Amber Archive Jul 2022: by subject

[AMBER] [amber.ambermd.org: Amber22 test suite results on a cray with AMD cores and A100 GPUs]
- accuratefreeenergy--- via AMBER (Thu Jul 21 2022 - 05:45:16 PDT)
[AMBER] acetonitrile
- Kshatresh Dutta Dubey via AMBER (Thu Jun 30 2022 - 13:30:32 PDT)
[AMBER] Advice on applying restraints
- David A Case via AMBER (Mon Jul 18 2022 - 05:20:45 PDT)
- Matthew Guberman-Pfeffer via AMBER (Sat Jul 16 2022 - 12:48:01 PDT)
[AMBER] Amber minimization with packmol failing with segmentation fault
- Carlos Simmerling via AMBER (Wed Jul 20 2022 - 14:35:15 PDT)
- Carlos Simmerling via AMBER (Wed Jul 20 2022 - 14:03:10 PDT)
- Christian Seitz via AMBER (Wed Jul 20 2022 - 13:52:23 PDT)
[AMBER] AMBER20 GPU error
- Prithviraj Nandigrami via AMBER (Thu Jul 28 2022 - 14:47:32 PDT)
[AMBER] AMBER22 pmemd.cuda installation ERROR
- Erdem Yeler via AMBER (Sat Jul 30 2022 - 03:23:33 PDT)
[AMBER] AmberTools installation issue
- Rybenkov, Valentin V. via AMBER (Tue Jul 19 2022 - 10:28:01 PDT)
- Rybenkov, Valentin V. via AMBER (Tue Jul 19 2022 - 08:51:00 PDT)
- David A Case via AMBER (Tue Jul 19 2022 - 05:48:27 PDT)
- Rybenkov, Valentin V. via AMBER (Sun Jul 17 2022 - 16:15:15 PDT)
[AMBER] Ambertools21 installation problems
- Gert Kruger via AMBER (Fri Jul 22 2022 - 01:52:45 PDT)
- Gert Kruger via AMBER (Fri Jul 22 2022 - 01:09:14 PDT)
[AMBER] appending to existing files
- Dr. Anselm Horn via AMBER (Mon Jul 18 2022 - 08:19:21 PDT)
- Suchetana Gupta via AMBER (Mon Jul 18 2022 - 06:52:59 PDT)
- Suchetana Gupta via AMBER (Mon Jul 18 2022 - 06:51:25 PDT)
- Giulia Sormani via AMBER (Mon Jul 18 2022 - 06:50:00 PDT)
[AMBER] Asking about any upcoming workshop
- Suchetana Gupta via AMBER (Fri Jul 29 2022 - 11:46:21 PDT)
[AMBER] atom charge from MD trajectory
- King Wu via AMBER (Wed Jul 20 2022 - 15:44:38 PDT)
[AMBER] atomic chaos in the equilibration trajectory
- 王展峰 via AMBER (Mon Jul 04 2022 - 04:41:23 PDT)
- David A Case via AMBER (Mon Jul 04 2022 - 04:36:00 PDT)
- Dr. Anselm Horn via AMBER (Mon Jul 04 2022 - 04:28:58 PDT)
- 王展峰 via AMBER (Sat Jul 02 2022 - 18:49:40 PDT)
- James Kress via AMBER (Sat Jul 02 2022 - 10:20:29 PDT)
- Carlos Simmerling via AMBER (Sat Jul 02 2022 - 05:39:37 PDT)
- 王展峰 via AMBER (Sat Jul 02 2022 - 05:27:40 PDT)
[AMBER] build with GPU issue
- David A Case via AMBER (Wed Jul 20 2022 - 07:18:34 PDT)
- Matthew Phanchana via AMBER (Wed Jul 20 2022 - 06:32:19 PDT)
[AMBER] Constant pH MD Simulation
- Adrian Roitberg via AMBER (Fri Jul 29 2022 - 08:50:37 PDT)
- Dulal Mondal via AMBER (Fri Jul 29 2022 - 00:28:41 PDT)
- Dr. Anselm Horn via AMBER (Wed Jul 20 2022 - 01:14:39 PDT)
- Dulal Mondal via AMBER (Tue Jul 19 2022 - 23:38:40 PDT)
[AMBER] Constant pH Molecular Dynamics Simulation
- Vinicius Wilian Cruzeiro via AMBER (Sat Jul 16 2022 - 00:44:39 PDT)
- Dulal Mondal via AMBER (Sat Jul 16 2022 - 00:31:07 PDT)
[AMBER] Conversion NETCDF trajectory to other formats
- Enrico Martinez via AMBER (Fri Jul 15 2022 - 04:33:59 PDT)
[AMBER] cpptraj selection mask syntax issue during clustering
- Liao via AMBER (Thu Jul 14 2022 - 21:10:20 PDT)
- Liao via AMBER (Thu Jul 14 2022 - 20:35:23 PDT)
[AMBER] CPPTRAJ, Total H-Bond Count Question
- Marie Brut via AMBER (Fri Jul 22 2022 - 13:14:08 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:45 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:55 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:20 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:52 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:21 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:51 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:02 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:12 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:26 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:47:55 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:48 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:12 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:02 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:11 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:18 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:52 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:25 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:47:44 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:47:44 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:13 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:26 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:26 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:10 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:11 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:37 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:32 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:47:00 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:47:55 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:52 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:47:56 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:47:43 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:47:00 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:47:55 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:37 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:25 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:56 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:45 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:22 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:32 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:47:43 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:12 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:26 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:45 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:25 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:25 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:45 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:51 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:47:43 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:26 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:47:44 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:23 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:26 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:48:17 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 13:13:48 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:46:11 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:52 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:51 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:48 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:47 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:47 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:25 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:25 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:24 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:24 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:07 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:06 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:06 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:45:06 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:44:43 PDT)
- Marie Brut via AMBER (Fri Jul 22 2022 - 12:44:41 PDT)
- Daniel Roe via AMBER (Fri Jul 22 2022 - 12:41:37 PDT)
[AMBER] Creating rst7 file with CHARMM-GUI generated parm7 and pdb files (Charmm36 force field)
- Prathit Chatterjee via AMBER (Tue Jul 26 2022 - 07:32:52 PDT)
[AMBER] Different prmtop with reordered mol2 file
- Ali Morshedifard via AMBER (Wed Jul 20 2022 - 09:33:09 PDT)
- Ali Morshedi via AMBER (Tue Jul 19 2022 - 10:45:47 PDT)
[AMBER] Entropy value in MM/GBSA calculation
- SATYAJIT KHATUA via AMBER (Sat Jul 23 2022 - 01:15:50 PDT)
[AMBER] error opening OpenFabrics device
- Daniel Roe via AMBER (Fri Jul 22 2022 - 11:05:20 PDT)
- Daniel Roe via AMBER (Fri Jul 22 2022 - 07:37:16 PDT)
- Rybenkov, Valentin V. via AMBER (Fri Jul 22 2022 - 06:45:58 PDT)
[AMBER] Errors in test results for AMBER and AMBER.CUDA
- Matthew Phanchana via AMBER (Sun Jul 24 2022 - 02:39:24 PDT)
[AMBER] Fwd: Constant pH Molecular Dynamics Simulation
- Carlos Simmerling via AMBER (Mon Jul 18 2022 - 02:30:16 PDT)
- Dulal Mondal via AMBER (Sun Jul 17 2022 - 22:21:17 PDT)
[AMBER] Fwd: Entropy value in MM/GBSA calculation
- Liao via AMBER (Sun Jul 24 2022 - 06:45:19 PDT)
- SATYAJIT KHATUA via AMBER (Sat Jul 23 2022 - 23:28:01 PDT)
[AMBER] Fwd: MOPAC
- Gustavo Seabra via AMBER (Fri Jul 15 2022 - 08:21:04 PDT)
[AMBER] How to avoid SHAKE on a specific QM hydrogen atom in QM/MM simulations without compromising qmshake=1 flag
- Amit, Amit \(amit.amit--- via AMBER (Fri Jul 22 2022 - 01:46:35 PDT)
- David A Case via AMBER (Thu Jul 21 2022 - 05:27:48 PDT)
- Amit, Amit \(amit.amit--- via AMBER (Thu Jul 21 2022 - 03:38:52 PDT)
[AMBER] how to convert the eigenvector projection to a free energy landscape plotting
- Daniel Roe via AMBER (Fri Jul 22 2022 - 07:32:39 PDT)
- ning via AMBER (Tue Jul 19 2022 - 20:24:22 PDT)
[AMBER] how to use Amber patched with Plumed
- Domenico Marson via AMBER (Tue Jul 19 2022 - 03:02:09 PDT)
- Giulia Sormani via AMBER (Tue Jul 19 2022 - 02:34:58 PDT)
[AMBER] installing CUDA driver with ubuntu 20.04
- Enrico Martinez via AMBER (Tue Jul 19 2022 - 07:39:30 PDT)
- Enrico Martinez via AMBER (Tue Jul 19 2022 - 05:48:15 PDT)
[AMBER] Job Opening in the Laboratory of Computational Biology, NIH
- Daniel Roe via AMBER (Fri Jul 29 2022 - 09:31:39 PDT)
- Daniel Roe via AMBER (Thu Jul 28 2022 - 05:45:26 PDT)
[AMBER] Loading external basis sets with Gaussian to use in QMMM
- Kung, Ryan via AMBER (Tue Jul 19 2022 - 13:03:46 PDT)
- James Kress via AMBER (Tue Jul 19 2022 - 12:46:13 PDT)
[AMBER] Multiple cpu with Sander
- Enrico Martinez via AMBER (Tue Jul 19 2022 - 05:54:14 PDT)
- Enrico Martinez via AMBER (Tue Jul 19 2022 - 01:19:58 PDT)
- Dr. Anselm Horn via AMBER (Mon Jul 18 2022 - 06:02:52 PDT)
- Enrico Martinez via AMBER (Mon Jul 18 2022 - 02:43:47 PDT)
[AMBER] No PDB space group specified
- Daniel Roe via AMBER (Wed Jul 20 2022 - 08:06:05 PDT)
- David A Case via AMBER (Wed Jul 20 2022 - 07:34:50 PDT)
- Carlos Simmerling via AMBER (Tue Jul 19 2022 - 06:02:36 PDT)
- Saranya vasudevan via AMBER (Tue Jul 19 2022 - 05:53:08 PDT)
[AMBER] Number of atoms in the coordinate file does not match the parm file
- Daniel Roe via AMBER (Fri Jul 22 2022 - 07:25:46 PDT)
- Sruthi Sudhakar via AMBER (Tue Jul 19 2022 - 02:26:26 PDT)
- Carlos Simmerling via AMBER (Mon Jul 18 2022 - 07:34:26 PDT)
- Saranya vasudevan via AMBER (Mon Jul 18 2022 - 07:21:00 PDT)
[AMBER] One building error with MPI option
- ning via AMBER (Fri Jul 22 2022 - 14:42:33 PDT)
[AMBER] pairwise MMPBSA calculations
- Rana Rehan Khalid via AMBER (Fri Jul 22 2022 - 09:42:23 PDT)
[AMBER] Partial charge discrepancy between AM1-BCC small molecule charge and FF library charges
- Carlos Simmerling via AMBER (Thu Jul 28 2022 - 02:48:19 PDT)
- Liao via AMBER (Wed Jul 27 2022 - 17:05:50 PDT)
- Shiji Zhao via AMBER (Wed Jul 27 2022 - 14:24:43 PDT)
- Liao via AMBER (Wed Jul 27 2022 - 13:45:03 PDT)
[AMBER] Problems with Antechamber leading to failed minimization
- Charlotta Lebedenko via AMBER (Sun Jul 31 2022 - 13:16:15 PDT)
[AMBER] RDF vs, Coordination numbers
- Daniel Roe via AMBER (Fri Jul 22 2022 - 07:16:51 PDT)
[AMBER] regarding "watershell" command of cpptraj
- Deepshikha Ghosh 19310001 via AMBER (Sun Jul 03 2022 - 22:09:35 PDT)
[AMBER] Regarding increase in size of combine trajectory
- Daniel Roe via AMBER (Fri Jul 29 2022 - 06:06:21 PDT)
- Carlos Simmerling via AMBER (Fri Jul 29 2022 - 04:45:34 PDT)
- Rajarshi Roy via AMBER (Fri Jul 29 2022 - 04:20:11 PDT)
[AMBER] restraint definitions
- Carlos Simmerling via AMBER (Fri Jul 22 2022 - 09:39:51 PDT)
- Jordi Bujons via AMBER (Fri Jul 22 2022 - 09:38:15 PDT)
[AMBER] tleap: position of the ligand in the input pdb for protein-ligand complex
- Enrico Martinez via AMBER (Mon Jul 25 2022 - 01:43:06 PDT)
[AMBER] Unwrapping in MSD calculations with pytraj/cpptraj
- Daniel Roe via AMBER (Sun Jul 31 2022 - 07:54:14 PDT)
- Daniel Roe via AMBER (Fri Jul 29 2022 - 12:51:13 PDT)
- Daniel Roe via AMBER (Fri Jul 29 2022 - 12:49:55 PDT)
- Cianna Calia via AMBER (Mon Jul 25 2022 - 05:57:56 PDT)
[AMBER] what is hx atomtype?
- Dr. Anselm Horn via AMBER (Tue Jul 26 2022 - 00:26:27 PDT)
- Ranajit Saha via AMBER (Mon Jul 25 2022 - 18:41:31 PDT)
[AMBER] What is the compatible versions of the MKL for Amber22?
- Gao Zhenting via AMBER (Sat Jul 02 2022 - 19:09:34 PDT)
- Gao Zhenting via AMBER (Thu Jun 30 2022 - 17:45:37 PDT)
Average number of water molecules per GIST group
- Miroslav Dikov via AMBER (Thu Jul 21 2022 - 03:18:32 PDT)
- Franz Waibl via AMBER (Thu Jul 21 2022 - 03:12:44 PDT)
- Miroslav Dikov via AMBER (Thu Jul 21 2022 - 03:03:52 PDT)
- Franz Waibl via AMBER (Wed Jul 20 2022 - 05:27:18 PDT)
- Miroslav Dikov via AMBER (Wed Jul 20 2022 - 03:52:23 PDT)
CPPTRAJ, Total H-Bond Count Question
- Daniel Roe via AMBER (Fri Jul 22 2022 - 15:50:59 PDT)

Amber Archive Jul 2022 by subject