Amber Archive Mar 2015: by subject

[AMBER] "Error opening unit 30: File "inpcrd" is missing or unreadable" on Tutorial A15
- christian.yongky.ui.ac.id (Mon Mar 23 2015 - 03:24:20 PDT)
- Jason Swails (Mon Mar 23 2015 - 02:33:58 PDT)
- christian.yongky.ui.ac.id (Sun Mar 22 2015 - 23:47:08 PDT)
[AMBER] ** No torsion terms
- Evans, Shalton (Sun Mar 15 2015 - 17:57:30 PDT)
[AMBER] **No Torsion terms
- David A Case (Wed Mar 18 2015 - 10:39:51 PDT)
- David A Case (Wed Mar 18 2015 - 06:35:28 PDT)
- Evans, Shalton (Tue Mar 17 2015 - 09:28:47 PDT)
[AMBER] 10-12 Potentials, HBOND
- Jason Swails (Sat Mar 14 2015 - 16:12:10 PDT)
- David Poole (Fri Mar 13 2015 - 20:37:13 PDT)
[AMBER] : Dimer Imaging Problem
- Waldner, Birgit (Wed Mar 11 2015 - 09:41:00 PDT)
- Daniel Roe (Wed Mar 11 2015 - 09:31:23 PDT)
- Waldner, Birgit (Wed Mar 11 2015 - 09:28:35 PDT)
[AMBER] [Fwd: ]
- vladimir.palivec.marge.uochb.cas.cz (Sat Mar 21 2015 - 04:46:19 PDT)
[AMBER] [q4md-fft] Fwd: D- amino acids in ff10
- Carlos Simmerling (Fri Mar 13 2015 - 11:28:17 PDT)
- FyD (Fri Mar 13 2015 - 10:51:42 PDT)
- Carlos Simmerling (Fri Mar 13 2015 - 10:01:04 PDT)
- FyD (Fri Mar 13 2015 - 09:51:04 PDT)
[AMBER] [q4md-fft] Modify RNA's sugar and adding partial charges
- FyD (Mon Mar 16 2015 - 00:15:03 PDT)
[AMBER] a question on molecular dynamics simulation
- David A Case (Fri Mar 06 2015 - 07:09:44 PST)
- Jason Swails (Fri Mar 06 2015 - 07:03:48 PST)
- Brett (Fri Mar 06 2015 - 05:14:35 PST)
[AMBER] About generalized restraints in AMBER14 with GPU support
- Jason Swails (Tue Mar 24 2015 - 07:48:46 PDT)
- Attilio Vittorio Vargiu (Tue Mar 24 2015 - 07:29:28 PDT)
[AMBER] About TIP4-Ew water model usage
- Saikat Dutta chowdhury (Thu Mar 19 2015 - 01:25:35 PDT)
- Carlos Simmerling (Wed Mar 18 2015 - 03:16:36 PDT)
- Saikat Dutta chowdhury (Tue Mar 17 2015 - 23:47:16 PDT)
- Jason Swails (Tue Mar 17 2015 - 05:53:54 PDT)
- Saikat Dutta chowdhury (Tue Mar 17 2015 - 03:31:56 PDT)
[AMBER] acetyl lysine
- achim.sandmann.chemie.stud.uni-erlangen.de (Mon Mar 09 2015 - 02:04:34 PDT)
- David A Case (Sat Mar 07 2015 - 17:43:48 PST)
- Dhiraj Srivastava (Sat Mar 07 2015 - 14:15:29 PST)
[AMBER] Amber 14 tests errors
- David A Case (Wed Mar 18 2015 - 17:41:34 PDT)
- Gustavo Avelar Molina (Wed Mar 18 2015 - 16:34:26 PDT)
[AMBER] AMBER Digest, Vol 1160, Issue 1
- Sohag Biswas (Tue Mar 17 2015 - 01:39:53 PDT)
[AMBER] AMBER Digest, Vol 1169, Issue 1
- Arjun Sharma (Wed Mar 25 2015 - 14:54:31 PDT)
[AMBER] Amber on Red Hat?
- Agnieszka Szarecka (Tue Mar 17 2015 - 13:29:19 PDT)
- Jason Swails (Tue Mar 17 2015 - 12:36:37 PDT)
- Agnieszka Szarecka (Tue Mar 17 2015 - 12:23:04 PDT)
[AMBER] Amber standard residue name
- wjli (Thu Mar 19 2015 - 03:45:34 PDT)
[AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files
- Ross Walker (Tue Mar 31 2015 - 23:33:34 PDT)
- Ross Walker (Tue Mar 31 2015 - 20:39:06 PDT)
- Bill Ross (Tue Mar 31 2015 - 18:00:34 PDT)
- Ross Walker (Tue Mar 31 2015 - 11:06:19 PDT)
- Himanshu Joshi (Tue Mar 31 2015 - 10:58:51 PDT)
[AMBER] aMD boost parameters for CHARMM force field?
- Daniel Roe (Fri Mar 27 2015 - 08:43:13 PDT)
- Brian Radak (Fri Mar 27 2015 - 08:39:13 PDT)
[AMBER] ante-mmpbsa.py: problem with the mask syntax
- George Tzotzos (Mon Mar 16 2015 - 12:59:49 PDT)
- Jason Swails (Mon Mar 16 2015 - 12:18:13 PDT)
- George Tzotzos (Mon Mar 16 2015 - 12:12:44 PDT)
- Jason Swails (Mon Mar 16 2015 - 11:37:47 PDT)
- Kenneth Huang (Mon Mar 16 2015 - 11:21:13 PDT)
- George Tzotzos (Mon Mar 16 2015 - 10:26:16 PDT)
[AMBER] Antechamber - TURBOMOLE
- hannes.loeffler.stfc.ac.uk (Thu Mar 26 2015 - 05:03:54 PDT)
- Sanja Zivanovic (Thu Mar 26 2015 - 04:48:26 PDT)
[AMBER] ATP and ADP-Pi simulations
- FyD (Wed Mar 04 2015 - 23:33:12 PST)
- Joseph Baker (Wed Mar 04 2015 - 21:38:33 PST)
- FyD (Wed Mar 04 2015 - 00:56:52 PST)
- Joseph Baker (Tue Mar 03 2015 - 21:36:07 PST)
- David A Case (Tue Mar 03 2015 - 06:05:19 PST)
- FyD (Tue Mar 03 2015 - 01:28:50 PST)
- Joseph Baker (Mon Mar 02 2015 - 20:05:25 PST)
- David A Case (Mon Mar 02 2015 - 17:38:22 PST)
- Joseph Baker (Mon Mar 02 2015 - 13:04:45 PST)
[AMBER] Backbone Rmsd
- Daniel Roe (Sat Mar 21 2015 - 08:44:56 PDT)
- Jason Swails (Fri Mar 20 2015 - 18:26:32 PDT)
- jacob wick (Fri Mar 20 2015 - 03:03:43 PDT)
- David A Case (Tue Mar 17 2015 - 04:52:50 PDT)
- jacob wick (Tue Mar 17 2015 - 03:17:46 PDT)
[AMBER] Bond distance and Box shape
- Daniel Roe (Fri Mar 20 2015 - 07:34:53 PDT)
- Arjun Sharma (Fri Mar 20 2015 - 07:21:58 PDT)
[AMBER] calculating angle between to vectors
- Vijay Achari (Thu Mar 12 2015 - 03:14:19 PDT)
- Vijay Achari (Wed Mar 11 2015 - 22:22:45 PDT)
- Daniel Roe (Wed Mar 11 2015 - 07:39:54 PDT)
- Vijay Achari (Wed Mar 11 2015 - 01:01:28 PDT)
[AMBER] calculating HB lifetime
- Vijay Achari (Mon Mar 09 2015 - 23:52:03 PDT)
[AMBER] CHAMBER and CMAP difficulty
- Brian Radak (Wed Mar 18 2015 - 09:59:33 PDT)
- Jason Swails (Wed Mar 18 2015 - 09:50:17 PDT)
- Brian Radak (Wed Mar 18 2015 - 09:31:55 PDT)
- Brian Radak (Wed Mar 18 2015 - 09:13:28 PDT)
- Jason Swails (Wed Mar 18 2015 - 09:03:47 PDT)
- Brian Radak (Wed Mar 18 2015 - 08:54:10 PDT)
- Jason Swails (Wed Mar 18 2015 - 08:36:33 PDT)
- Brian Radak (Wed Mar 18 2015 - 08:27:29 PDT)
- Jason Swails (Wed Mar 18 2015 - 08:14:29 PDT)
- Brian Radak (Wed Mar 18 2015 - 08:03:53 PDT)
[AMBER] Chamber problem
- Jason Swails (Mon Mar 02 2015 - 12:07:38 PST)
- Shukla, Saurabh (Mon Mar 02 2015 - 11:50:29 PST)
[AMBER] Citation from the apostrophe police
- David A Case (Fri Mar 20 2015 - 06:13:07 PDT)
[AMBER] clustering in ptraj
- Mary Varughese (Tue Mar 10 2015 - 08:12:32 PDT)
- Daniel Roe (Tue Mar 10 2015 - 07:08:14 PDT)
- Mary Varughese (Mon Mar 09 2015 - 10:39:33 PDT)
- Daniel Roe (Mon Mar 09 2015 - 07:12:25 PDT)
- Mary Varughese (Sun Mar 08 2015 - 23:48:43 PDT)
[AMBER] Cofactor parametrization
- FyD (Thu Mar 05 2015 - 07:43:44 PST)
- Hannes Loeffler (Thu Mar 05 2015 - 05:34:00 PST)
- Carlos Simmerling (Thu Mar 05 2015 - 05:04:09 PST)
- Francesca Tessaro (Thu Mar 05 2015 - 04:55:06 PST)
- FyD (Tue Mar 03 2015 - 04:47:26 PST)
- Dr. M. Shahid (Tue Mar 03 2015 - 03:18:01 PST)
- FyD (Tue Mar 03 2015 - 01:18:13 PST)
- Hannes Loeffler (Mon Mar 02 2015 - 03:29:31 PST)
- Francesca Tessaro (Mon Mar 02 2015 - 03:08:08 PST)
[AMBER] COM restrain support in Amber14
- Jason Swails (Mon Mar 02 2015 - 05:36:05 PST)
- Srinivasaraghavan Kannan (Mon Mar 02 2015 - 02:29:42 PST)
[AMBER] combinatorial library
- Hector A. Baldoni (Thu Mar 26 2015 - 17:22:05 PDT)
[AMBER] concave edge on torus has mismatched atoms
- Sylvester Tumusiime (Tue Mar 24 2015 - 13:06:15 PDT)
- Daniel Roe (Tue Mar 24 2015 - 13:02:16 PDT)
- Sylvester Tumusiime (Tue Mar 24 2015 - 12:28:12 PDT)
[AMBER] CpHMD-pHREX AMBER14
- Jason Swails (Tue Mar 24 2015 - 18:36:02 PDT)
- Arjun Sharma (Tue Mar 24 2015 - 10:37:29 PDT)
[AMBER] cpptraj H-bond: clarification sought
- Daniel Roe (Mon Mar 09 2015 - 07:29:22 PDT)
- George Tzotzos (Sat Mar 07 2015 - 15:12:12 PST)
- Daniel Roe (Sat Mar 07 2015 - 14:38:03 PST)
- George Tzotzos (Fri Mar 06 2015 - 09:44:55 PST)
[AMBER] CUDA problems
- Ross Walker (Mon Mar 23 2015 - 09:52:29 PDT)
- Beale, John (Mon Mar 23 2015 - 07:41:30 PDT)
[AMBER] D- amino acids in ff10
- FyD (Fri Mar 13 2015 - 09:21:03 PDT)
- Carlos Simmerling (Wed Mar 11 2015 - 06:55:01 PDT)
- Neha Gandhi (Wed Mar 11 2015 - 06:45:07 PDT)
[AMBER] Decomposition of the MMGBSA based on multi trajectory input
- James Starlight (Mon Mar 16 2015 - 06:42:16 PDT)
- James Starlight (Mon Mar 16 2015 - 06:00:19 PDT)
- Bill Miller III (Thu Mar 05 2015 - 04:44:26 PST)
- James Starlight (Thu Mar 05 2015 - 03:39:16 PST)
- James Starlight (Thu Mar 05 2015 - 02:45:02 PST)
- Bill Miller III (Wed Mar 04 2015 - 07:38:10 PST)
- James Starlight (Wed Mar 04 2015 - 06:48:34 PST)
- James Starlight (Wed Mar 04 2015 - 06:10:46 PST)
- Bill Miller III (Tue Mar 03 2015 - 07:23:56 PST)
- James Starlight (Tue Mar 03 2015 - 03:58:44 PST)
[AMBER] Dielectric constant for dna-ligand in TIP3P system
- Him Shweta (Wed Mar 18 2015 - 03:09:10 PDT)
- Thomas Cheatham (Tue Mar 17 2015 - 08:40:36 PDT)
- Jason Swails (Tue Mar 17 2015 - 08:15:01 PDT)
- Him Shweta (Tue Mar 17 2015 - 07:49:59 PDT)
- Him Shweta (Tue Mar 17 2015 - 07:45:13 PDT)
[AMBER] Differences in AMBER force fields
- Jiri Sponer (Fri Mar 20 2015 - 09:03:07 PDT)
- Petr Jurecka (Tue Mar 17 2015 - 10:47:57 PDT)
- David A Case (Tue Mar 17 2015 - 04:49:08 PDT)
- Thomas Exner (Tue Mar 17 2015 - 02:46:24 PDT)
[AMBER] diisopropylethylene parameter
- Hannes Loeffler (Mon Mar 16 2015 - 03:37:41 PDT)
- Jennifer Vo (Mon Mar 16 2015 - 03:06:47 PDT)
[AMBER] Drifting molecules despite strong restraints
- Jason Swails (Fri Mar 20 2015 - 08:23:15 PDT)
- Sanmeet Chahal (Fri Mar 20 2015 - 07:18:19 PDT)
- Jason Swails (Fri Mar 20 2015 - 05:22:03 PDT)
- Sanmeet Chahal (Thu Mar 19 2015 - 15:32:42 PDT)
[AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA
- Gerald Monard (Fri Mar 27 2015 - 01:27:39 PDT)
- psu4.uic.edu (Tue Mar 24 2015 - 10:06:49 PDT)
[AMBER] Error during Adding Fragment（about MCPB ）
- David A Case (Thu Mar 19 2015 - 05:11:34 PDT)
- wjli (Thu Mar 19 2015 - 03:33:23 PDT)
[AMBER] error in antechamber: Bond types are assigned for valence state 1 with penalty of 1
- Hannes Loeffler (Fri Mar 13 2015 - 02:59:40 PDT)
- Rebeca García Fandiño (Fri Mar 13 2015 - 02:24:20 PDT)
[AMBER] error in MMPBSA.py
- Bill Miller III (Thu Mar 05 2015 - 07:04:45 PST)
- Emilio Angelina (Thu Mar 05 2015 - 03:26:43 PST)
[AMBER] Error message from FEW in Amber14 tutorial A24
- Jason Swails (Mon Mar 23 2015 - 13:24:57 PDT)
- hannes.loeffler.stfc.ac.uk (Mon Mar 23 2015 - 12:05:52 PDT)
- David A Case (Mon Mar 23 2015 - 11:50:59 PDT)
- Hannes Loeffler (Mon Mar 23 2015 - 08:51:59 PDT)
- Jason Swails (Mon Mar 23 2015 - 08:17:31 PDT)
- Hannes Loeffler (Mon Mar 23 2015 - 07:52:14 PDT)
- Jason Swails (Mon Mar 23 2015 - 07:41:10 PDT)
- Michael Shokhen (Mon Mar 23 2015 - 04:57:50 PDT)
- Jason Swails (Sun Mar 22 2015 - 13:22:37 PDT)
- Michele Bonus (Sun Mar 22 2015 - 11:19:28 PDT)
- Michael Shokhen (Sun Mar 22 2015 - 06:44:30 PDT)
[AMBER] ERROR no map function for FE2 FE2 :data= 91 CYS SG 170 FE2 FE2 2.4
- Pragya Priyadarshini (Mon Mar 02 2015 - 03:37:48 PST)
[AMBER] error when doing lifetime calculation
- Daniel Roe (Mon Mar 23 2015 - 12:34:00 PDT)
- Vijay Achari (Mon Mar 23 2015 - 09:06:44 PDT)
- Daniel Roe (Mon Mar 23 2015 - 07:32:08 PDT)
- Vijay Achari (Sun Mar 22 2015 - 23:32:36 PDT)
[AMBER] Error while creating force field
- Hannes Loeffler (Tue Mar 03 2015 - 03:59:39 PST)
- Hannes Loeffler (Tue Mar 03 2015 - 03:55:24 PST)
- Akash Deep Biswas (Tue Mar 03 2015 - 03:50:12 PST)
- Swithin Hanosh (Tue Mar 03 2015 - 03:35:37 PST)
- FyD (Tue Mar 03 2015 - 01:15:25 PST)
- Hannes Loeffler (Mon Mar 02 2015 - 02:28:57 PST)
- Swithin Hanosh (Mon Mar 02 2015 - 02:21:07 PST)
[AMBER] error with mmpbsa.py
- Norbert GARNIER (Fri Mar 20 2015 - 10:08:52 PDT)
- Jason Swails (Fri Mar 20 2015 - 09:23:29 PDT)
- Kenneth Huang (Fri Mar 20 2015 - 09:21:05 PDT)
- Norbert GARNIER (Fri Mar 20 2015 - 08:32:24 PDT)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
- Jordan Graziadei (Thu Mar 12 2015 - 09:33:19 PDT)
- Jason Swails (Fri Mar 06 2015 - 11:22:16 PST)
- Jordan Graziadei (Fri Mar 06 2015 - 11:11:54 PST)
- Jordan Graziadei (Mon Mar 02 2015 - 14:01:41 PST)
[AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program
- David A Case (Sat Mar 28 2015 - 15:10:25 PDT)
- Jason Swails (Sat Mar 28 2015 - 11:51:53 PDT)
- vijay kumar narsapuram (Sat Mar 28 2015 - 04:47:48 PDT)
- David A Case (Fri Mar 13 2015 - 04:06:53 PDT)
- vijay kumar narsapuram (Fri Mar 13 2015 - 02:12:01 PDT)
- vijay kumar narsapuram (Fri Mar 06 2015 - 08:56:46 PST)
- Jason Swails (Fri Mar 06 2015 - 07:28:14 PST)
- vijay kumar narsapuram (Fri Mar 06 2015 - 07:22:58 PST)
[AMBER] Errors in AmberTools14
- Jason Swails (Fri Mar 13 2015 - 13:32:13 PDT)
- Jonathan Gough (Fri Mar 13 2015 - 12:28:53 PDT)
- Jason Swails (Fri Mar 13 2015 - 12:27:36 PDT)
- Jonathan Gough (Fri Mar 13 2015 - 12:27:23 PDT)
- Jason Swails (Fri Mar 13 2015 - 12:21:24 PDT)
- Jonathan Gough (Fri Mar 13 2015 - 11:31:49 PDT)
- Jason Swails (Fri Mar 13 2015 - 11:14:58 PDT)
- Jonathan Gough (Fri Mar 13 2015 - 10:54:38 PDT)
- Jonathan Gough (Fri Mar 13 2015 - 10:52:33 PDT)
[AMBER] Evaluating hydrogen boding lifetime
- Vijay Achari (Mon Mar 23 2015 - 20:42:32 PDT)
- Vijay Achari (Sat Mar 21 2015 - 22:23:50 PDT)
- Daniel Roe (Sat Mar 21 2015 - 09:06:20 PDT)
- Vijay Achari (Mon Mar 16 2015 - 09:50:20 PDT)
- Daniel Roe (Thu Mar 12 2015 - 08:33:36 PDT)
- Vijay Achari (Thu Mar 12 2015 - 01:53:20 PDT)
- Daniel Roe (Wed Mar 11 2015 - 08:11:50 PDT)
- Vijay Achari (Tue Mar 10 2015 - 23:57:17 PDT)
- Daniel Roe (Tue Mar 10 2015 - 20:50:13 PDT)
- Vijay Achari (Tue Mar 10 2015 - 20:24:34 PDT)
- Daniel Roe (Tue Mar 10 2015 - 07:15:29 PDT)
- Vijay Achari (Tue Mar 10 2015 - 01:53:39 PDT)
[AMBER] facing problem to create a prmtop file for oxonium cation
- FyD (Mon Mar 16 2015 - 05:31:01 PDT)
- David A Case (Mon Mar 16 2015 - 04:47:41 PDT)
- Hannes Loeffler (Mon Mar 16 2015 - 03:32:25 PDT)
- Sohag Biswas (Mon Mar 16 2015 - 02:59:06 PDT)
[AMBER] finding angles
- Jason Swails (Tue Mar 17 2015 - 07:23:33 PDT)
- Daniel Roe (Tue Mar 17 2015 - 07:12:39 PDT)
- Vijay Achari (Mon Mar 16 2015 - 19:22:09 PDT)
- Jason Swails (Mon Mar 16 2015 - 17:23:18 PDT)
- Vijay Achari (Mon Mar 16 2015 - 15:36:03 PDT)
- Jason Swails (Mon Mar 16 2015 - 10:53:12 PDT)
- Vijay Achari (Mon Mar 16 2015 - 10:49:31 PDT)
- Daniel Roe (Mon Mar 16 2015 - 06:58:33 PDT)
- Vijay Achari (Mon Mar 16 2015 - 03:18:03 PDT)
- Vijay Achari (Thu Mar 12 2015 - 20:40:49 PDT)
- Daniel Roe (Thu Mar 12 2015 - 20:15:39 PDT)
- Vijay Achari (Thu Mar 12 2015 - 18:24:05 PDT)
- Daniel Roe (Thu Mar 12 2015 - 08:20:19 PDT)
- Vijay Achari (Thu Mar 12 2015 - 07:00:31 PDT)
[AMBER] Fitting velocity autocorrelation data
- DEBOSTUTI GHOSHDASTIDAR (Thu Mar 12 2015 - 03:27:00 PDT)
[AMBER] flag for fast water
- Jason Swails (Mon Mar 30 2015 - 05:27:04 PDT)
- David A Case (Mon Mar 30 2015 - 05:20:27 PDT)
- FyD (Sun Mar 29 2015 - 07:54:06 PDT)
[AMBER] Force field for Inositol triphosphate
- anu chandra (Fri Mar 13 2015 - 05:35:00 PDT)
[AMBER] force field parameter for fructose 1 6 bisphosphate
- Lachele Foley (Sat Mar 07 2015 - 22:23:35 PST)
- Dhiraj Srivastava (Sat Mar 07 2015 - 22:13:55 PST)
[AMBER] Format of solventhb.dat file in hydrogen bonding calculation
- Vijay Achari (Tue Mar 24 2015 - 01:14:54 PDT)
- Daniel Roe (Fri Mar 20 2015 - 07:23:26 PDT)
- Vijay Achari (Mon Mar 16 2015 - 19:10:40 PDT)
[AMBER] Free energy calculation: Thermodynamic integration with use of restraints
- hannes.loeffler.stfc.ac.uk (Fri Mar 27 2015 - 09:30:57 PDT)
- vladimir.palivec.marge.uochb.cas.cz (Fri Mar 27 2015 - 08:46:47 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Mar 26 2015 - 09:02:58 PDT)
- vladimir.palivec.marge.uochb.cas.cz (Thu Mar 26 2015 - 08:22:03 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Mar 26 2015 - 02:20:25 PDT)
- vladimir.palivec.marge.uochb.cas.cz (Thu Mar 26 2015 - 01:34:47 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Mar 26 2015 - 00:32:07 PDT)
- hannes.loeffler.stfc.ac.uk (Wed Mar 25 2015 - 12:12:34 PDT)
- vladimir.palivec.marge.uochb.cas.cz (Wed Mar 25 2015 - 10:55:45 PDT)
[AMBER] free energy plot
- Jason Swails (Sun Mar 08 2015 - 18:44:13 PDT)
- David A Case (Sun Mar 08 2015 - 10:50:18 PDT)
- zahra khatti (Sun Mar 08 2015 - 08:18:25 PDT)
- zahra khatti (Sat Mar 07 2015 - 22:12:53 PST)
- zahra khatti (Sat Mar 07 2015 - 22:09:59 PST)
[AMBER] Fwd: [Fwd: Purchase of Amber-14]
- N.R. Jena (Sat Mar 14 2015 - 12:14:23 PDT)
[AMBER] Fwd: CPPTRAJ trajout results "weird" pdb
- Daniel Roe (Thu Mar 19 2015 - 21:17:55 PDT)
- David A Case (Thu Mar 19 2015 - 05:03:07 PDT)
- Chinh Su Tran To (Wed Mar 18 2015 - 20:40:59 PDT)
[AMBER] Fwd: help in sdf
- Jason Swails (Sun Mar 01 2015 - 07:47:50 PST)
- Robin Jain (Sun Mar 01 2015 - 06:40:44 PST)
[AMBER] Fwd: Regarding the MCPB tutorial
- Garisekurthi Satheesh (Mon Mar 23 2015 - 02:41:35 PDT)
[AMBER] General question about MM-PB(GB)SA
- Jason Swails (Sun Mar 08 2015 - 18:40:24 PDT)
- Atila Petrosian (Sun Mar 08 2015 - 05:22:16 PDT)
- Jason Swails (Sat Mar 07 2015 - 04:25:14 PST)
- Atila Petrosian (Fri Mar 06 2015 - 21:56:14 PST)
[AMBER] Gromacs towards Amber conversion
- Karl Kirschner (Sun Mar 29 2015 - 03:12:51 PDT)
- Carlos Simmerling (Sat Mar 28 2015 - 07:30:07 PDT)
- Simone Fulle (Sat Mar 28 2015 - 07:25:27 PDT)
[AMBER] GTX TITAN X was introduced
- filip fratev (Thu Mar 05 2015 - 00:16:34 PST)
- Ross Walker (Wed Mar 04 2015 - 18:19:18 PST)
- filip fratev (Wed Mar 04 2015 - 13:38:54 PST)
[AMBER] heat capacity
- David A Case (Sat Mar 21 2015 - 06:17:25 PDT)
- Ahmet yıldırım (Fri Mar 20 2015 - 13:07:34 PDT)
[AMBER] help in getting 3D isodensity surface
- Daniel Roe (Wed Mar 11 2015 - 07:35:58 PDT)
- Jason Swails (Wed Mar 11 2015 - 07:15:52 PDT)
- Robin Jain (Wed Mar 11 2015 - 01:09:48 PDT)
[AMBER] help in hbond analysis
- Daniel Roe (Thu Mar 26 2015 - 10:33:46 PDT)
- Robin Jain (Tue Mar 17 2015 - 23:26:35 PDT)
[AMBER] Help regarding appropriate analysis for correlated motion using cpptraj
- Kshatresh Dutta Dubey (Mon Mar 30 2015 - 12:44:39 PDT)
[AMBER] Histogram analysis of the dihedral distributions using cpptraj
- Daniel Roe (Mon Mar 30 2015 - 07:04:50 PDT)
- James Starlight (Mon Mar 30 2015 - 06:02:18 PDT)
- James Starlight (Mon Mar 30 2015 - 03:52:48 PDT)
- Daniel Roe (Fri Mar 27 2015 - 09:33:10 PDT)
- James Starlight (Fri Mar 27 2015 - 09:28:07 PDT)
- Daniel Roe (Fri Mar 27 2015 - 08:39:26 PDT)
- James Starlight (Fri Mar 27 2015 - 08:13:10 PDT)
[AMBER] HMR
- Hai Nguyen (Mon Mar 16 2015 - 17:27:31 PDT)
- Parker de Waal (Mon Mar 16 2015 - 15:28:05 PDT)
- Adrian Roitberg (Mon Mar 16 2015 - 14:40:23 PDT)
[AMBER] How to calculate interaction energy between any two residues of one protein
- Jason Swails (Wed Mar 04 2015 - 04:45:32 PST)
- Biao Ma (Tue Mar 03 2015 - 21:24:28 PST)
- danieldefoe (Tue Mar 03 2015 - 21:04:40 PST)
[AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12
- Jason Swails (Mon Mar 30 2015 - 08:34:08 PDT)
- Christina Bergonzo (Mon Mar 30 2015 - 07:08:17 PDT)
- Wang Moye (Mon Mar 30 2015 - 05:39:03 PDT)
[AMBER] how to use cpptraj for pdb files generated from external software
- Hai Nguyen (Wed Mar 18 2015 - 09:37:58 PDT)
- Mahendra B Thapa (Wed Mar 18 2015 - 09:34:29 PDT)
[AMBER] ideal range values for distance restraint b/w 2 non-bonded atoms.
- GG Smith (Sun Mar 08 2015 - 23:02:01 PDT)
- GG Smith (Sat Mar 07 2015 - 05:56:18 PST)
- Jason Swails (Sat Mar 07 2015 - 04:30:39 PST)
- GG Smith (Sat Mar 07 2015 - 03:22:59 PST)
[AMBER] Immediate Postdoctoral Position Opening In Dr. Khaled Barakat’s Lab, Faculty Of Pharmacy, University Of Alberta
- Marawan Hussien (Sun Mar 22 2015 - 14:01:11 PDT)
[AMBER] Implicit solvent simulation with Andersen thermostat
- Jason Swails (Fri Mar 27 2015 - 04:43:16 PDT)
- Glenn Carrington [bs10g3c] (Fri Mar 27 2015 - 04:31:17 PDT)
- David A Case (Thu Mar 26 2015 - 09:33:31 PDT)
- Ross Walker (Thu Mar 26 2015 - 08:57:17 PDT)
- Ross Walker (Thu Mar 26 2015 - 08:54:14 PDT)
- Jason Swails (Thu Mar 26 2015 - 07:25:55 PDT)
- Glenn Carrington [bs10g3c] (Thu Mar 26 2015 - 04:59:42 PDT)
- Hai Nguyen (Wed Mar 25 2015 - 22:56:16 PDT)
- Jason Swails (Wed Mar 25 2015 - 19:06:18 PDT)
- Glenn Carrington [bs10g3c] (Wed Mar 25 2015 - 16:41:38 PDT)
[AMBER] Improper torsions in NMA
- FyD (Fri Mar 06 2015 - 00:02:49 PST)
[AMBER] Inability to use antechamber on Anion
- hannes.loeffler.stfc.ac.uk (Fri Mar 06 2015 - 23:50:52 PST)
- David A Case (Fri Mar 06 2015 - 18:06:11 PST)
- Robert Molt (Fri Mar 06 2015 - 17:43:23 PST)
[AMBER] Intel Compiler and MKL
- Scott Brozell (Fri Mar 27 2015 - 14:14:22 PDT)
- Novosielski, Ryan (Fri Mar 27 2015 - 13:39:16 PDT)
- Scott Brozell (Fri Mar 27 2015 - 13:04:44 PDT)
- Novosielski, Ryan (Fri Mar 27 2015 - 11:03:32 PDT)
[AMBER] Invitation to Computational Chemical Biology Conference (Aug 6th to 9th 2015), Cairns, Australia (http://tinyurl.com/nyblv7o)
- Ross Walker (Sun Mar 08 2015 - 18:14:45 PDT)
[AMBER] issue with LRT calculation in sander
- Emilio Angelina (Mon Mar 30 2015 - 13:01:18 PDT)
[AMBER] iterative calculation in CPPTRAJ using "for... do... done"
- Vijay Achari (Wed Mar 25 2015 - 09:53:56 PDT)
- Vijay Achari (Wed Mar 25 2015 - 09:51:56 PDT)
- Jason Swails (Wed Mar 25 2015 - 06:52:06 PDT)
- Daniel Roe (Wed Mar 25 2015 - 06:50:26 PDT)
- Vijay Achari (Wed Mar 25 2015 - 04:42:16 PDT)
[AMBER] leap and centering
- hannes.loeffler.stfc.ac.uk (Sun Mar 15 2015 - 01:52:02 PDT)
- David A Case (Sat Mar 14 2015 - 06:31:56 PDT)
- Hannes Loeffler (Fri Mar 13 2015 - 09:04:45 PDT)
- David A Case (Fri Mar 13 2015 - 08:32:09 PDT)
- Hannes Loeffler (Fri Mar 13 2015 - 08:20:35 PDT)
[AMBER] Leap warning
- Bill Ross (Fri Mar 20 2015 - 11:07:47 PDT)
- George Tzotzos (Fri Mar 20 2015 - 10:55:18 PDT)
[AMBER] Lipid14 POPE lipids
- Jason Swails (Tue Mar 10 2015 - 11:06:49 PDT)
- Joseph Baker (Tue Mar 10 2015 - 10:08:57 PDT)
[AMBER] loading molecule in xleap and saving it in mol2 format
- Bill Ross (Fri Mar 20 2015 - 08:31:38 PDT)
- Bill Ross (Fri Mar 20 2015 - 08:19:59 PDT)
- Hannes Loeffler (Fri Mar 20 2015 - 08:15:32 PDT)
- jacob wick (Fri Mar 20 2015 - 08:09:50 PDT)
- Bill Ross (Fri Mar 20 2015 - 07:45:23 PDT)
- jacob wick (Fri Mar 20 2015 - 04:01:49 PDT)
- Hannes Loeffler (Fri Mar 20 2015 - 03:37:29 PDT)
- FyD (Fri Mar 20 2015 - 03:14:19 PDT)
- hannes.loeffler.stfc.ac.uk (Fri Mar 20 2015 - 01:01:48 PDT)
- jacob wick (Fri Mar 20 2015 - 00:17:05 PDT)
[AMBER] loading molecule in xleap and saving it in mol2 formatDear
- jacob wick (Fri Mar 20 2015 - 07:27:21 PDT)
- Hannes Loeffler (Fri Mar 20 2015 - 07:14:23 PDT)
[AMBER] Manual still ambiguous about igb=8 and pmemd
- Jason Swails (Mon Mar 30 2015 - 09:39:55 PDT)
- Edwin Helbert Aponte Angarita (Mon Mar 30 2015 - 09:32:44 PDT)
[AMBER] matrix newtransform command
- Sylvester Tumusiime (Wed Mar 04 2015 - 14:51:46 PST)
- David A Case (Tue Mar 03 2015 - 14:35:19 PST)
- Sylvester Tumusiime (Tue Mar 03 2015 - 12:03:24 PST)
[AMBER] mm-pbsa & extra-point
- Emilio Angelina (Thu Mar 05 2015 - 19:43:23 PST)
- Jason Swails (Thu Mar 05 2015 - 17:36:04 PST)
- Emilio Angelina (Thu Mar 05 2015 - 16:21:21 PST)
- Jason Swails (Thu Mar 05 2015 - 14:38:29 PST)
- Emilio Angelina (Thu Mar 05 2015 - 13:42:19 PST)
[AMBER] MMGBSA error
- Kenneth Huang (Thu Mar 26 2015 - 05:55:35 PDT)
- Abhishek TYAGI (Wed Mar 25 2015 - 23:06:44 PDT)
[AMBER] MMGBSA pairwise decomposition - differences in Non-Polar Solv. & TOTAL for same residue pairs
- Jason Swails (Tue Mar 17 2015 - 19:25:47 PDT)
- Cassandra Churchill (Tue Mar 17 2015 - 14:53:43 PDT)
[AMBER] mmpbsa conflict with Ca2+ ?
- Jason Swails (Thu Mar 12 2015 - 05:32:59 PDT)
- Jinfeng Huang (Thu Mar 12 2015 - 01:31:01 PDT)
- Jinfeng Huang (Wed Mar 11 2015 - 19:35:09 PDT)
- Jason Swails (Wed Mar 11 2015 - 09:21:45 PDT)
- Bill Ross (Wed Mar 11 2015 - 08:40:00 PDT)
- Jinfeng Huang (Wed Mar 11 2015 - 07:52:10 PDT)
[AMBER] MMPBSA error
- Kenneth Huang (Fri Mar 27 2015 - 15:49:25 PDT)
- Jason Swails (Fri Mar 27 2015 - 10:56:03 PDT)
- Abhishek Tyagi (Fri Mar 27 2015 - 09:39:50 PDT)
[AMBER] MMPBSA tutorial: MMPBSA.py
- camm-kansai (Fri Mar 13 2015 - 06:18:22 PDT)
- David A Case (Tue Mar 10 2015 - 04:51:45 PDT)
- camm-kansai (Tue Mar 10 2015 - 04:32:06 PDT)
[AMBER] Multiple MEPs option in R.E.D tools
- Jason Swails (Tue Mar 31 2015 - 13:53:52 PDT)
- FyD (Tue Mar 31 2015 - 12:07:43 PDT)
- FyD (Tue Mar 31 2015 - 11:44:52 PDT)
- Jason Swails (Tue Mar 31 2015 - 05:07:41 PDT)
- Brent Krueger (Tue Mar 31 2015 - 04:40:40 PDT)
- Yip Yew Mun (Mon Mar 30 2015 - 19:26:05 PDT)
[AMBER] NetCDF AMBER file corrupted
- Daniel Roe (Thu Mar 19 2015 - 21:21:24 PDT)
- Jacopo Sgrignani (Thu Mar 19 2015 - 08:46:36 PDT)
- Jason Swails (Thu Mar 19 2015 - 08:26:55 PDT)
- Jacopo Sgrignani (Thu Mar 19 2015 - 07:20:09 PDT)
[AMBER] Non-Standard Residue / Non-Integer Charge
- FyD (Mon Mar 23 2015 - 09:27:28 PDT)
- Maral Aminpour (Fri Mar 20 2015 - 19:27:15 PDT)
- Bill Ross (Fri Mar 20 2015 - 11:03:14 PDT)
- Maral Aminpour (Fri Mar 20 2015 - 10:51:14 PDT)
- FyD (Thu Mar 19 2015 - 23:58:31 PDT)
- Maral Aminpour (Thu Mar 19 2015 - 12:35:39 PDT)
- David A Case (Wed Mar 18 2015 - 17:32:35 PDT)
- FyD (Wed Mar 18 2015 - 02:07:46 PDT)
- Maral Aminpour (Tue Mar 17 2015 - 14:09:50 PDT)
[AMBER] Nuclicacid forcefield in AMBER
- Nhai (Wed Mar 18 2015 - 08:20:35 PDT)
- Carlos Simmerling (Wed Mar 18 2015 - 05:01:29 PDT)
- Jason Swails (Wed Mar 18 2015 - 04:54:59 PDT)
- mish (Tue Mar 17 2015 - 09:27:54 PDT)
- David A Case (Sun Mar 15 2015 - 17:33:34 PDT)
- mish (Sun Mar 15 2015 - 12:12:49 PDT)
[AMBER] On the clustering of the ligand position within the cavity
- Daniel Roe (Fri Mar 20 2015 - 07:14:48 PDT)
- Kenneth Huang (Thu Mar 19 2015 - 10:23:21 PDT)
- James Starlight (Thu Mar 19 2015 - 09:30:57 PDT)
- James Starlight (Thu Mar 19 2015 - 08:50:12 PDT)
[AMBER] on the force field
- David A Case (Sun Mar 08 2015 - 06:18:30 PDT)
- Nhai (Sat Mar 07 2015 - 20:57:52 PST)
- Brett (Sat Mar 07 2015 - 19:04:55 PST)
[AMBER] organic molecule
- Jason Swails (Mon Mar 16 2015 - 07:15:59 PDT)
- Lara rajam (Mon Mar 16 2015 - 06:45:47 PDT)
[AMBER] Param PROC does not exist (MM-PBSA)
- Atila Petrosian (Sun Mar 01 2015 - 06:49:33 PST)
[AMBER] Param PROC does not exist --- MM-PBSA problem
- Atila Petrosian (Thu Mar 05 2015 - 08:39:33 PST)
- Jason Swails (Wed Mar 04 2015 - 04:43:11 PST)
- Atila Petrosian (Tue Mar 03 2015 - 23:49:18 PST)
[AMBER] PCA_representation_in_Cpptraj
- Jason Swails (Wed Mar 11 2015 - 07:30:22 PDT)
- Daniel Roe (Wed Mar 11 2015 - 07:25:57 PDT)
- Juan Eiros Zamora (Wed Mar 11 2015 - 05:52:48 PDT)
- Daniel Roe (Tue Mar 10 2015 - 07:46:46 PDT)
- Jason Swails (Tue Mar 10 2015 - 07:15:20 PDT)
- Juan Eiros Zamora (Tue Mar 10 2015 - 04:37:50 PDT)
- Daniel Roe (Mon Mar 09 2015 - 07:07:17 PDT)
- Jason Swails (Mon Mar 09 2015 - 05:52:07 PDT)
- abdennour braka (Mon Mar 09 2015 - 02:14:51 PDT)
[AMBER] Per-residue decomposition energy MMGBSA.py
- Jason Swails (Tue Mar 17 2015 - 05:45:47 PDT)
- maryam azimzadehirani (Mon Mar 16 2015 - 20:52:58 PDT)
- Jason Swails (Mon Mar 16 2015 - 07:26:57 PDT)
- maryam azimzadehirani (Mon Mar 16 2015 - 06:49:12 PDT)
[AMBER] pmemd.MPI error
- David A Case (Mon Mar 16 2015 - 14:48:39 PDT)
- George Tzotzos (Mon Mar 16 2015 - 13:07:55 PDT)
[AMBER] PMF for dimer dissociation
- Jason Swails (Tue Mar 17 2015 - 19:33:44 PDT)
- Sanmeet Chahal (Tue Mar 17 2015 - 19:04:53 PDT)
- Carlos Simmerling (Tue Mar 17 2015 - 16:25:07 PDT)
- Sanmeet Chahal (Tue Mar 17 2015 - 14:18:33 PDT)
[AMBER] post processing temperature replica exchange trajectories
- Jason Swails (Fri Mar 20 2015 - 05:24:02 PDT)
- Sandeep Somani (Fri Mar 20 2015 - 04:42:42 PDT)
- Daniel Roe (Thu Mar 19 2015 - 19:57:03 PDT)
- Sandeep Somani (Thu Mar 19 2015 - 13:00:49 PDT)
[AMBER] Predefined number of water molecules in waterbox
- jacob wick (Fri Mar 13 2015 - 22:20:38 PDT)
- Michele Bonus (Thu Mar 12 2015 - 23:12:20 PDT)
- jacob wick (Thu Mar 12 2015 - 22:17:44 PDT)
[AMBER] Pressure units in 1D-RISM
- Tyler Luchko (Tue Mar 31 2015 - 22:00:08 PDT)
- Maksim Mišin (Tue Mar 31 2015 - 10:25:28 PDT)
- David A Case (Tue Mar 31 2015 - 09:09:08 PDT)
- Maksim Mišin (Tue Mar 31 2015 - 07:27:00 PDT)
[AMBER] Problem in calculation per residue free energy decomposition
- Jason Swails (Tue Mar 03 2015 - 05:53:42 PST)
- maryam azimzadehirani (Tue Mar 03 2015 - 02:04:42 PST)
[AMBER] Problem in capping ACE and NME.
- Jason Swails (Tue Mar 03 2015 - 05:27:54 PST)
- Harshala Haldankar (Mon Mar 02 2015 - 22:13:19 PST)
[AMBER] Problem in protonating.
- Jason Swails (Fri Mar 13 2015 - 05:14:42 PDT)
- Harshala Haldankar (Fri Mar 13 2015 - 04:16:02 PDT)
[AMBER] Problem Regarding Different PMF Graph
- Jason Swails (Mon Mar 30 2015 - 05:41:21 PDT)
- Shubhadip Das (Sun Mar 29 2015 - 22:02:34 PDT)
- Shubhadip Das (Thu Mar 26 2015 - 21:21:52 PDT)
[AMBER] Problem Regarding Different PMF Graphs
- Shubhadip Das (Sun Mar 29 2015 - 22:04:22 PDT)
[AMBER] Problem with Creating Unit for Non-standard N-Cap Residue
- FyD (Sun Mar 08 2015 - 09:56:43 PDT)
- Huang Tao (Sun Mar 08 2015 - 00:59:24 PST)
- FyD (Fri Mar 06 2015 - 08:20:06 PST)
- Huang Tao (Fri Mar 06 2015 - 00:26:24 PST)
- FyD (Tue Mar 03 2015 - 01:31:34 PST)
- Huang Tao (Mon Mar 02 2015 - 17:33:51 PST)
[AMBER] Problem with heating lipid bilayer in amber 12
- Ross Walker (Thu Mar 19 2015 - 14:49:30 PDT)
- Chris Gaughan (Thu Mar 19 2015 - 14:31:26 PDT)
[AMBER] Problems with Amber installation
- Jason Swails (Tue Mar 31 2015 - 08:40:14 PDT)
- Pinchas Aped (Tue Mar 31 2015 - 08:07:09 PDT)
- Gerald Monard (Tue Mar 31 2015 - 07:28:18 PDT)
- Pinchas Aped (Tue Mar 31 2015 - 06:45:53 PDT)
[AMBER] Projection on distance covariance modes
- Christina Bergonzo (Mon Mar 30 2015 - 06:49:08 PDT)
- Vishal Kumar Jaiswal (Mon Mar 30 2015 - 06:11:55 PDT)
[AMBER] Projection on modes calculated by distcovar matrix
- Daniel Roe (Sun Mar 29 2015 - 08:43:27 PDT)
- Vishal Kumar Jaiswal (Sun Mar 29 2015 - 02:53:00 PDT)
[AMBER] Putting oxygen molecules around protein structure
- David A Case (Thu Mar 12 2015 - 14:19:25 PDT)
- Shukla, Saurabh (Wed Mar 11 2015 - 20:38:24 PDT)
[AMBER] Reading two units from same .mol2 file
- Sanmeet Chahal (Mon Mar 09 2015 - 07:44:36 PDT)
- Daniel Roe (Mon Mar 09 2015 - 07:17:36 PDT)
- David A Case (Sat Mar 07 2015 - 17:45:36 PST)
- Sanmeet Chahal (Fri Mar 06 2015 - 17:16:10 PST)
[AMBER] Reduce not working properly
- David A Case (Fri Mar 20 2015 - 05:44:45 PDT)
- Francesco Gentile (Thu Mar 19 2015 - 21:47:14 PDT)
[AMBER] Reg: Query on distance restrain and its effect on conformation
- GG Smith (Wed Mar 11 2015 - 22:20:30 PDT)
- Jason Swails (Wed Mar 11 2015 - 08:41:12 PDT)
- GG Smith (Tue Mar 10 2015 - 21:41:18 PDT)
[AMBER] REGARDING ATOM TYPE ERROR
- hannes.loeffler.stfc.ac.uk (Sat Mar 28 2015 - 05:51:45 PDT)
- Swithin Hanosh (Sat Mar 28 2015 - 05:01:43 PDT)
[AMBER] REMD jobs crashing repeatedly on GPUs
- Christina Bergonzo (Wed Mar 04 2015 - 10:19:35 PST)
[AMBER] Replacing water with oxygen molecules
- David A Case (Mon Mar 02 2015 - 17:29:57 PST)
- Shukla, Saurabh (Mon Mar 02 2015 - 10:19:51 PST)
[AMBER] Replica Exchange on a single Titan-X GPU
- filip fratev (Mon Mar 23 2015 - 12:19:56 PDT)
- Ross Walker (Mon Mar 23 2015 - 11:28:30 PDT)
- Ross Walker (Mon Mar 23 2015 - 10:01:04 PDT)
- filip fratev (Mon Mar 23 2015 - 08:35:13 PDT)
- amr hamed (Mon Mar 23 2015 - 08:19:09 PDT)
[AMBER] Restrained MD
- David A Case (Tue Mar 31 2015 - 09:01:29 PDT)
- James Starlight (Tue Mar 31 2015 - 07:03:34 PDT)
- David A Case (Tue Mar 31 2015 - 05:32:04 PDT)
- James Starlight (Tue Mar 31 2015 - 05:09:02 PDT)
- James Starlight (Tue Mar 31 2015 - 04:58:59 PDT)
- David A Case (Mon Mar 30 2015 - 08:19:30 PDT)
- James Starlight (Mon Mar 30 2015 - 05:38:46 PDT)
- David A Case (Sun Mar 29 2015 - 07:42:50 PDT)
- James Starlight (Sun Mar 29 2015 - 03:50:31 PDT)
[AMBER] RMSF & changes of the secondary structure of protein
- Daniel Roe (Mon Mar 23 2015 - 11:50:55 PDT)
- shahab shariati (Mon Mar 23 2015 - 11:45:41 PDT)
[AMBER] RNA Simulation
- jacob wick (Thu Mar 12 2015 - 22:17:12 PDT)
- Bill Ross (Thu Mar 12 2015 - 14:15:29 PDT)
- Jiri Sponer (Thu Mar 12 2015 - 12:28:48 PDT)
- Jiri Sponer (Thu Mar 12 2015 - 12:16:10 PDT)
- jacob wick (Thu Mar 12 2015 - 11:28:59 PDT)
[AMBER] RNA's sugar modification
- Bill Ross (Sun Mar 15 2015 - 13:17:57 PDT)
- Bill Ross (Sun Mar 15 2015 - 13:13:20 PDT)
- jacob wick (Sun Mar 15 2015 - 11:05:20 PDT)
[AMBER] sander.MPI error
- Jason Swails (Thu Mar 19 2015 - 11:13:52 PDT)
- George Tzotzos (Thu Mar 19 2015 - 11:06:41 PDT)
- George Tzotzos (Thu Mar 19 2015 - 11:02:40 PDT)
[AMBER] script to convert the Gromacs topology to Amber topology?
- Jason Swails (Tue Mar 17 2015 - 05:39:36 PDT)
- Josep Maria Campanera Alsina (Tue Mar 17 2015 - 02:57:59 PDT)
[AMBER] set command and VMD
- David A Case (Sun Mar 15 2015 - 17:45:43 PDT)
- Jason Swails (Sat Mar 14 2015 - 18:16:02 PDT)
- Arjun Sharma (Sat Mar 14 2015 - 15:44:23 PDT)
[AMBER] SMD average work
- Adrian Roitberg (Tue Mar 03 2015 - 09:04:06 PST)
- Mahmood Jasim (Tue Mar 03 2015 - 07:58:09 PST)
[AMBER] Solvent Box Issue When Running AMBER Dynamics
- Zhang, Sixue (Mon Mar 09 2015 - 13:58:53 PDT)
- Daniel Roe (Mon Mar 09 2015 - 07:58:42 PDT)
- David A Case (Thu Mar 05 2015 - 05:12:44 PST)
- Zhang, Sixue (Wed Mar 04 2015 - 18:44:51 PST)
- David Case (Wed Mar 04 2015 - 17:02:12 PST)
- Zhang, Sixue (Wed Mar 04 2015 - 14:46:37 PST)
[AMBER] Stability MMPBSA
- Jason Swails (Tue Mar 31 2015 - 05:05:52 PDT)
- Kenneth Huang (Mon Mar 30 2015 - 19:47:59 PDT)
- Parker de Waal (Mon Mar 30 2015 - 19:47:00 PDT)
- Parker de Waal (Mon Mar 30 2015 - 18:44:20 PDT)
[AMBER] Starting antechamber for preparing ligand molecule
- David A Case (Wed Mar 18 2015 - 06:37:27 PDT)
- FyD (Wed Mar 18 2015 - 06:09:04 PDT)
- Hannes Loeffler (Wed Mar 18 2015 - 02:15:38 PDT)
- Anasuya Dighe (Tue Mar 17 2015 - 10:23:51 PDT)
[AMBER] Sudden RMSD blow-up in trajectory analysis
- Daniel Roe (Tue Mar 10 2015 - 07:23:49 PDT)
- Himanshu Joshi (Tue Mar 10 2015 - 03:27:56 PDT)
- Carlos Simmerling (Tue Mar 10 2015 - 03:25:03 PDT)
- Anasuya Dighe (Tue Mar 10 2015 - 02:54:17 PDT)
[AMBER] Syntax Confusion on Radial Command
- Thomas Cheatham (Sun Mar 08 2015 - 15:29:37 PDT)
- Robert Molt (Sun Mar 08 2015 - 14:55:59 PDT)
[AMBER] Targeted MD shows blank output file!
- Pallavi Mohanty (Wed Mar 04 2015 - 22:10:50 PST)
- Carlos Simmerling (Wed Mar 04 2015 - 05:37:23 PST)
- Jason Swails (Wed Mar 04 2015 - 05:12:47 PST)
- Pallavi Mohanty (Wed Mar 04 2015 - 05:05:07 PST)
- Jason Swails (Wed Mar 04 2015 - 04:53:05 PST)
- Pallavi Mohanty (Wed Mar 04 2015 - 04:21:32 PST)
- Carlos Simmerling (Wed Mar 04 2015 - 04:13:07 PST)
- Pallavi Mohanty (Wed Mar 04 2015 - 02:44:22 PST)
[AMBER] temp ramping in tutorial A5
- Robert Wohlhueter (Tue Mar 31 2015 - 13:22:30 PDT)
- Jason Swails (Tue Mar 31 2015 - 07:38:38 PDT)
- Robert Wohlhueter (Tue Mar 31 2015 - 06:52:12 PDT)
- Jason Swails (Tue Mar 31 2015 - 05:11:41 PDT)
- Robert Wohlhueter (Mon Mar 30 2015 - 15:33:31 PDT)
[AMBER] The unperturbed charge of the unit: -2.980000 is not integral
- George Tzotzos (Tue Mar 24 2015 - 19:48:08 PDT)
- Jason Swails (Tue Mar 24 2015 - 19:06:34 PDT)
- 王华 (Tue Mar 24 2015 - 18:40:20 PDT)
[AMBER] tleap box neutralization
- Sergio Decherchi (Mon Mar 02 2015 - 06:01:28 PST)
- Jason Swails (Mon Mar 02 2015 - 05:55:57 PST)
- Sergio Decherchi (Mon Mar 02 2015 - 01:13:58 PST)
[AMBER] topology file, segment id and the pathways plugin
- Jason Swails (Tue Mar 17 2015 - 13:54:18 PDT)
- Shoresh Shafei (Tue Mar 17 2015 - 13:33:32 PDT)
[AMBER] trajectory of minimization using generalized Born
- Jason Swails (Mon Mar 23 2015 - 11:36:20 PDT)
- Edwin Helbert Aponte Angarita (Mon Mar 23 2015 - 04:47:37 PDT)
- Edwin Helbert Aponte Angarita (Sat Mar 21 2015 - 04:48:56 PDT)
- Carlos Simmerling (Fri Mar 20 2015 - 14:08:47 PDT)
- Edwin Helbert Aponte Angarita (Fri Mar 20 2015 - 13:47:16 PDT)
- Carlos Simmerling (Fri Mar 20 2015 - 13:00:08 PDT)
- Jason Swails (Fri Mar 20 2015 - 12:49:50 PDT)
- Edwin Helbert Aponte Angarita (Fri Mar 20 2015 - 12:03:27 PDT)
- Carlos Simmerling (Fri Mar 20 2015 - 08:26:05 PDT)
- Carlos Simmerling (Fri Mar 20 2015 - 06:25:47 PDT)
- Jason Swails (Fri Mar 20 2015 - 06:23:50 PDT)
- Edwin Helbert Aponte Angarita (Fri Mar 20 2015 - 06:13:25 PDT)
- Jason Swails (Fri Mar 20 2015 - 05:29:03 PDT)
- Edwin Helbert Aponte Angarita (Thu Mar 19 2015 - 16:00:42 PDT)
- Carlos Simmerling (Thu Mar 19 2015 - 15:26:50 PDT)
- Edwin Helbert Aponte Angarita (Thu Mar 19 2015 - 15:05:25 PDT)
- Carlos Simmerling (Thu Mar 19 2015 - 13:35:48 PDT)
- Edwin Helbert Aponte Angarita (Thu Mar 19 2015 - 13:21:55 PDT)
- Edwin Helbert Aponte Angarita (Thu Mar 19 2015 - 12:30:23 PDT)
- Daniel Roe (Wed Mar 18 2015 - 19:50:25 PDT)
- David A Case (Wed Mar 18 2015 - 15:03:54 PDT)
- Jason Swails (Wed Mar 18 2015 - 14:03:42 PDT)
- Edwin Helbert Aponte Angarita (Wed Mar 18 2015 - 13:27:44 PDT)
- Edwin Helbert Aponte Angarita (Wed Mar 18 2015 - 09:41:43 PDT)
[AMBER] trouble running pmemd.cuda
- Jason Swails (Thu Mar 26 2015 - 11:14:57 PDT)
- Brian Radak (Thu Mar 26 2015 - 11:08:24 PDT)
- Ross Walker (Thu Mar 26 2015 - 10:17:54 PDT)
- Jason Swails (Thu Mar 26 2015 - 10:17:07 PDT)
- Brian Radak (Thu Mar 26 2015 - 10:08:54 PDT)
- Jason Swails (Thu Mar 26 2015 - 09:46:51 PDT)
- Ross Walker (Thu Mar 26 2015 - 08:49:53 PDT)
- Jason Swails (Thu Mar 26 2015 - 08:07:05 PDT)
- Brian Radak (Thu Mar 26 2015 - 07:41:38 PDT)
- Jason Swails (Wed Mar 25 2015 - 11:49:52 PDT)
- Brian Radak (Wed Mar 25 2015 - 11:46:24 PDT)
- Ross Walker (Wed Mar 25 2015 - 10:41:27 PDT)
- Brian Radak (Wed Mar 25 2015 - 10:30:23 PDT)
[AMBER] Truncated octahedron
- Jason Swails (Wed Mar 11 2015 - 09:19:03 PDT)
- Jason Swails (Wed Mar 11 2015 - 09:06:19 PDT)
- Crowley, Michael (Wed Mar 11 2015 - 08:39:03 PDT)
- Bill Ross (Wed Mar 11 2015 - 08:35:36 PDT)
- Arjun Sharma (Wed Mar 11 2015 - 08:24:31 PDT)
[AMBER] Tutorial B0
- Jason Swails (Mon Mar 09 2015 - 19:10:12 PDT)
- David A Case (Mon Mar 09 2015 - 14:57:31 PDT)
- Sanmeet Chahal (Mon Mar 09 2015 - 14:11:17 PDT)
- Sanmeet Chahal (Fri Mar 06 2015 - 16:06:18 PST)
- Sanmeet Chahal (Fri Mar 06 2015 - 13:25:27 PST)
- Jason Swails (Wed Mar 04 2015 - 13:33:11 PST)
- Jason Swails (Wed Mar 04 2015 - 13:32:49 PST)
- Sanmeet Chahal (Wed Mar 04 2015 - 13:32:28 PST)
- Sanmeet Chahal (Wed Mar 04 2015 - 13:29:24 PST)
- Sanmeet Chahal (Wed Mar 04 2015 - 08:49:48 PST)
- Sanmeet Chahal (Wed Mar 04 2015 - 08:47:02 PST)
- Sanmeet Chahal (Wed Mar 04 2015 - 08:44:43 PST)
- Sanmeet Chahal (Wed Mar 04 2015 - 08:34:51 PST)
- David A Case (Wed Mar 04 2015 - 05:10:17 PST)
- Jason Swails (Wed Mar 04 2015 - 04:58:59 PST)
- Sanmeet Chahal (Tue Mar 03 2015 - 15:05:57 PST)
[AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14)
- Lachele Foley (Sat Mar 14 2015 - 12:36:06 PDT)
- Jason Swails (Sat Mar 14 2015 - 08:56:22 PDT)
- Pedro Swagger (Sat Mar 14 2015 - 08:04:09 PDT)
- Lachele Foley (Fri Mar 13 2015 - 17:40:33 PDT)
- Pedro Swagger (Fri Mar 13 2015 - 17:28:43 PDT)
[AMBER] unfolding protein and solvent density
- Jason Swails (Tue Mar 17 2015 - 06:05:21 PDT)
- Ibrahim Said (Tue Mar 17 2015 - 03:54:10 PDT)
- Carlos Simmerling (Tue Mar 17 2015 - 03:30:29 PDT)
- Ibrahim Said (Tue Mar 17 2015 - 02:32:03 PDT)
[AMBER] using internal geometry
- newamber list (Mon Mar 02 2015 - 11:34:11 PST)
- Jason Swails (Mon Mar 02 2015 - 10:35:10 PST)
- newamber list (Mon Mar 02 2015 - 10:07:47 PST)
[AMBER] Using WHAM to get 3D free energy surface in AMBER12
- Wang Moye (Wed Mar 18 2015 - 18:21:21 PDT)
- Jason Swails (Mon Mar 16 2015 - 18:44:53 PDT)
- Wang Moye (Mon Mar 16 2015 - 18:06:56 PDT)
- Jason Swails (Mon Mar 16 2015 - 05:19:18 PDT)
- Wang Moye (Mon Mar 16 2015 - 00:30:40 PDT)
[AMBER] vdw energy and electrostatic energy calculation for osmolyte
- Jason Swails (Thu Mar 26 2015 - 07:29:28 PDT)
- MOHD HOMAIDUR RAHMAN (Wed Mar 25 2015 - 22:59:40 PDT)
- Daniel Roe (Wed Mar 25 2015 - 12:18:47 PDT)
- Jason Swails (Wed Mar 25 2015 - 11:47:02 PDT)
- Subrata Paul (Wed Mar 25 2015 - 11:40:58 PDT)
- Jason Swails (Wed Mar 25 2015 - 05:14:00 PDT)
- Subrata Paul (Tue Mar 24 2015 - 22:30:26 PDT)
- Jason Swails (Tue Mar 24 2015 - 06:55:54 PDT)
- Subrata Paul (Tue Mar 24 2015 - 00:31:49 PDT)
[AMBER] Water sigma parameters
- David A Case (Thu Mar 26 2015 - 14:38:43 PDT)
- Paolo Tosco (Thu Mar 26 2015 - 13:16:44 PDT)
[AMBER] | ERROR: PMEMD does not support intermolecular PRFs!
- Jason Swails (Fri Mar 20 2015 - 05:06:49 PDT)
- Jorgen Simonsen (Thu Mar 19 2015 - 15:12:50 PDT)
- Jorgen Simonsen (Thu Mar 19 2015 - 12:51:16 PDT)
- Jorgen Simonsen (Thu Mar 19 2015 - 12:31:19 PDT)
- Jason Swails (Thu Mar 19 2015 - 11:34:33 PDT)
- Jorgen Simonsen (Thu Mar 19 2015 - 11:15:30 PDT)
GTX980 PERFORMANCE
- carmendigiovanni75.alice.it (Mon Mar 02 2015 - 01:22:28 PST)
how to use cpptraj for pdb files generated from external software
- Mahendra B Thapa (Wed Mar 18 2015 - 09:57:18 PDT)

Amber Archive Mar 2015 by subject