Amber Archive Jun 2014: by subject

[AMBER] "Invalid start to time: 28..." error
- Daniel Roe (Sat Jun 14 2014 - 11:41:58 PDT)
- Bill Ross (Fri Jun 13 2014 - 18:21:38 PDT)
- Jason Swails (Fri Jun 13 2014 - 16:05:22 PDT)
- Vu Truong (Fri Jun 13 2014 - 14:35:42 PDT)
- Bill Ross (Thu Jun 12 2014 - 17:20:10 PDT)
- David A Case (Thu Jun 12 2014 - 13:37:13 PDT)
- Daniel Roe (Thu Jun 12 2014 - 13:09:06 PDT)
- Vu Truong (Thu Jun 12 2014 - 11:43:21 PDT)
[AMBER] (probably) benign error when writing iapbs-pot.dx files with sander.APBS
- Brian Radak (Tue Jun 03 2014 - 10:03:21 PDT)
[AMBER] 3D-RISM: charge density, charge distribution, and electrostatic potential
- T Luchko (Lists) (Fri Jun 27 2014 - 11:53:33 PDT)
- Brian Radak (Thu Jun 26 2014 - 14:06:16 PDT)
[AMBER] [Amber 14] multi-GPU calculation error occers when specify eight GPUs with Tesla K20Xm
- Scott Le Grand (Mon Jun 09 2014 - 09:50:56 PDT)
- Ross Walker (Mon Jun 09 2014 - 05:42:42 PDT)
- Keisuke Aono (Mon Jun 09 2014 - 04:17:52 PDT)
[AMBER] about setting iwrap
- Daniel Roe (Tue Jun 24 2014 - 08:27:59 PDT)
- kirtana S (Tue Jun 24 2014 - 08:04:15 PDT)
[AMBER] active site water cluster analysis
- Ahmet yıldırım (Tue Jun 03 2014 - 02:41:47 PDT)
[AMBER] Adding residue in two end of DNA
- FyD (Sat Jun 14 2014 - 10:08:01 PDT)
- mehdi bagherpoor (Thu Jun 12 2014 - 09:59:50 PDT)
[AMBER] AMBER 12 Nucleic Acid Builder (NAB) language
- loue chen (Sun Jun 22 2014 - 08:50:09 PDT)
[AMBER] Amber scaling on culster
- George Tzotzos (Wed Jun 25 2014 - 06:29:56 PDT)
- Ross Walker (Tue Jun 24 2014 - 14:11:49 PDT)
- Ross Walker (Tue Jun 24 2014 - 13:48:46 PDT)
- Roitberg,Adrian E (Tue Jun 24 2014 - 13:39:18 PDT)
- George Tzotzos (Tue Jun 24 2014 - 13:19:24 PDT)
[AMBER] AmberTools14 installation
- Gerald Monard (Fri Jun 20 2014 - 02:12:56 PDT)
- zahra khatti (Fri Jun 20 2014 - 01:30:18 PDT)
[AMBER] Analysis of CHARMM DNA trajectory using nastruct
- Jason Swails (Wed Jun 04 2014 - 12:40:11 PDT)
- Geoffrey Gray (Wed Jun 04 2014 - 12:11:48 PDT)
- Daniel Roe (Wed Jun 04 2014 - 12:06:06 PDT)
- Geoffrey Gray (Wed Jun 04 2014 - 08:38:07 PDT)
[AMBER] Analyze properties of in parallel MD
- Jason Swails (Fri Jun 27 2014 - 08:41:38 PDT)
- Brian Radak (Fri Jun 27 2014 - 08:09:00 PDT)
- Valentina Romano (Fri Jun 27 2014 - 07:37:34 PDT)
[AMBER] bash scripting for MD tasks
- Parker de Waal (Mon Jun 23 2014 - 07:30:54 PDT)
- James Starlight (Mon Jun 23 2014 - 04:48:29 PDT)
- Parker de Waal (Sun Jun 22 2014 - 07:07:17 PDT)
- Parker de Waal (Sun Jun 22 2014 - 07:04:13 PDT)
- James Starlight (Sun Jun 22 2014 - 06:24:34 PDT)
- Daniel Roe (Fri Jun 20 2014 - 07:47:22 PDT)
- James Starlight (Fri Jun 20 2014 - 07:25:06 PDT)
- James Starlight (Thu Jun 19 2014 - 06:52:51 PDT)
- Jason Swails (Tue Jun 17 2014 - 12:25:49 PDT)
- Lachele Foley (Tue Jun 17 2014 - 11:38:30 PDT)
- James Starlight (Tue Jun 17 2014 - 11:16:31 PDT)
- Daniel Roe (Mon Jun 16 2014 - 14:11:03 PDT)
- James Starlight (Mon Jun 16 2014 - 12:59:08 PDT)
[AMBER] Calculating absolute binding free energy
- menwer momo (Wed Jun 04 2014 - 00:04:41 PDT)
[AMBER] calculating absolute binding free energy using MMPBSA
- David A Case (Wed Jun 04 2014 - 12:24:46 PDT)
- Jason Swails (Wed Jun 04 2014 - 04:55:57 PDT)
- menwer momo (Wed Jun 04 2014 - 02:17:49 PDT)
[AMBER] calculation diffusion coefficient
- David A Case (Sun Jun 01 2014 - 04:37:50 PDT)
- Sohag Biswas (Sun Jun 01 2014 - 02:28:21 PDT)
[AMBER] charmmlipid2amber.py
- James Starlight (Thu Jun 12 2014 - 12:49:23 PDT)
- Benjamin D Madej (Thu Jun 12 2014 - 11:27:54 PDT)
- James Starlight (Wed Jun 11 2014 - 22:45:00 PDT)
- Benjamin D Madej (Wed Jun 11 2014 - 13:47:58 PDT)
- James Starlight (Wed Jun 11 2014 - 00:16:33 PDT)
- James Starlight (Tue Jun 10 2014 - 23:54:48 PDT)
- James Starlight (Tue Jun 10 2014 - 22:15:49 PDT)
- Bill Ross (Tue Jun 10 2014 - 13:43:35 PDT)
- Benjamin D Madej (Tue Jun 10 2014 - 13:38:54 PDT)
- James Starlight (Tue Jun 10 2014 - 12:39:24 PDT)
- Benjamin D Madej (Tue Jun 10 2014 - 12:16:41 PDT)
- James Starlight (Tue Jun 10 2014 - 12:04:30 PDT)
- Benjamin D Madej (Tue Jun 10 2014 - 11:51:40 PDT)
- James Starlight (Tue Jun 10 2014 - 09:06:49 PDT)
- James Starlight (Mon Jun 09 2014 - 22:47:52 PDT)
- James Starlight (Mon Jun 09 2014 - 22:36:06 PDT)
- Benjamin D Madej (Mon Jun 09 2014 - 15:48:20 PDT)
- James Starlight (Mon Jun 09 2014 - 12:18:47 PDT)
- Benjamin D Madej (Mon Jun 09 2014 - 12:02:09 PDT)
- James Starlight (Fri Jun 06 2014 - 09:26:53 PDT)
- James Starlight (Fri Jun 06 2014 - 07:40:45 PDT)
[AMBER] Clustering using CPPTRAJ
- Jason Swails (Mon Jun 23 2014 - 12:35:25 PDT)
- Soumendranath Bhakat (Mon Jun 23 2014 - 12:08:50 PDT)
- Jason Swails (Mon Jun 23 2014 - 08:19:04 PDT)
- Soumendranath Bhakat (Mon Jun 23 2014 - 07:45:54 PDT)
- Soumendranath Bhakat (Mon Jun 23 2014 - 07:07:47 PDT)
- Daniel Roe (Mon Jun 23 2014 - 06:58:50 PDT)
- Soumendranath Bhakat (Mon Jun 23 2014 - 06:51:15 PDT)
[AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10
- Benjamin D Madej (Wed Jun 04 2014 - 13:43:33 PDT)
- Thomas Evangelidis (Wed Jun 04 2014 - 04:03:04 PDT)
- Hannes Loeffler (Wed Jun 04 2014 - 03:07:33 PDT)
- Jason Swails (Tue Jun 03 2014 - 14:58:11 PDT)
- Thomas Evangelidis (Tue Jun 03 2014 - 14:30:21 PDT)
[AMBER] Condensed Glycam notation for gammacyclodextrin
- Lachele Foley (Mon Jun 23 2014 - 10:49:16 PDT)
- Shreeramesh (Mon Jun 23 2014 - 05:08:09 PDT)
[AMBER] Constant surface tension on the membrane
- Benjamin D Madej (Mon Jun 09 2014 - 16:19:53 PDT)
- James Starlight (Mon Jun 09 2014 - 12:24:08 PDT)
- Benjamin D Madej (Mon Jun 09 2014 - 11:53:29 PDT)
- Jason Swails (Fri Jun 06 2014 - 05:27:01 PDT)
- James Starlight (Fri Jun 06 2014 - 01:28:27 PDT)
[AMBER] Contributing new water models
- Jason Swails (Mon Jun 02 2014 - 04:18:52 PDT)
- adm (Mon Jun 02 2014 - 00:35:57 PDT)
[AMBER] Could not find angle parameter: S - S - S
- Sangita Kachhap (Tue Jun 03 2014 - 03:55:30 PDT)
- Hector A. Baldoni (Tue Jun 03 2014 - 03:47:48 PDT)
- Sangita Kachhap (Tue Jun 03 2014 - 02:49:52 PDT)
[AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1.
- mish (Thu Jun 05 2014 - 07:49:33 PDT)
- Daniel Roe (Wed Jun 04 2014 - 10:54:02 PDT)
- Daniel Roe (Wed Jun 04 2014 - 10:15:58 PDT)
- mish (Wed Jun 04 2014 - 08:43:48 PDT)
- Daniel Roe (Wed Jun 04 2014 - 08:26:12 PDT)
- mish (Wed Jun 04 2014 - 08:11:47 PDT)
[AMBER] cpptraj error : not parsing mdvel file
- Himanshu Joshi (Sat Jun 07 2014 - 05:17:41 PDT)
- Daniel Roe (Fri Jun 06 2014 - 06:53:53 PDT)
- Himanshu Joshi (Fri Jun 06 2014 - 04:00:17 PDT)
[AMBER] cpptraj hbond - warning message
- Jason Swails (Wed Jun 18 2014 - 08:13:00 PDT)
- Mahendra B Thapa (Tue Jun 17 2014 - 16:16:16 PDT)
[AMBER] cpptraj: arithmetic on data sets?
- Brian Radak (Mon Jun 30 2014 - 07:24:47 PDT)
[AMBER] defining reaction coordinate for umbrella sampling
- Jason Swails (Sun Jun 01 2014 - 19:09:50 PDT)
- Jorgen Simonsen (Sun Jun 01 2014 - 18:12:32 PDT)
[AMBER] Deleting Box info from trajectory
- Kshatresh Dutta Dubey (Sun Jun 15 2014 - 00:47:00 PDT)
- Jason Swails (Sat Jun 14 2014 - 22:03:19 PDT)
- Kshatresh Dutta Dubey (Sat Jun 14 2014 - 20:53:05 PDT)
- David A Case (Sat Jun 14 2014 - 20:32:31 PDT)
- Kshatresh Dutta Dubey (Sat Jun 14 2014 - 14:40:35 PDT)
- Daniel Roe (Sat Jun 14 2014 - 14:27:11 PDT)
- David A Case (Sat Jun 14 2014 - 13:51:36 PDT)
- Kshatresh Dutta Dubey (Sat Jun 14 2014 - 13:09:26 PDT)
[AMBER] Density Plot
- Jason Swails (Fri Jun 06 2014 - 05:21:43 PDT)
- Jurgens de Bruin (Fri Jun 06 2014 - 00:58:32 PDT)
[AMBER] Derive charge of multiple molecules
- Soumendranath Bhakat (Sun Jun 22 2014 - 06:44:31 PDT)
- Soumendranath Bhakat (Sun Jun 22 2014 - 06:34:13 PDT)
- Daniel Roe (Sat Jun 21 2014 - 08:45:29 PDT)
- sunita gupta (Fri Jun 20 2014 - 22:29:14 PDT)
- Jason Swails (Thu Jun 19 2014 - 12:02:16 PDT)
- sunita gupta (Thu Jun 19 2014 - 11:38:45 PDT)
[AMBER] different number of waters
- Brian Radak (Wed Jun 18 2014 - 08:01:27 PDT)
- David A Case (Wed Jun 18 2014 - 07:49:05 PDT)
- newamber list (Wed Jun 18 2014 - 07:30:05 PDT)
- Brian Radak (Wed Jun 18 2014 - 07:09:48 PDT)
- newamber list (Wed Jun 18 2014 - 06:43:34 PDT)
- David A Case (Sun Jun 15 2014 - 08:52:48 PDT)
- newamber list (Sun Jun 15 2014 - 08:06:10 PDT)
- newamber list (Sun Jun 15 2014 - 07:18:48 PDT)
- Jason Swails (Sat Jun 14 2014 - 22:07:41 PDT)
- MURAT OZTURK (Sat Jun 14 2014 - 16:07:34 PDT)
- newamber list (Fri Jun 13 2014 - 06:04:22 PDT)
[AMBER] Distance matrix time series
- Daniel Roe (Tue Jun 03 2014 - 07:22:47 PDT)
- Eugene Yedvabny (Mon Jun 02 2014 - 15:19:35 PDT)
[AMBER] Disulfide Bond Info and XMIN Stuck Problems
- Daniel Roe (Thu Jun 19 2014 - 14:17:33 PDT)
- Guqin Shi (Tue Jun 17 2014 - 14:15:49 PDT)
- Guqin Shi (Tue Jun 17 2014 - 14:11:23 PDT)
- Daniel Roe (Sat Jun 14 2014 - 10:49:48 PDT)
- David A Case (Thu Jun 12 2014 - 13:39:40 PDT)
[AMBER] donor and acceptor group in hbond
- Daniel Roe (Wed Jun 04 2014 - 06:47:16 PDT)
- Arunima Shilpi (Tue Jun 03 2014 - 21:59:17 PDT)
[AMBER] EAMBER (non-restraint) in sander output
- Duggan, Brendan (Thu Jun 19 2014 - 14:55:12 PDT)
- David A Case (Wed Jun 18 2014 - 20:25:07 PDT)
- Duggan, Brendan (Wed Jun 18 2014 - 11:26:37 PDT)
[AMBER] Early termination of parallel MD
- Jason Swails (Mon Jun 30 2014 - 06:30:44 PDT)
- Anselm Horn (Mon Jun 30 2014 - 03:20:17 PDT)
- Valentina Romano (Mon Jun 30 2014 - 01:49:07 PDT)
- Anna Bauß (Mon Jun 30 2014 - 01:32:04 PDT)
- Valentina Romano (Mon Jun 30 2014 - 00:52:24 PDT)
[AMBER] Efficient, accurate estimation of relative binding free energies
- Jason Swails (Mon Jun 30 2014 - 06:17:01 PDT)
- Guo, Zhuyan (Mon Jun 30 2014 - 05:13:50 PDT)
[AMBER] Equilibration of membrane protein
- James Starlight (Tue Jun 10 2014 - 22:13:36 PDT)
- Benjamin D Madej (Tue Jun 10 2014 - 12:04:41 PDT)
- James Starlight (Tue Jun 10 2014 - 00:05:13 PDT)
[AMBER] Error in cpptraj remlog command
- Daniel Roe (Tue Jun 03 2014 - 12:20:05 PDT)
- Daniel Roe (Mon Jun 02 2014 - 19:54:21 PDT)
- Eugene Yedvabny (Mon Jun 02 2014 - 17:25:04 PDT)
[AMBER] error in hbond analysis
- Jason Swails (Fri Jun 06 2014 - 05:15:25 PDT)
- Arunima Shilpi (Thu Jun 05 2014 - 23:51:22 PDT)
[AMBER] error in hydrogen bond
- Soumendranath Bhakat (Sat Jun 07 2014 - 06:43:18 PDT)
- Jason Swails (Sat Jun 07 2014 - 04:24:26 PDT)
- Arunima Shilpi (Fri Jun 06 2014 - 21:48:04 PDT)
[AMBER] error in MMPBSA
- Ray Luo, Ph.D. (Mon Jun 02 2014 - 15:39:54 PDT)
- Lara rajam (Mon Jun 02 2014 - 13:48:47 PDT)
[AMBER] error in plot of interaction energy in xmgrace
- Soumendranath Bhakat (Sun Jun 01 2014 - 13:24:11 PDT)
- Asaminew Haile (Sun Jun 01 2014 - 09:30:24 PDT)
- Arunima Shilpi (Sun Jun 01 2014 - 09:05:15 PDT)
[AMBER] error in using pmemd
- Jason Swails (Tue Jun 10 2014 - 08:22:20 PDT)
- Valentina Romano (Tue Jun 10 2014 - 08:13:26 PDT)
[AMBER] Falling apart of membrane
- Benjamin D Madej (Mon Jun 30 2014 - 13:58:14 PDT)
- Gözde YALÇIN (Mon Jun 30 2014 - 07:07:26 PDT)
[AMBER] FF12SB (and FF14?) - any benchmarks/evidence of its quality?
- Carlos Simmerling (Sun Jun 01 2014 - 12:59:19 PDT)
- Hai Nguyen (Sun Jun 01 2014 - 12:09:44 PDT)
- Marc van der Kamp (Sun Jun 01 2014 - 07:39:27 PDT)
[AMBER] filter trajectory with modes same number of frames
- newamber list (Tue Jun 24 2014 - 17:28:08 PDT)
- Daniel Roe (Tue Jun 24 2014 - 08:42:55 PDT)
- newamber list (Sat Jun 21 2014 - 18:34:01 PDT)
- Daniel Roe (Sat Jun 21 2014 - 13:48:33 PDT)
- newamber list (Sat Jun 21 2014 - 10:07:53 PDT)
[AMBER] fitting of atomic structures to cryo-em maps
- Jason Swails (Mon Jun 16 2014 - 07:07:03 PDT)
- Asmita Gupta (Mon Jun 16 2014 - 06:36:41 PDT)
- Jason Swails (Mon Jun 16 2014 - 06:17:41 PDT)
- Asmita Gupta (Mon Jun 16 2014 - 06:12:02 PDT)
[AMBER] Force field for carbohydrates-Reg.
- Lachele Foley (Wed Jun 25 2014 - 07:46:57 PDT)
- Lachele Foley (Wed Jun 25 2014 - 07:46:20 PDT)
- FyD (Tue Jun 24 2014 - 23:14:23 PDT)
- Shreeramesh (Tue Jun 24 2014 - 01:56:11 PDT)
[AMBER] formal charge of the ligand
- Mary Varughese (Fri Jun 27 2014 - 23:13:21 PDT)
- Soumendranath Bhakat (Fri Jun 27 2014 - 09:40:19 PDT)
- Jason Swails (Fri Jun 27 2014 - 06:52:36 PDT)
- Soumendranath Bhakat (Fri Jun 27 2014 - 05:33:59 PDT)
- Jason Swails (Fri Jun 27 2014 - 05:05:29 PDT)
- Mary Varughese (Fri Jun 27 2014 - 02:35:55 PDT)
[AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py
- Senthil Natesan (Tue Jun 10 2014 - 11:08:01 PDT)
- Jason Swails (Tue Jun 10 2014 - 10:06:17 PDT)
- Jason Swails (Tue Jun 10 2014 - 09:26:48 PDT)
- Senthil Natesan (Tue Jun 10 2014 - 08:57:51 PDT)
- Jason Swails (Tue Jun 10 2014 - 08:39:03 PDT)
- Senthil Natesan (Tue Jun 10 2014 - 08:22:38 PDT)
[AMBER] Fwd: problem while USING GLYCAM for Gammacyclodextrin-Reg.
- Lachele Foley (Thu Jun 26 2014 - 11:13:14 PDT)
- Shreeramesh (Thu Jun 26 2014 - 05:46:31 PDT)
[AMBER] Fwd: Substrate moving out of the box during MD simulation-- reg
- Jason Swails (Mon Jun 09 2014 - 05:24:05 PDT)
- Rajeswari A. (Mon Jun 09 2014 - 04:10:35 PDT)
[AMBER] GAFFlipid parameters
- Dickson, Callum J (Wed Jun 11 2014 - 04:25:31 PDT)
- Alexandra Antipina (Wed Jun 11 2014 - 02:35:02 PDT)
- Benjamin D Madej (Wed Jun 04 2014 - 14:13:51 PDT)
- Aldo Segura (Wed Jun 04 2014 - 05:56:48 PDT)
- Dickson, Callum J (Wed Jun 04 2014 - 05:52:44 PDT)
- Антипина Александра (Wed Jun 04 2014 - 05:24:17 PDT)
- Dickson, Callum J (Wed Jun 04 2014 - 04:37:42 PDT)
- Антипина Александра (Wed Jun 04 2014 - 02:01:16 PDT)
[AMBER] GLYCAM parameter ATOM TYPE
- Soumendranath Bhakat (Thu Jun 12 2014 - 01:42:07 PDT)
- Lachele Foley (Wed Jun 11 2014 - 12:34:17 PDT)
- Soumendranath Bhakat (Wed Jun 11 2014 - 11:54:15 PDT)
[AMBER] GLYCAM_06 reference
- Lachele Foley (Tue Jun 17 2014 - 07:55:59 PDT)
- Chinthaka Ratnaweera (Tue Jun 17 2014 - 00:18:35 PDT)
[AMBER] Glycophosphate parametrization using GLYCAM
- FyD (Fri Jun 20 2014 - 01:46:35 PDT)
- Lachele Foley (Thu Jun 19 2014 - 08:46:31 PDT)
- Jochen Heil (Thu Jun 19 2014 - 04:57:00 PDT)
- FyD (Thu Jun 19 2014 - 01:53:30 PDT)
- Thomas Pochapsky (Wed Jun 18 2014 - 11:15:10 PDT)
- Thomas Pochapsky (Wed Jun 18 2014 - 11:13:31 PDT)
- Lachele Foley (Wed Jun 18 2014 - 10:48:44 PDT)
- Jochen Heil (Wed Jun 18 2014 - 02:23:33 PDT)
- FyD (Tue Jun 17 2014 - 23:34:08 PDT)
- Lachele Foley (Tue Jun 17 2014 - 09:57:47 PDT)
- Raj Schneider (Tue Jun 17 2014 - 09:26:51 PDT)
[AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
- Ross Walker (Thu Jun 12 2014 - 19:10:20 PDT)
- Keiran Rowell (Thu Jun 12 2014 - 18:40:14 PDT)
- Scott Le Grand (Mon Jun 02 2014 - 22:45:38 PDT)
- Keiran Rowell (Mon Jun 02 2014 - 18:34:17 PDT)
- Scott Le Grand (Mon Jun 02 2014 - 17:05:22 PDT)
- Keiran Rowell (Mon Jun 02 2014 - 16:54:55 PDT)
[AMBER] Hbond analysi
- Daniel Roe (Sun Jun 08 2014 - 19:23:24 PDT)
- Arunima Shilpi (Sun Jun 08 2014 - 16:41:45 PDT)
[AMBER] hbond analysis
- Arunima Shilpi (Sun Jun 08 2014 - 06:05:47 PDT)
[AMBER] help in calculating Angular distribution function
- Robin Jain (Tue Jun 03 2014 - 00:12:16 PDT)
[AMBER] help in grid command
- Jason Swails (Tue Jun 03 2014 - 05:52:56 PDT)
- Robin Jain (Mon Jun 02 2014 - 23:17:08 PDT)
[AMBER] Hi
- Daniel Roe (Thu Jun 19 2014 - 13:58:44 PDT)
- Him Shweta (Thu Jun 19 2014 - 12:30:32 PDT)
[AMBER] image distances
- Daniel Roe (Wed Jun 04 2014 - 11:06:55 PDT)
- newamber list (Wed Jun 04 2014 - 07:06:05 PDT)
- newamber list (Mon Jun 02 2014 - 08:36:34 PDT)
- Daniel Roe (Mon Jun 02 2014 - 07:50:22 PDT)
- newamber list (Mon Jun 02 2014 - 07:46:38 PDT)
[AMBER] Integration scheme used in Amber 9 and 11 ?
- Ravi Tripathi (Sun Jun 15 2014 - 21:14:00 PDT)
- Kshatresh Dutta Dubey (Sat Jun 14 2014 - 06:28:40 PDT)
- Jason Swails (Sat Jun 14 2014 - 06:07:45 PDT)
- Kshatresh Dutta Dubey (Sat Jun 14 2014 - 02:03:56 PDT)
- Ravi Tripathi (Fri Jun 13 2014 - 23:30:57 PDT)
[AMBER] Is it possible to tleap a protein molecule without adding terminal atoms?
- Ray Luo, Ph.D. (Mon Jun 09 2014 - 10:13:40 PDT)
- Jason Swails (Mon Jun 09 2014 - 05:33:49 PDT)
- #YIP YEW MUN# (Mon Jun 09 2014 - 05:12:30 PDT)
[AMBER] Isopeptide bond Asp-Lys - parameters?
- FyD (Wed Jun 04 2014 - 22:56:03 PDT)
- Anselm Horn (Wed Jun 04 2014 - 05:08:17 PDT)
[AMBER] Issues in .out trying to simulat a polymer in AMBER
- Andrew.Warden.csiro.au (Wed Jun 25 2014 - 13:28:30 PDT)
- David A Case (Wed Jun 25 2014 - 04:42:05 PDT)
- Andrew.Warden.csiro.au (Tue Jun 24 2014 - 22:23:34 PDT)
[AMBER] Leapfrog algorithm
- David A Case (Wed Jun 18 2014 - 13:34:09 PDT)
- Jason Swails (Wed Jun 18 2014 - 11:12:35 PDT)
- zahra khatti (Wed Jun 18 2014 - 10:20:48 PDT)
[AMBER] Ligand movement in protein cavatiy
- Jurgens de Bruin (Wed Jun 04 2014 - 05:56:18 PDT)
- Jason Swails (Wed Jun 04 2014 - 05:55:59 PDT)
- Jurgens de Bruin (Wed Jun 04 2014 - 05:14:19 PDT)
- Jurgens de Bruin (Mon Jun 02 2014 - 23:09:41 PDT)
- Aldo Segura (Mon Jun 02 2014 - 06:12:26 PDT)
- Jurgens de Bruin (Mon Jun 02 2014 - 05:22:59 PDT)
- Soumendranath Bhakat (Mon Jun 02 2014 - 04:59:04 PDT)
- Jason Swails (Mon Jun 02 2014 - 04:47:37 PDT)
- Jurgens de Bruin (Mon Jun 02 2014 - 04:31:09 PDT)
- Jason Swails (Mon Jun 02 2014 - 04:25:24 PDT)
- Jurgens de Bruin (Sun Jun 01 2014 - 22:22:41 PDT)
- Aldo Segura (Sun Jun 01 2014 - 20:34:56 PDT)
- Jurgens de Bruin (Sun Jun 01 2014 - 19:20:10 PDT)
[AMBER] Loop refirement
- James Starlight (Sat Jun 14 2014 - 13:21:02 PDT)
- James Starlight (Fri Jun 13 2014 - 12:50:36 PDT)
[AMBER] Low performance in multi-pmemd.mpi
- Daniel Roe (Mon Jun 23 2014 - 06:52:58 PDT)
- James Starlight (Mon Jun 23 2014 - 04:38:32 PDT)
[AMBER] Magnesium FATAL error
- David A Case (Thu Jun 12 2014 - 04:10:36 PDT)
- Soumendranath Bhakat (Thu Jun 12 2014 - 01:46:00 PDT)
[AMBER] Membrane protein tutorial
- James Starlight (Tue Jun 10 2014 - 11:36:59 PDT)
- Jason Swails (Tue Jun 10 2014 - 10:48:31 PDT)
- Brian Radak (Tue Jun 10 2014 - 10:03:45 PDT)
- Jason Swails (Tue Jun 10 2014 - 09:35:56 PDT)
- Brian Radak (Tue Jun 10 2014 - 09:19:08 PDT)
- James Starlight (Tue Jun 10 2014 - 08:58:13 PDT)
[AMBER] Metal Center Parameter Builder (MCPB) manual
- Senthil Natesan (Thu Jun 12 2014 - 11:24:00 PDT)
- Senthil Natesan (Thu Jun 12 2014 - 10:47:07 PDT)
- Jason Swails (Thu Jun 12 2014 - 10:32:53 PDT)
- Senthil Natesan (Wed Jun 11 2014 - 14:49:41 PDT)
- Senthil Natesan (Wed Jun 11 2014 - 10:19:27 PDT)
[AMBER] metal ion parameterisation problem
- Pengfei Li (Wed Jun 25 2014 - 13:25:54 PDT)
- Kshatresh Dutta Dubey (Mon Jun 23 2014 - 12:52:07 PDT)
- Pengfei Li (Mon Jun 23 2014 - 11:53:46 PDT)
- Kshatresh Dutta Dubey (Mon Jun 23 2014 - 08:02:06 PDT)
- Ken Merz (Mon Jun 23 2014 - 07:10:40 PDT)
- Ben Roberts (Sun Jun 22 2014 - 14:57:11 PDT)
- Kshatresh Dutta Dubey (Fri Jun 20 2014 - 14:29:30 PDT)
[AMBER] Mistake in water density
- David A Case (Tue Jun 03 2014 - 05:14:20 PDT)
- Vu Truong (Mon Jun 02 2014 - 15:50:08 PDT)
[AMBER] MM/PBSA calculation.
- Him Shweta (Mon Jun 23 2014 - 23:02:51 PDT)
- Jason Swails (Mon Jun 23 2014 - 12:01:27 PDT)
- Him Shweta (Mon Jun 23 2014 - 10:21:17 PDT)
- Jason Swails (Mon Jun 23 2014 - 05:51:47 PDT)
- Him Shweta (Mon Jun 23 2014 - 03:09:47 PDT)
[AMBER] MMPBSA - calculating energy decomposition by residue in a trajectory without a ligand
- Andrew.Warden.csiro.au (Mon Jun 23 2014 - 14:11:40 PDT)
- Bill Miller III (Wed Jun 18 2014 - 15:40:42 PDT)
- Andrew.Warden.csiro.au (Wed Jun 18 2014 - 14:53:57 PDT)
[AMBER] MMPBSA error
- zahra khatti (Fri Jun 20 2014 - 08:03:32 PDT)
- Ray Luo, Ph.D. (Tue Jun 10 2014 - 12:58:53 PDT)
- zahra khatti (Fri Jun 06 2014 - 05:57:41 PDT)
- Ray Luo, Ph.D. (Thu Jun 05 2014 - 16:25:43 PDT)
- zahra khatti (Thu Jun 05 2014 - 00:28:06 PDT)
- zahra khatti (Wed Jun 04 2014 - 11:43:38 PDT)
- Ray Luo, Ph.D. (Wed Jun 04 2014 - 10:52:40 PDT)
- Jason Swails (Wed Jun 04 2014 - 06:02:14 PDT)
- zahra khatti (Wed Jun 04 2014 - 05:46:48 PDT)
- zahra khatti (Tue Jun 03 2014 - 13:17:48 PDT)
- Jason Swails (Tue Jun 03 2014 - 08:11:32 PDT)
- zahra khatti (Tue Jun 03 2014 - 07:15:45 PDT)
[AMBER] MMPBSA huge VDW values
- maryam azimzadehirani (Thu Jun 12 2014 - 04:44:16 PDT)
- Jason Swails (Thu Jun 12 2014 - 04:11:39 PDT)
- maryam azimzadehirani (Thu Jun 12 2014 - 00:28:36 PDT)
[AMBER] mmpbsa.py
- zahra khatti (Mon Jun 02 2014 - 07:54:40 PDT)
[AMBER] MPI and parallel installation
- Jason Swails (Wed Jun 18 2014 - 12:09:36 PDT)
- Gerald Monard (Wed Jun 18 2014 - 12:06:49 PDT)
- Simone Fulle (Wed Jun 18 2014 - 10:44:26 PDT)
[AMBER] MTK++ Error
- Kshatresh Dutta Dubey (Sat Jun 21 2014 - 16:00:46 PDT)
- Kshatresh Dutta Dubey (Sat Jun 21 2014 - 13:43:44 PDT)
[AMBER] MTKPP installation error
- Kshatresh Dutta Dubey (Wed Jun 04 2014 - 04:46:23 PDT)
- Jason Swails (Wed Jun 04 2014 - 04:39:45 PDT)
- Kshatresh Dutta Dubey (Tue Jun 03 2014 - 22:07:44 PDT)
- Kshatresh Dutta Dubey (Tue Jun 03 2014 - 13:04:09 PDT)
- Jason Swails (Tue Jun 03 2014 - 12:52:03 PDT)
- Kshatresh Dutta Dubey (Tue Jun 03 2014 - 12:47:12 PDT)
[AMBER] No VDWAALS EEL in PB MMPBSA.py job
- Ray Luo, Ph.D. (Fri Jun 27 2014 - 09:57:28 PDT)
- JPB (Fri Jun 27 2014 - 08:27:25 PDT)
[AMBER] NVT equilibration crash using CUDA
- Daniel Roe (Tue Jun 10 2014 - 07:39:26 PDT)
- Jason Swails (Tue Jun 10 2014 - 05:10:03 PDT)
- James Starlight (Tue Jun 10 2014 - 02:36:04 PDT)
- James Starlight (Mon Jun 09 2014 - 11:13:26 PDT)
- Jason Swails (Mon Jun 09 2014 - 08:39:34 PDT)
- James Starlight (Mon Jun 09 2014 - 07:59:44 PDT)
- Jason Swails (Mon Jun 09 2014 - 05:21:06 PDT)
- James Starlight (Mon Jun 09 2014 - 03:26:08 PDT)
- Soumendranath Bhakat (Mon Jun 09 2014 - 02:15:27 PDT)
- James Starlight (Mon Jun 09 2014 - 01:34:29 PDT)
- James Starlight (Mon Jun 09 2014 - 01:17:04 PDT)
[AMBER] On the choosing of coordinate for the umbrella sampling
- Carlos Simmerling (Thu Jun 05 2014 - 12:28:32 PDT)
- Brian Radak (Thu Jun 05 2014 - 06:37:29 PDT)
- Jason Swails (Thu Jun 05 2014 - 04:45:56 PDT)
- James Starlight (Thu Jun 05 2014 - 04:03:46 PDT)
[AMBER] On the usage of the position restrains during equilibration
- Jason Swails (Sun Jun 22 2014 - 12:34:06 PDT)
- James Starlight (Fri Jun 20 2014 - 22:23:38 PDT)
- Bill Ross (Fri Jun 20 2014 - 18:57:36 PDT)
- Bill Ross (Fri Jun 20 2014 - 18:48:33 PDT)
- James Starlight (Fri Jun 20 2014 - 11:31:33 PDT)
- Bill Ross (Fri Jun 20 2014 - 08:36:06 PDT)
- James Starlight (Fri Jun 20 2014 - 07:30:50 PDT)
[AMBER] Parametrization of non-standart residues
- James Starlight (Tue Jun 03 2014 - 08:15:55 PDT)
- Parker de Waal (Tue Jun 03 2014 - 06:15:30 PDT)
- James Starlight (Tue Jun 03 2014 - 05:57:57 PDT)
[AMBER] Parametrization of the protein with the assigned protonation states
- Jason Swails (Wed Jun 04 2014 - 07:35:02 PDT)
- James Starlight (Wed Jun 04 2014 - 06:43:53 PDT)
- Jason Swails (Tue Jun 03 2014 - 10:59:34 PDT)
- James Starlight (Tue Jun 03 2014 - 10:44:07 PDT)
[AMBER] Per residue rmsd
- Daniel Roe (Fri Jun 27 2014 - 16:07:53 PDT)
- Soumendranath Bhakat (Fri Jun 27 2014 - 15:56:31 PDT)
- Jason Swails (Fri Jun 27 2014 - 15:50:54 PDT)
- Chinthaka Ratnaweera (Fri Jun 27 2014 - 14:46:58 PDT)
- Soumendranath Bhakat (Fri Jun 27 2014 - 14:19:40 PDT)
- Chinthaka Ratnaweera (Fri Jun 27 2014 - 13:59:49 PDT)
[AMBER] periodic box drifted during NVE run
- David A Case (Sat Jun 28 2014 - 08:45:39 PDT)
- Quynh Vo (Thu Jun 26 2014 - 15:56:25 PDT)
[AMBER] plot in xmgrace (interaction energy per residues)
- David A Case (Mon Jun 02 2014 - 04:07:10 PDT)
- Arunima Shilpi (Sun Jun 01 2014 - 23:45:18 PDT)
[AMBER] Pressure fluctuation problem during NPT simulation
- Saikat Dutta chowdhury (Mon Jun 02 2014 - 04:41:19 PDT)
- Jason Swails (Mon Jun 02 2014 - 04:35:00 PDT)
- Saikat Dutta chowdhury (Mon Jun 02 2014 - 03:53:30 PDT)
[AMBER] principal axes error using cpptraj
- Daniel Roe (Wed Jun 04 2014 - 06:05:24 PDT)
- Asmita Gupta (Wed Jun 04 2014 - 03:16:43 PDT)
[AMBER] Printing out matrix labels
- Daniel Roe (Mon Jun 30 2014 - 06:41:12 PDT)
- Jason Swails (Mon Jun 30 2014 - 06:37:50 PDT)
- Eugene Yedvabny (Sun Jun 29 2014 - 21:51:09 PDT)
- Eugene Yedvabny (Sun Jun 29 2014 - 21:44:08 PDT)
- Daniel Roe (Fri Jun 27 2014 - 21:13:10 PDT)
- Eugene Yedvabny (Fri Jun 27 2014 - 18:09:12 PDT)
[AMBER] problem during add ions
- Parvesh Singh (Mon Jun 09 2014 - 07:08:50 PDT)
- David A Case (Mon Jun 09 2014 - 05:02:49 PDT)
- Sohag Biswas (Mon Jun 09 2014 - 03:21:02 PDT)
[AMBER] Problem in creating prmtop inpcrd file in leap
- 肖立 (Wed Jun 25 2014 - 10:25:42 PDT)
- David A Case (Tue Jun 24 2014 - 18:20:52 PDT)
- Bill Ross (Tue Jun 24 2014 - 18:06:02 PDT)
- 肖立 (Tue Jun 24 2014 - 17:31:37 PDT)
[AMBER] Problem using charmmlipid2amber.py with VMD
- Benjamin D Madej (Mon Jun 09 2014 - 17:10:36 PDT)
- Thomas Evangelidis (Mon Jun 09 2014 - 12:48:40 PDT)
- Benjamin D Madej (Mon Jun 09 2014 - 12:18:57 PDT)
- Benjamin D Madej (Mon Jun 09 2014 - 12:03:13 PDT)
- James Starlight (Sun Jun 08 2014 - 00:52:22 PDT)
- wmsmith.uci.edu (Fri Jun 06 2014 - 09:27:59 PDT)
[AMBER] QM/MM and spin parameter
- Jason Swails (Tue Jun 03 2014 - 08:18:47 PDT)
- Brian Radak (Tue Jun 03 2014 - 08:16:36 PDT)
- Jinfeng Huang (Tue Jun 03 2014 - 07:39:10 PDT)
[AMBER] QM/MMPBSA
- Jason Swails (Wed Jun 11 2014 - 10:14:06 PDT)
- John Smith (Wed Jun 11 2014 - 09:53:15 PDT)
- Jason Swails (Wed Jun 11 2014 - 09:32:02 PDT)
- Brian Radak (Wed Jun 11 2014 - 09:24:26 PDT)
- John Smith (Wed Jun 11 2014 - 09:01:42 PDT)
- Jason Swails (Wed Jun 11 2014 - 05:35:07 PDT)
- John Smith (Wed Jun 11 2014 - 04:31:29 PDT)
[AMBER] QMMM NEB reaction pathway calculation with AMBER
- Teerapong Pirojsirikul (Mon Jun 30 2014 - 11:17:51 PDT)
- Jason Swails (Sun Jun 29 2014 - 17:52:49 PDT)
- Teerapong Pirojsirikul (Sat Jun 28 2014 - 17:50:17 PDT)
[AMBER] Queries about QM/MM
- Brian Radak (Wed Jun 18 2014 - 07:03:36 PDT)
- David A Case (Wed Jun 18 2014 - 05:54:51 PDT)
- Jason Swails (Wed Jun 18 2014 - 05:41:31 PDT)
- Tanmoy Paul (Tue Jun 17 2014 - 23:36:51 PDT)
[AMBER] Query about GPU model
- Indrajit Deb (Tue Jun 10 2014 - 12:25:16 PDT)
- Scott Le Grand (Tue Jun 10 2014 - 10:28:21 PDT)
- Ross Walker (Tue Jun 10 2014 - 09:27:10 PDT)
- Indrajit Deb (Tue Jun 10 2014 - 01:19:19 PDT)
[AMBER] Query about parallel GPU multijob
- Kshatresh Dutta Dubey (Mon Jun 23 2014 - 14:27:35 PDT)
- Ross Walker (Mon Jun 23 2014 - 14:15:11 PDT)
- Kshatresh Dutta Dubey (Mon Jun 23 2014 - 13:54:22 PDT)
- Ross Walker (Mon Jun 23 2014 - 13:45:57 PDT)
- Kshatresh Dutta Dubey (Mon Jun 23 2014 - 13:44:14 PDT)
- Ross Walker (Mon Jun 23 2014 - 13:37:43 PDT)
- Kshatresh Dutta Dubey (Mon Jun 23 2014 - 13:36:45 PDT)
- Kshatresh Dutta Dubey (Mon Jun 23 2014 - 13:25:18 PDT)
- Ross Walker (Mon Jun 23 2014 - 13:04:44 PDT)
- Kshatresh Dutta Dubey (Mon Jun 23 2014 - 12:43:59 PDT)
[AMBER] Query about QM/MM calculation using Amber/Gaussian interface
- Kshatresh Dutta Dubey (Fri Jun 13 2014 - 14:24:54 PDT)
- Gerald Monard (Fri Jun 13 2014 - 12:39:14 PDT)
- David A Case (Fri Jun 13 2014 - 12:08:35 PDT)
- Kshatresh Dutta Dubey (Fri Jun 13 2014 - 07:58:59 PDT)
- Kshatresh Dutta Dubey (Fri Jun 13 2014 - 06:01:00 PDT)
- Gerald Monard (Fri Jun 13 2014 - 06:48:11 PDT)
- Soumendranath Bhakat (Fri Jun 13 2014 - 04:42:31 PDT)
- Kshatresh Dutta Dubey (Fri Jun 13 2014 - 04:44:39 PDT)
- Soumendranath Bhakat (Fri Jun 13 2014 - 04:34:47 PDT)
- Soumendranath Bhakat (Fri Jun 13 2014 - 04:36:26 PDT)
- Kshatresh Dutta Dubey (Fri Jun 13 2014 - 04:31:51 PDT)
- Kshatresh Dutta Dubey (Fri Jun 13 2014 - 04:26:48 PDT)
- Soumendranath Bhakat (Fri Jun 13 2014 - 04:01:44 PDT)
- Jason Swails (Fri Jun 13 2014 - 03:54:41 PDT)
- Kshatresh Dutta Dubey (Fri Jun 13 2014 - 02:50:31 PDT)
- Gerald Monard (Fri Jun 13 2014 - 02:31:17 PDT)
- Kshatresh Dutta Dubey (Fri Jun 13 2014 - 02:16:03 PDT)
[AMBER] Question about how a charged system can be simulated using PBC?
- Jason Swails (Sun Jun 08 2014 - 18:26:37 PDT)
- yuandandan05.gmail.com (Sun Jun 08 2014 - 18:13:31 PDT)
- Dr. Vitaly Chaban (Sun Jun 08 2014 - 03:27:05 PDT)
- yuandandan05.gmail.com (Sat Jun 07 2014 - 21:12:27 PDT)
[AMBER] RDF Plot
- Jason Swails (Wed Jun 04 2014 - 09:08:42 PDT)
- zahra khatti (Wed Jun 04 2014 - 08:04:57 PDT)
[AMBER] Regarding molecule's breaking during simulation.
- Jason Swails (Mon Jun 02 2014 - 05:12:38 PDT)
- richa anand (Mon Jun 02 2014 - 04:52:09 PDT)
[AMBER] remd
- Daniel Roe (Thu Jun 19 2014 - 13:57:09 PDT)
- whb (Wed Jun 18 2014 - 17:35:19 PDT)
[AMBER] request for help in plotting distance matrix plot
- Soumendranath Bhakat (Sun Jun 01 2014 - 09:53:55 PDT)
- Daniel Roe (Sun Jun 01 2014 - 09:35:30 PDT)
[AMBER] restarting MDs generated in Amber10 with Amber12
- David A Case (Wed Jun 11 2014 - 04:29:24 PDT)
- Silvia Bonomo (Wed Jun 11 2014 - 01:52:29 PDT)
[AMBER] Rmsd with reference structure having different number of total atoms
- Rajeswari A. (Fri Jun 13 2014 - 07:26:25 PDT)
- Rajeswari A. (Fri Jun 13 2014 - 07:13:05 PDT)
[AMBER] sander14 MPI produces different results depending on number of used cores
- David A Case (Tue Jun 03 2014 - 06:10:59 PDT)
- David Abia (Tue Jun 03 2014 - 05:00:53 PDT)
[AMBER] Se atom type
- David A Case (Mon Jun 23 2014 - 05:04:42 PDT)
- Krisztina Feher (Mon Jun 23 2014 - 04:43:35 PDT)
- Jason Swails (Sat Jun 21 2014 - 20:16:18 PDT)
- Krisztina Feher (Sat Jun 21 2014 - 05:37:34 PDT)
- Krisztina Feher (Thu Jun 19 2014 - 11:29:18 PDT)
- Krisztina Feher (Thu Jun 19 2014 - 08:32:24 PDT)
[AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14
- Gerald Monard (Thu Jun 19 2014 - 03:09:55 PDT)
- 余青芬 (Thu Jun 19 2014 - 02:27:21 PDT)
- Gerald Monard (Wed Jun 18 2014 - 12:44:13 PDT)
- David A Case (Wed Jun 18 2014 - 06:02:45 PDT)
- 余青芬 (Wed Jun 18 2014 - 03:03:55 PDT)
- Gerald Monard (Mon Jun 16 2014 - 06:04:37 PDT)
- 余青芬 (Mon Jun 16 2014 - 02:26:38 PDT)
- Gerald Monard (Sun Jun 15 2014 - 00:27:25 PDT)
- 余青芬 (Sat Jun 14 2014 - 23:26:54 PDT)
[AMBER] segmentation_fault_loading_pdb in tleap
- Shomesankar Bhunia (Sat Jun 21 2014 - 06:45:30 PDT)
- Soumendranath Bhakat (Sat Jun 21 2014 - 06:34:50 PDT)
- Shomesankar Bhunia (Sat Jun 21 2014 - 05:56:11 PDT)
[AMBER] set up for the ScaledMD
- Neha Gandhi (Wed Jun 04 2014 - 00:10:49 PDT)
- zhou gong (Tue Jun 03 2014 - 23:55:06 PDT)
[AMBER] Setting up z-constraint
- Ross Walker (Mon Jun 23 2014 - 08:04:56 PDT)
- Pierpaolo Cacciotto (Mon Jun 23 2014 - 03:20:29 PDT)
- Scott Le Grand (Fri Jun 20 2014 - 09:16:37 PDT)
- Scott Le Grand (Fri Jun 20 2014 - 09:13:01 PDT)
- Ross Walker (Fri Jun 20 2014 - 08:57:56 PDT)
- Pierpaolo Cacciotto (Fri Jun 20 2014 - 03:26:48 PDT)
- Benjamin D Madej (Thu Jun 19 2014 - 19:40:27 PDT)
- Pierpaolo Cacciotto (Wed Jun 18 2014 - 10:03:31 PDT)
- Brian Radak (Wed Jun 18 2014 - 09:11:22 PDT)
- Ylenia Cau (Wed Jun 18 2014 - 08:47:03 PDT)
[AMBER] Side chain and backbone-specific parameters.
- Jason Swails (Tue Jun 10 2014 - 12:07:35 PDT)
- Lee-Ping Wang (Tue Jun 10 2014 - 11:50:40 PDT)
- Jason Swails (Tue Jun 10 2014 - 11:30:03 PDT)
- Lee-Ping Wang (Tue Jun 10 2014 - 10:50:35 PDT)
- Jason Swails (Tue Jun 10 2014 - 10:46:32 PDT)
- Lee-Ping Wang (Tue Jun 10 2014 - 10:25:24 PDT)
[AMBER] simulation differences in pmemd.MPI and pmemd.cuda
- Manikanthan Bhavaraju (Wed Jun 25 2014 - 18:33:00 PDT)
- Ross Walker (Wed Jun 25 2014 - 17:57:26 PDT)
- Soumendranath Bhakat (Wed Jun 25 2014 - 15:13:53 PDT)
- Manikanthan Bhavaraju (Wed Jun 25 2014 - 14:56:45 PDT)
[AMBER] Simulation of the protein with internal water
- Bill Ross (Thu Jun 05 2014 - 19:04:21 PDT)
[AMBER] Sirius executable not available anymore?
- David A Case (Thu Jun 26 2014 - 04:30:55 PDT)
- Felix Terwesten (Thu Jun 26 2014 - 04:05:23 PDT)
- Ross Walker (Tue Jun 24 2014 - 11:09:49 PDT)
- David A Case (Tue Jun 24 2014 - 04:53:18 PDT)
- Felix Terwesten (Tue Jun 24 2014 - 04:19:57 PDT)
[AMBER] SolvateBox command
- Bill Ross (Mon Jun 02 2014 - 17:18:41 PDT)
[AMBER] Some error in output file and restart
- Ross Walker (Tue Jun 24 2014 - 09:59:27 PDT)
- kirtana S (Mon Jun 23 2014 - 21:42:24 PDT)
- Ross Walker (Mon Jun 23 2014 - 13:11:59 PDT)
- Jason Swails (Mon Jun 23 2014 - 09:54:08 PDT)
- kirtana S (Mon Jun 23 2014 - 08:40:35 PDT)
[AMBER] sudden and rapid configuration change in NVT simulation
- yjlee (Fri Jun 06 2014 - 05:46:03 PDT)
- Jason Swails (Thu Jun 05 2014 - 05:40:17 PDT)
- yjlee (Thu Jun 05 2014 - 04:47:02 PDT)
- Daniel Roe (Tue Jun 03 2014 - 07:12:07 PDT)
- Soumendranath Bhakat (Tue Jun 03 2014 - 06:46:30 PDT)
- Jason Swails (Tue Jun 03 2014 - 06:23:09 PDT)
- yjlee (Mon Jun 02 2014 - 23:43:02 PDT)
- Jason Swails (Mon Jun 02 2014 - 04:20:43 PDT)
- yjlee (Sun Jun 01 2014 - 23:47:17 PDT)
[AMBER] The linkage of Amber and Gaussian in Amber 14.
- Jason Swails (Sat Jun 14 2014 - 06:05:39 PDT)
- Jinfeng Huang (Sat Jun 14 2014 - 01:41:41 PDT)
[AMBER] tleap for gammacyclodextrin-Reg.
- Lachele Foley (Tue Jun 24 2014 - 10:54:54 PDT)
- Lachele Foley (Tue Jun 24 2014 - 10:32:00 PDT)
- Shreeramesh (Tue Jun 24 2014 - 08:18:25 PDT)
[AMBER] tleap using GLYCAM force field
- Lachele Foley (Mon Jun 23 2014 - 08:32:51 PDT)
- Shreeramesh (Mon Jun 23 2014 - 05:00:49 PDT)
[AMBER] Topology issue with MMPBSA.py
- Daniel Roe (Thu Jun 19 2014 - 14:24:40 PDT)
- Jason Swails (Mon Jun 16 2014 - 07:03:43 PDT)
- JPB (Mon Jun 16 2014 - 06:37:06 PDT)
- Jason Swails (Mon Jun 16 2014 - 05:27:52 PDT)
- JPB (Mon Jun 16 2014 - 03:29:39 PDT)
[AMBER] torsion restraint violation reporting
- Duggan, Brendan (Wed Jun 18 2014 - 11:36:08 PDT)
[AMBER] Torsional profile of butane
- Yingjie Wang (Fri Jun 27 2014 - 07:38:41 PDT)
- FyD (Thu Jun 26 2014 - 22:55:02 PDT)
- Jason Swails (Thu Jun 26 2014 - 15:14:00 PDT)
- Yingjie Wang (Thu Jun 26 2014 - 13:08:32 PDT)
- Jason Swails (Thu Jun 26 2014 - 11:54:25 PDT)
- Yingjie Wang (Thu Jun 26 2014 - 10:57:32 PDT)
[AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex
- Jason Swails (Mon Jun 02 2014 - 05:15:48 PDT)
- Soumendranath Bhakat (Mon Jun 02 2014 - 05:10:57 PDT)
- Roza M (Mon Jun 02 2014 - 05:02:15 PDT)
- Jason Swails (Mon Jun 02 2014 - 04:27:13 PDT)
- Roza M (Mon Jun 02 2014 - 04:04:28 PDT)
[AMBER] Using MM-PBSA to find binding free energy for Zif268-DNA complex
- Roza M (Mon Jun 02 2014 - 06:20:04 PDT)
[AMBER] VMD and binary trajectories
- James Starlight (Thu Jun 05 2014 - 07:19:08 PDT)
- Jason Swails (Thu Jun 05 2014 - 04:39:54 PDT)
- James Starlight (Thu Jun 05 2014 - 01:00:45 PDT)
[AMBER] WaterBox Dimensions
- David A Case (Tue Jun 03 2014 - 05:10:35 PDT)
- Ahmed Ayoub (Mon Jun 02 2014 - 14:53:00 PDT)
[AMBER] zlib issues during compilation.
- Harris, Danni (Tue Jun 10 2014 - 04:56:02 PDT)
- Daniel Roe (Mon Jun 09 2014 - 20:17:41 PDT)
- Harris, Danni (Mon Jun 09 2014 - 16:29:24 PDT)
- Daniel Roe (Mon Jun 09 2014 - 14:44:56 PDT)
- Harris, Danni (Mon Jun 09 2014 - 12:46:51 PDT)
[AMBER] 【amber】center of mass&umbrella sampling
- Daniel Roe (Fri Jun 06 2014 - 06:57:16 PDT)
- Jason Swails (Fri Jun 06 2014 - 05:20:20 PDT)
- whb (Fri Jun 06 2014 - 00:11:40 PDT)
RDF Plot
- zahra khatti (Wed Jun 04 2014 - 08:13:45 PDT)

Amber Archive Jun 2014 by subject