Amber Archive Nov 2019: by subject

[AMBER] 2D graphic visualisation
- Giulia Paiardi (Wed Nov 13 2019 - 08:42:54 PST)
[AMBER] [Bug-Report] NAB: TER record need a serial number
- Daniel Roe (Mon Nov 25 2019 - 05:21:42 PST)
- Johannes Kalliauer (Mon Nov 25 2019 - 03:06:57 PST)
[AMBER] absolute binding free energy calculations
- Debarati DasGupta (Fri Nov 22 2019 - 10:37:22 PST)
[AMBER] amber 16 with nVIDIA Tesla T4 GPU
- Schröder, David Christopher (Tue Nov 19 2019 - 03:51:35 PST)
[AMBER] amber maillist
- Q Yu (Mon Nov 18 2019 - 08:41:09 PST)
[AMBER] Amber updates brings duplicate patch
- David A Case (Thu Nov 21 2019 - 05:29:41 PST)
- viktor drobot (Thu Nov 21 2019 - 04:03:52 PST)
- David A Case (Wed Nov 20 2019 - 10:57:07 PST)
- viktor drobot (Wed Nov 20 2019 - 06:27:24 PST)
- David A Case (Wed Nov 20 2019 - 06:21:41 PST)
- viktor drobot (Wed Nov 20 2019 - 01:50:44 PST)
[AMBER] amber15 cpptraj closest
- Daniel Roe (Fri Nov 22 2019 - 09:07:35 PST)
- Q Yu (Fri Nov 22 2019 - 08:55:56 PST)
- Daniel Roe (Thu Nov 21 2019 - 08:52:18 PST)
- Q Yu (Mon Nov 18 2019 - 10:34:43 PST)
[AMBER] AMBER18/16 12-6-4LJ Sander TI problem
- Pengfei Li (Sat Nov 16 2019 - 18:13:15 PST)
- Paulius Kantakevicius (Sat Nov 16 2019 - 03:20:35 PST)
- Pengfei Li (Fri Nov 15 2019 - 15:32:10 PST)
- Paulius Kantakevicius (Tue Nov 12 2019 - 02:58:51 PST)
[AMBER] antechamber QM calculation/qmcharge error
- Rui Chen (Thu Nov 21 2019 - 08:48:38 PST)
- David A Case (Thu Nov 21 2019 - 05:34:06 PST)
- Rui Chen (Wed Nov 20 2019 - 21:25:53 PST)
[AMBER] ATP gamma phosphate distorted in MD
- Qing Lv (Fri Nov 22 2019 - 22:04:09 PST)
- Zachary Fallon (Fri Nov 22 2019 - 10:26:28 PST)
- Qing Lv (Fri Nov 22 2019 - 10:11:23 PST)
[AMBER] Broken AmberTools19 cpptraj compilation for GNU, Intel and PGI on a Cray with -crayxt5 flag
- Daniel Roe (Fri Nov 15 2019 - 11:50:58 PST)
- Victor Holanda Rusu (Fri Nov 15 2019 - 08:42:20 PST)
[AMBER] building openMP cpptraj with intel compiler
- Daniel Roe (Tue Nov 12 2019 - 10:26:10 PST)
- Vlad Cojocaru (Tue Nov 12 2019 - 10:13:26 PST)
- Daniel Roe (Tue Nov 12 2019 - 07:03:42 PST)
- Vlad Cojocaru (Tue Nov 12 2019 - 06:59:38 PST)
- Daniel Roe (Tue Nov 12 2019 - 06:49:44 PST)
- Vlad Cojocaru (Fri Nov 08 2019 - 05:34:36 PST)
- Vlad Cojocaru (Fri Nov 08 2019 - 05:13:14 PST)
[AMBER] Calculate MMGBSA keeping water in binding site
- Rosellen, Martin (Fri Nov 01 2019 - 10:24:54 PDT)
[AMBER] Calculation Tetrahedral Order Parameter of Water
- Ajeet Kumar Yadav (Thu Nov 14 2019 - 10:22:44 PST)
[AMBER] Charge neutrality in QM/MM system
- James Kress (Mon Nov 18 2019 - 20:51:09 PST)
- David Case (Mon Nov 18 2019 - 18:25:13 PST)
- James Kress (Mon Nov 18 2019 - 15:13:42 PST)
- James Kress (Thu Nov 14 2019 - 06:46:21 PST)
[AMBER] Citation for GAFF2
- Gustaf Olsson (Mon Nov 25 2019 - 07:02:59 PST)
[AMBER] compiling Amber with gcc 9.2 and intel mpi 2019
- Vlad Cojocaru (Thu Nov 07 2019 - 11:56:57 PST)
- David A Case (Thu Nov 07 2019 - 11:50:49 PST)
- Vlad Cojocaru (Thu Nov 07 2019 - 06:47:09 PST)
[AMBER] Conformation of NEB end states changing during 1HEAT
- Madhur Aggarwal (Wed Nov 20 2019 - 00:15:46 PST)
- Carlos Simmerling (Tue Nov 19 2019 - 07:53:13 PST)
- Ghoreishi, Delaram (Tue Nov 19 2019 - 07:48:53 PST)
- Madhur Aggarwal (Tue Nov 19 2019 - 06:51:36 PST)
- Ghoreishi, Delaram (Mon Nov 18 2019 - 22:55:15 PST)
- Madhur Aggarwal (Mon Nov 18 2019 - 11:44:29 PST)
- Carlos Simmerling (Mon Nov 18 2019 - 09:40:13 PST)
- Ghoreishi, Delaram (Mon Nov 18 2019 - 09:29:36 PST)
- Madhur Aggarwal (Mon Nov 18 2019 - 09:09:59 PST)
[AMBER] cpptraj msd of center -of-mass motion
- Daniel Roe (Tue Nov 12 2019 - 08:22:29 PST)
- David A Case (Tue Nov 12 2019 - 05:43:00 PST)
- 조준범 (Mon Nov 11 2019 - 18:11:02 PST)
[AMBER] cpptraj.MPI query
- Debarati DasGupta (Mon Nov 04 2019 - 12:50:11 PST)
- Debarati DasGupta (Mon Nov 04 2019 - 12:38:13 PST)
- Daniel Roe (Mon Nov 04 2019 - 12:28:49 PST)
- Debarati DasGupta (Mon Nov 04 2019 - 12:07:53 PST)
- Daniel Roe (Mon Nov 04 2019 - 11:54:10 PST)
- Debarati DasGupta (Mon Nov 04 2019 - 11:41:05 PST)
- Daniel Roe (Mon Nov 04 2019 - 11:17:11 PST)
- Debarati DasGupta (Mon Nov 04 2019 - 07:34:59 PST)
- Daniel Roe (Mon Nov 04 2019 - 07:20:00 PST)
- Debarati DasGupta (Mon Nov 04 2019 - 06:01:28 PST)
- Daniel Roe (Sun Nov 03 2019 - 17:00:50 PST)
- Debarati DasGupta (Sun Nov 03 2019 - 09:39:14 PST)
[AMBER] decompose MMGBSA error
- Elvis Martis (Thu Nov 28 2019 - 05:12:04 PST)
- Nisha Amarnath Jonniya (Thu Nov 28 2019 - 04:56:40 PST)
- Elvis Martis (Thu Nov 21 2019 - 20:32:48 PST)
- Nisha Amarnath Jonniya (Thu Nov 21 2019 - 20:27:25 PST)
- David A Case (Thu Nov 21 2019 - 05:36:03 PST)
- Nisha Amarnath Jonniya (Wed Nov 20 2019 - 22:46:36 PST)
- Elvis Martis (Wed Nov 20 2019 - 04:38:41 PST)
- Nisha Amarnath Jonniya (Wed Nov 20 2019 - 03:43:21 PST)
- Nisha Amarnath Jonniya (Mon Nov 18 2019 - 20:50:34 PST)
- David Case (Mon Nov 18 2019 - 04:35:12 PST)
- Elvis Martis (Mon Nov 18 2019 - 00:45:20 PST)
- Nisha Amarnath Jonniya (Mon Nov 18 2019 - 00:19:05 PST)
- Elvis Martis (Sun Nov 17 2019 - 22:07:41 PST)
- Nisha Amarnath Jonniya (Sat Nov 16 2019 - 18:53:35 PST)
- Elvis Martis (Fri Nov 15 2019 - 22:21:15 PST)
- Nisha Amarnath Jonniya (Fri Nov 15 2019 - 21:58:59 PST)
[AMBER] different radii sets and GB models
- Pietro Aronica (Thu Nov 14 2019 - 18:29:23 PST)
- Neha Gandhi (Thu Nov 14 2019 - 18:21:57 PST)
[AMBER] Does amber work with NVIDIA RTX6000?
- David Cerutti (Sat Nov 16 2019 - 09:05:16 PST)
- Shenglong Wang (Fri Nov 15 2019 - 19:33:27 PST)
- David Cerutti (Fri Nov 15 2019 - 19:16:01 PST)
- Shenglong Wang (Fri Nov 15 2019 - 08:35:56 PST)
[AMBER] error in namelist
- David A Case (Tue Nov 05 2019 - 09:47:52 PST)
- Debarati DasGupta (Tue Nov 05 2019 - 06:29:22 PST)
[AMBER] Error in PMEMD installation with MPI
- David Case (Mon Nov 18 2019 - 04:22:38 PST)
- Rahul Verma (Sun Nov 17 2019 - 21:01:52 PST)
[AMBER] Error in the namelist cntrl
- David A Case (Fri Nov 22 2019 - 05:30:33 PST)
- Airy Sanjeev (Thu Nov 21 2019 - 22:04:00 PST)
[AMBER] Error in themodynamic integration with PMEMD.CUDA
- David A Case (Thu Nov 21 2019 - 11:53:55 PST)
- HOCHEOL LIM (Thu Nov 21 2019 - 07:32:29 PST)
- HOCHEOL LIM (Thu Nov 21 2019 - 07:06:28 PST)
- HOCHEOL LIM (Mon Nov 18 2019 - 04:37:49 PST)
[AMBER] Error parameterizing a heme using MCPB
- Pengfei Li (Mon Nov 25 2019 - 18:04:28 PST)
- Mohamed M. Aboelnga (Thu Nov 21 2019 - 05:50:13 PST)
- Pengfei Li (Wed Nov 20 2019 - 19:29:33 PST)
- Mohamed M. Aboelnga (Tue Nov 19 2019 - 09:20:01 PST)
[AMBER] Error with addIons
- David Case (Tue Nov 19 2019 - 05:14:10 PST)
- Bill Ross (Mon Nov 18 2019 - 23:22:42 PST)
- 조준범 (Mon Nov 18 2019 - 23:22:03 PST)
- 조준범 (Mon Nov 18 2019 - 23:09:33 PST)
- Bill Ross (Mon Nov 18 2019 - 22:56:45 PST)
- 조준범 (Mon Nov 18 2019 - 22:49:37 PST)
- 조준범 (Mon Nov 18 2019 - 22:45:54 PST)
- Bill Ross (Mon Nov 18 2019 - 22:17:02 PST)
- 조준범 (Mon Nov 18 2019 - 22:10:09 PST)
[AMBER] ff19SB inpcrd test file missing
- David Case (Thu Nov 28 2019 - 05:48:07 PST)
- Chuan Tian (Wed Nov 27 2019 - 14:48:39 PST)
- David Wang (Wed Nov 27 2019 - 11:57:37 PST)
[AMBER] Finding radial distribution function using cpptraj
- Daniel Roe (Mon Nov 25 2019 - 05:16:02 PST)
- Raghav Arora (Mon Nov 25 2019 - 03:57:22 PST)
[AMBER] Force-field with only Bond parameters
- Stefano Motta (Fri Nov 22 2019 - 01:07:02 PST)
- David A Case (Thu Nov 21 2019 - 11:47:45 PST)
- Stefano Motta (Thu Nov 21 2019 - 05:19:53 PST)
- Carlos Simmerling (Thu Nov 21 2019 - 03:59:52 PST)
- Stefano Motta (Thu Nov 21 2019 - 03:27:39 PST)
- Carlos Simmerling (Thu Nov 21 2019 - 03:21:37 PST)
- Stefano Motta (Thu Nov 21 2019 - 03:12:33 PST)
- Carlos Simmerling (Thu Nov 21 2019 - 02:59:24 PST)
- Stefano Motta (Thu Nov 21 2019 - 02:48:57 PST)
- Carlos Simmerling (Thu Nov 21 2019 - 02:12:33 PST)
- Stefano Motta (Thu Nov 21 2019 - 02:04:44 PST)
[AMBER] Fwd: Error in PMEMD installation with MPI
- Rahul Verma (Wed Nov 20 2019 - 19:42:30 PST)
[AMBER] help on this error
- David Case (Fri Nov 29 2019 - 18:10:18 PST)
- Debarati DasGupta (Fri Nov 29 2019 - 06:29:45 PST)
[AMBER] How can I calculate dihedral distribution through CPPTRAJ
- Daniel Roe (Tue Nov 12 2019 - 08:21:14 PST)
- Elvis Martis (Tue Nov 12 2019 - 02:00:53 PST)
- 조준범 (Tue Nov 12 2019 - 00:16:39 PST)
- Elvis Martis (Mon Nov 11 2019 - 19:32:48 PST)
- 조준범 (Mon Nov 11 2019 - 18:23:40 PST)
- David A Case (Mon Nov 11 2019 - 04:50:07 PST)
- 조준범 (Mon Nov 11 2019 - 03:21:01 PST)
[AMBER] How to check the convergence of NEB calculation?
- Charles-Alexandre Mattelaer (Mon Nov 11 2019 - 04:16:37 PST)
- Bill Ross (Mon Nov 11 2019 - 03:40:58 PST)
- Charles-Alexandre Mattelaer (Mon Nov 11 2019 - 00:33:05 PST)
[AMBER] how to cluster by cpptraj
- Daniel Roe (Tue Nov 12 2019 - 07:58:52 PST)
- 石娜 (Mon Nov 11 2019 - 17:12:22 PST)
[AMBER] HTTP Error 500 - download
- Hai Nguyen (Fri Nov 29 2019 - 08:42:07 PST)
- Mattia Pini (Fri Nov 29 2019 - 00:16:59 PST)
[AMBER] jump in monomer position
- Fabian Glaser (Wed Nov 06 2019 - 23:26:23 PST)
- Carlos Simmerling (Wed Nov 06 2019 - 13:02:50 PST)
- Fabian Glaser (Wed Nov 06 2019 - 00:55:55 PST)
[AMBER] Large GPU performance difference for umbrella sampling methods: (infe=1 and &pmd) vs (nmropt=1 and disang-rst)
- accuratefreeenergy.gmail.com (Tue Nov 05 2019 - 04:55:49 PST)
- Åsmund Røhr Kjendseth (Tue Nov 05 2019 - 01:13:23 PST)
[AMBER] List of GAF2 atom types?
- David Case (Fri Nov 22 2019 - 18:55:26 PST)
- Gustavo Seabra (Fri Nov 22 2019 - 13:19:28 PST)
[AMBER] mac os catalina..... (oh my god)
- Fabian Glaser (Wed Nov 06 2019 - 00:58:05 PST)
- Gustaf Olsson (Wed Nov 06 2019 - 00:40:52 PST)
- Fabian Glaser (Wed Nov 06 2019 - 00:07:55 PST)
[AMBER] Making ParmEd play nice with OpenEye?
- Brian Radak (Mon Nov 11 2019 - 07:52:58 PST)
[AMBER] MD CYT C : heme bound
- emanuele falbo (Mon Nov 18 2019 - 07:58:40 PST)
[AMBER] md simulation with GPU -Geng Dong
- Ross Walker (Tue Nov 05 2019 - 18:09:35 PST)
- 东庚 (Tue Nov 05 2019 - 18:03:07 PST)
[AMBER] md simulation with GPU （Geng Dong）
- Gerardo Zerbetto De Palma (Tue Nov 05 2019 - 05:18:57 PST)
- 东庚 (Tue Nov 05 2019 - 00:44:27 PST)
[AMBER] Metal ion parameterization using MCPB.py
- Pengfei Li (Sat Nov 16 2019 - 20:20:08 PST)
- Abhilash J (Sat Nov 09 2019 - 10:42:25 PST)
[AMBER] Minimization of ethanol in water
- David Case (Wed Nov 06 2019 - 14:25:17 PST)
[AMBER] mmbpsa.py error
- David Case (Tue Nov 05 2019 - 17:45:29 PST)
- Alen Ahmetovic (Tue Nov 05 2019 - 16:25:26 PST)
[AMBER] MMGBSA error
- RITUPARNA ROY (Sat Nov 30 2019 - 08:48:26 PST)
[AMBER] Modification of gaff
- David A Case (Wed Nov 13 2019 - 04:42:21 PST)
- 조준범 (Tue Nov 12 2019 - 19:02:10 PST)
[AMBER] NMR refined MD
- maya nair (Tue Nov 12 2019 - 23:31:08 PST)
- maya nair (Tue Nov 12 2019 - 23:28:11 PST)
- David A Case (Tue Nov 12 2019 - 10:50:37 PST)
- Christina Bergonzo (Tue Nov 12 2019 - 10:18:39 PST)
- maya nair (Tue Nov 12 2019 - 09:20:03 PST)
[AMBER] Obtaining excess molar volumes using Molecular Dynamics
- Raghav Arora (Thu Nov 28 2019 - 02:58:30 PST)
[AMBER] Open Scientific Computing Roles at GSK.
- Ross Walker (Mon Nov 04 2019 - 12:48:59 PST)
[AMBER] Parameter file GTP or GMP containing tRNA
- David A Case (Mon Nov 04 2019 - 04:36:17 PST)
- student_cbc_1 nnlab (Mon Nov 04 2019 - 02:27:35 PST)
[AMBER] Parameter file not saved
- David Case (Sun Nov 03 2019 - 04:54:31 PST)
- Carlos Simmerling (Sun Nov 03 2019 - 04:47:19 PST)
- Bill Ross (Sun Nov 03 2019 - 03:47:49 PST)
- student_cbc_1 nnlab (Sun Nov 03 2019 - 03:11:19 PST)
[AMBER] PIMD restart error in Amber18
- David A Case (Thu Nov 21 2019 - 11:56:49 PST)
- jinfeng liu (Mon Nov 18 2019 - 19:36:35 PST)
[AMBER] Problem in generating the .rst file
- Carlos Simmerling (Tue Nov 19 2019 - 02:42:40 PST)
- Airy Sanjeev (Mon Nov 18 2019 - 21:44:33 PST)
[AMBER] Problem in Leap PDB Reading
- Yong Duan (Tue Nov 05 2019 - 21:48:40 PST)
- Robert Molt (Sun Nov 03 2019 - 16:31:04 PST)
- Yong Duan (Sun Nov 03 2019 - 15:07:38 PST)
- Robert Molt (Sun Nov 03 2019 - 14:25:08 PST)
[AMBER] Problem running production run
- Bill Ross (Sat Nov 16 2019 - 01:33:23 PST)
- Bill Ross (Sat Nov 16 2019 - 00:54:11 PST)
- Airy Sanjeev (Sat Nov 16 2019 - 00:48:04 PST)
[AMBER] Problem with ABMD simulation
- Feng Pan (Sun Nov 03 2019 - 11:39:16 PST)
- Federico Iacovelli (Sun Nov 03 2019 - 06:47:39 PST)
[AMBER] problem with MM/PB(GB)SA (Geng Dong)
- Ray Luo (Wed Nov 06 2019 - 09:28:37 PST)
- 东庚 (Tue Nov 05 2019 - 00:21:53 PST)
[AMBER] Provisional RTX2080 AMBER 18 Performance Numbers
- Daniel Roe (Mon Nov 25 2019 - 05:31:23 PST)
- Charles-Alexandre Mattelaer (Wed Nov 20 2019 - 09:55:15 PST)
- Ross Walker (Wed Nov 20 2019 - 08:53:46 PST)
- Charles-Alexandre Mattelaer (Tue Nov 19 2019 - 14:49:20 PST)
[AMBER] question about prmtop file
- David A Case (Thu Nov 14 2019 - 05:38:23 PST)
- 조준범 (Thu Nov 14 2019 - 01:22:43 PST)
[AMBER] Regarding Amber16 installation
- David Case (Tue Nov 26 2019 - 04:57:34 PST)
- dilrajl.bii.a-star.edu.sg (Tue Nov 26 2019 - 04:15:09 PST)
[AMBER] reinstallation of amber 14
- Sruthi Sudhakar (Fri Nov 01 2019 - 22:41:49 PDT)
[AMBER] RROR: I could not understand line - during US
- David A Case (Wed Nov 20 2019 - 10:46:49 PST)
- Fabian Glaser (Wed Nov 20 2019 - 06:57:09 PST)
- David A Case (Wed Nov 20 2019 - 06:04:59 PST)
- Fabian Glaser (Wed Nov 20 2019 - 05:16:10 PST)
- Bill Ross (Wed Nov 20 2019 - 03:50:16 PST)
- Fabian Glaser (Wed Nov 20 2019 - 03:44:35 PST)
- David Case (Tue Nov 19 2019 - 12:41:43 PST)
- Fabian Glaser (Tue Nov 19 2019 - 07:55:59 PST)
[AMBER] Simulation run issue
- David Case (Mon Nov 18 2019 - 04:27:52 PST)
- Sayan Poddar (Sun Nov 17 2019 - 22:03:03 PST)
[AMBER] steered md at constant force
- Wesley Michael Botello-Smith (Thu Nov 07 2019 - 16:15:58 PST)
[AMBER] strip problem in cpptraj
- Daniel Roe (Tue Nov 12 2019 - 05:52:07 PST)
[AMBER] There is an bug in how Amber preserves charge neutrality in QM/MM system when ORCA is the targeted QM tool.
- James Kress (Sat Nov 16 2019 - 08:08:40 PST)
[AMBER] tleap error
- David A Case (Fri Nov 08 2019 - 05:25:11 PST)
- Bill Ross (Fri Nov 08 2019 - 04:14:30 PST)
- MYRIAN TORRES RICO (Fri Nov 08 2019 - 04:11:38 PST)
- Akinpelu Olayinka (Fri Nov 08 2019 - 03:50:09 PST)
- MYRIAN TORRES RICO (Fri Nov 08 2019 - 03:31:45 PST)
- MYRIAN TORRES RICO (Fri Nov 08 2019 - 03:31:02 PST)
[AMBER] Tleap-complex PDB problem
- Rui Chen (Wed Nov 27 2019 - 14:01:40 PST)
- Rui Chen (Wed Nov 27 2019 - 08:52:12 PST)
- David A Case (Wed Nov 27 2019 - 08:42:31 PST)
- Rui Chen (Wed Nov 27 2019 - 07:37:19 PST)
- Lachele Foley (Tue Nov 26 2019 - 21:07:36 PST)
- Rui Chen (Tue Nov 26 2019 - 17:52:10 PST)
[AMBER] umbrella box size for protein-protein
- Fabian Glaser (Tue Nov 26 2019 - 01:38:39 PST)
[AMBER] Using NetCDF trajectory files as ParmEd structure
- Jason Swails (Wed Nov 27 2019 - 10:58:18 PST)
- Brian Radak (Wed Nov 20 2019 - 07:44:15 PST)
[AMBER] Using the polarizable FF GolP
- Lucas Bandeira (Tue Nov 12 2019 - 11:42:18 PST)
[AMBER] velocity autocorrelation
- Daniel Roe (Mon Nov 04 2019 - 11:27:17 PST)
- Ajeet Kumar Yadav (Sun Nov 03 2019 - 10:00:28 PST)
[AMBER] Workshop on Free Energy calculations in Muenster March 11-13 2020
- Vlad Cojocaru (Thu Nov 14 2019 - 02:41:29 PST)

Amber Archive Nov 2019 by subject