas Cheatham (Mon Mar 26 2012 - 13:21:22 PDT)
- Jason Swails (Mon Mar 26 2012 - 13:15:55 PDT)
- Aronica, Pietro (Mon Mar 26 2012 - 10:05:41 PDT)
- Ross Walker (Mon Mar 26 2012 - 09:44:30 PDT)
- Aronica, Pietro (Mon Mar 26 2012 - 08:04:45 PDT)
[AMBER] Amber for Cuda on Mac OSX
- Jason Swails (Fri Mar 16 2012 - 12:03:52 PDT)
- George Tzotzos (Fri Mar 16 2012 - 07:35:38 PDT)
[AMBER] AMBER force calculations
- Jason Swails (Fri Mar 16 2012 - 15:01:19 PDT)
- David Condon (Fri Mar 16 2012 - 13:30:45 PDT)
- Brian Radak (Fri Mar 16 2012 - 13:10:53 PDT)
- David Condon (Fri Mar 16 2012 - 13:03:29 PDT)
- Brian Radak (Fri Mar 02 2012 - 06:47:43 PST)
- David Condon (Fri Mar 02 2012 - 06:25:10 PST)
[AMBER] amber parameters for cytochrome c
- Jason Swails (Sat Mar 24 2012 - 08:49:23 PDT)
- Gurunath Katagi (Thu Mar 22 2012 - 19:42:03 PDT)
[AMBER] Amber10 paralel installation
- Jason Swails (Sat Mar 10 2012 - 13:08:21 PST)
- Shaandar Nyamtulga (Fri Mar 09 2012 - 19:06:01 PST)
[AMBER] Amber10 parallel installation test error
- David A Case (Thu Mar 15 2012 - 12:29:09 PDT)
- Shaandar Nyamtulga (Wed Mar 14 2012 - 22:48:45 PDT)
[AMBER] Amber10 parallel installation test example
- David A Case (Fri Mar 23 2012 - 05:21:38 PDT)
- Shaandar Nyamtulga (Fri Mar 23 2012 - 01:08:31 PDT)
[AMBER] Amber10 parallel installation test example run error
- Daniel Roe (Thu Mar 15 2012 - 03:16:25 PDT)
- Shaandar Nyamtulga (Wed Mar 14 2012 - 20:50:37 PDT)
[AMBER] Amber10 parallel test example run error
- Shaandar Nyamtulga (Fri Mar 30 2012 - 01:04:16 PDT)
- Shaandar Nyamtulga (Thu Mar 29 2012 - 23:25:32 PDT)
[AMBER] Amber11 Intel compiler version 12 make parallel fail
- David Case (Fri Mar 09 2012 - 17:44:03 PST)
- Andrew Petersen (Fri Mar 09 2012 - 14:34:32 PST)
[AMBER] amber12
- Jason Swails (Tue Mar 27 2012 - 06:16:40 PDT)
- Elisa Frezza (Tue Mar 27 2012 - 05:35:44 PDT)
- Ross Walker (Mon Mar 26 2012 - 09:35:22 PDT)
- Jason Swails (Mon Mar 26 2012 - 08:32:45 PDT)
- Elisa Frezza (Mon Mar 26 2012 - 02:26:39 PDT)
[AMBER] Amber8 and RAMD
- Vlad Cojocaru (Sun Mar 18 2012 - 02:54:15 PDT)
- xiaojiong (Sun Mar 18 2012 - 01:59:00 PDT)
[AMBER] AmberGS forcefield
- Carlos Simmerling (Tue Mar 27 2012 - 08:17:19 PDT)
- steinbrt.rci.rutgers.edu (Tue Mar 27 2012 - 07:57:05 PDT)
[AMBER] ANAL
- wei wang (Sat Mar 24 2012 - 20:32:47 PDT)
- 王伟 (Sat Mar 24 2012 - 20:17:43 PDT)
- 王伟 (Sat Mar 24 2012 - 00:57:41 PDT)
[AMBER] angle restraint
- Elisa Frezza (Tue Mar 27 2012 - 02:28:46 PDT)
[AMBER] Announcement: 2012 summer intern position at GSK
- 肖立 (Sun Mar 25 2012 - 16:24:55 PDT)
[AMBER] Announcement: Large biomolecule benchmark report
- Hannes Loeffler (Thu Mar 15 2012 - 05:50:10 PDT)
[AMBER] Another question about Amber 12
- Tong Zhu (Wed Mar 28 2012 - 18:51:25 PDT)
- Ross Walker (Tue Mar 27 2012 - 10:25:43 PDT)
- Tong Zhu (Mon Mar 26 2012 - 18:04:31 PDT)
[AMBER] antechamber error
- David A Case (Fri Mar 16 2012 - 05:16:22 PDT)
- Syed Tarique Moin (Wed Mar 14 2012 - 03:59:45 PDT)
[AMBER] April 3 deadline for application for ACS computational chemistry awards for the Fall 2012 national meeting
- Carlos Simmerling (Mon Mar 12 2012 - 10:02:19 PDT)
[AMBER] Asking About Differences between amber force field ff10 and ff03
- David A Case (Fri Mar 30 2012 - 09:27:54 PDT)
- Aron Broom (Fri Mar 30 2012 - 07:21:30 PDT)
- setyanto md (Fri Mar 30 2012 - 02:50:59 PDT)
[AMBER] asking about mden
- setyanto md (Mon Mar 12 2012 - 03:26:43 PDT)
- Ben Roberts (Sun Mar 11 2012 - 23:35:11 PDT)
- setyanto md (Sun Mar 11 2012 - 22:33:57 PDT)
[AMBER] Assignment of partial charge to a molecule
- Aron Broom (Tue Mar 06 2012 - 10:18:47 PST)
- gargi borgohai (Tue Mar 06 2012 - 10:05:07 PST)
[AMBER] assignment of partial charge to fullerene2160
- FyD (Tue Mar 27 2012 - 05:55:04 PDT)
- steinbrt.rci.rutgers.edu (Tue Mar 27 2012 - 01:05:44 PDT)
- gargi borgohai (Tue Mar 27 2012 - 00:15:21 PDT)
[AMBER] atom type of Sulphur in CYS/CYM (MCPB)
- ashwini gupta (Sun Mar 25 2012 - 21:33:53 PDT)
- Ben Roberts (Sun Mar 25 2012 - 11:02:04 PDT)
- Tong Zhu (Fri Mar 23 2012 - 02:12:32 PDT)
- ashwini gupta (Thu Mar 22 2012 - 23:39:03 PDT)
[AMBER] ATP minimization
- FyD (Tue Mar 06 2012 - 01:17:28 PST)
- Sangita Kachhap (Mon Mar 05 2012 - 21:58:33 PST)
[AMBER] Base stacking
- amirhossein taghavi (Fri Mar 09 2012 - 07:33:51 PST)
- amir abbasi (Thu Mar 08 2012 - 11:10:11 PST)
- francesco oteri (Thu Mar 08 2012 - 11:00:49 PST)
- Ilyas Yildirim (Thu Mar 08 2012 - 10:39:13 PST)
- amir abbasi (Thu Mar 08 2012 - 10:11:12 PST)
- amirhossein taghavi (Thu Mar 08 2012 - 09:18:27 PST)
- amirhossein taghavi (Thu Mar 08 2012 - 09:17:06 PST)
- amir abbasi (Thu Mar 08 2012 - 03:13:51 PST)
[AMBER] Best way to implement PBC
- steinbrt.rci.rutgers.edu (Wed Mar 07 2012 - 13:22:35 PST)
- Ben Ahmady (Wed Mar 07 2012 - 07:26:35 PST)
[AMBER] binding free energy
- David A Case (Thu Mar 15 2012 - 05:51:43 PDT)
- David A. Case (Wed Mar 14 2012 - 14:49:23 PDT)
- David A. Case (Wed Mar 14 2012 - 14:16:20 PDT)
- Sushil Mishra (Tue Mar 13 2012 - 00:55:33 PDT)
- kirtana S (Tue Mar 13 2012 - 00:35:19 PDT)
[AMBER] both parallel and serial
- Jason Swails (Wed Mar 14 2012 - 07:10:59 PDT)
- amir abbasi (Wed Mar 14 2012 - 06:57:34 PDT)
[AMBER] Can I use Amber 10 PRMTOP with Amber 11?
- Jason Swails (Thu Mar 08 2012 - 12:41:53 PST)
- Kasprzak, Wojciech (NIH/NCI) [C] (Thu Mar 08 2012 - 10:40:32 PST)
[AMBER] charges for ion and surrounding residues at the active site
- Jorge Iulek (Wed Mar 21 2012 - 09:07:08 PDT)
- FyD (Wed Mar 21 2012 - 00:02:44 PDT)
- Jorge Iulek (Tue Mar 20 2012 - 17:28:36 PDT)
- FyD (Tue Mar 20 2012 - 04:55:07 PDT)
- Jorge Iulek (Mon Mar 19 2012 - 17:33:10 PDT)
- JORGE IULEK (Mon Mar 19 2012 - 12:51:05 PDT)
[AMBER] cluster configuration help
- Sangeetha B (Sun Mar 11 2012 - 08:11:30 PDT)
- Thomas Cheatham (Sat Mar 10 2012 - 10:24:33 PST)
- Sangeetha B (Fri Mar 09 2012 - 09:16:42 PST)
- Sangeetha B (Tue Mar 06 2012 - 19:27:09 PST)
[AMBER] COM
- David A. Case (Wed Mar 28 2012 - 12:25:45 PDT)
- Olena Dobrovolska (Wed Mar 28 2012 - 08:40:02 PDT)
- David A. Case (Wed Mar 28 2012 - 07:53:38 PDT)
- Olena Dobrovolska (Tue Mar 27 2012 - 08:01:27 PDT)
[AMBER] Comparison of the results
- manikanthan bhavaraju (Thu Mar 08 2012 - 14:19:50 PST)
- Jason Swails (Thu Mar 08 2012 - 14:00:20 PST)
- manikanthan bhavaraju (Wed Mar 07 2012 - 14:23:54 PST)
[AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
- Jason Swails (Sun Mar 11 2012 - 14:42:36 PDT)
- David A. Case (Sun Mar 11 2012 - 10:54:23 PDT)
- Jan-Philip Gehrcke (Fri Mar 09 2012 - 06:28:38 PST)
[AMBER] compiling failure on ibm
- Yubo Fan (Mon Mar 26 2012 - 13:50:06 PDT)
- Jason Swails (Mon Mar 26 2012 - 12:51:48 PDT)
- Scott Brozell (Mon Mar 26 2012 - 12:20:00 PDT)
- Yubo Fan (Mon Mar 26 2012 - 11:44:03 PDT)
[AMBER] Conflict between AmberTools 1.5 and Cuda
- Jan-Philip Gehrcke (Sat Mar 24 2012 - 05:23:38 PDT)
- Adam Jion (Sat Mar 24 2012 - 04:26:21 PDT)
- David A Case (Fri Mar 23 2012 - 11:11:32 PDT)
- Adam Jion (Fri Mar 23 2012 - 10:09:32 PDT)
- Ross Walker (Fri Mar 23 2012 - 09:19:07 PDT)
- Daniel Roe (Fri Mar 23 2012 - 09:16:55 PDT)
- Adam Jion (Fri Mar 23 2012 - 08:18:55 PDT)
[AMBER] control_rmsd_in TMD
- neha sree (Fri Mar 02 2012 - 11:57:42 PST)
[AMBER] Converting Gromacs coordinate file to Amber input files for molecular dynamics
- Alex Rodriguez (Wed Mar 21 2012 - 10:13:23 PDT)
- Adam Jion (Wed Mar 21 2012 - 10:00:23 PDT)
[AMBER] Converting Gromacs coordinate file to Amber input files formolecular dynamics
- Vlad Cojocaru (Wed Mar 21 2012 - 10:10:52 PDT)
[AMBER] correct inconsistencies in [DR]NA_CI.lib
- Jason Swails (Tue Mar 06 2012 - 20:38:09 PST)
- Thomas Gaillard (Tue Mar 06 2012 - 08:57:36 PST)
[AMBER] covert CHARMM format PDB file to AMBER formart
- case (Wed Mar 07 2012 - 05:09:19 PST)
- c00jsw00.nchc.narl.org.tw (Wed Mar 07 2012 - 03:11:32 PST)
- Tong Zhu (Wed Mar 07 2012 - 02:25:05 PST)
[AMBER] cpptraj hbond
- George Tzotzos (Mon Mar 26 2012 - 12:10:43 PDT)
- Daniel Roe (Mon Mar 26 2012 - 12:06:57 PDT)
- George Tzotzos (Mon Mar 26 2012 - 11:13:55 PDT)
- George Tzotzos (Mon Mar 26 2012 - 07:26:28 PDT)
[AMBER] cpptraj surf Segmentation fault
- Daniel Roe (Wed Mar 07 2012 - 08:12:46 PST)
- Guillermo Mulliert Carlín (Wed Mar 07 2012 - 07:51:07 PST)
[AMBER] Dedication from Ibrahim - Manchester/Minia
- David A Case (Wed Mar 07 2012 - 12:01:38 PST)
- Mahmoud Ibrahim (Tue Mar 06 2012 - 14:17:57 PST)
[AMBER] Defining sulfonyl halide atom type
- FyD (Sat Mar 03 2012 - 10:39:04 PST)
- Chris Bryant (Fri Mar 02 2012 - 09:03:08 PST)
[AMBER] different residues use different force to restrict
- David A Case (Mon Mar 05 2012 - 05:15:04 PST)
- xiaojiong (Sun Mar 04 2012 - 17:41:16 PST)
[AMBER] Dihedral analysis
- g t (Tue Mar 13 2012 - 10:41:45 PDT)
- CHAMI F. (Thu Mar 08 2012 - 08:47:45 PST)
- Ibrahim Moustafa (Thu Mar 08 2012 - 08:06:33 PST)
- Niel Henriksen (Thu Mar 08 2012 - 06:10:26 PST)
- Ibrahim Moustafa (Wed Mar 07 2012 - 10:05:00 PST)
[AMBER] Distance plot
- Beale, John (Fri Mar 02 2012 - 06:50:18 PST)
- Cannon, John F. (Fri Mar 02 2012 - 06:42:27 PST)
- Beale, John (Fri Mar 02 2012 - 05:57:35 PST)
[AMBER] disulfide bond warnings
- Jason Swails (Tue Mar 20 2012 - 18:45:32 PDT)
- George Tzotzos (Tue Mar 20 2012 - 16:19:41 PDT)
- Jason Swails (Tue Mar 20 2012 - 16:01:09 PDT)
- George Tzotzos (Tue Mar 20 2012 - 11:30:29 PDT)
[AMBER] Energy and Coordinate Outputs
- David Minh (Sat Mar 17 2012 - 05:03:28 PDT)
- David A. Case (Wed Mar 14 2012 - 14:49:53 PDT)
- David A. Case (Wed Mar 14 2012 - 14:15:58 PDT)
- Jason Swails (Tue Mar 13 2012 - 15:22:11 PDT)
- David Minh (Mon Mar 12 2012 - 08:55:38 PDT)
- David A. Case (Sat Mar 10 2012 - 10:13:00 PST)
- David Minh (Fri Mar 09 2012 - 18:26:39 PST)
- David Case (Fri Mar 09 2012 - 17:37:45 PST)
- David Minh (Fri Mar 09 2012 - 13:47:53 PST)
[AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
- Adam Jion (Sat Mar 24 2012 - 20:28:04 PDT)
- Jason Swails (Sat Mar 24 2012 - 19:33:37 PDT)
- Adam Jion (Sat Mar 24 2012 - 17:45:47 PDT)
- Jason Swails (Sat Mar 24 2012 - 17:15:42 PDT)
- Adam Jion (Sat Mar 24 2012 - 17:12:48 PDT)
- Adam Jion (Sat Mar 24 2012 - 10:29:09 PDT)
- Jason Swails (Sat Mar 24 2012 - 10:06:02 PDT)
- Scott Le Grand (Sat Mar 24 2012 - 09:49:42 PDT)
- Adam Jion (Sat Mar 24 2012 - 09:38:16 PDT)
- Jason Swails (Sat Mar 24 2012 - 08:17:58 PDT)
- Adam Jion (Sat Mar 24 2012 - 06:03:58 PDT)
[AMBER] Error in amber output files
- Jason Swails (Tue Mar 06 2012 - 07:44:32 PST)
- David A Case (Tue Mar 06 2012 - 04:50:08 PST)
- souvik sur (Mon Mar 05 2012 - 21:11:01 PST)
- Jason Swails (Mon Mar 05 2012 - 13:34:51 PST)
- souvik sur (Mon Mar 05 2012 - 05:19:40 PST)
[AMBER] error in nmode calculations
- David A. Case (Thu Mar 29 2012 - 06:09:53 PDT)
- Jason Swails (Wed Mar 28 2012 - 14:46:54 PDT)
- manikanthan bhavaraju (Wed Mar 28 2012 - 14:18:06 PDT)
- Cannon, John F. (Wed Mar 28 2012 - 13:11:03 PDT)
- Bill Miller III (Wed Mar 28 2012 - 12:05:14 PDT)
- manikanthan bhavaraju (Wed Mar 28 2012 - 11:41:04 PDT)
[AMBER] error in sander_com.1.out
- Nadine.Homeyer.uni-duesseldorf.de (Thu Mar 01 2012 - 03:12:05 PST)
- kureeckal ramesh (Thu Mar 01 2012 - 02:30:54 PST)
[AMBER] esp and resp comparison
- FyD (Fri Mar 23 2012 - 08:01:27 PDT)
- jun kit (Fri Mar 23 2012 - 01:23:49 PDT)
[AMBER] External Force Method in pmemd.cuda
- Ismail, Mohd F. (Wed Mar 21 2012 - 10:46:59 PDT)
- Jason Swails (Wed Mar 21 2012 - 10:35:52 PDT)
- Ismail, Mohd F. (Wed Mar 21 2012 - 10:28:43 PDT)
[AMBER] Extra Bonds For Water
- Adrian Roitberg (Tue Mar 13 2012 - 15:44:59 PDT)
- Kyle Greenway (Tue Mar 13 2012 - 15:37:33 PDT)
[AMBER] Fast ibelly?
- David Minh (Wed Mar 21 2012 - 07:22:59 PDT)
- David A Case (Tue Mar 20 2012 - 13:22:15 PDT)
- Ross Walker (Tue Mar 20 2012 - 11:31:10 PDT)
- David Minh (Tue Mar 20 2012 - 11:10:15 PDT)
- Ross Walker (Tue Mar 20 2012 - 10:09:47 PDT)
- David Minh (Tue Mar 20 2012 - 08:29:00 PDT)
[AMBER] Fast moving system in targeted MD
- Thomas Exner (Fri Mar 30 2012 - 05:16:18 PDT)
[AMBER] Force Field Parameterization -- Torsion Potentials
- Karl N. Kirschner (Mon Mar 19 2012 - 05:50:46 PDT)
- Ismail, Mohd F. (Thu Mar 15 2012 - 22:31:02 PDT)
- Karl N. Kirschner (Wed Mar 14 2012 - 04:53:23 PDT)
- Ismail, Mohd F. (Tue Mar 13 2012 - 15:14:08 PDT)
- Ismail, Mohd F. (Tue Mar 13 2012 - 15:08:48 PDT)
[AMBER] Free Energy Calculate
- David A Case (Mon Mar 05 2012 - 05:24:28 PST)
- mehdi bagherpoor (Mon Mar 05 2012 - 04:41:05 PST)
[AMBER] Fwd: Comparison of the results
- manikanthan bhavaraju (Wed Mar 07 2012 - 22:31:48 PST)
[AMBER] Fwd: PB with inp=2 doesn't recognize ff10 atom types?
- Ray Luo, Ph.D. (Sat Mar 17 2012 - 19:33:14 PDT)
[AMBER] Fwd: SASA Plot
- João Ribeiro (Wed Mar 07 2012 - 02:16:53 PST)
[AMBER] Fwd: V limit
- David A Case (Thu Mar 29 2012 - 13:20:05 PDT)
- Jason Swails (Thu Mar 29 2012 - 12:04:41 PDT)
- Ross Walker (Thu Mar 29 2012 - 11:47:37 PDT)
- David A Case (Thu Mar 29 2012 - 09:18:59 PDT)
- RAMON (Mon Mar 26 2012 - 07:21:46 PDT)
[AMBER] GBSA - surface tension question for calculation of ΔGnonpolar
- g t (Wed Mar 21 2012 - 23:18:34 PDT)
- Carlos Simmerling (Wed Mar 21 2012 - 04:08:30 PDT)
- g t (Tue Mar 20 2012 - 16:02:06 PDT)
- Carlos Simmerling (Tue Mar 20 2012 - 10:44:37 PDT)
- g t (Tue Mar 20 2012 - 10:34:48 PDT)
[AMBER] glycine sidechain contribution in MM-GBSA decompostion
- Carlos Simmerling (Tue Mar 27 2012 - 03:01:13 PDT)
- Jason Swails (Mon Mar 26 2012 - 21:52:10 PDT)
- caobb0214 (Mon Mar 26 2012 - 18:56:22 PDT)
- Carlos Simmerling (Mon Mar 26 2012 - 18:08:33 PDT)
- caobb0214 (Mon Mar 26 2012 - 18:05:04 PDT)
[AMBER] GPU performance and GPU Direct
- Gould, Ian R (Wed Mar 07 2012 - 06:14:08 PST)
- steinbrt.rci.rutgers.edu (Wed Mar 07 2012 - 05:26:53 PST)
[AMBER] GTX680
- Scott Le Grand (Thu Mar 29 2012 - 08:39:21 PDT)
- Fenley, Andrew (Wed Mar 28 2012 - 19:33:53 PDT)
- Aron Broom (Wed Mar 28 2012 - 15:11:26 PDT)
- Ross Walker (Wed Mar 28 2012 - 13:39:14 PDT)
- Aron Broom (Wed Mar 28 2012 - 10:45:45 PDT)
- Scott Le Grand (Wed Mar 28 2012 - 10:40:40 PDT)
- Aron Broom (Wed Mar 28 2012 - 10:30:30 PDT)
- Scott Le Grand (Wed Mar 28 2012 - 10:07:57 PDT)
- Aron Broom (Wed Mar 28 2012 - 09:54:11 PDT)
- Scott Le Grand (Wed Mar 28 2012 - 09:33:39 PDT)
- Scott Le Grand (Fri Mar 23 2012 - 11:57:00 PDT)
- Ross Walker (Fri Mar 23 2012 - 11:49:15 PDT)
- filip fratev (Fri Mar 23 2012 - 11:37:02 PDT)
[AMBER] Harmonic Restraint in pmemd.cuda
- Adrian Roitberg (Wed Mar 07 2012 - 15:16:33 PST)
- Aron Broom (Wed Mar 07 2012 - 15:14:40 PST)
- Adrian Roitberg (Wed Mar 07 2012 - 15:10:07 PST)
- Aron Broom (Wed Mar 07 2012 - 15:01:37 PST)
[AMBER] Help with solvating organic molecule with input .prmtop file
- Jason Swails (Thu Mar 01 2012 - 12:33:32 PST)
- Andy Ballard (Thu Mar 01 2012 - 09:28:23 PST)
[AMBER] How to calculate the energy contributed by hydrogen bonds?
- bin wang (Wed Mar 21 2012 - 20:58:22 PDT)
- Jason Swails (Tue Mar 20 2012 - 10:01:24 PDT)
- bin wang (Tue Mar 20 2012 - 07:17:29 PDT)
- Jason Swails (Mon Mar 19 2012 - 19:27:01 PDT)
- bin wang (Mon Mar 19 2012 - 14:00:51 PDT)
[AMBER] How to convert multiple mdcrd files to single files with minimium size?
- Aron Broom (Thu Mar 08 2012 - 08:08:47 PST)
- Marc van der Kamp (Thu Mar 08 2012 - 07:53:35 PST)
- Catein Catherine (Thu Mar 08 2012 - 07:47:26 PST)
[AMBER] How to get the information of hydrophobic contact?
- g t (Tue Mar 13 2012 - 10:39:44 PDT)
- qiao xue (Wed Mar 07 2012 - 19:03:48 PST)
[AMBER] how to keep atom restrained in R.E.D?
- Albert (Tue Mar 06 2012 - 22:45:37 PST)
[AMBER] how to measure atom distance in md trajectories using ptraj program
- Daniel Roe (Wed Mar 28 2012 - 12:37:04 PDT)
- Jason Swails (Wed Mar 28 2012 - 12:23:30 PDT)
- Bala Subramani (Wed Mar 28 2012 - 11:25:41 PDT)
- Daniel Roe (Wed Mar 28 2012 - 10:33:39 PDT)
- Bala Subramani (Wed Mar 28 2012 - 10:26:21 PDT)
[AMBER] how to merge 10 trajectory files
- Ben Roberts (Wed Mar 28 2012 - 21:42:41 PDT)
- BALASUBRAMANI G L (Wed Mar 28 2012 - 21:35:42 PDT)
[AMBER] Hydrogen bond analysis
- Daniel Roe (Fri Mar 09 2012 - 04:34:41 PST)
- tdo.chem.ucsb.edu (Thu Mar 08 2012 - 23:48:00 PST)
[AMBER] implicit and explicit
- Carlos Simmerling (Sun Mar 04 2012 - 04:35:12 PST)
[AMBER] Implicit MD run
- Aditya Padhi (Tue Mar 20 2012 - 04:12:04 PDT)
- Carlos Simmerling (Tue Mar 20 2012 - 04:02:13 PDT)
- Aditya Padhi (Mon Mar 19 2012 - 22:52:57 PDT)
- Carlos Simmerling (Mon Mar 19 2012 - 05:42:34 PDT)
- Aditya Padhi (Mon Mar 19 2012 - 04:11:35 PDT)
- Carlos Simmerling (Mon Mar 19 2012 - 03:30:27 PDT)
- Aditya Padhi (Sun Mar 18 2012 - 21:30:51 PDT)
- Carlos Simmerling (Sat Mar 17 2012 - 04:20:00 PDT)
- Aditya Padhi (Fri Mar 16 2012 - 23:19:21 PDT)
- Aron Broom (Fri Mar 16 2012 - 23:06:13 PDT)
- Aditya Padhi (Fri Mar 16 2012 - 22:57:20 PDT)
- Aron Broom (Fri Mar 16 2012 - 22:53:08 PDT)
- Aditya Padhi (Fri Mar 16 2012 - 21:29:00 PDT)
[AMBER] is GB/SA suitable for nonaqueous solvent?
- Alex Rodriguez (Mon Mar 19 2012 - 10:25:15 PDT)
- Dean Cuebas (Mon Mar 19 2012 - 09:51:28 PDT)
- Carlos Simmerling (Sun Mar 18 2012 - 07:25:35 PDT)
- Junjian Miao (Sun Mar 18 2012 - 07:21:42 PDT)
[AMBER] Is it possible to cluster several mdcrd files based on a dihedral angles of a particular residues?
- Catein Catherine (Thu Mar 15 2012 - 07:16:56 PDT)
[AMBER] Is it possible to just calculate translational and rotational entropy?
- David A Case (Thu Mar 22 2012 - 05:23:10 PDT)
- Tan Yaw Sing (Thu Mar 22 2012 - 03:57:57 PDT)
[AMBER] Is there some constrains required for the REMD simulation on disaccharide in Amber11?
- 黄恋琦 (Tue Mar 20 2012 - 00:42:05 PDT)
[AMBER] Issue with running sander
- Jason Swails (Fri Mar 30 2012 - 10:56:15 PDT)
- David A Case (Fri Mar 30 2012 - 09:39:47 PDT)
- Jason Swails (Fri Mar 30 2012 - 07:13:14 PDT)
- 板垣哲彦 (Fri Mar 30 2012 - 05:37:21 PDT)
[AMBER] Job Opening at Simbios/Stanford University
- Ross Walker (Fri Mar 09 2012 - 13:19:54 PST)
[AMBER] Large Energy Jump in TMD simulation - Regarding
- Jason Swails (Fri Mar 30 2012 - 15:51:50 PDT)
- Fredrick Devadoss (Fri Mar 30 2012 - 15:15:50 PDT)
- Jason Swails (Fri Mar 30 2012 - 12:25:40 PDT)
- Fredrick Devadoss (Fri Mar 30 2012 - 11:06:02 PDT)
- Carlos Simmerling (Fri Mar 30 2012 - 08:57:53 PDT)
- Fredrick Devadoss (Fri Mar 30 2012 - 06:49:21 PDT)
- Carlos Simmerling (Fri Mar 30 2012 - 06:41:13 PDT)
- Fredrick Devadoss (Fri Mar 30 2012 - 06:34:11 PDT)
- Carlos Simmerling (Fri Mar 30 2012 - 05:52:35 PDT)
- Fredrick Devadoss (Fri Mar 30 2012 - 05:19:56 PDT)
[AMBER] Mac OSX 10.7
- Jason Swails (Thu Mar 08 2012 - 12:36:00 PST)
- George Tzotzos (Thu Mar 08 2012 - 11:05:05 PST)
[AMBER] MD and RAMD
- Vlad Cojocaru (Tue Mar 20 2012 - 00:59:52 PDT)
- xiaojiong (Tue Mar 20 2012 - 00:12:20 PDT)
[AMBER] md sticking!
- amir abbasi (Sat Mar 03 2012 - 04:37:25 PST)
[AMBER] MM-PBSA: different dielectric constants for ligand and receptor?
- David A Case (Mon Mar 05 2012 - 05:20:10 PST)
- Antonija Tomić (Mon Mar 05 2012 - 02:07:38 PST)
[AMBER] mm_pbsa error: Flag "RADII" not found in PARM file
- g t (Thu Mar 01 2012 - 08:32:45 PST)
- Jason Swails (Thu Mar 01 2012 - 07:24:57 PST)
- g t (Thu Mar 01 2012 - 06:59:07 PST)
- g t (Thu Mar 01 2012 - 06:40:24 PST)
[AMBER] MMGBSA residue-wise decomposition
- Jason Swails (Thu Mar 15 2012 - 07:10:50 PDT)
- Rajeswari A. (Wed Mar 14 2012 - 23:58:35 PDT)
- Jason Swails (Wed Mar 14 2012 - 06:34:40 PDT)
- Carlos Simmerling (Wed Mar 14 2012 - 06:05:01 PDT)
- Rajeswari A. (Tue Mar 13 2012 - 04:42:53 PDT)
- Rajeswari A. (Wed Mar 07 2012 - 21:10:52 PST)
- Rajeswari A. (Tue Mar 06 2012 - 21:18:28 PST)
[AMBER] MMPB(GB)SA: two questions
- George Tzotzos (Mon Mar 05 2012 - 09:23:06 PST)
- Cannon, John F. (Mon Mar 05 2012 - 05:37:16 PST)
- George Tzotzos (Sat Mar 03 2012 - 05:05:05 PST)
[AMBER] MMPBSA
- George Tzotzos (Tue Mar 13 2012 - 13:43:36 PDT)
- Dmitry Mukha (Tue Mar 13 2012 - 13:15:21 PDT)
- George Tzotzos (Tue Mar 13 2012 - 12:28:12 PDT)
- Dmitry Mukha (Tue Mar 13 2012 - 12:19:19 PDT)
- George Tzotzos (Tue Mar 13 2012 - 10:26:43 PDT)
- Aron Broom (Tue Mar 13 2012 - 10:13:04 PDT)
- George Tzotzos (Tue Mar 13 2012 - 10:08:47 PDT)
- George Tzotzos (Tue Mar 13 2012 - 10:06:14 PDT)
[AMBER] MMPBSA and explicit ions: what should I do?
- David A Case (Thu Mar 01 2012 - 05:11:42 PST)
- tommaso.casalini.mail.polimi.it (Thu Mar 01 2012 - 02:21:51 PST)
[AMBER] MMPBSA issue: incosistency within internal potential error
- tommaso.casalini.mail.polimi.it (Thu Mar 01 2012 - 07:30:36 PST)
[AMBER] MMPBSA, in parallel?
- Jason Swails (Fri Mar 16 2012 - 06:41:07 PDT)
- Fernando Blanco (Fri Mar 16 2012 - 05:30:17 PDT)
[AMBER] MMPBSA.py - Internal energy
- George Tzotzos (Fri Mar 16 2012 - 12:13:40 PDT)
- Jason Swails (Fri Mar 16 2012 - 12:05:58 PDT)
- George Tzotzos (Fri Mar 16 2012 - 11:58:40 PDT)
[AMBER] Modified phosphotyrosine parameters
- FyD (Tue Mar 06 2012 - 02:18:37 PST)
- Ilya Belalov (Mon Mar 05 2012 - 17:32:44 PST)
[AMBER] MP2 for RESP
- Ben Roberts (Mon Mar 26 2012 - 13:26:07 PDT)
- Tong Zhu (Mon Mar 26 2012 - 01:46:36 PDT)
[AMBER] mpi-allreduce in AMBER11
- Carlos Sosa (Fri Mar 16 2012 - 09:36:59 PDT)
- Jason Swails (Fri Mar 16 2012 - 06:38:40 PDT)
- Carlos Sosa (Fri Mar 16 2012 - 06:23:16 PDT)
[AMBER] NAB segmentation fault
- case (Tue Mar 20 2012 - 18:26:52 PDT)
- Brian Wolfe (Tue Mar 20 2012 - 17:34:19 PDT)
- Michael F. Bruist (Fri Mar 16 2012 - 09:32:33 PDT)
- David A. Case (Tue Mar 13 2012 - 00:28:08 PDT)
- Michael F. Bruist (Mon Mar 12 2012 - 11:34:46 PDT)
- David A. Case (Sun Mar 11 2012 - 10:57:16 PDT)
- Michael F. Bruist (Thu Mar 08 2012 - 08:03:12 PST)
[AMBER] No Na molecule type for genion
- M. L. Dodson (Sat Mar 17 2012 - 06:40:06 PDT)
- raghav singh (Fri Mar 16 2012 - 22:57:05 PDT)
- Wholly Peach (Fri Mar 16 2012 - 22:45:32 PDT)
[AMBER] Non - integral charge o unperturbed unit
- FyD (Fri Mar 23 2012 - 07:58:26 PDT)
- ashwini gupta (Thu Mar 22 2012 - 03:08:44 PDT)
[AMBER] non-linear PB solver within MMPBSA: questions regarding EEL, eneopt and cutnb
- Jason Swails (Sat Mar 10 2012 - 13:36:04 PST)
- Jan-Philip Gehrcke (Wed Mar 07 2012 - 08:23:32 PST)
[AMBER] on the AMBER advanced tutorial 3 MM-PBSA
- Aron Broom (Sat Mar 17 2012 - 11:40:25 PDT)
- Bill Miller III (Sat Mar 17 2012 - 11:19:03 PDT)
- Wholly Peach (Thu Mar 15 2012 - 17:18:01 PDT)
[AMBER] organics solvent radius
- setyanto md (Mon Mar 19 2012 - 23:04:23 PDT)
[AMBER] Parameters
- setyanto md (Wed Mar 07 2012 - 21:18:55 PST)
- FyD (Tue Mar 06 2012 - 01:48:22 PST)
- Maxier Acosta (Mon Mar 05 2012 - 20:27:45 PST)
[AMBER] parameters for Lys-sugar
- Lachele Foley (Lists) (Sun Mar 25 2012 - 13:10:23 PDT)
- Urszula Uciechowska (Sat Mar 24 2012 - 13:52:42 PDT)
- Urszula Uciechowska (Sat Mar 24 2012 - 13:41:00 PDT)
- Lachele Foley (Lists) (Sat Mar 24 2012 - 08:10:20 PDT)
- FyD (Sat Mar 24 2012 - 01:14:17 PDT)
- Lachele Foley (Lists) (Fri Mar 23 2012 - 12:39:04 PDT)
- Lachele Foley (Lists) (Fri Mar 23 2012 - 11:01:27 PDT)
- FyD (Fri Mar 23 2012 - 09:11:51 PDT)
- Urszula Uciechowska (Fri Mar 23 2012 - 08:26:19 PDT)
- Lachele Foley (Lists) (Fri Mar 23 2012 - 08:11:15 PDT)
- FyD (Fri Mar 23 2012 - 08:06:35 PDT)
- Urszula Uciechowska (Fri Mar 23 2012 - 05:15:38 PDT)
[AMBER] parameters for Lys-sugar P2N file
- FyD (Mon Mar 26 2012 - 05:47:17 PDT)
- Urszula Uciechowska (Sun Mar 25 2012 - 23:52:33 PDT)
[AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi
- Ross Walker (Fri Mar 30 2012 - 10:34:17 PDT)
- Adam Jion (Fri Mar 30 2012 - 04:08:07 PDT)
- Ben Roberts (Thu Mar 29 2012 - 17:38:00 PDT)
- Aron Broom (Thu Mar 29 2012 - 17:35:33 PDT)
- Adam Jion (Thu Mar 29 2012 - 17:05:16 PDT)
[AMBER] PB with inp=2 doesn't recognize ff10 atom types?
- Qin Cai (Mon Mar 19 2012 - 15:15:38 PDT)
- David Minh (Sat Mar 17 2012 - 11:10:45 PDT)
[AMBER] PBSA sprob question
- Jesper Sørensen (Wed Mar 14 2012 - 08:57:50 PDT)
- Qin Cai (Tue Mar 13 2012 - 16:46:48 PDT)
- Jesper Sørensen (Tue Mar 13 2012 - 15:58:18 PDT)
- Qin Cai (Tue Mar 13 2012 - 15:13:42 PDT)
- Jesper Sørensen (Tue Mar 13 2012 - 13:49:09 PDT)
[AMBER] PDB trajectory format
- Daniel Roe (Fri Mar 16 2012 - 09:30:34 PDT)
- Dmitry Osolodkin (Fri Mar 16 2012 - 09:11:26 PDT)
- Daniel Roe (Fri Mar 16 2012 - 08:43:20 PDT)
- Dmitry Osolodkin (Fri Mar 16 2012 - 08:08:48 PDT)
- Daniel Roe (Thu Mar 15 2012 - 09:46:40 PDT)
- Dmitry Osolodkin (Thu Mar 15 2012 - 09:15:21 PDT)
- Daniel Roe (Sat Mar 03 2012 - 10:53:39 PST)
- Aron Broom (Sat Mar 03 2012 - 08:45:16 PST)
- Dmitry Osolodkin (Sat Mar 03 2012 - 08:10:46 PST)
[AMBER] performance dependency on OS
- steinbrt.rci.rutgers.edu (Tue Mar 06 2012 - 02:56:09 PST)
- amir abbasi (Tue Mar 06 2012 - 02:41:18 PST)
[AMBER] Problem in Amber installation
- Jason Swails (Fri Mar 30 2012 - 07:09:11 PDT)
- setyanto md (Fri Mar 30 2012 - 02:21:57 PDT)
- Jason Swails (Thu Mar 29 2012 - 04:49:37 PDT)
- vishal Nemaysh (Wed Mar 28 2012 - 22:01:57 PDT)
- Jason Swails (Thu Mar 22 2012 - 06:09:39 PDT)
- David A Case (Thu Mar 22 2012 - 05:18:32 PDT)
- vishal Nemaysh (Thu Mar 22 2012 - 01:06:08 PDT)
[AMBER] Problem in creating topology of NAD
- FyD (Thu Mar 01 2012 - 23:18:29 PST)
- FyD (Thu Mar 01 2012 - 23:05:26 PST)
- Ashutosh Shandilya (Thu Mar 01 2012 - 22:55:25 PST)
- Ashutosh Shandilya (Thu Mar 01 2012 - 22:50:06 PST)
[AMBER] problem in output file of the awk script in tutorial A6
- g t (Thu Mar 22 2012 - 00:24:30 PDT)
[AMBER] Problem with installation of MTKPP
- setyanto md (Thu Mar 29 2012 - 03:55:07 PDT)
- Martin Peters (Thu Mar 29 2012 - 01:41:58 PDT)
- setyanto md (Wed Mar 28 2012 - 19:33:09 PDT)
[AMBER] problem with MMPBSA script
- David A Case (Thu Mar 01 2012 - 05:14:41 PST)
- Nadine.Homeyer.uni-duesseldorf.de (Thu Mar 01 2012 - 01:51:57 PST)
- kureeckal ramesh (Thu Mar 01 2012 - 00:52:39 PST)
[AMBER] Problems compiling pmemd.cuda - undefined reference to ...
- Jason Swails (Sat Mar 24 2012 - 09:06:43 PDT)
- Daniel Roe (Fri Mar 23 2012 - 11:10:19 PDT)
- Adam Jion (Fri Mar 23 2012 - 10:22:40 PDT)
- Ross Walker (Fri Mar 23 2012 - 09:17:06 PDT)
- Adam Jion (Fri Mar 23 2012 - 07:15:28 PDT)
[AMBER] Problems testing pmemd.cuda.MPI
- Ben Roberts (Sun Mar 25 2012 - 16:14:18 PDT)
- Adam Jion (Sat Mar 24 2012 - 19:21:02 PDT)
[AMBER] Problems with pmemd.cuda.mpi (again!)
- Adam Jion (Mon Mar 26 2012 - 10:25:30 PDT)
- Jason Swails (Mon Mar 26 2012 - 09:51:13 PDT)
- Adam Jion (Mon Mar 26 2012 - 09:13:05 PDT)
- Jason Swails (Mon Mar 26 2012 - 07:24:35 PDT)
- Adam Jion (Sun Mar 25 2012 - 09:58:48 PDT)
- Jason Swails (Sun Mar 25 2012 - 08:24:26 PDT)
- Adam Jion (Sun Mar 25 2012 - 07:34:28 PDT)
- Ross Walker (Sun Mar 25 2012 - 07:03:48 PDT)
- Adam Jion (Sun Mar 25 2012 - 04:51:53 PDT)
[AMBER] Problems with tetrahedral Al in antechamber
- case (Mon Mar 19 2012 - 05:11:32 PDT)
- Gonzalo Jimenez (Mon Mar 19 2012 - 02:16:35 PDT)
- Gonzalo Jimenez (Mon Mar 19 2012 - 01:44:19 PDT)
[AMBER] ptraj atomicfluct
- George Tzotzos (Sat Mar 24 2012 - 14:54:48 PDT)
- Thomas Cheatham (Sat Mar 24 2012 - 14:26:16 PDT)
- George Tzotzos (Sat Mar 24 2012 - 14:12:11 PDT)
[AMBER] ptraj removes my ligands
- Daniel Roe (Fri Mar 30 2012 - 11:36:23 PDT)
- Daniel Roe (Mon Mar 26 2012 - 21:10:01 PDT)
- DENILSON FERREIRA DE OLIVEIRA (Mon Mar 26 2012 - 19:22:48 PDT)
[AMBER] ptraj: SegFault during SOM clustering
- Anselm Horn (Fri Mar 30 2012 - 09:47:34 PDT)
[AMBER] ptraj: Sort trajectory based on protein-ligand distance
- g t (Wed Mar 14 2012 - 11:37:31 PDT)
- tdo.chem.ucsb.edu (Tue Mar 13 2012 - 18:27:05 PDT)
[AMBER] puting restrains
- Urszula Uciechowska (Fri Mar 16 2012 - 04:01:13 PDT)
- Brian Radak (Thu Mar 15 2012 - 06:59:11 PDT)
- Urszula Uciechowska (Thu Mar 15 2012 - 06:24:26 PDT)
[AMBER] Query on error
- abinayar.imsc.res.in (Fri Mar 30 2012 - 05:39:19 PDT)
[AMBER] Query on error :Atom does not have a type
- Jason Swails (Fri Mar 30 2012 - 07:15:33 PDT)
- abinayar.imsc.res.in (Fri Mar 30 2012 - 05:52:49 PDT)
[AMBER] Question about output files
- case (Wed Mar 07 2012 - 14:59:08 PST)
- lnedialkova.gmail.com (Wed Mar 07 2012 - 14:18:42 PST)
[AMBER] Question about Simulated Annealing procedure
- filip fratev (Mon Mar 05 2012 - 06:08:35 PST)
- Carlos Simmerling (Mon Mar 05 2012 - 05:19:43 PST)
- filip fratev (Sun Mar 04 2012 - 18:29:13 PST)
[AMBER] R: tleap and water molecules
- Giovanni Pavan (Tue Mar 13 2012 - 03:19:05 PDT)
[AMBER] RED resp step failed
- Albert (Wed Mar 07 2012 - 22:24:46 PST)
- Ismail, Mohd F. (Tue Mar 06 2012 - 13:41:45 PST)
- Albert (Tue Mar 06 2012 - 11:38:11 PST)
[AMBER] Replica Exchange
- Adrian Roitberg (Wed Mar 14 2012 - 08:40:46 PDT)
- Logan Ahlstrom (Wed Mar 14 2012 - 08:34:59 PDT)
- Alex Rodriguez (Wed Mar 14 2012 - 08:32:40 PDT)
- Carlos Simmerling (Wed Mar 14 2012 - 08:29:16 PDT)
- Indrajit Deb (Wed Mar 14 2012 - 08:29:19 PDT)
- Rajendra Sharma (Wed Mar 14 2012 - 08:22:38 PDT)
- Dmitry Mukha (Tue Mar 13 2012 - 13:34:23 PDT)
- Rajendra Sharma (Tue Mar 13 2012 - 08:08:06 PDT)
[AMBER] Residual Dipolar Coupling
- case (Wed Mar 07 2012 - 05:04:23 PST)
- Rahul Banerjee (Tue Mar 06 2012 - 13:32:27 PST)
[AMBER] restrain water in a solvatecap
- liu junjun (Mon Mar 19 2012 - 20:40:22 PDT)
- Yi An (Mon Mar 19 2012 - 13:01:44 PDT)
- Yi An (Thu Mar 15 2012 - 10:05:22 PDT)
[AMBER] rfree: Error decoding variable 1 3 from:
- Jason Swails (Thu Mar 29 2012 - 11:42:44 PDT)
- David A Case (Thu Mar 29 2012 - 07:47:25 PDT)
- Elisa Frezza (Thu Mar 29 2012 - 06:46:30 PDT)
- Jason Swails (Thu Mar 29 2012 - 06:33:42 PDT)
- Elisa Frezza (Thu Mar 29 2012 - 06:04:47 PDT)
[AMBER] rigid body simulation
- Ilyas Yildirim (Thu Mar 15 2012 - 12:36:48 PDT)
- David A Case (Thu Mar 15 2012 - 12:30:40 PDT)
- Qian Wang (Thu Mar 15 2012 - 08:19:06 PDT)
[AMBER] saltconc and string parameters in MM/PB(GB)SA
- Aron Broom (Thu Mar 08 2012 - 11:21:44 PST)
- mish (Thu Mar 08 2012 - 11:10:10 PST)
- Thomas Cheatham III (Thu Mar 08 2012 - 10:00:30 PST)
- mish (Thu Mar 08 2012 - 09:34:00 PST)
[AMBER] SASA Plot
- setyanto md (Wed Mar 07 2012 - 21:05:23 PST)
- Daniel Roe (Wed Mar 07 2012 - 09:27:56 PST)
- setyanto md (Wed Mar 07 2012 - 00:51:29 PST)
- Bruno Luís Pinto de Oliveira (Tue Mar 06 2012 - 07:00:49 PST)
- Daniel Roe (Tue Mar 06 2012 - 04:05:16 PST)
- Rajeswari A. (Tue Mar 06 2012 - 03:31:04 PST)
- Beale, John (Tue Mar 06 2012 - 03:08:06 PST)
[AMBER] Segmentation fault
- Ben Roberts (Thu Mar 29 2012 - 02:37:53 PDT)
- Agostino Bruno (Thu Mar 29 2012 - 01:06:09 PDT)
- Ben Roberts (Wed Mar 28 2012 - 13:22:06 PDT)
- Agostino Bruno (Wed Mar 28 2012 - 08:33:15 PDT)
[AMBER] separated thermostat in AMBER
- David A Case (Fri Mar 09 2012 - 06:54:24 PST)
- mjyang (Fri Mar 09 2012 - 05:25:57 PST)
[AMBER] SHAKE not available for parallel runs
- case (Wed Mar 07 2012 - 14:55:54 PST)
- CHAMI F. (Wed Mar 07 2012 - 12:30:51 PST)
[AMBER] simulation with metal-containing ligands
- Fati (Thu Mar 15 2012 - 05:01:04 PDT)
[AMBER] slow : amber job
- Aron Broom (Sat Mar 03 2012 - 20:03:51 PST)
- akshar bhosale (Sat Mar 03 2012 - 19:21:33 PST)
- Carlos Simmerling (Sat Mar 03 2012 - 10:35:22 PST)
- akshar bhosale (Sat Mar 03 2012 - 10:26:45 PST)
- Jason Swails (Sat Mar 03 2012 - 04:34:23 PST)
- akshar bhosale (Fri Mar 02 2012 - 19:14:20 PST)
- Cannon, John F. (Thu Mar 01 2012 - 10:27:29 PST)
- Aron Broom (Thu Mar 01 2012 - 10:02:55 PST)
- akshar bhosale (Thu Mar 01 2012 - 09:44:09 PST)
[AMBER] test failure in the AMBERTOOL installation
- Acoot Brett (Sat Mar 31 2012 - 23:26:34 PDT)
[AMBER] Test if MD converged or not.
- g t (Thu Mar 22 2012 - 00:14:36 PDT)
[AMBER] the problem of RAMD
- Vlad Cojocaru (Fri Mar 16 2012 - 03:52:47 PDT)
- xiaojiong (Fri Mar 16 2012 - 02:02:50 PDT)
[AMBER] The value of Delta G is positive after MMPBSA calculation for metalloprotein
- JiYuan Liu (Tue Mar 13 2012 - 20:02:24 PDT)
[AMBER] tleap and water molecules
- Enrico Caldarulo (Tue Mar 13 2012 - 03:05:36 PDT)
[AMBER] To generate more than one structure using ptraj
- Jason Swails (Tue Mar 20 2012 - 10:04:48 PDT)
- Souvik Sur (Mon Mar 19 2012 - 22:56:44 PDT)
- Jason Swails (Mon Mar 19 2012 - 08:17:12 PDT)
- Souvik Sur (Mon Mar 19 2012 - 06:36:31 PDT)
[AMBER] top and crd file error
- Aron Broom (Thu Mar 01 2012 - 23:34:47 PST)
- kanika sharma (Thu Mar 01 2012 - 23:22:07 PST)
- Aron Broom (Thu Mar 01 2012 - 23:13:01 PST)
- kanika sharma (Thu Mar 01 2012 - 22:59:03 PST)
[AMBER] turning off solute-solvent interactions
- Brian Radak (Mon Mar 05 2012 - 14:01:27 PST)
- Andy Ballard (Mon Mar 05 2012 - 13:22:17 PST)
[AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues
- FyD (Tue Mar 27 2012 - 06:30:52 PDT)
- Bala subramanian (Mon Mar 26 2012 - 12:05:29 PDT)
- Ross Walker (Mon Mar 26 2012 - 09:37:02 PDT)
- Bala subramanian (Mon Mar 26 2012 - 08:23:49 PDT)
[AMBER] Use of SLEF1 force field in Amber
- Gonzalo Jimenez (Wed Mar 14 2012 - 16:40:40 PDT)
- CHAMI F. (Wed Mar 14 2012 - 11:52:05 PDT)
- Gonzalo Jimenez (Tue Mar 13 2012 - 00:56:54 PDT)
[AMBER] using GAFF with TIP3P model for simulation of solvated organic molecule
- Jason Swails (Sun Mar 04 2012 - 17:46:13 PST)
- Andy Ballard (Sun Mar 04 2012 - 12:19:22 PST)
[AMBER] Velocity
- Adrian Roitberg (Wed Mar 07 2012 - 11:05:50 PST)
- kirtana S (Wed Mar 07 2012 - 11:02:32 PST)
[AMBER] Viewing with VMD bonds set by the "bond" command
- FyD (Fri Mar 09 2012 - 10:10:27 PST)
- Francesco Pietra (Thu Mar 08 2012 - 10:27:58 PST)
- francesco oteri (Thu Mar 08 2012 - 06:27:46 PST)
- FyD (Thu Mar 08 2012 - 03:48:31 PST)
- Francesco Pietra (Thu Mar 08 2012 - 03:30:29 PST)
- FyD (Thu Mar 08 2012 - 03:22:40 PST)
- Francesco Pietra (Thu Mar 08 2012 - 03:01:34 PST)
- Lorenzo Gontrani (Thu Mar 08 2012 - 02:21:57 PST)
- Francesco Pietra (Thu Mar 08 2012 - 01:48:48 PST)
- Lorenzo Gontrani (Thu Mar 08 2012 - 00:42:00 PST)
- Francesco Pietra (Wed Mar 07 2012 - 23:59:23 PST)
[AMBER] Water coordinated with transition metal
- ashwini gupta (Wed Mar 21 2012 - 04:40:32 PDT)
- Ben Roberts (Wed Mar 21 2012 - 03:41:10 PDT)
- ashwini gupta (Wed Mar 21 2012 - 03:33:29 PDT)
- Ben Roberts (Wed Mar 21 2012 - 02:40:50 PDT)
- ashwini gupta (Wed Mar 21 2012 - 02:09:04 PDT)
- Ben Roberts (Wed Mar 21 2012 - 00:21:35 PDT)
- ashwini gupta (Tue Mar 20 2012 - 23:36:40 PDT)
[AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW
- FyD (Tue Mar 20 2012 - 09:26:58 PDT)
- JiYuan Liu (Mon Mar 19 2012 - 05:51:51 PDT)
- Ben Roberts (Mon Mar 19 2012 - 01:30:42 PDT)
[AMBER] Which methodology could estimate the binding affinity of zinc containing metalloprotei(wrong string) �Cligand complex accurately?
- JiYuan Liu (Fri Mar 30 2012 - 08:00:35 PDT)
RED resp step failed
- FyD (Wed Mar 07 2012 - 23:30:59 PST)
Viewing with VMD bonds set by the "bond" command
- Francesco Pietra (Thu Mar 08 2012 - 23:39:17 PST)

Amber Archive Mar 2012 by subject