Amber Archive Jun 2015: by subject

[AMBER] 2nd mail: subroutine qm_write_pdb
- Hector A. Baldoni (Wed Jun 17 2015 - 06:47:41 PDT)
[AMBER] [cpptraj] Changing frames in a trajectory file
- Juan Eiros Zamora (Tue Jun 16 2015 - 12:44:19 PDT)
- Hai Nguyen (Tue Jun 16 2015 - 12:27:44 PDT)
- Juan Eiros Zamora (Tue Jun 16 2015 - 12:19:08 PDT)
[AMBER] A possible bug in t leap when creating topology file ?
- Arun Srikanth (Thu Jun 25 2015 - 11:41:28 PDT)
- Arun Srikanth (Thu Jun 25 2015 - 11:22:11 PDT)
- Arun Srikanth (Thu Jun 25 2015 - 08:21:30 PDT)
- David A Case (Thu Jun 25 2015 - 05:22:39 PDT)
- Arun Srikanth (Wed Jun 24 2015 - 20:59:57 PDT)
[AMBER] A problem in using tLeap
- David A Case (Mon Jun 15 2015 - 16:19:38 PDT)
- Morteza Chehel Amirani (Mon Jun 15 2015 - 11:12:50 PDT)
[AMBER] About OH conformation in protonated Asp/Glu (ASH/GLH)
- Jason Swails (Fri Jun 19 2015 - 09:09:36 PDT)
- Marc van der Kamp (Fri Jun 19 2015 - 04:29:02 PDT)
[AMBER] Abrupt RMSD change during DNA simulation for a short interval of time
- jacob wick (Fri Jun 05 2015 - 01:08:00 PDT)
- Jason Swails (Thu Jun 04 2015 - 09:17:44 PDT)
- Daniel Roe (Thu Jun 04 2015 - 08:20:22 PDT)
- jacob wick (Thu Jun 04 2015 - 06:59:23 PDT)
- Jason Swails (Thu Jun 04 2015 - 06:51:00 PDT)
- jacob wick (Thu Jun 04 2015 - 06:38:17 PDT)
[AMBER] accuracy of FEW free energy calculation
- Jason Swails (Sun Jun 21 2015 - 10:00:55 PDT)
- Robert Molt (Sun Jun 21 2015 - 09:43:10 PDT)
- Jason Swails (Sun Jun 21 2015 - 09:30:01 PDT)
- Jiri Sponer (Sun Jun 21 2015 - 02:16:12 PDT)
- Albert (Sun Jun 21 2015 - 00:10:37 PDT)
- Jason Swails (Sat Jun 20 2015 - 18:56:36 PDT)
- Ross Walker (Sat Jun 20 2015 - 15:54:36 PDT)
- Albert (Sat Jun 20 2015 - 12:07:42 PDT)
- Jiri Sponer (Sat Jun 20 2015 - 10:38:09 PDT)
- Jason Swails (Sat Jun 20 2015 - 09:29:10 PDT)
- Albert (Fri Jun 19 2015 - 22:08:42 PDT)
- filip fratev (Fri Jun 19 2015 - 15:25:54 PDT)
- Ross Walker (Fri Jun 19 2015 - 14:31:32 PDT)
- Albert (Fri Jun 19 2015 - 13:44:15 PDT)
[AMBER] acpype fails to run on provided tests
- Jason Swails (Mon Jun 29 2015 - 21:16:57 PDT)
- Daniel Bork (Mon Jun 29 2015 - 13:27:14 PDT)
[AMBER] Align 1000 frames into one .crd file
- Hadeer ELHabashy (Fri Jun 26 2015 - 06:48:49 PDT)
- Jason Swails (Fri Jun 26 2015 - 05:40:35 PDT)
- Hadeer ELHabashy (Fri Jun 26 2015 - 04:17:46 PDT)
[AMBER] Alternative Membrane System Tutorial
- Parker de Waal (Sat Jun 13 2015 - 18:08:29 PDT)
[AMBER] amber 15 compiled with multiple GPUs
- nam kim (Thu Jun 25 2015 - 14:17:27 PDT)
- Ross Walker (Fri Jun 19 2015 - 09:06:55 PDT)
- nam kim (Fri Jun 19 2015 - 08:47:12 PDT)
- Kenneth Huang (Fri Jun 19 2015 - 07:55:34 PDT)
- nam kim (Fri Jun 19 2015 - 07:47:04 PDT)
- Nhai (Fri Jun 19 2015 - 00:10:10 PDT)
- nam kim (Thu Jun 18 2015 - 22:43:01 PDT)
[AMBER] AMBER Digest, Vol 1220, Issue 1
- Jason Swails (Mon Jun 15 2015 - 22:51:44 PDT)
- Huang (Mon Jun 15 2015 - 21:45:01 PDT)
[AMBER] Amber14 compatibility with GTX-760 GPU card
- Elvis Martis (Sat Jun 27 2015 - 12:35:28 PDT)
[AMBER] Amber14 compatibilty with GTX-760 GPU card
- Ross Walker (Fri Jun 26 2015 - 21:01:50 PDT)
- Hector A. Baldoni (Fri Jun 26 2015 - 20:57:51 PDT)
- Elvis Martis (Fri Jun 26 2015 - 20:46:37 PDT)
[AMBER] aMD and scaled MD simulation-NVT production runs
- Vlad Cojocaru (Mon Jun 22 2015 - 00:43:57 PDT)
- Neha Gandhi (Sun Jun 21 2015 - 23:24:25 PDT)
[AMBER] Announcement: AMBER Workshop - London, Mon July 6th to Fri July 10th 2015 - Registration deadline June 15th (this coming Monday!)
- Ross Walker (Wed Jun 10 2015 - 09:23:17 PDT)
[AMBER] Antechamber on regular nucleotides
- hannes.loeffler.stfc.ac.uk (Thu Jun 11 2015 - 23:38:48 PDT)
- Mrinda Jones (Thu Jun 11 2015 - 22:58:14 PDT)
- David A Case (Thu Jun 11 2015 - 07:08:42 PDT)
- Mrinda Jones (Thu Jun 11 2015 - 05:58:14 PDT)
[AMBER] Arsenic force field parametrization
- Pengfei Li (Fri Jun 26 2015 - 12:36:18 PDT)
- Sushi Shilpa (Tue Jun 02 2015 - 23:17:32 PDT)
- Pengfei Li (Mon Jun 01 2015 - 15:56:59 PDT)
[AMBER] Bad Frames in Corrupted Trajectories
- Daniel Roe (Wed Jun 03 2015 - 12:40:59 PDT)
- Amanda Li (Wed Jun 03 2015 - 12:22:55 PDT)
[AMBER] basic question - sanity check
- Jonathan Gough (Wed Jun 10 2015 - 12:04:21 PDT)
- Jason Swails (Wed Jun 10 2015 - 11:09:52 PDT)
- Jason Swails (Wed Jun 10 2015 - 11:07:42 PDT)
- Jonathan Gough (Wed Jun 10 2015 - 10:48:32 PDT)
[AMBER] binding energy for the frames
- Maryam Hamzehee (Wed Jun 17 2015 - 04:14:53 PDT)
[AMBER] Bug or feature of tleap
- Pengfei Li (Tue Jun 02 2015 - 19:19:31 PDT)
- Julio Dominguez (Tue Jun 02 2015 - 13:48:13 PDT)
- Jason Swails (Mon Jun 01 2015 - 18:06:27 PDT)
- David A Case (Mon Jun 01 2015 - 18:00:39 PDT)
- Julio Dominguez (Mon Jun 01 2015 - 16:01:27 PDT)
[AMBER] built-in scc-dftb method amber15
- Hector A. Baldoni (Mon Jun 29 2015 - 05:22:55 PDT)
[AMBER] Centre of Mass or geometry issue
- Jason Swails (Tue Jun 09 2015 - 04:36:59 PDT)
- Juan Eiros Zamora (Tue Jun 09 2015 - 02:14:20 PDT)
- Soumendranath Bhakat (Tue Jun 09 2015 - 02:02:49 PDT)
- Juan Eiros Zamora (Tue Jun 09 2015 - 01:57:33 PDT)
- Juan Eiros Zamora (Tue Jun 09 2015 - 01:55:58 PDT)
- Soumendranath Bhakat (Tue Jun 09 2015 - 01:33:49 PDT)
[AMBER] Charges for H-atoms in GLYCAM?
- Lachele Foley (Wed Jun 10 2015 - 11:37:04 PDT)
- David A Case (Wed Jun 10 2015 - 11:20:39 PDT)
- Lachele Foley (Wed Jun 10 2015 - 10:44:33 PDT)
- Chris (Wed Jun 10 2015 - 10:32:57 PDT)
[AMBER] circle of correlation - PCA - AMBERtools
- Jose Manuel Gally (Wed Jun 03 2015 - 07:33:36 PDT)
[AMBER] combine multiple trajectory
- Daniel Roe (Thu Jun 18 2015 - 08:25:54 PDT)
- Hai Nguyen (Wed Jun 17 2015 - 13:45:28 PDT)
- Yin, Guowei (Wed Jun 17 2015 - 13:33:18 PDT)
[AMBER] Compile Failure
- Jim Wu (Tue Jun 30 2015 - 21:12:54 PDT)
- Jason Swails (Tue Jun 30 2015 - 20:20:21 PDT)
- Jim Wu (Tue Jun 30 2015 - 19:44:41 PDT)
- Jason Swails (Tue Jun 30 2015 - 19:40:34 PDT)
- Jim Wu (Tue Jun 30 2015 - 15:06:36 PDT)
[AMBER] Connect atoms in a pdb created with nab
- Jean-Patrick Francoia (Thu Jun 18 2015 - 07:09:19 PDT)
- Jason Swails (Thu Jun 18 2015 - 07:05:16 PDT)
- Jean-Patrick Francoia (Thu Jun 18 2015 - 06:59:15 PDT)
- Jason Swails (Thu Jun 18 2015 - 06:47:29 PDT)
- Jean-Patrick Francoia (Thu Jun 18 2015 - 01:31:52 PDT)
[AMBER] conserved water in MMPBSA
- Albert (Fri Jun 12 2015 - 07:16:56 PDT)
- George Tzotzos (Fri Jun 12 2015 - 06:31:38 PDT)
- Alessandro Contini (Fri Jun 12 2015 - 06:15:56 PDT)
- Albert (Fri Jun 12 2015 - 06:03:15 PDT)
[AMBER] Converting Gromacs topology files to Amber format
- Jason Swails (Mon Jun 15 2015 - 07:37:34 PDT)
- Sarah Witzke (Mon Jun 15 2015 - 06:46:59 PDT)
- Vishal Nemaysh (Mon Jun 08 2015 - 22:30:42 PDT)
- Jason Swails (Sun Jun 07 2015 - 09:25:52 PDT)
- Jason Swails (Sun Jun 07 2015 - 09:22:02 PDT)
- Vishal Nemaysh (Sun Jun 07 2015 - 02:12:49 PDT)
- MOHD HOMAIDUR RAHMAN (Sat Jun 06 2015 - 10:48:38 PDT)
- Jason Swails (Thu Jun 04 2015 - 06:33:09 PDT)
[AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized
- Jason Swails (Wed Jun 17 2015 - 21:18:49 PDT)
- Hai Nguyen (Wed Jun 17 2015 - 13:23:26 PDT)
- Gerald Monard (Wed Jun 17 2015 - 13:20:37 PDT)
- Marion, Antoine (Wed Jun 17 2015 - 13:03:52 PDT)
- David A Case (Wed Jun 17 2015 - 12:27:04 PDT)
- Gerald Monard (Wed Jun 17 2015 - 11:28:10 PDT)
- Marion, Antoine (Wed Jun 17 2015 - 09:37:41 PDT)
- Daniel Roe (Wed Jun 17 2015 - 07:24:35 PDT)
- Nhai (Wed Jun 17 2015 - 07:04:50 PDT)
- Marion, Antoine (Wed Jun 17 2015 - 06:37:47 PDT)
[AMBER] cpptraj crosscorr command
- Gard Nelson (Thu Jun 04 2015 - 11:22:05 PDT)
- Daniel Roe (Thu Jun 04 2015 - 11:00:56 PDT)
- Gard Nelson (Thu Jun 04 2015 - 10:44:38 PDT)
- Daniel Roe (Thu Jun 04 2015 - 09:00:39 PDT)
- Gard Nelson (Wed Jun 03 2015 - 16:53:25 PDT)
[AMBER] Cpptraj failure
- Lin Song (Tue Jun 30 2015 - 19:47:37 PDT)
[AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory
- Daniel Roe (Thu Jun 25 2015 - 07:28:55 PDT)
- bharat lakhani (Wed Jun 24 2015 - 20:52:03 PDT)
- Daniel Roe (Wed Jun 24 2015 - 20:02:32 PDT)
- bharat lakhani (Wed Jun 24 2015 - 19:58:20 PDT)
- bharat lakhani (Wed Jun 24 2015 - 18:38:04 PDT)
- Daniel Roe (Wed Jun 24 2015 - 14:01:19 PDT)
- bharat lakhani (Wed Jun 24 2015 - 13:35:03 PDT)
- Daniel Roe (Wed Jun 24 2015 - 12:56:23 PDT)
- bharat lakhani (Wed Jun 24 2015 - 10:56:18 PDT)
[AMBER] cpptraj matrix dist modifications
- Gard Nelson (Thu Jun 11 2015 - 11:59:19 PDT)
[AMBER] cuda7 not supported?
- Jason Swails (Tue Jun 30 2015 - 06:31:05 PDT)
- Albert (Tue Jun 30 2015 - 02:30:26 PDT)
- nam kim (Mon Jun 29 2015 - 14:45:47 PDT)
- Daniel Roe (Mon Jun 29 2015 - 14:27:42 PDT)
- Albert (Mon Jun 29 2015 - 10:34:15 PDT)
[AMBER] Defining the box dimensions while making the top and crd files
- David A Case (Fri Jun 26 2015 - 18:59:55 PDT)
- Iqbal, Muhammad Sajid (Fri Jun 26 2015 - 11:48:46 PDT)
- David A Case (Thu Jun 25 2015 - 07:14:17 PDT)
- Jason Swails (Thu Jun 25 2015 - 06:39:03 PDT)
- Iqbal, Muhammad Sajid (Wed Jun 24 2015 - 17:02:03 PDT)
[AMBER] Density for a protein ligand complex run
- Hector A. Baldoni (Sun Jun 07 2015 - 16:37:59 PDT)
- Jason Swails (Fri Jun 05 2015 - 11:31:59 PDT)
- Mrinda Jones (Fri Jun 05 2015 - 11:12:40 PDT)
- David A Case (Wed Jun 03 2015 - 06:14:39 PDT)
- Jason Swails (Wed Jun 03 2015 - 06:01:23 PDT)
- Hector A. Baldoni (Wed Jun 03 2015 - 05:58:49 PDT)
- Mrinda Jones (Tue Jun 02 2015 - 23:26:00 PDT)
- David A Case (Tue Jun 02 2015 - 12:41:53 PDT)
- Hector A. Baldoni (Tue Jun 02 2015 - 07:14:37 PDT)
- Mrinda Jones (Tue Jun 02 2015 - 05:16:03 PDT)
[AMBER] Dimer Rotations
- Kenneth Huang (Fri Jun 12 2015 - 15:18:33 PDT)
- Brittany Boykin (Fri Jun 12 2015 - 14:56:03 PDT)
[AMBER] distance restrain
- David A Case (Fri Jun 12 2015 - 05:54:00 PDT)
- Jason Swails (Fri Jun 12 2015 - 02:24:44 PDT)
- Lara rajam (Thu Jun 11 2015 - 13:11:38 PDT)
[AMBER] During MD simulation protein drifts out of periodic cell
- Michael Shokhen (Sun Jun 07 2015 - 03:35:23 PDT)
[AMBER] Energy contribution of phosphorylated residues
- Jason Swails (Fri Jun 19 2015 - 09:26:52 PDT)
- Kenneth Huang (Thu Jun 18 2015 - 14:28:40 PDT)
- Parker de Waal (Thu Jun 18 2015 - 13:50:54 PDT)
- Kenneth Huang (Thu Jun 18 2015 - 09:06:25 PDT)
- Parker de Waal (Thu Jun 18 2015 - 06:57:14 PDT)
[AMBER] energy difference between GBSA and PBSA
- Carlos Simmerling (Thu Jun 18 2015 - 05:36:37 PDT)
- Chris (Thu Jun 18 2015 - 05:30:15 PDT)
- Carlos Simmerling (Thu Jun 18 2015 - 05:05:11 PDT)
- Chris (Thu Jun 18 2015 - 02:32:58 PDT)
[AMBER] Entropy
- Vlad Cojocaru (Mon Jun 01 2015 - 00:07:11 PDT)
- Ramin Ekhteiari (Sun May 31 2015 - 23:25:36 PDT)
[AMBER] Error during action on loaded multiple trajectory in cpptraj 15
- MOHD HOMAIDUR RAHMAN (Mon Jun 29 2015 - 23:19:56 PDT)
- Daniel Roe (Mon Jun 29 2015 - 14:24:32 PDT)
- MOHD HOMAIDUR RAHMAN (Mon Jun 29 2015 - 13:46:49 PDT)
- MOHD HOMAIDUR RAHMAN (Wed Jun 24 2015 - 14:09:01 PDT)
- Daniel Roe (Wed Jun 24 2015 - 12:32:43 PDT)
- MOHD HOMAIDUR RAHMAN (Wed Jun 24 2015 - 05:52:14 PDT)
[AMBER] error encountered on extending production simulation on Amber14
- Jason Swails (Sat Jun 13 2015 - 03:49:20 PDT)
- Harmeet Kaur (Sat Jun 13 2015 - 01:30:01 PDT)
[AMBER] error in ante-MMPBSA.py
- Jason Swails (Tue Jun 16 2015 - 22:21:46 PDT)
- Chris (Tue Jun 16 2015 - 21:41:25 PDT)
[AMBER] error in MD simulation
- Jason Swails (Fri Jun 26 2015 - 05:25:40 PDT)
- erik.laurini.di3.units.it (Fri Jun 26 2015 - 05:15:40 PDT)
- Jason Swails (Thu Jun 25 2015 - 07:47:59 PDT)
- erik.laurini.di3.units.it (Thu Jun 25 2015 - 07:17:56 PDT)
[AMBER] error in parallel run
- David A Case (Tue Jun 30 2015 - 11:02:39 PDT)
- Lara rajam (Tue Jun 30 2015 - 10:20:37 PDT)
[AMBER] Error unknown flag: –O
- Michael Shokhen (Sat Jun 06 2015 - 02:40:55 PDT)
- hannes.loeffler.stfc.ac.uk (Sat Jun 06 2015 - 02:02:05 PDT)
- Michael Shokhen (Sat Jun 06 2015 - 01:24:19 PDT)
[AMBER] ERROR WHILE RUNNING ANTECHAMBER
- Aleksandra Skoric (Thu Jun 04 2015 - 03:47:14 PDT)
- Marc van der Kamp (Thu Jun 04 2015 - 02:20:35 PDT)
- ROOPALI VERMA (Thu Jun 04 2015 - 02:04:24 PDT)
- ROOPALI VERMA (Wed Jun 03 2015 - 21:58:18 PDT)
- ROOPALI VERMA (Wed Jun 03 2015 - 21:51:08 PDT)
- Aleksandra Skoric (Wed Jun 03 2015 - 02:36:02 PDT)
- Marc van der Kamp (Wed Jun 03 2015 - 01:41:57 PDT)
- Hannes Loeffler (Wed Jun 03 2015 - 01:40:39 PDT)
- ROOPALI VERMA (Wed Jun 03 2015 - 01:08:00 PDT)
[AMBER] Error while running leap for a protein containing Co2+
- Jason Swails (Mon Jun 08 2015 - 07:30:36 PDT)
- Kenneth Huang (Mon Jun 08 2015 - 07:21:23 PDT)
- Suchetana Gupta (Mon Jun 08 2015 - 05:05:38 PDT)
[AMBER] ERROR while running XLEAP
- Pierre Bertin (Fri Jun 19 2015 - 07:49:47 PDT)
- David A Case (Fri Jun 19 2015 - 06:59:54 PDT)
- Pierre Bertin (Thu Jun 18 2015 - 11:13:29 PDT)
[AMBER] Error: unspecified launch failure launching kernel kNLSkinTest
- David A Case (Wed Jun 17 2015 - 07:27:33 PDT)
- zayan alhalabi (Wed Jun 17 2015 - 06:18:26 PDT)
[AMBER] Experimental values about some orgnaic solvent BOX
- Karl Kirschner (Mon Jun 29 2015 - 05:04:36 PDT)
- David A Case (Mon Jun 29 2015 - 04:41:16 PDT)
- wangmt (Sun Jun 28 2015 - 23:43:41 PDT)
[AMBER] Explicit Solvent Constant pH MD
- Jason Swails (Tue Jun 30 2015 - 20:11:43 PDT)
- Rahul Ramesh (Tue Jun 30 2015 - 13:53:13 PDT)
[AMBER] Few queries about membrane protein simulations
- Joseph Baker (Sat Jun 13 2015 - 17:04:26 PDT)
- Ross Walker (Sat Jun 13 2015 - 10:48:05 PDT)
- Joseph Baker (Fri Jun 12 2015 - 21:07:48 PDT)
- Ross Walker (Fri Jun 12 2015 - 19:46:50 PDT)
- Joseph Baker (Fri Jun 12 2015 - 07:25:47 PDT)
- anu chandra (Fri Jun 12 2015 - 02:26:51 PDT)
- Ross Walker (Mon Jun 08 2015 - 09:17:38 PDT)
- Jason Swails (Mon Jun 08 2015 - 09:04:11 PDT)
- anu chandra (Mon Jun 08 2015 - 07:45:18 PDT)
[AMBER] folding RNA using SGLD
- Jason Swails (Tue Jun 30 2015 - 08:30:40 PDT)
- Wu, Xiongwu (NIH/NHLBI) [E] (Tue Jun 30 2015 - 07:44:37 PDT)
- Asmita Gupta (Tue Jun 30 2015 - 07:11:21 PDT)
[AMBER] force-momentum based SGLD algorithm
- Wu, Xiongwu (NIH/NHLBI) [E] (Thu Jun 04 2015 - 08:14:51 PDT)
- barbara rossi (Wed Jun 03 2015 - 02:22:16 PDT)
[AMBER] Free Energy Landscape for cMD
- bharat lakhani (Wed Jun 17 2015 - 12:53:05 PDT)
[AMBER] Free Energy Landscape for cMD Help
- Daniel Roe (Thu Jun 18 2015 - 08:16:07 PDT)
- Jason Swails (Wed Jun 17 2015 - 21:26:18 PDT)
- bharat lakhani (Wed Jun 17 2015 - 19:17:04 PDT)
[AMBER] Freezing atoms in space during a simulation
- Jonathan Gough (Wed Jun 17 2015 - 06:22:54 PDT)
- Gustavo Seabra (Tue Jun 16 2015 - 13:38:19 PDT)
- David A Case (Tue Jun 16 2015 - 13:19:00 PDT)
- Jonathan Gough (Tue Jun 16 2015 - 11:06:30 PDT)
[AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)???
- Chinh Su Tran To (Thu Jun 04 2015 - 22:43:57 PDT)
- Jason Swails (Thu Jun 04 2015 - 20:32:16 PDT)
- Chinh Su Tran To (Thu Jun 04 2015 - 18:59:16 PDT)
- Jason Swails (Thu Jun 04 2015 - 05:51:11 PDT)
- Patrick McGrath (Thu Jun 04 2015 - 05:35:51 PDT)
- Jason Swails (Thu Jun 04 2015 - 05:15:12 PDT)
- Gerald Monard (Thu Jun 04 2015 - 05:04:59 PDT)
- Chinh Su Tran To (Thu Jun 04 2015 - 03:58:08 PDT)
- Gerald Monard (Thu Jun 04 2015 - 02:52:32 PDT)
- Chinh Su Tran To (Thu Jun 04 2015 - 01:13:55 PDT)
[AMBER] Fwd: Question about building a branched levan oligosaccharide
- Surasak Chunsrivirot (Tue Jun 09 2015 - 19:47:41 PDT)
- Lachele Foley (Tue Jun 09 2015 - 15:35:11 PDT)
- Surasak Chunsrivirot (Tue Jun 09 2015 - 04:05:08 PDT)
- Lachele Foley (Mon Jun 08 2015 - 11:42:19 PDT)
- Surasak Chunsrivirot (Mon Jun 08 2015 - 07:26:17 PDT)
[AMBER] Generating RESP Charges For Tightly-Bound Complexes - Charges from the complexes or the fragments?
- David A Case (Sun Jun 28 2015 - 05:09:52 PDT)
- Damian G. Allis, Ph.D. (Sat Jun 27 2015 - 19:08:43 PDT)
[AMBER] generating topology without loading Frcmod file
- Arun Srikanth (Wed Jun 24 2015 - 16:01:50 PDT)
- Arun Srikanth (Wed Jun 24 2015 - 15:13:00 PDT)
- Jason Swails (Wed Jun 24 2015 - 14:26:16 PDT)
- Arun Srikanth (Wed Jun 24 2015 - 13:45:40 PDT)
- Jason Swails (Wed Jun 24 2015 - 10:19:01 PDT)
- Arun Srikanth (Wed Jun 24 2015 - 10:07:08 PDT)
[AMBER] Get energy information
- Jason Swails (Thu Jun 18 2015 - 06:42:01 PDT)
- loic etheve (Thu Jun 18 2015 - 00:28:09 PDT)
[AMBER] GPI-anchor protein cleavage
- Aditya Padhi (Wed Jun 17 2015 - 07:18:58 PDT)
- Jason Swails (Tue Jun 16 2015 - 19:11:34 PDT)
- Aditya Padhi (Tue Jun 16 2015 - 17:36:11 PDT)
- Jason Swails (Tue Jun 16 2015 - 17:06:20 PDT)
- Aditya Padhi (Tue Jun 16 2015 - 11:49:04 PDT)
[AMBER] GPU machines in the UK.
- George Tzotzos (Tue Jun 02 2015 - 10:01:19 PDT)
- Gould, Ian R (Tue Jun 02 2015 - 09:05:31 PDT)
- Ross Walker (Tue Jun 02 2015 - 08:53:15 PDT)
- Peter Winn (Tue Jun 02 2015 - 06:49:33 PDT)
[AMBER] Halogen at the dftb level
- Hector A. Baldoni (Fri Jun 26 2015 - 12:42:54 PDT)
[AMBER] hbond
- Daniel Roe (Wed Jun 24 2015 - 14:50:47 PDT)
- zahra khatti (Wed Jun 24 2015 - 14:37:12 PDT)
[AMBER] hbond lifetime cpptraj
- Daniel Roe (Wed Jun 24 2015 - 14:00:06 PDT)
- Lara rajam (Wed Jun 24 2015 - 13:32:44 PDT)
- Daniel Roe (Wed Jun 24 2015 - 13:17:36 PDT)
- Lara rajam (Wed Jun 24 2015 - 11:48:08 PDT)
[AMBER] Help - setting up parallel machine
- Jason Swails (Fri Jun 12 2015 - 02:32:50 PDT)
- anu chandra (Fri Jun 12 2015 - 02:31:16 PDT)
- David A Case (Thu Jun 11 2015 - 07:00:55 PDT)
- David A Case (Thu Jun 11 2015 - 05:17:33 PDT)
- anu chandra (Thu Jun 11 2015 - 03:39:26 PDT)
[AMBER] help in radial command
- newamber list (Fri Jun 26 2015 - 04:01:49 PDT)
- Robin Jain (Thu Jun 25 2015 - 22:20:22 PDT)
- Daniel Roe (Wed Jun 17 2015 - 07:34:15 PDT)
- Robin Jain (Wed Jun 17 2015 - 01:32:19 PDT)
[AMBER] HMR
- Ross Walker (Tue Jun 09 2015 - 11:34:47 PDT)
- Parker de Waal (Tue Jun 09 2015 - 11:09:43 PDT)
[AMBER] How can I do a thermodynamic integration using Simpson's rules ?
- Jinfeng Huang (Tue Jun 02 2015 - 07:04:07 PDT)
- Hannes Loeffler (Tue Jun 02 2015 - 06:18:43 PDT)
- Jinfeng Huang (Tue Jun 02 2015 - 06:03:27 PDT)
- Hannes Loeffler (Tue Jun 02 2015 - 02:43:52 PDT)
- Jinfeng Huang (Tue Jun 02 2015 - 02:20:25 PDT)
[AMBER] How to avoid protein drift?
- Jason Swails (Sun Jun 07 2015 - 09:36:51 PDT)
- Michael Shokhen (Sun Jun 07 2015 - 05:08:36 PDT)
[AMBER] how to convert pdb to rst file ?
- Indrajit Deb (Fri Jun 05 2015 - 10:21:36 PDT)
- Jason Swails (Fri Jun 05 2015 - 09:54:24 PDT)
- Indrajit Deb (Fri Jun 05 2015 - 09:35:38 PDT)
- Indrajit Deb (Fri Jun 05 2015 - 09:34:01 PDT)
- Kenneth Huang (Fri Jun 05 2015 - 08:49:47 PDT)
- Jason Swails (Fri Jun 05 2015 - 08:49:44 PDT)
- Indrajit Deb (Fri Jun 05 2015 - 08:26:47 PDT)
[AMBER] how to export pdb in 'cluster' with 'autoimage'
- Daniel Roe (Mon Jun 22 2015 - 09:09:18 PDT)
- windy (Mon Jun 22 2015 - 02:11:32 PDT)
[AMBER] How to generate Phi_Psi by cpptraj ?
- Daniel Roe (Mon Jun 01 2015 - 16:40:40 PDT)
- Jason Swails (Mon Jun 01 2015 - 14:33:02 PDT)
- Hai Nguyen (Mon Jun 01 2015 - 14:03:28 PDT)
- Soumendranath Bhakat (Mon Jun 01 2015 - 13:41:11 PDT)
- James Maier (Mon Jun 01 2015 - 12:44:35 PDT)
- Michael Shokhen (Mon Jun 01 2015 - 12:27:19 PDT)
[AMBER] How to Simulate Monoclinic crystal packing arrangement.
- srilaxmi reddy (Mon Jun 01 2015 - 05:17:32 PDT)
- David A Case (Mon Jun 01 2015 - 04:54:20 PDT)
- srilaxmi reddy (Mon Jun 01 2015 - 02:55:20 PDT)
[AMBER] Hydrogen bond bridges
- DEBOSTUTI GHOSHDASTIDAR (Mon Jun 29 2015 - 10:16:48 PDT)
- Daniel Roe (Sat Jun 27 2015 - 06:36:10 PDT)
- DEBOSTUTI GHOSHDASTIDAR (Fri Jun 26 2015 - 21:45:16 PDT)
- Daniel Roe (Fri Jun 26 2015 - 10:25:33 PDT)
- DEBOSTUTI GHOSHDASTIDAR (Thu Jun 25 2015 - 21:48:05 PDT)
- Daniel Roe (Thu Jun 25 2015 - 07:48:44 PDT)
- DEBOSTUTI GHOSHDASTIDAR (Wed Jun 24 2015 - 23:38:43 PDT)
- DEBOSTUTI GHOSHDASTIDAR (Wed Jun 24 2015 - 23:35:01 PDT)
- Daniel Roe (Wed Jun 24 2015 - 12:50:48 PDT)
- DEBOSTUTI GHOSHDASTIDAR (Wed Jun 24 2015 - 06:52:23 PDT)
[AMBER] Imaging & centering
- de Manzanos Guinot, Angela (Tue Jun 02 2015 - 10:11:44 PDT)
- Daniel Roe (Tue Jun 02 2015 - 10:05:27 PDT)
- Jason Swails (Tue Jun 02 2015 - 09:49:42 PDT)
- Angela de Manzanos (Tue Jun 02 2015 - 09:33:58 PDT)
[AMBER] Installation Question - Missing file?
- David A Case (Tue Jun 30 2015 - 04:43:49 PDT)
- Jason Swails (Mon Jun 29 2015 - 21:01:40 PDT)
- Jim Wu (Mon Jun 29 2015 - 15:36:19 PDT)
[AMBER] Is there a way to do simultaneous Cartesian position and distance restraints in amber?
- David A Case (Mon Jun 22 2015 - 10:29:55 PDT)
- Arthur Roberts (Mon Jun 22 2015 - 09:53:42 PDT)
[AMBER] Issue Lennard jones interaction
- Jason Swails (Sat Jun 13 2015 - 04:02:20 PDT)
- Loic ETHEVE (Sat Jun 13 2015 - 02:01:33 PDT)
[AMBER] Leap : problem with copying and combining DNA items
- Jason Swails (Mon Jun 08 2015 - 05:19:12 PDT)
- Jérémie Knoops (Sun Jun 07 2015 - 23:58:18 PDT)
[AMBER] lifetime
- Daniel Roe (Sun Jun 28 2015 - 15:48:46 PDT)
- zahra khatti (Sun Jun 28 2015 - 15:06:50 PDT)
- zahra khatti (Sun Jun 28 2015 - 14:53:54 PDT)
[AMBER] lifetime analysis
- Jason Swails (Mon Jun 29 2015 - 05:08:38 PDT)
- zahra khatti (Sun Jun 28 2015 - 14:34:26 PDT)
- zahra khatti (Sun Jun 28 2015 - 14:22:52 PDT)
- zahra khatti (Sat Jun 27 2015 - 15:12:00 PDT)
[AMBER] Ligand entry and exit path
- Vlad Cojocaru (Mon Jun 22 2015 - 08:55:34 PDT)
- Debodyuti Dutta (Mon Jun 22 2015 - 08:26:41 PDT)
[AMBER] Lipid 14 force field
- Benjamin D Madej (Fri Jun 26 2015 - 10:48:26 PDT)
- Ning Xiang (Fri Jun 26 2015 - 07:16:24 PDT)
[AMBER] Load "library" of custom residues
- David A Case (Sun Jun 21 2015 - 10:14:20 PDT)
- Jean-Patrick Francoia (Sun Jun 21 2015 - 08:43:50 PDT)
- David A Case (Sun Jun 21 2015 - 08:26:37 PDT)
- Jean-Patrick Francoia (Sun Jun 21 2015 - 04:57:55 PDT)
[AMBER] MMGBSA on Protein-DNA/RNA complex
- Muthukumaran R (Wed Jun 24 2015 - 09:58:45 PDT)
- Jason Swails (Wed Jun 24 2015 - 07:46:02 PDT)
- Vlad Cojocaru (Wed Jun 24 2015 - 06:47:39 PDT)
- Vlad Cojocaru (Wed Jun 24 2015 - 06:21:40 PDT)
- Jason Swails (Wed Jun 24 2015 - 05:27:32 PDT)
- Muthukumaran R (Wed Jun 24 2015 - 01:02:59 PDT)
- Vlad Cojocaru (Tue Jun 23 2015 - 09:16:12 PDT)
- Muthukumaran R (Tue Jun 23 2015 - 09:04:31 PDT)
- Carlos Simmerling (Tue Jun 23 2015 - 04:49:57 PDT)
- Vlad Cojocaru (Tue Jun 23 2015 - 04:32:42 PDT)
- Muthukumaran R (Tue Jun 23 2015 - 03:32:15 PDT)
[AMBER] MMPBSA on DNA-Protein-Ligand complex
- Vlad Cojocaru (Mon Jun 29 2015 - 04:39:35 PDT)
- Norbert GARNIER (Mon Jun 29 2015 - 04:31:33 PDT)
- Ray Luo, Ph.D. (Wed Jun 24 2015 - 10:06:34 PDT)
- Norbert GARNIER (Wed Jun 24 2015 - 08:32:44 PDT)
- Ray Luo, Ph.D. (Tue Jun 23 2015 - 10:35:57 PDT)
- Norbert GARNIER (Tue Jun 23 2015 - 08:00:47 PDT)
- Vlad Cojocaru (Tue Jun 23 2015 - 05:53:10 PDT)
- Jason Swails (Tue Jun 23 2015 - 05:37:10 PDT)
- Norbert GARNIER (Tue Jun 23 2015 - 05:26:07 PDT)
[AMBER] MMPBSA sasopt problem
- Jason Swails (Fri Jun 12 2015 - 02:32:22 PDT)
- Debodyuti Dutta (Thu Jun 11 2015 - 23:40:31 PDT)
[AMBER] MMPBSA: Generalised Born Warning
- Jason Swails (Mon Jun 15 2015 - 06:22:25 PDT)
- George Tzotzos (Mon Jun 15 2015 - 06:13:47 PDT)
[AMBER] MMPBSA_API: AmberTools13 vs. 15
- Jason Swails (Tue Jun 23 2015 - 07:52:07 PDT)
- Gerald Monard (Tue Jun 23 2015 - 07:46:42 PDT)
- Jason Swails (Tue Jun 23 2015 - 07:32:56 PDT)
- Gerald Monard (Tue Jun 23 2015 - 06:49:27 PDT)
[AMBER] modifying cpptraj
- Gard Nelson (Fri Jun 12 2015 - 14:16:03 PDT)
- Daniel Roe (Fri Jun 12 2015 - 13:19:46 PDT)
- Gard Nelson (Fri Jun 12 2015 - 10:16:32 PDT)
[AMBER] NMR restraints with pmemd.cuda problem
- Miroslav Krepl (Wed Jun 17 2015 - 11:50:13 PDT)
- Ross Walker (Wed Jun 17 2015 - 08:00:52 PDT)
- David A Case (Wed Jun 17 2015 - 07:23:42 PDT)
- Miroslav Krepl (Tue Jun 16 2015 - 14:25:41 PDT)
[AMBER] Normal mode calculation was failed with MMPBSA.py
- Jason Swails (Mon Jun 29 2015 - 21:05:13 PDT)
- wliu (Mon Jun 29 2015 - 19:30:00 PDT)
[AMBER] Only -mpi option creates the python modules. Is this right?
- Eduardo Almeida Costa (Tue Jun 02 2015 - 08:06:21 PDT)
- Jason Swails (Tue Jun 02 2015 - 07:58:42 PDT)
- Eduardo Almeida Costa (Tue Jun 02 2015 - 07:26:47 PDT)
[AMBER] Output format in sander
- John Dood (Tue Jun 30 2015 - 11:38:17 PDT)
- David A Case (Tue Jun 30 2015 - 11:00:19 PDT)
- John Dood (Tue Jun 30 2015 - 10:03:01 PDT)
[AMBER] Pairwise Interaction Energy between two urea pairs
- Jason Swails (Fri Jun 12 2015 - 05:42:12 PDT)
- MOHD HOMAIDUR RAHMAN (Fri Jun 12 2015 - 05:15:32 PDT)
- Jason Swails (Fri Jun 12 2015 - 02:20:57 PDT)
- MOHD HOMAIDUR RAHMAN (Thu Jun 11 2015 - 23:45:51 PDT)
[AMBER] Parmed.py_ImportError: No module named ParmedTools.logos
- Sheehan, Alice (Thu Jun 11 2015 - 02:45:29 PDT)
- Jason Swails (Wed Jun 10 2015 - 09:22:39 PDT)
- Sheehan, Alice (Wed Jun 10 2015 - 08:54:20 PDT)
[AMBER] parmwrite in cpptraj: AmberTools13 vs. 15
- Gerald Monard (Tue Jun 23 2015 - 09:00:00 PDT)
- Daniel Roe (Tue Jun 23 2015 - 08:47:39 PDT)
- Gerald Monard (Tue Jun 23 2015 - 07:59:49 PDT)
- Daniel Roe (Tue Jun 23 2015 - 07:42:43 PDT)
- Gerald Monard (Tue Jun 23 2015 - 05:15:21 PDT)
[AMBER] PCA Calculations
- Daniel Roe (Tue Jun 30 2015 - 08:44:44 PDT)
- Parker de Waal (Mon Jun 29 2015 - 19:43:43 PDT)
[AMBER] Per residue rmsd
- Daniel Roe (Tue Jun 23 2015 - 07:55:01 PDT)
- bharat lakhani (Mon Jun 22 2015 - 09:59:05 PDT)
[AMBER] pmemd.cuda.MPI vs openmpi
- Ross Walker (Wed Jun 03 2015 - 13:42:43 PDT)
- Victor Ma (Wed Jun 03 2015 - 13:29:13 PDT)
- Ross Walker (Wed Jun 03 2015 - 12:29:00 PDT)
- Victor Ma (Wed Jun 03 2015 - 11:58:01 PDT)
- Ross Walker (Wed Jun 03 2015 - 11:31:48 PDT)
- Victor Ma (Wed Jun 03 2015 - 10:54:44 PDT)
[AMBER] Population analysis
- Kshatresh Dutta Dubey (Mon Jun 15 2015 - 08:33:46 PDT)
- Daniel Roe (Mon Jun 15 2015 - 08:21:29 PDT)
- Kshatresh Dutta Dubey (Mon Jun 15 2015 - 07:51:11 PDT)
- Parker de Waal (Mon Jun 15 2015 - 06:39:44 PDT)
- Jason Swails (Mon Jun 15 2015 - 06:25:08 PDT)
- Kshatresh Dutta Dubey (Mon Jun 15 2015 - 00:54:25 PDT)
[AMBER] Post processing of trajectory with sander
- Jason Swails (Tue Jun 30 2015 - 08:26:01 PDT)
- MOHD HOMAIDUR RAHMAN (Tue Jun 30 2015 - 05:59:02 PDT)
[AMBER] problem
- zayan alhalabi (Sat Jun 20 2015 - 06:25:59 PDT)
- Bill Ross (Wed Jun 17 2015 - 09:01:25 PDT)
- zayan alhalabi (Wed Jun 17 2015 - 07:47:30 PDT)
- Daniel Roe (Wed Jun 17 2015 - 07:27:10 PDT)
- zayan alhalabi (Wed Jun 17 2015 - 06:52:01 PDT)
[AMBER] Problem generating peptide
- Harshala Haldankar (Tue Jun 16 2015 - 04:38:50 PDT)
[AMBER] problem in .pdb after md simulation
- Soumendranath Bhakat (Tue Jun 16 2015 - 00:54:25 PDT)
- Soong Jiaxin (Tue Jun 16 2015 - 00:52:22 PDT)
- Vishal Nemaysh (Tue Jun 16 2015 - 00:34:54 PDT)
- Vishal Nemaysh (Tue Jun 16 2015 - 00:34:28 PDT)
- Soong Jiaxin (Mon Jun 15 2015 - 23:55:01 PDT)
- Vishal Nemaysh (Mon Jun 15 2015 - 23:52:58 PDT)
[AMBER] Problem in Radial command
- Daniel Roe (Thu Jun 25 2015 - 07:46:12 PDT)
- Robin Jain (Wed Jun 24 2015 - 22:43:01 PDT)
[AMBER] problem with extraction of potential energy for the ligand
- Maryam Hamzehee (Thu Jun 11 2015 - 04:46:39 PDT)
- Bill Ross (Wed Jun 10 2015 - 13:32:50 PDT)
- Maryam Hamzehee (Wed Jun 10 2015 - 12:03:44 PDT)
- Jason Swails (Wed Jun 10 2015 - 11:16:33 PDT)
- Maryam Hamzehee (Wed Jun 10 2015 - 10:45:29 PDT)
- Bill Ross (Wed Jun 10 2015 - 07:29:48 PDT)
- Maryam Hamzehee (Wed Jun 10 2015 - 02:50:14 PDT)
- Bill Ross (Sun Jun 07 2015 - 14:20:28 PDT)
- Maryam Hamzehee (Sun Jun 07 2015 - 10:14:26 PDT)
[AMBER] Problem with stripped combined mdcrd files
- Soong Jiaxin (Fri Jun 12 2015 - 00:20:09 PDT)
- Daniel Roe (Thu Jun 11 2015 - 21:17:43 PDT)
- Soong Jiaxin (Thu Jun 11 2015 - 21:04:57 PDT)
- Daniel Roe (Thu Jun 11 2015 - 20:49:21 PDT)
- Soong Jiaxin (Thu Jun 11 2015 - 20:40:25 PDT)
- Hai Nguyen (Thu Jun 11 2015 - 20:39:02 PDT)
- Soong Jiaxin (Thu Jun 11 2015 - 20:29:50 PDT)
- Hai Nguyen (Thu Jun 11 2015 - 20:14:36 PDT)
- Soong Jiaxin (Thu Jun 11 2015 - 19:48:06 PDT)
[AMBER] problems with relative TI calculations
- hannes.loeffler.stfc.ac.uk (Thu Jun 18 2015 - 09:18:34 PDT)
- Brian Radak (Thu Jun 18 2015 - 09:01:48 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Jun 18 2015 - 02:35:42 PDT)
[AMBER] proxy configuration
- Jason Swails (Thu Jun 04 2015 - 05:09:12 PDT)
- abdennour braka (Thu Jun 04 2015 - 02:48:45 PDT)
[AMBER] Python: AttributeError: 'dict' object has no attribute 'property'
- Jason Swails (Mon Jun 15 2015 - 06:18:31 PDT)
- Gerald Monard (Mon Jun 15 2015 - 02:40:23 PDT)
- Jean-Patrick Francoia (Mon Jun 15 2015 - 02:02:41 PDT)
- Hannes Loeffler (Mon Jun 15 2015 - 01:57:04 PDT)
- Hai Nguyen (Mon Jun 15 2015 - 01:55:59 PDT)
- Jean-Patrick Francoia (Mon Jun 15 2015 - 01:45:23 PDT)
- Gerald Monard (Sun Jun 14 2015 - 13:40:29 PDT)
- Jean-Patrick Francoia (Sun Jun 14 2015 - 10:44:43 PDT)
[AMBER] QM-MM Equilibration of the System
- Gustavo Seabra (Mon Jun 15 2015 - 09:26:31 PDT)
- Brittany Boykin (Mon Jun 15 2015 - 09:11:25 PDT)
[AMBER] QM-MM Equilibration Step
- Gustavo Seabra (Thu Jun 18 2015 - 11:06:23 PDT)
- Brittany Boykin (Thu Jun 18 2015 - 10:06:34 PDT)
[AMBER] Quantifying Membrane Contact or insertion
- Parker de Waal (Mon Jun 29 2015 - 11:39:35 PDT)
[AMBER] Quasi harmonic bad eigenvalue error
- Jason Swails (Sat Jun 20 2015 - 09:33:36 PDT)
- D.J. Pattinson (Sat Jun 20 2015 - 07:28:45 PDT)
[AMBER] Question About RESP/AmberTools14
- ivan.gladich.marge.uochb.cas.cz (Wed Jun 24 2015 - 03:05:08 PDT)
- ivan.gladich.marge.uochb.cas.cz (Tue Jun 23 2015 - 23:12:39 PDT)
- David A Case (Tue Jun 23 2015 - 05:16:39 PDT)
- ivan.gladich.marge.uochb.cas.cz (Mon Jun 22 2015 - 22:49:54 PDT)
[AMBER] Recover .lib from .prmtop and .inpcrd
- Yin, Xing (Thu Jun 18 2015 - 14:15:29 PDT)
- Jason Swails (Thu Jun 18 2015 - 09:18:59 PDT)
- Yin, Xing (Thu Jun 18 2015 - 08:35:14 PDT)
[AMBER] Recover the water model and periodic box from built parm files
- Yin, Xing (Tue Jun 23 2015 - 07:04:17 PDT)
- Jason Swails (Mon Jun 22 2015 - 13:52:46 PDT)
- Brian Radak (Mon Jun 22 2015 - 13:34:03 PDT)
- David A Case (Mon Jun 22 2015 - 10:17:26 PDT)
- Brian Radak (Mon Jun 22 2015 - 08:44:06 PDT)
- Jason Swails (Mon Jun 22 2015 - 07:12:59 PDT)
- Yin, Xing (Mon Jun 22 2015 - 07:01:10 PDT)
[AMBER] Regarding calculation of viscosity of system
- David A Case (Fri Jun 26 2015 - 08:38:25 PDT)
- MOHD HOMAIDUR RAHMAN (Fri Jun 26 2015 - 05:09:56 PDT)
[AMBER] Regarding creating Mg2+ ions topology and parameter file
- Kenneth Huang (Mon Jun 08 2015 - 07:12:55 PDT)
- David A Case (Mon Jun 08 2015 - 04:49:30 PDT)
- ROOPALI VERMA (Mon Jun 08 2015 - 03:31:53 PDT)
[AMBER] Regarding dihedral scanning
- Daniel Roe (Fri Jun 12 2015 - 12:48:31 PDT)
- Soumendranath Bhakat (Mon Jun 08 2015 - 02:48:09 PDT)
- Daniel Roe (Fri Jun 05 2015 - 13:03:16 PDT)
- Soumendranath Bhakat (Fri Jun 05 2015 - 02:45:12 PDT)
- Soumendranath Bhakat (Thu Jun 04 2015 - 08:49:40 PDT)
- Daniel Roe (Thu Jun 04 2015 - 08:30:26 PDT)
- Soumendranath Bhakat (Thu Jun 04 2015 - 01:36:21 PDT)
[AMBER] Regarding hydrogen bond time correlation function in cpptraj
- Daniel Roe (Sat Jun 20 2015 - 09:53:08 PDT)
- MOHD HOMAIDUR RAHMAN (Sat Jun 20 2015 - 03:27:34 PDT)
[AMBER] Regarding the protonation states of Histidine
- Soumendranath Bhakat (Thu Jun 11 2015 - 01:13:13 PDT)
- muhammad tahir ayub (Wed Jun 10 2015 - 23:50:10 PDT)
[AMBER] relaxation in t/xleap
- newamber list (Mon Jun 29 2015 - 03:46:04 PDT)
- Bill Ross (Sat Jun 27 2015 - 16:15:14 PDT)
- David A Case (Thu Jun 25 2015 - 05:14:31 PDT)
- newamber list (Thu Jun 25 2015 - 03:35:08 PDT)
- David A Case (Wed Jun 24 2015 - 18:07:53 PDT)
- newamber list (Wed Jun 24 2015 - 15:33:51 PDT)
[AMBER] Required time for a typical MD run
- David A Case (Mon Jun 22 2015 - 17:53:44 PDT)
- Jason Swails (Mon Jun 22 2015 - 17:22:55 PDT)
- Daniel Roe (Mon Jun 22 2015 - 14:32:31 PDT)
- Kenneth Huang (Mon Jun 22 2015 - 14:23:01 PDT)
- Morteza Chehel Amirani (Mon Jun 22 2015 - 14:10:39 PDT)
[AMBER] RESP charge derivation
- Suman Chakrabarty (Sun Jun 21 2015 - 06:25:37 PDT)
- Jason Swails (Fri Jun 19 2015 - 19:47:18 PDT)
- Neelanjana Sengupta (Fri Jun 19 2015 - 14:17:43 PDT)
- Jason Swails (Fri Jun 19 2015 - 12:31:37 PDT)
- Neelanjana Sengupta (Fri Jun 19 2015 - 10:56:08 PDT)
[AMBER] RESP Charge Fit - Intramolecular Hydrogen Bond
- Yip Yew Mun (Tue Jun 30 2015 - 07:48:36 PDT)
[AMBER] RESP: charges on equivalent atoms
- David A Case (Tue Jun 30 2015 - 04:50:46 PDT)
- Neelanjana Sengupta (Tue Jun 30 2015 - 01:55:20 PDT)
[AMBER] resp: errors in reading the electrostatic potential
- David A Case (Sun Jun 21 2015 - 08:40:54 PDT)
- Neelanjana Sengupta (Sun Jun 21 2015 - 05:29:47 PDT)
- Neelanjana Sengupta (Sun Jun 21 2015 - 02:51:03 PDT)
[AMBER] Restraining distance between molecules initially
- jacob wick (Wed Jun 10 2015 - 23:40:55 PDT)
[AMBER] Rms fitting to a reference structure with a differnt number atoms to top file
- Daniel Roe (Tue Jun 30 2015 - 13:15:56 PDT)
- George Green (Tue Jun 30 2015 - 12:54:53 PDT)
- George Green (Tue Jun 30 2015 - 12:42:12 PDT)
[AMBER] Running amber forcefield in NAMD
- Jason Swails (Mon Jun 29 2015 - 05:12:52 PDT)
- Yogeeshwar Ajjugal (Mon Jun 29 2015 - 05:02:32 PDT)
[AMBER] savepdb command not working in xleap
- David A Case (Wed Jun 17 2015 - 09:27:21 PDT)
- muhammad tahir ayub (Wed Jun 17 2015 - 08:20:02 PDT)
[AMBER] simulation phosphorylated complex of protein
- David A Case (Tue Jun 30 2015 - 09:11:52 PDT)
- Ziba Bahadori (Tue Jun 30 2015 - 07:24:36 PDT)
[AMBER] solid surface interacting with organic
- Jason Swails (Fri Jun 19 2015 - 09:59:38 PDT)
- Azade Yazdan Yar (Fri Jun 19 2015 - 03:12:55 PDT)
[AMBER] some doubts about simulation analysis
- Jiri Sponer (Sat Jun 27 2015 - 01:28:59 PDT)
- Mary Varughese (Sat Jun 27 2015 - 00:53:28 PDT)
[AMBER] Spreading water molecules over the simulation time
- Daniel Roe (Thu Jun 18 2015 - 08:18:17 PDT)
- Jason Swails (Wed Jun 17 2015 - 21:19:57 PDT)
- windy (Wed Jun 17 2015 - 18:30:28 PDT)
- Morteza Chehel Amirani (Wed Jun 17 2015 - 12:40:34 PDT)
[AMBER] standard and non-standard residues
- Ramin Ekhteiari (Sun Jun 21 2015 - 01:37:55 PDT)
- Jason Swails (Sat Jun 20 2015 - 09:39:44 PDT)
- Ramin Ekhteiari (Sat Jun 20 2015 - 08:09:43 PDT)
[AMBER] Steered Molecular Dynamics
- Marcos Serrou do Amaral (Wed Jun 10 2015 - 13:35:09 PDT)
- Brittany Boykin (Wed Jun 10 2015 - 09:35:53 PDT)
[AMBER] subroutine qm_write_pdb
- Hector A. Baldoni (Wed Jun 17 2015 - 06:30:25 PDT)
[AMBER] svdcmp in sander/ncsu-rmsd.F90 (AmberTools15) is sensitive to higher optimizations, suggest using lapack routine instead
- Åke Sandgren (Mon Jun 29 2015 - 23:41:35 PDT)
[AMBER] tcorr and order parameters
- Travis Hughes (Tue Jun 16 2015 - 12:49:48 PDT)
- Daniel Roe (Mon Jun 15 2015 - 20:27:00 PDT)
- Travis Hughes (Mon Jun 15 2015 - 16:08:30 PDT)
[AMBER] The respective references suggested by the developers of Amber and HADDOCK
- Zhichao Lou (Tue Jun 16 2015 - 20:38:19 PDT)
- Hai Nguyen (Tue Jun 16 2015 - 20:15:46 PDT)
- Zhichao Lou (Tue Jun 16 2015 - 20:01:30 PDT)
[AMBER] tinker_to_amber doesn't like AMOEBA reference frames for chloride
- David A Case (Thu Jun 11 2015 - 11:08:18 PDT)
- David A Case (Thu Jun 11 2015 - 11:05:58 PDT)
- Baker, Lewis Robert (Thu Jun 11 2015 - 10:30:02 PDT)
[AMBER] To Add or Not To Add - Salt Conc in Explicit Solvent
- Marc van der Kamp (Thu Jun 18 2015 - 01:10:20 PDT)
- Yip Yew Mun (Thu Jun 18 2015 - 00:32:41 PDT)
[AMBER] Torsion restraints with pmemd.amoeba
- David A Case (Thu Jun 04 2015 - 09:12:53 PDT)
- Karl Debiec (Thu Jun 04 2015 - 08:41:41 PDT)
[AMBER] torsions in parm10.dat
- Jason Swails (Tue Jun 02 2015 - 08:05:04 PDT)
- Jeffrey Teillet (Tue Jun 02 2015 - 01:28:58 PDT)
[AMBER] united atom force field
- anu chandra (Mon Jun 22 2015 - 07:26:54 PDT)
[AMBER] unsaturated sugars
- Lara rajam (Fri Jun 26 2015 - 09:08:47 PDT)
- Lachele Foley (Wed Jun 24 2015 - 10:31:25 PDT)
- Lara rajam (Wed Jun 24 2015 - 07:06:07 PDT)
[AMBER] Use of OPLS-AA/M force field in AMBER via CHAMBER
- Brian Radak (Mon Jun 22 2015 - 13:30:52 PDT)
- Karl Debiec (Mon Jun 22 2015 - 08:54:31 PDT)
[AMBER] using AMBER 14sb force-field in CHARMM program
- Iceriver Forever (Sun Jun 21 2015 - 09:21:50 PDT)
[AMBER] what's the default radius?
- Albert (Tue Jun 16 2015 - 02:26:01 PDT)
- Carlos Simmerling (Tue Jun 16 2015 - 02:23:30 PDT)
- Albert (Mon Jun 15 2015 - 23:06:31 PDT)
[AMBER] write PCA mode trajectory with cpptraj
- Daniel Roe (Fri Jun 05 2015 - 13:10:06 PDT)
- Vlad Cojocaru (Fri Jun 05 2015 - 01:18:35 PDT)
[AMBER] ΑΠ: Regarding dihedral scanning
- Jason Swails (Fri Jun 05 2015 - 04:39:03 PDT)
- Antonios Kolocouris (Fri Jun 05 2015 - 02:51:35 PDT)

Amber Archive Jun 2015 by subject