Amber Archive May 2018: by subject

[AMBER] .rst and .mdcrd file outputted in ascii
- David A Case (Wed May 02 2018 - 11:36:59 PDT)
[AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1"
- PRITI ROY (Thu May 17 2018 - 22:22:51 PDT)
- Leena Aggarwal (Thu May 17 2018 - 21:36:09 PDT)
- PRITI ROY (Thu May 17 2018 - 09:18:50 PDT)
- David A Case (Thu May 17 2018 - 09:11:23 PDT)
- Tyler Luchko (Lists) (Thu May 17 2018 - 08:47:57 PDT)
- Leena Aggarwal (Thu May 17 2018 - 06:23:15 PDT)
- PRITI ROY (Thu May 17 2018 - 06:04:08 PDT)
- Leena Aggarwal (Thu May 17 2018 - 05:06:37 PDT)
- PRITI ROY (Thu May 17 2018 - 02:45:51 PDT)
[AMBER] 1x PCI-E Riser card for MD/TI?
- Hadházi Ádám (Tue May 22 2018 - 14:42:29 PDT)
- Ross Walker (Tue May 22 2018 - 14:08:48 PDT)
- Hadházi Ádám (Tue May 22 2018 - 07:20:46 PDT)
[AMBER] [cpptraj] Angle between atom and two centroids
- Daniel Roe (Fri May 18 2018 - 05:05:26 PDT)
- David A Case (Fri May 18 2018 - 05:04:34 PDT)
- Eiros Zamora, Juan (Fri May 18 2018 - 04:14:11 PDT)
[AMBER] ABMD with multiple walkers
- Qinghua Liao (Tue May 29 2018 - 00:31:31 PDT)
- Feng Pan (Mon May 28 2018 - 18:01:21 PDT)
- Qinghua Liao (Mon May 28 2018 - 05:36:21 PDT)
- Feng Pan (Sun May 27 2018 - 19:05:45 PDT)
- Qinghua Liao (Sun May 27 2018 - 14:08:12 PDT)
- Feng Pan (Sat May 26 2018 - 19:16:09 PDT)
- Qinghua Liao (Fri May 25 2018 - 16:00:01 PDT)
[AMBER] adding NME and ACE terminals
- ABEL Stephane (Wed May 09 2018 - 10:45:59 PDT)
- roja rahmani (Wed May 09 2018 - 10:41:15 PDT)
- ABEL Stephane (Wed May 09 2018 - 10:36:28 PDT)
- roja rahmani (Wed May 09 2018 - 08:53:15 PDT)
- David A Case (Wed May 09 2018 - 07:23:48 PDT)
- roja rahmani (Wed May 09 2018 - 05:21:18 PDT)
- roja rahmani (Wed May 09 2018 - 05:08:59 PDT)
- Juan Eiros (Wed May 09 2018 - 03:56:23 PDT)
- roja rahmani (Wed May 09 2018 - 03:40:10 PDT)
[AMBER] Advice on SMD QM/MM for Cyanogenic Glucoside
- senal dinuka (Mon May 07 2018 - 23:34:21 PDT)
[AMBER] Amber 18 manual shows TI as not supported in pmemd.cuda
- David A Case (Thu May 24 2018 - 04:34:27 PDT)
- Patricio German Barletta Roldan (Wed May 23 2018 - 13:47:48 PDT)
[AMBER] Amber 18 Thermodynamic integration question
- David A Case (Wed May 09 2018 - 07:29:18 PDT)
- David Wifling (Mon May 07 2018 - 12:27:18 PDT)
[AMBER] AMBER Digest, Vol 2280, Issue 1
- David A Case (Fri May 04 2018 - 05:21:02 PDT)
- Kadir Ozcan (Thu May 03 2018 - 15:19:23 PDT)
[AMBER] AMBER NFE SMD calculation with new collective variable
- Feng Pan (Wed May 30 2018 - 11:20:39 PDT)
- georg.kuenze.vanderbilt.edu (Mon May 28 2018 - 13:51:41 PDT)
[AMBER] AMBER TI more examples
- David A Case (Tue May 29 2018 - 06:24:41 PDT)
- Omoto, Kiyoyuki (Thu May 24 2018 - 08:30:55 PDT)
[AMBER] Amber16 pmemd.cuda.MPI simulation can drop a frame with an inopportune node crash
- Chris Neale (Sat May 19 2018 - 15:04:04 PDT)
- David Cerutti (Sat May 19 2018 - 04:30:27 PDT)
- Chris Neale (Sat May 19 2018 - 00:07:06 PDT)
[AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory
- Chris Neale (Thu May 10 2018 - 12:16:16 PDT)
- David A Case (Wed May 09 2018 - 05:20:48 PDT)
- Chris Neale (Tue May 08 2018 - 16:58:41 PDT)
[AMBER] AMBER: trouble while running constant pH simulation
- Cruzeiro,Vinicius Wilian D (Tue May 29 2018 - 05:58:06 PDT)
- 李耀 (Tue May 29 2018 - 00:54:18 PDT)
- 李耀 (Mon May 28 2018 - 19:35:06 PDT)
[AMBER] AMBER: trouble while running constant pH simulation > (Cruzeiro, Vinicius Wilian D)
- Cruzeiro,Vinicius Wilian D (Wed May 30 2018 - 09:03:55 PDT)
- 李耀 (Wed May 30 2018 - 08:48:29 PDT)
[AMBER] Angle calculation between three amino acids
- maryam azimzadehirani (Fri May 11 2018 - 06:35:05 PDT)
- Daniel Roe (Fri May 11 2018 - 06:10:00 PDT)
- maryam azimzadehirani (Thu May 10 2018 - 23:45:27 PDT)
[AMBER] autoimage problem
- Daniel Roe (Wed May 16 2018 - 06:46:09 PDT)
- David A Case (Wed May 16 2018 - 05:59:17 PDT)
- Ming Tang (Mon May 14 2018 - 06:59:14 PDT)
[AMBER] Automatic patching failed!
- David A Case (Wed May 30 2018 - 05:42:42 PDT)
- senal dinuka (Wed May 30 2018 - 00:49:40 PDT)
- Charles Lin (Tue May 29 2018 - 22:11:09 PDT)
- senal dinuka (Tue May 29 2018 - 21:30:50 PDT)
- Charles Lin (Tue May 29 2018 - 21:24:18 PDT)
- senal dinuka (Tue May 29 2018 - 21:10:54 PDT)
[AMBER] Boost not linking when compiling on Mac
- Scott Brozell (Wed May 02 2018 - 17:30:23 PDT)
- Gustaf Olsson (Wed May 02 2018 - 05:53:36 PDT)
- David A Case (Wed May 02 2018 - 04:48:41 PDT)
- Gustaf Olsson (Tue May 01 2018 - 23:44:30 PDT)
[AMBER] calculation of cavity water
- Tousif Hossen (Mon May 07 2018 - 11:09:26 PDT)
- Tom Kurtzman (Mon May 07 2018 - 09:13:15 PDT)
- Tousif Hossen (Mon May 07 2018 - 08:22:41 PDT)
- Kenneth Huang (Mon May 07 2018 - 07:47:36 PDT)
- Tousif Hossen (Mon May 07 2018 - 06:38:35 PDT)
- Tousif Hossen (Sun May 06 2018 - 22:41:24 PDT)
- Kenneth Huang (Sun May 06 2018 - 07:35:01 PDT)
- Kenneth Huang (Sun May 06 2018 - 07:28:37 PDT)
- Tousif Hossen (Sat May 05 2018 - 23:29:43 PDT)
- Leena Aggarwal (Fri May 04 2018 - 21:13:08 PDT)
- Kenneth Huang (Fri May 04 2018 - 13:15:16 PDT)
- Tousif Hossen (Fri May 04 2018 - 04:11:33 PDT)
[AMBER] change the charge of the chlorine ion
- Saikat Pal (Sun May 13 2018 - 21:43:43 PDT)
- David A Case (Sat May 12 2018 - 10:13:23 PDT)
- Saikat Pal (Sat May 12 2018 - 05:13:21 PDT)
[AMBER] combining trajectories with different parameter files
- Daniel Roe (Mon May 14 2018 - 06:18:23 PDT)
- Chetna Tyagi (Mon May 14 2018 - 05:17:12 PDT)
- David A Case (Mon May 14 2018 - 05:09:20 PDT)
- Chetna Tyagi (Mon May 14 2018 - 04:31:36 PDT)
[AMBER] Computing interaction energies from trajectory
- Aravind Ravichandran (Tue May 01 2018 - 06:59:32 PDT)
[AMBER] Conda Installation error
- Scott Brozell (Thu May 31 2018 - 09:18:24 PDT)
- Hai Nguyen (Thu May 31 2018 - 09:11:38 PDT)
- Scott Brozell (Thu May 31 2018 - 09:06:54 PDT)
- Hai Nguyen (Thu May 31 2018 - 07:18:30 PDT)
- andreas.tosstorff.cup.uni-muenchen.de (Wed May 30 2018 - 10:51:25 PDT)
[AMBER] Configure CUDA issues
- David A Case (Thu May 03 2018 - 10:35:32 PDT)
- Kadir Ozcan (Thu May 03 2018 - 08:55:34 PDT)
[AMBER] CPPTRAJ Ensemble Keyword: "Too Many Open Files"
- Daniel Roe (Thu May 03 2018 - 07:28:19 PDT)
- Jason Ku Wang (Tue May 01 2018 - 16:55:15 PDT)
[AMBER] Creating a Gold surface library file
- David A Case (Tue May 22 2018 - 17:43:01 PDT)
- Timothy Cholko (Tue May 22 2018 - 15:37:29 PDT)
- David A Case (Sat May 19 2018 - 06:53:59 PDT)
- Timothy Cholko (Fri May 18 2018 - 15:03:41 PDT)
- David A Case (Fri May 18 2018 - 04:51:42 PDT)
- Timothy Cholko (Thu May 17 2018 - 14:49:53 PDT)
- David A Case (Mon May 14 2018 - 18:20:45 PDT)
- Timothy Cholko (Mon May 14 2018 - 17:35:06 PDT)
[AMBER] Cremer Pucker values using Pytraj
- Vivek Bharadwaj (Tue May 01 2018 - 07:31:34 PDT)
[AMBER] CUDA v9.0 with AMBER16 Question
- David A Case (Sat May 26 2018 - 06:14:01 PDT)
- Korey M Reid (Fri May 25 2018 - 16:56:43 PDT)
[AMBER] DEADLINE EXTENDED: Call for Papers, GCC 2018, 14th German Conference on Chemoinformatics
- Stefan.Guessregen.sanofi.com (Mon May 28 2018 - 04:56:58 PDT)
[AMBER] DFT method for calculating amino acids partial charges in AMBER99
- roja rahmani (Fri May 18 2018 - 05:33:26 PDT)
- David A Case (Fri May 18 2018 - 05:10:07 PDT)
- FyD (Thu May 17 2018 - 03:19:32 PDT)
- roja rahmani (Thu May 17 2018 - 03:10:43 PDT)
[AMBER] Different outputs of external electric field
- David A Case (Thu May 10 2018 - 06:05:56 PDT)
- David A Case (Thu May 10 2018 - 04:17:56 PDT)
- Meng Wu (Wed May 09 2018 - 20:16:44 PDT)
- David A Case (Wed May 09 2018 - 07:20:33 PDT)
- Meng Wu (Wed May 09 2018 - 04:05:42 PDT)
[AMBER] Dimension Box visualization
- Matias Machado (Thu May 31 2018 - 04:45:13 PDT)
- David A Case (Thu May 31 2018 - 04:29:35 PDT)
- Aashish Bhatt (Wed May 30 2018 - 23:00:50 PDT)
[AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon
- Thomas Exner (Thu May 24 2018 - 04:43:18 PDT)
[AMBER] eCheminfo Oxford, UK Training and Innovation Course in Drug Design 2018, first announcement
- Thomas Exner (Wed May 30 2018 - 02:59:48 PDT)
[AMBER] Electrostatic potential calculation
- Daniel Roe (Fri May 18 2018 - 07:49:11 PDT)
- Meng Wu (Thu May 17 2018 - 23:45:54 PDT)
- Meng Wu (Tue May 15 2018 - 19:52:18 PDT)
[AMBER] error in rst file during Minimization
- Subrata Paul (Mon May 28 2018 - 09:04:38 PDT)
- Stephan Schott (Mon May 28 2018 - 06:03:57 PDT)
- Subrata Paul (Mon May 28 2018 - 05:37:08 PDT)
[AMBER] Error in using pdb4amber command
- Aashish Bhatt (Thu May 24 2018 - 06:04:45 PDT)
- senal dinuka (Thu May 24 2018 - 04:55:14 PDT)
- David A Case (Thu May 24 2018 - 04:49:10 PDT)
- senal dinuka (Thu May 24 2018 - 03:14:03 PDT)
[AMBER] Error: No data sets selected - Problem or not?
- Gustaf Olsson (Wed May 09 2018 - 05:34:07 PDT)
- Daniel Roe (Wed May 09 2018 - 05:25:27 PDT)
- Gustaf Olsson (Wed May 09 2018 - 04:15:55 PDT)
[AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda
- David A Case (Tue May 22 2018 - 12:21:31 PDT)
- David A Case (Tue May 15 2018 - 13:12:53 PDT)
- David Adrian Saez San Martin (Mon May 14 2018 - 18:58:02 PDT)
- David Sáez (Mon May 14 2018 - 18:49:05 PDT)
[AMBER] Extracting infromation from topology file
- Hai Nguyen (Tue May 08 2018 - 22:47:07 PDT)
- anu chandra (Tue May 08 2018 - 22:36:23 PDT)
[AMBER] Facing problem to generate ala10_chir.dat in REMD tutorial
- David A Case (Fri May 18 2018 - 07:03:50 PDT)
- Saikat Pal (Fri May 18 2018 - 05:29:21 PDT)
[AMBER] GBNSR6 with MMPBSA.py
- Jose Manuel Granadino Roldán (Tue May 08 2018 - 02:08:38 PDT)
[AMBER] GPU benchmark - Amber18
- David A Case (Wed May 02 2018 - 05:18:39 PDT)
- Hadházi Ádám (Wed May 02 2018 - 02:00:19 PDT)
[AMBER] GPU questions
- Daniel Roe (Thu May 17 2018 - 08:25:32 PDT)
- 陈金峰 (Thu May 17 2018 - 07:54:17 PDT)
[AMBER] GUI for TI setup
- James Kress (Mon May 14 2018 - 14:11:00 PDT)
- Charles Lin (Mon May 14 2018 - 12:53:58 PDT)
- Hadházi Ádám (Mon May 14 2018 - 06:38:43 PDT)
[AMBER] How to evaluate the impact of PH on protein structures by Amber
- Lei Zhao (Thu May 24 2018 - 07:49:38 PDT)
[AMBER] How to extract frames with particular hydrogen bonds only
- Daniel Roe (Thu May 03 2018 - 07:42:05 PDT)
- Stejskal, Lenka (Wed May 02 2018 - 08:31:59 PDT)
[AMBER] How to prepare prmtop and inpcrd files from a PDB file?
- Markowska (Fri May 25 2018 - 05:37:18 PDT)
- Carlos Simmerling (Thu May 24 2018 - 06:53:04 PDT)
- Kshatresh Dutta Dubey (Thu May 24 2018 - 06:27:03 PDT)
- Markowska (Thu May 24 2018 - 06:07:13 PDT)
- Carlos Simmerling (Thu May 24 2018 - 05:56:20 PDT)
- Markowska (Thu May 24 2018 - 05:52:59 PDT)
- Gustaf Olsson (Thu May 24 2018 - 05:19:18 PDT)
- Carlos Simmerling (Thu May 24 2018 - 05:17:26 PDT)
- Gustaf Olsson (Thu May 24 2018 - 05:15:47 PDT)
- Markowska (Thu May 24 2018 - 05:07:20 PDT)
[AMBER] Hydrogen Bond Occupancy
- Jerrano Bowleg (Wed May 23 2018 - 06:44:22 PDT)
- Gustaf Olsson (Tue May 22 2018 - 23:27:45 PDT)
- David A Case (Tue May 22 2018 - 17:46:00 PDT)
- Jerrano Bowleg (Tue May 22 2018 - 10:13:42 PDT)
[AMBER] I: help please
- David A Case (Fri May 18 2018 - 05:18:16 PDT)
- giuseppe gatti (Wed May 16 2018 - 08:10:19 PDT)
[AMBER] info grafic about MD
- Rosellen, Martin (Mon May 21 2018 - 05:45:42 PDT)
[AMBER] Initial configuration of ADP and ion simulation using AMBER.
- Abhilash J (Thu May 31 2018 - 09:45:12 PDT)
[AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem
- Chetna Tyagi (Thu May 03 2018 - 07:36:12 PDT)
- Daniel Roe (Thu May 03 2018 - 07:32:30 PDT)
- Gustaf Olsson (Thu May 03 2018 - 07:28:47 PDT)
- Chetna Tyagi (Thu May 03 2018 - 07:18:54 PDT)
[AMBER] lipid 14 MSD with OPC water
- Chitrak Gupta (Sun May 13 2018 - 12:30:48 PDT)
[AMBER] lipid MSD values for lipid 14 FF
- Chitrak Gupta (Sat May 12 2018 - 14:56:12 PDT)
[AMBER] MD stops due to the distortion of a molecule
- Sergey Samsonov (Thu May 17 2018 - 23:13:43 PDT)
- David A Case (Thu May 17 2018 - 05:11:48 PDT)
- Sergey Samsonov (Thu May 17 2018 - 01:23:57 PDT)
[AMBER] MMPBSA energy decomposition
- Yuxin Xie (Wed May 16 2018 - 11:38:47 PDT)
[AMBER] MMPBSA.py - PrmtopError: Inconsistent charge definition for atom
- David A Case (Wed May 16 2018 - 05:49:18 PDT)
- Rodrigo Galindo-Murillo (Tue May 15 2018 - 14:41:50 PDT)
[AMBER] MMPBSA.py execution error
- Jose Manuel Granadino Roldán (Fri May 11 2018 - 00:27:52 PDT)
- Hai Nguyen (Thu May 10 2018 - 13:24:22 PDT)
- David A Case (Thu May 10 2018 - 12:11:56 PDT)
- Daniel Roe (Thu May 10 2018 - 11:15:38 PDT)
- Jose Manuel Granadino Roldán (Thu May 10 2018 - 09:14:27 PDT)
[AMBER] MMPBSA.py.MPI and matching topology files a problem
- Kasprzak, Wojciech (NIH/NCI) [C] (Tue May 08 2018 - 09:17:21 PDT)
[AMBER] MMPBSA.py.MPI: questions about output warnings and discrepancies
- Kasprzak, Wojciech (NIH/NCI) [C] (Fri May 11 2018 - 06:59:40 PDT)
[AMBER] Multiple temperature groups
- David A Case (Wed May 09 2018 - 18:52:59 PDT)
- I Lőrincz (Thu May 03 2018 - 07:03:13 PDT)
[AMBER] nativecontacts command in CPPTRAJ
- Ruth Helena Tichauer (Wed May 23 2018 - 08:28:49 PDT)
- Ruth Helena Tichauer (Wed May 23 2018 - 01:43:43 PDT)
- Andreas Tosstorff (Wed May 23 2018 - 01:15:51 PDT)
- Ruth Helena Tichauer (Wed May 23 2018 - 01:09:47 PDT)
- Daniel Roe (Tue May 22 2018 - 06:33:38 PDT)
- Ruth Helena Tichauer (Tue May 22 2018 - 06:25:33 PDT)
- Sowmya Indrakumar (Sun May 06 2018 - 09:26:52 PDT)
- Ruth Helena Tichauer (Sun May 06 2018 - 08:58:09 PDT)
- Sowmya Indrakumar (Sun May 06 2018 - 08:13:32 PDT)
- Ruth Helena Tichauer (Sun May 06 2018 - 07:57:01 PDT)
- Andreas Tosstorff (Sun May 06 2018 - 05:05:41 PDT)
- Ruth Helena Tichauer (Sun May 06 2018 - 03:31:06 PDT)
[AMBER] need QMMM interface for TURBOMOLE
- Holger Kruse (Wed May 09 2018 - 05:26:25 PDT)
- Scott Brozell (Tue May 08 2018 - 12:47:04 PDT)
- Antoine MARION (Tue May 08 2018 - 08:19:17 PDT)
- Goetz, Andreas (Mon May 07 2018 - 10:26:15 PDT)
- David A Case (Mon May 07 2018 - 04:39:11 PDT)
- 陈金峰 (Wed May 02 2018 - 16:38:09 PDT)
[AMBER] NetCDF error: NetCDF: Not a valid ID
- David A Case (Fri May 18 2018 - 05:34:43 PDT)
- Midhun K Madhu (Mon May 14 2018 - 14:12:46 PDT)
[AMBER] Novice Question: MD Visualisation in VMD
- James Kress (Sun May 13 2018 - 12:18:14 PDT)
- David A Case (Sun May 13 2018 - 10:59:33 PDT)
- Horn, Anselm (Sun May 13 2018 - 05:07:40 PDT)
[AMBER] optimization of QM zone in QM/MM-GBSA calculations.
- David A Case (Thu May 24 2018 - 04:46:03 PDT)
- mish (Thu May 24 2018 - 00:10:19 PDT)
[AMBER] Parametrization of Small Molecules
- David A Case (Fri May 18 2018 - 04:58:13 PDT)
- Johannes Loeffler (Fri May 18 2018 - 02:44:56 PDT)
[AMBER] Parametrization: consistency with gaff force field
- Alechania Misturini (Tue May 15 2018 - 04:55:07 PDT)
- David A Case (Mon May 14 2018 - 07:25:43 PDT)
- Alechania Misturini (Tue May 08 2018 - 11:25:50 PDT)
[AMBER] parmed/chamber verify including CMAP corrections
- Robin Betz (Wed May 23 2018 - 12:06:19 PDT)
- David Sáez (Wed May 23 2018 - 12:00:26 PDT)
[AMBER] PC modes per residue from existing evecs file?
- Kenneth Huang (Mon May 07 2018 - 08:15:27 PDT)
[AMBER] PhD/Junior position, AMBER sims DNA/RNA
- Jiri Sponer (Wed May 02 2018 - 03:54:35 PDT)
[AMBER] Plotting phi-psi plots with free energy scale
- Carlos Simmerling (Thu May 24 2018 - 07:13:33 PDT)
- Chetna Tyagi (Thu May 24 2018 - 07:01:19 PDT)
[AMBER] pmemd.MPI compatible for REMD simulation IN AMBER package
- Cruzeiro,Vinicius Wilian D (Wed May 16 2018 - 05:39:37 PDT)
- Saikat Pal (Tue May 15 2018 - 22:48:07 PDT)
[AMBER] pmemd.MPI won't work in Amber 18
- Ross Walker (Thu May 24 2018 - 15:08:11 PDT)
- Hai Long (Thu May 24 2018 - 14:44:40 PDT)
- David A Case (Thu May 24 2018 - 04:38:09 PDT)
- Hai Long (Wed May 23 2018 - 14:37:27 PDT)
[AMBER] Poly amino acid helix form topology files
- Carlos Simmerling (Mon May 07 2018 - 04:59:51 PDT)
- ABEL Stephane (Mon May 07 2018 - 04:00:58 PDT)
- roja rahmani (Mon May 07 2018 - 03:19:01 PDT)
- ABEL Stephane (Mon May 07 2018 - 03:02:53 PDT)
- roja rahmani (Sun May 06 2018 - 06:29:52 PDT)
- Carlos Simmerling (Sun May 06 2018 - 06:20:18 PDT)
- roja rahmani (Sun May 06 2018 - 06:15:12 PDT)
- Carlos Simmerling (Sun May 06 2018 - 06:01:08 PDT)
- roja rahmani (Sat May 05 2018 - 23:53:31 PDT)
[AMBER] Possible memory leak with LMOD
- David A Case (Thu May 31 2018 - 12:43:12 PDT)
- David A Case (Thu May 24 2018 - 04:31:06 PDT)
- Charo del Genio (Wed May 23 2018 - 10:31:11 PDT)
- David A Case (Tue May 22 2018 - 13:08:59 PDT)
- Charo del Genio (Tue May 22 2018 - 09:39:08 PDT)
[AMBER] Problem in distance restraint
- David A Case (Fri May 04 2018 - 10:47:07 PDT)
- Kshatresh Dutta Dubey (Fri May 04 2018 - 05:01:57 PDT)
[AMBER] Problem with g++ compiler with boost (AmberTools18)
- Matias Machado (Thu May 31 2018 - 05:10:54 PDT)
- David A Case (Thu May 31 2018 - 04:21:47 PDT)
- Matias Machado (Wed May 30 2018 - 19:12:28 PDT)
[AMBER] problems with MCPY.py step 2
- Cristián Ferretti (Wed May 30 2018 - 03:03:02 PDT)
[AMBER] QM/MM issue with boron containing compound (AMBER16)
- Bodee Nutho (Thu May 10 2018 - 19:02:07 PDT)
- David A Case (Thu May 10 2018 - 11:48:01 PDT)
- Bodee Nutho (Thu May 10 2018 - 08:04:32 PDT)
[AMBER] QM/MM minimization issue using sander (AMBER 18)
- Abhilash J (Tue May 01 2018 - 08:47:49 PDT)
- Abhilash J (Tue May 01 2018 - 06:03:28 PDT)
- Goetz, Andreas (Mon Apr 30 2018 - 17:01:55 PDT)
[AMBER] QMMM surface scan
- 陈金峰 (Fri May 18 2018 - 07:55:39 PDT)
[AMBER] Query related to the Umbrella sampling method
- Saikat Pal (Tue May 08 2018 - 23:00:50 PDT)
[AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version).
- DHEERAJ CHITARA (Thu May 17 2018 - 05:08:50 PDT)
- David A Case (Thu May 17 2018 - 05:02:00 PDT)
- DHEERAJ CHITARA (Thu May 17 2018 - 04:41:08 PDT)
- Carlos Simmerling (Thu May 17 2018 - 04:27:37 PDT)
- DHEERAJ CHITARA (Thu May 17 2018 - 01:04:54 PDT)
[AMBER] Reg. generating empty frcmod file for ligand molecule
- DHEERAJ CHITARA (Thu May 17 2018 - 05:40:57 PDT)
- Aashish Bhatt (Thu May 17 2018 - 05:16:09 PDT)
- DHEERAJ CHITARA (Thu May 17 2018 - 05:03:01 PDT)
[AMBER] Request of help on Leap PDB preparation error "atom does not have a type"
- David A Case (Wed May 30 2018 - 05:46:50 PDT)
- Carlos Simmerling (Wed May 30 2018 - 05:09:31 PDT)
- Gustaf Olsson (Tue May 29 2018 - 23:36:40 PDT)
- 符哲瀚 (Tue May 29 2018 - 21:32:33 PDT)
[AMBER] Reservoir REMD using GPUs
- koushik kasavajhala (Thu May 31 2018 - 12:47:15 PDT)
- Hurst, Travis C (MU-Student) (Tue May 29 2018 - 08:09:01 PDT)
- Carlos Simmerling (Fri May 25 2018 - 10:07:02 PDT)
- Hurst, Travis C (MU-Student) (Wed May 16 2018 - 15:25:55 PDT)
[AMBER] Restart From Check point File
- Stephan Schott (Tue May 22 2018 - 05:36:12 PDT)
- Midhun K Madhu (Mon May 21 2018 - 22:22:46 PDT)
- Stephan Schott (Sun May 20 2018 - 08:27:10 PDT)
- Midhun K Madhu (Sun May 20 2018 - 05:47:24 PDT)
[AMBER] S-S bond
- roja rahmani (Wed May 23 2018 - 22:45:13 PDT)
- FyD (Wed May 23 2018 - 22:24:55 PDT)
- roja rahmani (Wed May 23 2018 - 02:47:29 PDT)
[AMBER] sander failed with prmtop complex.top!
- Urszula Uciechowska (Tue May 29 2018 - 23:52:54 PDT)
[AMBER] Scabilility of the code in cpus
- David A Case (Tue May 22 2018 - 13:38:59 PDT)
- Ana Luisa Novo de Oliveira (Tue May 22 2018 - 09:45:39 PDT)
[AMBER] Setting initial velocities
- David A Case (Wed May 09 2018 - 05:27:58 PDT)
- Hai Nguyen (Tue May 08 2018 - 20:22:29 PDT)
- Hai Nguyen (Tue May 08 2018 - 20:18:27 PDT)
- diego.soler.uam.es (Fri May 04 2018 - 05:42:39 PDT)
[AMBER] SGLD
- Piotr Fajer (Sat May 05 2018 - 19:19:12 PDT)
- David A Case (Sat May 05 2018 - 19:10:14 PDT)
- Piotr Fajer (Sat May 05 2018 - 12:52:40 PDT)
[AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model
- Sadegh Faramarzi Ganjabad (Mon May 28 2018 - 13:29:46 PDT)
- Sadegh Faramarzi Ganjabad (Wed May 23 2018 - 12:36:30 PDT)
- David A Case (Tue May 22 2018 - 12:53:54 PDT)
- David A Case (Tue May 22 2018 - 05:15:20 PDT)
- Karla Galdamez (Mon May 21 2018 - 18:54:49 PDT)
- Sadegh Faramarzi Ganjabad (Mon May 21 2018 - 11:24:52 PDT)
[AMBER] Simulation does not restart from restart file written in previous step.
- Abhilash J (Fri May 04 2018 - 05:19:38 PDT)
[AMBER] TI for side chain mutation in dimer protein
- Josephine la sala (Wed May 30 2018 - 06:29:22 PDT)
- Josephine la sala (Wed May 30 2018 - 02:55:48 PDT)
[AMBER] TiMergeError: Cannot have dihedral cross through softcore region
- Jissy Akkarapattiakal Kuriappan (Wed May 30 2018 - 06:07:15 PDT)
[AMBER] tleap error 'FATAL: Atom .R<NMET 1>.A<CAY 20> does not have a type'
- David A Case (Mon May 14 2018 - 05:06:22 PDT)
- Midhun K Madhu (Mon May 14 2018 - 00:26:01 PDT)
[AMBER] TMD : Doubts regarding TGTMDFRC
- Carlos Simmerling (Mon May 14 2018 - 05:12:01 PDT)
- Aravind Ravichandran (Sun May 13 2018 - 23:44:25 PDT)
- Carlos Simmerling (Sat May 12 2018 - 10:58:54 PDT)
- Aravind Ravichandran (Fri May 11 2018 - 23:25:58 PDT)
[AMBER] Total Energy Decomposition
- daniele selli (Wed May 23 2018 - 05:06:43 PDT)
- David A Case (Tue May 22 2018 - 05:12:46 PDT)
- daniele selli (Mon May 21 2018 - 04:06:56 PDT)
[AMBER] Troubleshooting SHAKE problems in minimization
- David A Case (Sun May 27 2018 - 06:06:47 PDT)
- Alen Ahmetovic (Sat May 26 2018 - 21:07:29 PDT)
[AMBER] Ubuntu 18
- Scott Brozell (Thu May 31 2018 - 08:55:40 PDT)
- Sepideh Jafari (Thu May 31 2018 - 07:29:24 PDT)
- David A Case (Thu May 31 2018 - 07:10:58 PDT)
- Sepideh Jafari (Thu May 31 2018 - 06:22:00 PDT)
[AMBER] update ambertools
- Kevin Keane (Wed May 02 2018 - 10:20:30 PDT)
- David A Case (Wed May 02 2018 - 05:26:34 PDT)
- Tousif Hossen (Wed May 02 2018 - 02:33:16 PDT)
- Tousif Hossen (Wed May 02 2018 - 02:28:52 PDT)
[AMBER] update_amber URL time out problem
- David A Case (Thu May 24 2018 - 04:45:05 PDT)
- Meng Wu (Wed May 23 2018 - 20:07:55 PDT)
- David A Case (Wed May 23 2018 - 05:13:09 PDT)
- Meng Wu (Wed May 23 2018 - 01:29:11 PDT)
[AMBER] Use of Amber12 and 14 on the same simulation
- David A Case (Thu May 24 2018 - 04:28:45 PDT)
- JoAnne Babula (Wed May 23 2018 - 09:09:08 PDT)
[AMBER] Using infe = 1, &pmd, and pmemd.cuda (AMBER16)
- Feng Pan (Wed May 02 2018 - 13:40:13 PDT)
- Lenz, Stefan (Tue May 01 2018 - 09:04:27 PDT)
[AMBER] Using multiple CPU threads
- David A Case (Sat May 26 2018 - 06:19:21 PDT)
- senal dinuka (Sat May 26 2018 - 01:17:55 PDT)
[AMBER] VMD window
- Karla Galdamez (Wed May 23 2018 - 07:24:27 PDT)
- Gustaf Olsson (Wed May 23 2018 - 00:48:40 PDT)
- Karla Galdamez (Tue May 22 2018 - 23:53:14 PDT)
- Gustaf Olsson (Tue May 22 2018 - 23:05:11 PDT)
- Karla Galdamez (Tue May 22 2018 - 20:43:23 PDT)
[AMBER] what are the benefits of cuda9 vs. 8 with amber 18?
- Chris Neale (Wed May 09 2018 - 08:32:08 PDT)
- David A Case (Wed May 09 2018 - 07:18:28 PDT)
- Chris Neale (Tue May 08 2018 - 21:41:11 PDT)
SHAKEH: Extra bond between hydrogen atoms of TIP3 water model
- David A Case (Tue May 22 2018 - 17:32:17 PDT)
- Sadegh Faramarzi Ganjabad (Tue May 22 2018 - 12:59:21 PDT)

Amber Archive May 2018 by subject