Amber Archive Aug 2022: by subject

[AMBER] [AmberTools22 installation] I installed AmberTools22 on my Windows WSL2 but there is no sander.MPI
- David A Case via AMBER (Thu Aug 25 2022 - 08:38:49 PDT)
- 이동언 via AMBER (Wed Aug 24 2022 - 19:35:58 PDT)
[AMBER] Amber 20 - error with PI parallel install
- David A Case via AMBER (Mon Aug 01 2022 - 18:10:00 PDT)
- Gert Kruger via AMBER (Mon Aug 01 2022 - 05:04:49 PDT)
[AMBER] AMBER NME caps not recognized
- Carlos Simmerling via AMBER (Thu Aug 04 2022 - 12:28:30 PDT)
- Carlos Simmerling via AMBER (Thu Aug 04 2022 - 10:31:30 PDT)
- Dr. Anselm Horn via AMBER (Thu Aug 04 2022 - 09:51:07 PDT)
- David A Case via AMBER (Thu Aug 04 2022 - 09:40:50 PDT)
- Debarati DasGupta via AMBER (Thu Aug 04 2022 - 08:39:36 PDT)
- Kellon Belfon via AMBER (Thu Aug 04 2022 - 05:49:42 PDT)
- Valentin Hörschinger via AMBER (Thu Aug 04 2022 - 01:18:27 PDT)
- Dr. Anselm Horn via AMBER (Wed Aug 03 2022 - 22:33:04 PDT)
[AMBER] AMBER to LAMMPS Conversion
- Cianna Calia via AMBER (Fri Aug 05 2022 - 14:18:16 PDT)
[AMBER] AMBER tutorial 5.4 original publication?
- Maria Nagan via AMBER (Mon Aug 29 2022 - 05:22:06 PDT)
- Michael Shokhen via AMBER (Mon Aug 29 2022 - 01:21:02 PDT)
[AMBER] AMBER/ORCA for QM/MM
- Adrian Roitberg via AMBER (Wed Aug 17 2022 - 10:22:37 PDT)
- James Kress via AMBER (Wed Aug 17 2022 - 10:16:59 PDT)
- 许茂峰 via AMBER (Mon Aug 15 2022 - 18:56:44 PDT)
[AMBER] Amber21: rism3d.periodic/1ahoa test fails for number of CPUs > 2
- tluchko via AMBER (Tue Aug 02 2022 - 13:22:22 PDT)
- Vlad via AMBER (Mon Aug 01 2022 - 19:16:27 PDT)
[AMBER] AMBER22 failed during installation on CUDA and centos 7.9
- Rybenkov, Valentin V. via AMBER (Wed Aug 24 2022 - 18:27:36 PDT)
- David A Case via AMBER (Wed Aug 24 2022 - 17:34:34 PDT)
- Hamza, Adel via AMBER (Wed Aug 24 2022 - 09:15:56 PDT)
[AMBER] Amber22 incompatible CUDA version - how to solve this?
- Markowska (Thu Aug 18 2022 - 04:06:07 PDT)
[AMBER] Amber22 installation
- David A Case via AMBER (Tue Aug 23 2022 - 05:08:56 PDT)
- Rybenkov, Valentin V. via AMBER (Mon Aug 22 2022 - 13:40:31 PDT)
- David A Case via AMBER (Mon Aug 01 2022 - 18:13:43 PDT)
[AMBER] analysis of the Hydrogen bonds
- Enrico Martinez via AMBER (Wed Aug 31 2022 - 07:26:15 PDT)
[AMBER] any ideas on this?
- Debarati DasGupta via AMBER (Thu Aug 04 2022 - 08:43:54 PDT)
[AMBER] Automatic glycan bonds in tleap?
- Dr. Anselm Horn via AMBER (Fri Aug 26 2022 - 07:57:31 PDT)
- Daniel Roe via AMBER (Fri Aug 26 2022 - 07:37:04 PDT)
- Dr. Anselm Horn via AMBER (Fri Aug 26 2022 - 07:31:20 PDT)
- Daniel Roe via AMBER (Fri Aug 26 2022 - 06:54:39 PDT)
- Dr. Anselm Horn via AMBER (Fri Aug 26 2022 - 05:35:24 PDT)
[AMBER] Backbone decomposition values all zero upon successful MMPBSA.py run
- Miroslav Suruzhon via AMBER (Fri Aug 19 2022 - 03:28:31 PDT)
- Bill Miller III via AMBER (Thu Aug 18 2022 - 13:57:37 PDT)
- Miroslav Suruzhon via AMBER (Wed Aug 17 2022 - 05:24:32 PDT)
[AMBER] Bond energy discrepancy between amber simulated results and cpptraj
- Daniel Roe via AMBER (Tue Aug 30 2022 - 07:29:07 PDT)
- Carlos Simmerling via AMBER (Mon Aug 29 2022 - 06:22:35 PDT)
- Ruihan Zhou via AMBER (Mon Aug 29 2022 - 05:27:56 PDT)
[AMBER] Bridge hydrogen bonds
- Umesh Roy via AMBER (Tue Aug 16 2022 - 07:35:02 PDT)
[AMBER] Confusion of difference EPB value of me and tutorial of MMPBSA.py
- Ray Luo via AMBER (Sat Aug 27 2022 - 10:34:27 PDT)
- Dongxiao Yue \(LHS, 220059036\) via AMBER (Fri Aug 26 2022 - 21:03:07 PDT)
[AMBER] Conversion NETCDF trajectory to other formats
- Daniel Roe via AMBER (Mon Aug 08 2022 - 07:10:09 PDT)
- Daniel Roe via AMBER (Mon Aug 08 2022 - 05:31:04 PDT)
[AMBER] CpHMD
- David A Case via AMBER (Mon Aug 29 2022 - 13:20:55 PDT)
- Adrian Roitberg via AMBER (Mon Aug 29 2022 - 13:07:21 PDT)
- Dulal Mondal via AMBER (Mon Aug 29 2022 - 06:58:00 PDT)
[AMBER] CPPTRAJ: sign convention for dihedral angles!!
- Daniel Roe via AMBER (Fri Aug 19 2022 - 07:30:32 PDT)
- Cenk Andac via AMBER (Fri Aug 19 2022 - 00:28:21 PDT)
[AMBER] Creating rst7 file with CHARMM-GUI generated parm7 and pdb files (Charmm36 force field)
- Daniel Roe via AMBER (Mon Aug 08 2022 - 07:15:08 PDT)
[AMBER] Dealing with DU atom types in parmchk2
- He, Amy via AMBER (Sat Aug 27 2022 - 19:33:46 PDT)
[AMBER] Does Parmed tiMerge accept all ambmasks?
- Wong, Sergio E. via AMBER (Thu Aug 25 2022 - 16:04:20 PDT)
[AMBER] Dumping different trajectories at time
- angad sharma via AMBER (Fri Aug 26 2022 - 02:55:48 PDT)
[AMBER] error with parmed in MCPB and pdb4amber
- Nishad Ankita Rudal via AMBER (Fri Aug 19 2022 - 21:01:39 PDT)
[AMBER] Error: an illegal memory access was encountered launching kernel kNLSkinTest
- Christian Seitz via AMBER (Wed Aug 31 2022 - 10:37:55 PDT)
- David A Case via AMBER (Tue Aug 23 2022 - 05:12:11 PDT)
- Christian Seitz via AMBER (Tue Aug 23 2022 - 00:17:43 PDT)
[AMBER] Extracting residue number from a given resname - Pytraj
- Hai Nguyen via AMBER (Fri Aug 12 2022 - 17:28:02 PDT)
[AMBER] Frames are zero for prmtop file
- Carlos Simmerling via AMBER (Mon Aug 29 2022 - 09:15:24 PDT)
- Sneha Kandapal via AMBER (Mon Aug 29 2022 - 09:07:38 PDT)
[AMBER] Fwd: Extracting residue number from a given resname - Pytraj
- Carlos Navarro via AMBER (Mon Aug 08 2022 - 07:17:43 PDT)
[AMBER] Fwd: MOPAC
- Gustavo Seabra via AMBER (Mon Aug 08 2022 - 10:37:43 PDT)
[AMBER] gremd_acyc keyword for H-REMD
- accuratefreeenergy--- via AMBER (Tue Aug 16 2022 - 19:52:08 PDT)
- Brian Radak via AMBER (Tue Aug 16 2022 - 11:00:04 PDT)
- Adrian Roitberg via AMBER (Tue Aug 16 2022 - 08:44:05 PDT)
- Zhuoran Long via AMBER (Mon Aug 15 2022 - 13:42:18 PDT)
- Adrian Roitberg via AMBER (Mon Aug 15 2022 - 12:59:38 PDT)
- Zhuoran Long via AMBER (Mon Aug 15 2022 - 12:48:57 PDT)
[AMBER] How can I install AmberTools22?
- David A Case via AMBER (Thu Aug 04 2022 - 10:01:11 PDT)
- 清川慎介 via AMBER (Thu Aug 04 2022 - 07:44:48 PDT)
[AMBER] How to convert the dihedral dataset into a probability mass function plotting
- Daniel Roe via AMBER (Wed Aug 24 2022 - 07:55:27 PDT)
- Carlos Simmerling via AMBER (Wed Aug 24 2022 - 07:11:40 PDT)
- ning via AMBER (Wed Aug 24 2022 - 07:05:51 PDT)
[AMBER] how to convert the eigenvector projection to a free energy landscape plotting
- Daniel Roe via AMBER (Fri Aug 12 2022 - 09:41:58 PDT)
[AMBER] How to do multiple 'watershell' analysis in cpptraj
- Daniel Roe via AMBER (Tue Aug 16 2022 - 04:59:21 PDT)
- XP Chen via AMBER (Tue Aug 16 2022 - 02:07:33 PDT)
[AMBER] How to extract last snapshot from the trajectory with re imaging?
- Enrico Martinez via AMBER (Tue Aug 16 2022 - 01:19:39 PDT)
- Enrico Martinez via AMBER (Fri Aug 12 2022 - 08:18:53 PDT)
[AMBER] How to generate PCA and porcupine analysis for crystal structure from X-ray study using AMBER 16
- priya murugan via AMBER (Mon Aug 22 2022 - 02:15:04 PDT)
[AMBER] Hydrogen bonding !
- angad sharma via AMBER (Mon Aug 29 2022 - 00:21:51 PDT)
[AMBER] idecomp in PMEMD?
- Matthew Guberman-Pfeffer via AMBER (Thu Aug 25 2022 - 06:23:49 PDT)
- David A Case via AMBER (Thu Aug 25 2022 - 06:04:36 PDT)
- Matthew Guberman-Pfeffer via AMBER (Tue Aug 23 2022 - 22:25:31 PDT)
[AMBER] Inquiry regarding pmemd and gem.pmemd
- Elvis Martis via AMBER (Wed Aug 03 2022 - 19:15:52 PDT)
- Jiaqiao Zhou via AMBER (Wed Aug 03 2022 - 18:33:48 PDT)
[AMBER] installing CUDA driver with ubuntu 20.04
- Enrico Martinez via AMBER (Fri Aug 05 2022 - 06:24:35 PDT)
- Enrico Martinez via AMBER (Fri Aug 05 2022 - 03:37:40 PDT)
- Enrico Martinez via AMBER (Thu Aug 04 2022 - 06:33:28 PDT)
- Enrico Martinez via AMBER (Thu Aug 04 2022 - 01:15:31 PDT)
- David A Case via AMBER (Wed Aug 03 2022 - 10:12:53 PDT)
- Enrico Martinez via AMBER (Wed Aug 03 2022 - 09:05:02 PDT)
[AMBER] makeANG_RST
- David A Case via AMBER (Tue Aug 30 2022 - 14:14:08 PDT)
- Osman, Roman via AMBER (Tue Aug 30 2022 - 12:54:28 PDT)
[AMBER] MD simulation of complexes with Ag+ ions in Chimera
- David A Case via AMBER (Mon Aug 29 2022 - 13:13:23 PDT)
- Dr. Anselm Horn via AMBER (Mon Aug 29 2022 - 01:17:14 PDT)
- 幅田揚一 via AMBER (Mon Aug 29 2022 - 00:24:54 PDT)
[AMBER] method to change residue numbering for amber masks after production
- Daniel Roe via AMBER (Mon Aug 08 2022 - 06:33:56 PDT)
- Daniel Roe via AMBER (Mon Aug 08 2022 - 06:32:02 PDT)
- Murray, Makay via AMBER (Fri Aug 05 2022 - 10:41:19 PDT)
[AMBER] MMPBSA with implicit radii error
- King Wu via AMBER (Fri Aug 12 2022 - 16:50:46 PDT)
- King Wu via AMBER (Fri Aug 12 2022 - 12:05:50 PDT)
[AMBER] nvcc fatal : Unsupported gpu architecture 'compute_75'
- Erdem Yeler via AMBER (Wed Aug 17 2022 - 06:59:13 PDT)
- Erdem Yeler via AMBER (Fri Aug 12 2022 - 10:26:07 PDT)
[AMBER] one error from MMPBSA.py
- David A Case via AMBER (Wed Aug 31 2022 - 06:55:18 PDT)
- laura zhang via AMBER (Tue Aug 30 2022 - 18:05:50 PDT)
[AMBER] one question about setting up scmask and timask
- laura zhang via AMBER (Mon Aug 22 2022 - 12:21:36 PDT)
- laura zhang via AMBER (Sun Aug 21 2022 - 05:10:55 PDT)
[AMBER] pmemd.cuda crash
- Enrico Martinez via AMBER (Mon Aug 08 2022 - 07:28:02 PDT)
- Enrico Martinez via AMBER (Fri Aug 05 2022 - 06:26:06 PDT)
- Enrico Martinez via AMBER (Fri Aug 05 2022 - 01:24:31 PDT)
- Enrico Martinez via AMBER (Thu Aug 04 2022 - 08:58:42 PDT)
[AMBER] pmemd.mpi crashes
- David A Case via AMBER (Fri Aug 26 2022 - 05:48:51 PDT)
- Rybenkov, Valentin V. via AMBER (Thu Aug 25 2022 - 22:31:02 PDT)
[AMBER] problem with MMPBSA.py.mpi
- Enrico Martinez via AMBER (Mon Aug 08 2022 - 07:05:25 PDT)
- Enrico Martinez via AMBER (Mon Aug 08 2022 - 02:24:52 PDT)
- Enrico Martinez via AMBER (Fri Aug 05 2022 - 07:40:04 PDT)
[AMBER] problem: TIP3P model with tleap in Amber22
- David A Case via AMBER (Thu Aug 25 2022 - 05:48:03 PDT)
- Carlos Simmerling via AMBER (Tue Aug 23 2022 - 19:43:38 PDT)
- 王怡文 via AMBER (Tue Aug 23 2022 - 19:22:41 PDT)
[AMBER] Problems with Antechamber leading to failed minimization
- David A Case via AMBER (Mon Aug 01 2022 - 05:45:57 PDT)
[AMBER] Query about Constant pH MD simulation
- Dulal Mondal via AMBER (Thu Aug 18 2022 - 07:10:27 PDT)
[AMBER] Query regarding calculation of peptide-peptide hydrogen bond lifetime
- Daniel Roe via AMBER (Tue Aug 30 2022 - 11:06:41 PDT)
- RIMJHIM MORAL via AMBER (Tue Aug 30 2022 - 08:51:35 PDT)
[AMBER] Query regarding glycoprotein RMSD calculation
- Carlos Simmerling via AMBER (Thu Aug 25 2022 - 03:25:09 PDT)
- Sayan Poddar via AMBER (Thu Aug 25 2022 - 00:02:33 PDT)
[AMBER] Question about cpptraj analysis
- Daniel Roe via AMBER (Fri Aug 19 2022 - 07:21:53 PDT)
- Enrico Martinez via AMBER (Tue Aug 09 2022 - 02:24:41 PDT)
[AMBER] Question about histograms analysis with multiple values
- Suchetana Gupta via AMBER (Mon Aug 22 2022 - 10:52:50 PDT)
- Suchetana Gupta via AMBER (Tue Aug 16 2022 - 14:41:25 PDT)
[AMBER] Question about NAB package usage in AMBER
- Qinsi Xiong via AMBER (Tue Aug 30 2022 - 16:42:41 PDT)
[AMBER] question about run TI with REMD (amber20)
- 费俊文 via AMBER (Mon Aug 08 2022 - 01:29:49 PDT)
[AMBER] Questions about MMPBSA.py
- Enrico Martinez via AMBER (Thu Aug 18 2022 - 00:31:53 PDT)
- Enrico Martinez via AMBER (Wed Aug 10 2022 - 02:18:11 PDT)
- Enrico Martinez via AMBER (Tue Aug 09 2022 - 07:31:53 PDT)
- Enrico Martinez via AMBER (Tue Aug 09 2022 - 00:12:39 PDT)
- Enrico Martinez via AMBER (Mon Aug 08 2022 - 07:48:26 PDT)
[AMBER] Restraints with replica exchange MD
- Carlos Simmerling via AMBER (Thu Aug 04 2022 - 07:33:25 PDT)
- Juliette Newell via AMBER (Thu Aug 04 2022 - 07:14:37 PDT)
[AMBER] running pmemd.cuda with 2 GPUs
- Enrico Martinez via AMBER (Thu Aug 04 2022 - 03:45:21 PDT)
- Enrico Martinez via AMBER (Thu Aug 04 2022 - 03:10:51 PDT)
[AMBER] Software announcement: Release of PUPIL 4.0
- Juan Torras Costa via AMBER (Thu Aug 04 2022 - 02:04:25 PDT)
[AMBER] Some basic questions about cpptraj
- Enrico Martinez via AMBER (Thu Aug 11 2022 - 03:58:22 PDT)
[AMBER] The file contained 6 atoms not in residue templates
- Rodrigo Galindo-Murillo via AMBER (Wed Aug 17 2022 - 09:32:11 PDT)
- Sneha Kandapal via AMBER (Wed Aug 17 2022 - 09:21:02 PDT)
[AMBER] Thermodynamic integration for covalently bound ligands
- Ali Morshedifard via AMBER (Sun Aug 21 2022 - 23:06:14 PDT)
[AMBER] Thermodynamic Integration simulation in pmemd.cuda
- Suguna Sakkiah via AMBER (Mon Aug 22 2022 - 16:33:23 PDT)
[AMBER] TI and periodic boundaries?
- Matthew Guberman-Pfeffer via AMBER (Sun Aug 21 2022 - 21:58:13 PDT)
[AMBER] timask vs. scmask question
- Matthew Guberman-Pfeffer via AMBER (Mon Aug 29 2022 - 14:25:34 PDT)
- David A Case via AMBER (Mon Aug 29 2022 - 13:37:44 PDT)
- Matthew Guberman-Pfeffer via AMBER (Mon Aug 29 2022 - 06:58:52 PDT)
[AMBER] Timelagged Independent Component plots with Amber?
- Suchetana Gupta via AMBER (Wed Aug 31 2022 - 11:51:13 PDT)
- Suchetana Gupta via AMBER (Wed Aug 31 2022 - 10:04:20 PDT)
- Valentin Hörschinger via AMBER (Wed Aug 31 2022 - 05:27:25 PDT)
- Suchetana Gupta via AMBER (Tue Aug 30 2022 - 11:10:28 PDT)
- Suchetana Gupta via AMBER (Fri Aug 26 2022 - 16:08:20 PDT)
[AMBER] TiMerge doesn't work, or what am I doing wrong?
- Matthew Guberman-Pfeffer via AMBER (Thu Aug 25 2022 - 17:06:03 PDT)
- Josiah Bones via AMBER (Thu Aug 25 2022 - 15:06:36 PDT)
- Matthew Guberman-Pfeffer via AMBER (Thu Aug 18 2022 - 07:40:58 PDT)
[AMBER] tleap: position of the ligand in the input pdb for protein-ligand complex
- Daniel Roe via AMBER (Mon Aug 08 2022 - 07:18:34 PDT)
[AMBER] Unwrapping in MSD calculations with pytraj/cpptraj
- Daniel Roe via AMBER (Tue Aug 16 2022 - 04:53:24 PDT)
- Daniel Roe via AMBER (Wed Aug 10 2022 - 13:06:20 PDT)
- Daniel Roe via AMBER (Tue Aug 09 2022 - 15:42:28 PDT)
- Daniel Roe via AMBER (Tue Aug 09 2022 - 12:44:18 PDT)
- Daniel Roe via AMBER (Tue Aug 09 2022 - 11:43:36 PDT)
- Daniel Roe via AMBER (Tue Aug 09 2022 - 07:26:10 PDT)
AMBER22 failed during installation on CUDA and centos 7.9
- Hamza, Adel via AMBER (Fri Aug 26 2022 - 06:58:19 PDT)
timask vs. scmask question
- Ali Morshedifard via AMBER (Tue Aug 30 2022 - 15:05:59 PDT)
- David A Case via AMBER (Tue Aug 30 2022 - 14:09:51 PDT)
- Matthew Guberman-Pfeffer via AMBER (Mon Aug 29 2022 - 18:36:24 PDT)

Amber Archive Aug 2022 by subject