Amber Archive Dec 2015: by subject

[AMBER] [Amber] Imaginary Frequencies from nmode()
- Guqin Shi (Tue Dec 15 2015 - 13:51:27 PST)
- David A Case (Sat Dec 12 2015 - 13:32:03 PST)
- Guqin Shi (Tue Dec 08 2015 - 13:19:53 PST)
[AMBER] [Amber] nmode() results with imaginary frequencies
- Guqin Shi (Sun Dec 06 2015 - 11:13:28 PST)
- Guqin Shi (Wed Dec 02 2015 - 06:15:58 PST)
- Jason Swails (Tue Dec 01 2015 - 19:05:55 PST)
- Guqin Shi (Tue Dec 01 2015 - 15:18:17 PST)
[AMBER] A problem about using AMBER
- 东不拉 (Sun Dec 27 2015 - 21:34:01 PST)
[AMBER] Add charges to new molecule with out Gaussian package
- V. Kumar (Sat Dec 05 2015 - 12:01:09 PST)
- Karl Kirschner (Sat Dec 05 2015 - 06:42:07 PST)
- V. Kumar (Sat Dec 05 2015 - 06:08:41 PST)
[AMBER] AMBER 12 XLEAP options were disabled
- V. Kumar (Thu Dec 03 2015 - 06:14:02 PST)
- David A Case (Thu Dec 03 2015 - 05:28:32 PST)
- Jason Swails (Thu Dec 03 2015 - 04:36:01 PST)
- V. Kumar (Thu Dec 03 2015 - 03:36:58 PST)
[AMBER] Amber 14, sander.MPI, NaN
- David A Case (Sat Dec 12 2015 - 07:42:14 PST)
- Starovoytov, Oleg (Tue Dec 08 2015 - 12:38:07 PST)
[AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera
- V. Kumar (Wed Dec 02 2015 - 12:42:01 PST)
- V. Kumar (Wed Dec 02 2015 - 12:17:32 PST)
- Daniel Roe (Wed Dec 02 2015 - 12:06:07 PST)
- Carlos Simmerling (Wed Dec 02 2015 - 11:56:23 PST)
- V. Kumar (Wed Dec 02 2015 - 11:38:00 PST)
[AMBER] average structure
- Ross Walker (Thu Dec 17 2015 - 14:44:04 PST)
- Hai Nguyen (Thu Dec 17 2015 - 14:43:59 PST)
- Andrew Bostick (Thu Dec 17 2015 - 14:35:59 PST)
[AMBER] bond connections
- mohammad r (Mon Dec 07 2015 - 00:08:15 PST)
- Jason Swails (Sun Dec 06 2015 - 16:54:45 PST)
- mohammad r (Sun Dec 06 2015 - 14:53:43 PST)
- Jason Swails (Sun Dec 06 2015 - 06:07:45 PST)
- Bill (Sun Dec 06 2015 - 01:24:34 PST)
- mohammad r (Sun Dec 06 2015 - 00:59:33 PST)
- Jonathan Sheehan (Sun Dec 06 2015 - 00:41:34 PST)
- Jason Swails (Sat Dec 05 2015 - 12:05:47 PST)
- Jason Swails (Thu Dec 03 2015 - 20:39:04 PST)
- Jason Swails (Thu Dec 03 2015 - 12:59:30 PST)
- mohammad r (Thu Dec 03 2015 - 11:27:51 PST)
- Brian Radak (Thu Dec 03 2015 - 10:16:56 PST)
- Jason Swails (Thu Dec 03 2015 - 10:05:15 PST)
- David A Case (Thu Dec 03 2015 - 05:26:15 PST)
- Jason Swails (Thu Dec 03 2015 - 04:41:11 PST)
- mohammad r (Thu Dec 03 2015 - 04:26:05 PST)
- Bill (Wed Dec 02 2015 - 23:51:04 PST)
- mohammad r (Wed Dec 02 2015 - 23:02:03 PST)
[AMBER] bug or not bug ????
- David A Case (Sun Dec 20 2015 - 08:42:40 PST)
- Åke Sandgren (Sat Dec 19 2015 - 05:24:05 PST)
- Min Li (Tue Dec 01 2015 - 19:54:38 PST)
[AMBER] Can I use the Nose-Hoover thermostat in Amber
- Jason Swails (Tue Dec 01 2015 - 19:02:59 PST)
- jfliu (Tue Dec 01 2015 - 18:12:54 PST)
[AMBER] charge fitting procedure in amber
- Karl Kirschner (Tue Dec 15 2015 - 02:16:13 PST)
- Karl Kirschner (Tue Dec 15 2015 - 00:16:51 PST)
- conor parks (Mon Dec 14 2015 - 13:27:21 PST)
[AMBER] Charmm-gui conversion
- mohammad r (Fri Dec 11 2015 - 07:30:06 PST)
- Jason Swails (Fri Dec 11 2015 - 05:40:43 PST)
- Jason Swails (Fri Dec 11 2015 - 04:07:01 PST)
- Bill Ross (Fri Dec 11 2015 - 00:05:29 PST)
- mohammad r (Thu Dec 10 2015 - 21:06:04 PST)
- David A Case (Thu Dec 10 2015 - 13:34:08 PST)
- mohammad r (Thu Dec 10 2015 - 13:28:46 PST)
- mohammad r (Thu Dec 10 2015 - 13:13:25 PST)
- Brian Radak (Thu Dec 10 2015 - 13:12:26 PST)
- mohammad r (Thu Dec 10 2015 - 12:57:17 PST)
- Bill Ross (Thu Dec 10 2015 - 12:31:36 PST)
- mohammad r (Thu Dec 10 2015 - 12:25:11 PST)
- Brian Radak (Wed Dec 09 2015 - 12:55:29 PST)
- Bill Ross (Wed Dec 09 2015 - 12:48:44 PST)
- mohammad r (Wed Dec 09 2015 - 12:31:01 PST)
- Arnoult, Eric [JRDUS] (Wed Dec 09 2015 - 12:31:09 PST)
- Bill Ross (Wed Dec 09 2015 - 12:07:49 PST)
- mohammad r (Wed Dec 09 2015 - 11:58:29 PST)
- Arnoult, Eric [JRDUS] (Wed Dec 09 2015 - 10:26:54 PST)
- Brian Radak (Wed Dec 09 2015 - 08:10:06 PST)
- mohammad r (Wed Dec 09 2015 - 08:02:20 PST)
[AMBER] confusion in xleap for ligand and comlex
- David A Case (Tue Dec 15 2015 - 04:53:20 PST)
- Ayesha Kanwal (Mon Dec 14 2015 - 23:50:07 PST)
[AMBER] Confusion on "No Pressure"
- Jason Swails (Thu Dec 17 2015 - 09:27:41 PST)
- Robert Molt (Thu Dec 17 2015 - 08:38:13 PST)
[AMBER] cpptraj average structure warning
- George Tzotzos (Thu Dec 17 2015 - 02:22:12 PST)
- George Tzotzos (Thu Dec 17 2015 - 01:05:26 PST)
[AMBER] cpptraj grid command
- Thomas Fox (Mon Dec 14 2015 - 08:24:46 PST)
[AMBER] cpptraj: grid and gist
- Thomas Fox (Tue Dec 08 2015 - 08:50:15 PST)
- Jason Swails (Tue Dec 08 2015 - 05:28:50 PST)
- Thomas Fox (Tue Dec 08 2015 - 05:15:38 PST)
- Steven Ramsey (Mon Dec 07 2015 - 08:34:29 PST)
- Daniel Roe (Mon Dec 07 2015 - 07:39:02 PST)
- Thomas Fox (Mon Dec 07 2015 - 02:22:19 PST)
[AMBER] different dielectric constant value for polar non-polar hydrophobic residue in MMGBSA
- David A Case (Wed Dec 30 2015 - 05:30:30 PST)
- bharat lakhani (Tue Dec 29 2015 - 21:47:05 PST)
[AMBER] Docking before MD of scratch ligands OR not
- Jason Swails (Tue Dec 01 2015 - 05:13:12 PST)
- muhammad tahir ayub (Mon Nov 30 2015 - 23:49:57 PST)
[AMBER] Error in running AMBER 12 GPU simulations
- David A Case (Thu Dec 31 2015 - 08:22:59 PST)
- Yogeeshwar Ajjugal (Thu Dec 31 2015 - 05:35:30 PST)
[AMBER] Error message while running alanine dipeptide tutorial (minimization)
- David A Case (Fri Dec 04 2015 - 05:13:37 PST)
- Bill (Fri Dec 04 2015 - 01:02:05 PST)
- Nikolay N. Kuzmich (Fri Dec 04 2015 - 00:51:21 PST)
- Bill (Tue Dec 01 2015 - 02:13:33 PST)
- Nikolay N. Kuzmich (Tue Dec 01 2015 - 01:27:53 PST)
- Nikolay N. Kuzmich (Tue Dec 01 2015 - 01:08:49 PST)
[AMBER] External forces
- Christina Bergonzo (Tue Dec 08 2015 - 07:26:42 PST)
- Josh Berryman (Tue Dec 08 2015 - 02:12:00 PST)
- Jack Shepherd (Mon Dec 07 2015 - 09:29:07 PST)
[AMBER] Finding PDF of individual dihedral angles
- Mahendra B Thapa (Mon Dec 21 2015 - 09:27:37 PST)
[AMBER] free energy of solvation of small molecules
- Hannes Loeffler (Mon Dec 14 2015 - 01:35:43 PST)
- Fabian gmail (Sun Dec 13 2015 - 06:10:25 PST)
- Fabian Glaser (Mon Dec 07 2015 - 13:07:03 PST)
- David A Case (Mon Dec 07 2015 - 07:06:33 PST)
- Fabian gmail (Mon Dec 07 2015 - 06:58:51 PST)
- Fabian Glaser (Fri Dec 04 2015 - 07:06:22 PST)
- Hannes Loeffler (Fri Dec 04 2015 - 06:21:23 PST)
- Fabian Glaser (Fri Dec 04 2015 - 04:09:29 PST)
- Hannes Loeffler (Fri Dec 04 2015 - 01:44:40 PST)
- Fabian gmail (Thu Dec 03 2015 - 04:15:17 PST)
- Hannes Loeffler (Thu Dec 03 2015 - 03:46:45 PST)
- Hannes Loeffler (Thu Dec 03 2015 - 03:35:12 PST)
- Fabian gmail (Wed Dec 02 2015 - 06:55:43 PST)
- Fabian gmail (Wed Dec 02 2015 - 06:49:20 PST)
- Jason Swails (Wed Dec 02 2015 - 05:42:10 PST)
- Fabian gmail (Wed Dec 02 2015 - 04:41:31 PST)
[AMBER] gnu plot of cpptraj Secstruct
- George Tzotzos (Fri Dec 11 2015 - 11:32:42 PST)
- Lachele Foley (Fri Dec 11 2015 - 11:28:53 PST)
- George Tzotzos (Fri Dec 11 2015 - 07:58:36 PST)
- Daniel Roe (Fri Dec 11 2015 - 07:55:28 PST)
- George Tzotzos (Fri Dec 11 2015 - 06:01:54 PST)
- Jason Swails (Fri Dec 11 2015 - 05:43:30 PST)
- George Tzotzos (Fri Dec 11 2015 - 04:22:28 PST)
- Lachele Foley (Thu Dec 10 2015 - 20:55:47 PST)
- George Tzotzos (Thu Dec 10 2015 - 13:42:20 PST)
[AMBER] GPU support
- Rupak Pal (Tue Dec 22 2015 - 01:03:46 PST)
- Jason Swails (Mon Dec 21 2015 - 08:53:38 PST)
- Ross Walker (Mon Dec 21 2015 - 08:31:07 PST)
- Rupak Pal (Sun Dec 20 2015 - 22:51:10 PST)
[AMBER] Group specification
- David A Case (Tue Dec 29 2015 - 17:43:05 PST)
- Havva Mehralitabar (Mon Dec 28 2015 - 12:52:51 PST)
[AMBER] HBOND_water mediated
- Lara rajam (Thu Dec 17 2015 - 06:49:00 PST)
- Daniel Roe (Tue Dec 15 2015 - 09:01:24 PST)
- Lara rajam (Mon Dec 14 2015 - 07:16:58 PST)
[AMBER] High PB deltaG values from MMPBSA.py calculation
- anu chandra (Sat Dec 05 2015 - 03:46:40 PST)
- Ray Luo, Ph.D. (Thu Dec 03 2015 - 10:26:51 PST)
- anu chandra (Thu Dec 03 2015 - 02:28:58 PST)
- Ray Luo, Ph.D. (Wed Dec 02 2015 - 16:09:14 PST)
- anu chandra (Wed Dec 02 2015 - 06:48:05 PST)
- Jason Swails (Wed Dec 02 2015 - 06:25:20 PST)
- anu chandra (Wed Dec 02 2015 - 05:59:48 PST)
[AMBER] How does the collision frequency gamma_ln value affect the temperature in Langevin dynamics
- David A Case (Wed Dec 02 2015 - 06:03:08 PST)
- jfliu (Tue Dec 01 2015 - 18:07:17 PST)
[AMBER] How to calculate the interplanar angle between 2 Trp residues?
- Daniel Roe (Mon Dec 21 2015 - 08:38:44 PST)
- Yew Mun Yip (Sun Dec 20 2015 - 01:12:00 PST)
[AMBER] How to have special residues in trajectory file using cpptraj
- Daniel Roe (Thu Dec 17 2015 - 07:23:29 PST)
- Kenneth Huang (Thu Dec 17 2015 - 06:39:14 PST)
- shahab shariati (Thu Dec 17 2015 - 06:14:43 PST)
[AMBER] How to run two single-card jobs on the node with two GPU cards
- Kenneth Huang (Mon Nov 30 2015 - 22:34:36 PST)
- Stephen Wang (Mon Nov 30 2015 - 22:25:57 PST)
[AMBER] ig=-1 for multi production runs
- Jason Swails (Mon Dec 21 2015 - 06:38:43 PST)
- Fabian gmail (Mon Dec 21 2015 - 05:36:04 PST)
- David A Case (Mon Dec 21 2015 - 05:20:50 PST)
- Jason Swails (Mon Dec 21 2015 - 05:09:40 PST)
- Fabian gmail (Mon Dec 21 2015 - 04:31:01 PST)
[AMBER] Irregular ligand positioning in simulations
- Daniel Roe (Tue Dec 15 2015 - 08:38:36 PST)
- Carlos Simmerling (Tue Dec 15 2015 - 03:08:32 PST)
- Anasuya Dighe (Mon Dec 14 2015 - 22:58:43 PST)
[AMBER] Is triplicate analysis required for pmemd.MPI and ig=-1?
- Ross Walker (Thu Dec 17 2015 - 14:56:01 PST)
- Morrow,John Kenneth (Thu Dec 17 2015 - 14:25:51 PST)
[AMBER] kinetic
- Andrea Spitaleri (Fri Dec 04 2015 - 06:24:20 PST)
- David A Case (Wed Dec 02 2015 - 06:06:13 PST)
- Jason Swails (Wed Dec 02 2015 - 05:34:35 PST)
- Ziba Bahadori (Wed Dec 02 2015 - 04:14:32 PST)
[AMBER] ligand is not opening in the binding site of protein
- Bill Ross (Fri Dec 11 2015 - 00:36:03 PST)
- muhammad tahir ayub (Fri Dec 11 2015 - 00:22:36 PST)
[AMBER] Ligand's parameterization
- Karl Kirschner (Thu Dec 17 2015 - 04:02:27 PST)
- Mathy Froeyen (Wed Dec 16 2015 - 06:47:50 PST)
- Carlos Simmerling (Wed Dec 16 2015 - 06:20:13 PST)
- Trang Nguyen (Wed Dec 16 2015 - 06:07:55 PST)
[AMBER] mac hangs when compile ambertools15 on El capitan
- Jason Swails (Wed Dec 02 2015 - 04:40:26 PST)
- Yong Yao (Tue Dec 01 2015 - 20:10:45 PST)
- Jason Swails (Tue Dec 01 2015 - 05:07:45 PST)
- Yong Yao (Mon Nov 30 2015 - 20:54:28 PST)
- Yong Yao (Mon Nov 30 2015 - 19:13:31 PST)
[AMBER] malloc error during MM-PBSA calculation on AMBER14 ... mmpbsa_py_energy: malloc.c:2372: sysmalloc
- Jason Swails (Tue Dec 01 2015 - 08:50:04 PST)
- Mijiddorj Batsaikhan (Tue Dec 01 2015 - 08:44:19 PST)
[AMBER] mbar
- Hannes Loeffler (Tue Dec 15 2015 - 09:02:41 PST)
- Johannes Löffler (Tue Dec 15 2015 - 08:42:25 PST)
- Hannes Loeffler (Tue Dec 15 2015 - 08:14:07 PST)
- Brian Radak (Tue Dec 15 2015 - 07:35:36 PST)
- Johannes Loeffler (Tue Dec 15 2015 - 07:24:02 PST)
- Hannes Loeffler (Tue Dec 15 2015 - 07:17:05 PST)
- Johannes Loeffler (Tue Dec 15 2015 - 06:42:18 PST)
- Hannes Loeffler (Tue Dec 15 2015 - 05:46:51 PST)
- Johannes Loeffler (Tue Dec 15 2015 - 05:36:06 PST)
[AMBER] MD study of transition of protein from one conformation to another
- Abhilash J (Mon Dec 28 2015 - 20:58:55 PST)
- David A Case (Mon Dec 28 2015 - 12:42:40 PST)
- Abhilash J (Mon Dec 28 2015 - 09:40:28 PST)
[AMBER] Minimization after simulated annealing (0° C) ans CSH script need to be combined
- V. Kumar (Wed Dec 16 2015 - 09:14:26 PST)
[AMBER] mmgbsa_CalcError
- Jason Swails (Tue Dec 01 2015 - 11:08:10 PST)
- Atila Petrosian (Tue Dec 01 2015 - 10:59:15 PST)
- Jason Swails (Tue Dec 01 2015 - 05:19:25 PST)
- Atila Petrosian (Tue Dec 01 2015 - 04:13:48 PST)
[AMBER] MMPBSA bad atom type error persisting
- Kenneth Huang (Mon Dec 07 2015 - 10:40:13 PST)
[AMBER] MMPBSA error
- Jason Swails (Wed Dec 23 2015 - 10:09:59 PST)
- Lara rajam (Wed Dec 23 2015 - 10:05:05 PST)
[AMBER] MMPBSA.py.MPI compling issue
- Daniel Roe (Tue Dec 15 2015 - 08:51:57 PST)
- Marc Zhang (Mon Dec 14 2015 - 13:22:14 PST)
[AMBER] Not matching test AMBER14 with CUDA
- Jason Swails (Tue Dec 01 2015 - 04:55:29 PST)
- Mijiddorj Batsaikhan (Mon Nov 30 2015 - 20:20:13 PST)
[AMBER] OSX 10.11.1: Amber installation problem
- George Tzotzos (Thu Dec 10 2015 - 02:16:14 PST)
- Jason Swails (Wed Dec 09 2015 - 12:34:25 PST)
- George Tzotzos (Wed Dec 09 2015 - 10:19:47 PST)
[AMBER] per-residue or pairwise per-residue basis in decomposing the free energy contributions to the binding free energy
- Jason Swails (Sun Dec 06 2015 - 13:38:32 PST)
- Andrew Bostick (Sun Dec 06 2015 - 10:45:18 PST)
- Jason Swails (Sat Dec 05 2015 - 12:06:57 PST)
- Andrew Bostick (Sat Dec 05 2015 - 11:20:19 PST)
[AMBER] pH-REMD GPU runs
- Jason Swails (Wed Dec 02 2015 - 06:23:26 PST)
- Adrian Roitberg (Wed Dec 02 2015 - 06:01:16 PST)
- Arjun Sharma (Wed Dec 02 2015 - 05:53:22 PST)
[AMBER] pmemd issue
- David A Case (Mon Dec 21 2015 - 05:18:42 PST)
- Jason Swails (Mon Dec 21 2015 - 05:03:42 PST)
- Mahmoud A. A. Ibrahim (Mon Dec 21 2015 - 02:04:08 PST)
[AMBER] pmemd.cuda with CoM restraints
- Charles Lin (Thu Dec 03 2015 - 22:30:04 PST)
- 達南杰 (Thu Dec 03 2015 - 20:09:24 PST)
- Marc van der Kamp (Thu Dec 03 2015 - 09:25:00 PST)
- Charles Lin (Thu Dec 03 2015 - 09:22:33 PST)
- 達南杰 (Thu Dec 03 2015 - 06:56:20 PST)
[AMBER] Principal Component Analysis
- Daniel Roe (Wed Dec 02 2015 - 10:00:49 PST)
- Jason Swails (Wed Dec 02 2015 - 05:50:24 PST)
- Beale, John (Wed Dec 02 2015 - 02:23:57 PST)
[AMBER] problem in adding ACE and NME to CSX.
- Jason Swails (Sun Dec 13 2015 - 08:28:16 PST)
- Saman Yousuf ali (Sun Dec 13 2015 - 04:58:06 PST)
[AMBER] Problem in interpreting snapshot_statistics.out after per-residue decomposition analysis
- Soong Jiaxin (Wed Dec 30 2015 - 19:36:54 PST)
[AMBER] problem in plotting secondary structure graph
- Daniel Roe (Tue Dec 15 2015 - 08:12:41 PST)
- Sehrish Naz (Mon Dec 14 2015 - 23:19:32 PST)
[AMBER] problem with "closest" waters being wrapped
- Thomas Cheatham (Thu Dec 03 2015 - 14:53:25 PST)
- Marc van der Kamp (Thu Dec 03 2015 - 14:45:40 PST)
- Kalenkiewicz, Andrew (NIH/NICHD) [F] (Thu Dec 03 2015 - 14:34:59 PST)
- Daniel Roe (Thu Dec 03 2015 - 13:20:04 PST)
- Kalenkiewicz, Andrew (NIH/NICHD) [F] (Thu Dec 03 2015 - 13:17:57 PST)
[AMBER] Problem with GPU equilibration step [ cudaMalloc GpuBuffer::Allocate failed out of memory]
- Yogeeshwar Ajjugal (Wed Dec 09 2015 - 22:04:51 PST)
- Jason Swails (Wed Dec 09 2015 - 04:46:00 PST)
- Yogeeshwar Ajjugal (Tue Dec 08 2015 - 21:42:25 PST)
[AMBER] problem with hist command in cpptraj in AmberTools15
- Osman, Roman (Tue Dec 08 2015 - 16:35:56 PST)
- Daniel Roe (Tue Dec 08 2015 - 14:03:47 PST)
- Osman, Roman (Tue Dec 08 2015 - 13:22:19 PST)
- Daniel Roe (Tue Dec 08 2015 - 13:00:53 PST)
- Osman, Roman (Tue Dec 08 2015 - 12:59:46 PST)
[AMBER] Problem with initial complex structure for TI
- Kalenkiewicz, Andrew (NIH/NICHD) [F] (Mon Dec 14 2015 - 13:37:56 PST)
- Kalenkiewicz, Andrew (NIH/NICHD) [F] (Fri Dec 11 2015 - 15:17:11 PST)
[AMBER] Problems regarding using ZAFF
- Bill Ross (Sun Dec 13 2015 - 23:01:56 PST)
[AMBER] QM/MM Implementation Details
- Jim William Snyder Jr (Thu Dec 03 2015 - 10:38:35 PST)
[AMBER] Question Regarding Input File Preparation
- David A Case (Fri Dec 04 2015 - 05:10:24 PST)
- Jason Swails (Fri Dec 04 2015 - 04:29:44 PST)
- Ziheng Wang (Thu Dec 03 2015 - 18:35:49 PST)
[AMBER] RED vIII for Amber
- Steven M. Graham (Sun Dec 20 2015 - 15:40:56 PST)
- Nash, Anthony (Sun Dec 20 2015 - 09:23:28 PST)
- Nash, Anthony (Sun Dec 13 2015 - 23:50:56 PST)
- Karl Kirschner (Sun Dec 13 2015 - 23:42:54 PST)
- Nash, Anthony (Sun Dec 13 2015 - 13:41:19 PST)
[AMBER] restraints on group of atoms
- David A Case (Mon Dec 14 2015 - 05:06:57 PST)
- Dhananjay (Mon Dec 14 2015 - 01:47:47 PST)
[AMBER] rmsd as order parameter in umbrella sampling
- Carlos Simmerling (Mon Dec 07 2015 - 03:18:25 PST)
- Srinivasaraghavan Kannan (Sun Dec 06 2015 - 19:09:46 PST)
[AMBER] Simulation of the docked complex with phosphorylated tyrosine
- Pallavi Mohanty (Fri Dec 04 2015 - 01:27:35 PST)
- David A Case (Thu Dec 03 2015 - 05:33:30 PST)
- Pallavi Mohanty (Thu Dec 03 2015 - 03:53:38 PST)
[AMBER] standard deviation of Hbond lengths and angles
- Hai Nguyen (Mon Dec 07 2015 - 12:24:16 PST)
- Daniel Roe (Mon Dec 07 2015 - 08:04:07 PST)
- Hadeer ELHabashy (Sun Dec 06 2015 - 07:20:12 PST)
[AMBER] Termodinamic Integration setup error
- Hannes Loeffler (Thu Dec 17 2015 - 01:59:01 PST)
- Claire Coderch Boué (Thu Dec 17 2015 - 01:46:17 PST)
[AMBER] TI/MBAR energy re-calculating with imin5
- wliu (Wed Dec 23 2015 - 01:16:12 PST)
[AMBER] Time Step
- Wong Li Zhe (Mon Dec 14 2015 - 16:21:37 PST)
- Jason Swails (Mon Dec 14 2015 - 09:05:29 PST)
- Bill Ross (Sun Dec 13 2015 - 23:10:05 PST)
- Wong Li Zhe (Sun Dec 13 2015 - 23:01:18 PST)
[AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures
- V. Kumar (Sun Dec 20 2015 - 07:23:18 PST)
- Carlos Simmerling (Sun Dec 20 2015 - 06:44:15 PST)
- V. Kumar (Sun Dec 20 2015 - 05:27:03 PST)
- Carlos Simmerling (Sun Dec 20 2015 - 05:04:31 PST)
- V. Kumar (Sun Dec 20 2015 - 04:23:27 PST)
[AMBER] Utilizing two different nodes simultaneously for one job
- Jason Swails (Tue Dec 01 2015 - 05:11:15 PST)
- muhammad tahir ayub (Mon Nov 30 2015 - 22:35:26 PST)
[AMBER] Warning regarding "triangular bond"
- Bill Ross (Wed Dec 16 2015 - 11:45:48 PST)
- David A Case (Wed Dec 16 2015 - 04:57:44 PST)
- Xiong Jiawei (Tue Dec 15 2015 - 23:30:52 PST)
[AMBER] WARNING: There is a bond of 420.000806 angstroms between: ------- .R<LIG 546>.A<O2 28> and .R<LIG 546>.A<H2 31>
- Carlos Simmerling (Fri Dec 11 2015 - 07:48:59 PST)
- Andrew Bostick (Fri Dec 11 2015 - 07:30:16 PST)
[AMBER] Water model
- David A Case (Fri Dec 18 2015 - 08:17:38 PST)
- jfliu (Thu Dec 17 2015 - 05:07:40 PST)
[AMBER] weird output of SMD simulation combined with Constant pH
- Jason Swails (Mon Dec 07 2015 - 18:55:31 PST)
- Gustavo Seabra (Mon Dec 07 2015 - 17:34:47 PST)
- Jason Swails (Mon Dec 07 2015 - 12:14:30 PST)
- Gustavo Seabra (Mon Dec 07 2015 - 11:38:49 PST)
- Jason Swails (Mon Dec 07 2015 - 06:29:41 PST)
- zhonghe xu (Mon Dec 07 2015 - 06:25:27 PST)
[AMBER] which chain to select for MD simulation.
- Jason Swails (Wed Dec 30 2015 - 17:55:44 PST)
- Saman Yousuf ali (Wed Dec 30 2015 - 11:58:24 PST)
[AMBER] xleap terminal terminate
- Jason Swails (Fri Dec 04 2015 - 04:11:48 PST)
- Mary Dutta (Fri Dec 04 2015 - 02:22:17 PST)
- Ayesha Kanwal (Fri Dec 04 2015 - 00:36:07 PST)
- Jason Swails (Thu Dec 03 2015 - 04:42:50 PST)
- Ayesha Kanwal (Thu Dec 03 2015 - 04:33:08 PST)
[AMBER] xparmed.py
- Jason Swails (Tue Dec 08 2015 - 12:07:38 PST)
- Nathalie Willems (Tue Dec 08 2015 - 08:12:21 PST)
- Jason Swails (Tue Dec 08 2015 - 07:55:02 PST)
- Nathalie Willems (Tue Dec 08 2015 - 07:23:19 PST)
[AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond
- V. Kumar (Sat Dec 12 2015 - 05:58:42 PST)
- Pengfei Li (Fri Dec 11 2015 - 19:59:11 PST)
- V. Kumar (Thu Dec 10 2015 - 12:34:16 PST)
- Carlos Simmerling (Thu Dec 10 2015 - 12:08:08 PST)
- V. Kumar (Thu Dec 10 2015 - 08:05:43 PST)
- V. Kumar (Mon Nov 30 2015 - 23:54:06 PST)
- V. Kumar (Mon Nov 30 2015 - 23:52:56 PST)
How to use "divergence" command
- Daniel Roe (Wed Dec 09 2015 - 08:51:15 PST)
- Jason Swails (Wed Dec 09 2015 - 05:28:22 PST)
- Mahendra B Thapa (Wed Dec 09 2015 - 05:08:30 PST)

Amber Archive Dec 2015 by subject