Amber Archive Sep 2022: by subject

[AMBER] [amber.ambermd.org: Fwd: Failed TI heating simulation (RBFE) using Amber22]
- accuratefreeenergy--- via AMBER (Sat Sep 10 2022 - 10:33:20 PDT)
[AMBER] [NEB] Convergence criteria
- Madhur Aggarwal via AMBER (Wed Sep 21 2022 - 06:23:32 PDT)
[AMBER] Amber 22 Installation
- Scott Brozell via AMBER (Tue Sep 27 2022 - 14:22:41 PDT)
- Nagar, Hemant via AMBER (Tue Sep 27 2022 - 13:42:27 PDT)
[AMBER] AMBER 22 installation with CUDA support
- SATYAJIT KHATUA via AMBER (Sun Sep 04 2022 - 04:02:12 PDT)
- SATYAJIT KHATUA via AMBER (Sat Sep 03 2022 - 10:37:06 PDT)
[AMBER] Amber patched with Plumed, units conversion
- Giulia Sormani via AMBER (Wed Sep 07 2022 - 01:40:28 PDT)
[AMBER] AMBER22 INSTALLATION
- Edivaldo Rodrigues via AMBER (Tue Sep 06 2022 - 14:51:57 PDT)
- Edivaldo Rodrigues via AMBER (Tue Sep 06 2022 - 14:10:55 PDT)
[AMBER] AMBER22 INSTALLING
- Edivaldo Rodrigues via AMBER (Tue Sep 06 2022 - 12:34:38 PDT)
- David A Case via AMBER (Tue Sep 06 2022 - 12:09:05 PDT)
- Edivaldo Rodrigues via AMBER (Tue Sep 06 2022 - 11:59:57 PDT)
[AMBER] Amber22, no DV/DL value with option gti_lam_sch
- Domenico Marson via AMBER (Thu Sep 29 2022 - 11:02:37 PDT)
- Domenico Marson via AMBER (Tue Sep 27 2022 - 07:54:35 PDT)
- Domenico Marson via AMBER (Fri Sep 23 2022 - 11:10:10 PDT)
[AMBER] any parameter settings in paramfit for a short restrained minimization before fitting?
- Cenk Andac via AMBER (Fri Sep 30 2022 - 11:14:26 PDT)
- Cenk Andac via AMBER (Thu Sep 22 2022 - 15:33:18 PDT)
- Cenk Andac via AMBER (Thu Sep 22 2022 - 10:50:53 PDT)
- Cenk Andac via AMBER (Thu Sep 22 2022 - 10:39:34 PDT)
[AMBER] ATOMIC NUMBER section in prmtop file - sulfur atom in ligand is -1?
- He, Amy via AMBER (Tue Sep 06 2022 - 13:01:22 PDT)
- He, Amy via AMBER (Mon Sep 05 2022 - 10:21:17 PDT)
- David A Case via AMBER (Mon Sep 05 2022 - 06:14:12 PDT)
- He, Amy via AMBER (Sun Sep 04 2022 - 21:52:38 PDT)
[AMBER] Autocorrelation time
- Charo del Genio via AMBER (Sun Sep 11 2022 - 22:48:00 PDT)
- He, Amy via AMBER (Sun Sep 11 2022 - 14:19:55 PDT)
[AMBER] Bump "Distance restraint and periodic boundary conditions"
- Demian Riccardi via AMBER (Fri Sep 16 2022 - 09:45:53 PDT)
[AMBER] Calculation of dihedral angle using cpptraj in CpHMD simulation
- Carlos Simmerling via AMBER (Thu Sep 01 2022 - 06:45:32 PDT)
- Daniel Roe via AMBER (Thu Sep 01 2022 - 06:38:34 PDT)
- Dulal Mondal via AMBER (Thu Sep 01 2022 - 06:31:14 PDT)
[AMBER] Can restraints on protein substitute membrane?
- Rafał Madaj via AMBER (Mon Sep 26 2022 - 10:59:57 PDT)
[AMBER] crash o the pmemd.cuda
- Enrico Martinez via AMBER (Mon Sep 05 2022 - 00:45:26 PDT)
- Enrico Martinez via AMBER (Fri Sep 02 2022 - 01:02:10 PDT)
[AMBER] Data set math gives "size is 0"
- Rodrigo Galindo-Murillo via AMBER (Thu Sep 22 2022 - 21:44:10 PDT)
- Chunsheng Lin via AMBER (Thu Sep 22 2022 - 21:03:32 PDT)
[AMBER] Define angle between planes of monomers in a hexamer
- David A Case via AMBER (Thu Sep 29 2022 - 10:13:26 PDT)
- Rosellen, Martin via AMBER (Thu Sep 29 2022 - 06:28:52 PDT)
[AMBER] Error in calculation of Binding free energy !
- angad sharma via AMBER (Mon Sep 12 2022 - 02:19:53 PDT)
[AMBER] Error: an illegal memory access was encountered launching kernel kNLSkinTest
- Daniel Roe via AMBER (Thu Sep 01 2022 - 10:08:05 PDT)
- Christian Seitz via AMBER (Thu Sep 01 2022 - 08:59:14 PDT)
- David A Case via AMBER (Thu Sep 01 2022 - 04:43:11 PDT)
[AMBER] FATAL Error Issue
- Carlos Simmerling via AMBER (Mon Sep 26 2022 - 02:33:09 PDT)
- Amara Jabeen via AMBER (Mon Sep 26 2022 - 01:06:00 PDT)
- Tamsila Parveen via AMBER (Mon Sep 26 2022 - 00:56:49 PDT)
- David A Case via AMBER (Wed Sep 21 2022 - 05:19:32 PDT)
- Tamsila Parveen via AMBER (Wed Sep 21 2022 - 01:12:02 PDT)
[AMBER] Force field parameters for non canonical amino acids
- Suchetana Gupta via AMBER (Thu Sep 15 2022 - 17:53:33 PDT)
- Suchetana Gupta via AMBER (Thu Sep 15 2022 - 17:10:03 PDT)
[AMBER] Fwd: AMBER 22 installation with CUDA support
- SATYAJIT KHATUA via AMBER (Mon Sep 05 2022 - 10:09:58 PDT)
- SATYAJIT KHATUA via AMBER (Mon Sep 05 2022 - 09:53:50 PDT)
- SATYAJIT KHATUA via AMBER (Mon Sep 05 2022 - 09:02:04 PDT)
[AMBER] Fwd: CPPTRAJ: sign convention for dihedral angles!!
- Cenk Andac via AMBER (Sat Sep 03 2022 - 07:15:37 PDT)
- Cenk Andac via AMBER (Sat Sep 03 2022 - 07:14:21 PDT)
[AMBER] Fwd: Failed TI heating simulation (RBFE) using Amber22
- Pengfei Li via AMBER (Sun Sep 04 2022 - 18:59:56 PDT)
[AMBER] Histidine tautomer state and pKa?
- Carlos Simmerling via AMBER (Sat Sep 03 2022 - 20:01:53 PDT)
- Liao via AMBER (Sat Sep 03 2022 - 18:53:15 PDT)
[AMBER] How to determine the optimal number of cluster in cpptraj or other something
- SATYAJIT KHATUA via AMBER (Fri Sep 09 2022 - 08:00:51 PDT)
- Carlos Simmerling via AMBER (Fri Sep 09 2022 - 07:56:52 PDT)
- Rybenkov, Valentin V. via AMBER (Fri Sep 09 2022 - 07:56:21 PDT)
- ning via AMBER (Fri Sep 09 2022 - 07:48:34 PDT)
[AMBER] interpreting paramfit results
- Barış KURT via AMBER (Wed Sep 21 2022 - 02:13:34 PDT)
- David A Case via AMBER (Mon Sep 19 2022 - 07:35:35 PDT)
- Cenk Andac via AMBER (Sun Sep 18 2022 - 01:18:49 PDT)
- Cenk Andac via AMBER (Sun Sep 18 2022 - 01:04:19 PDT)
- David A Case via AMBER (Fri Sep 16 2022 - 08:18:55 PDT)
- Cenk Andac via AMBER (Thu Sep 15 2022 - 13:41:11 PDT)
[AMBER] MM-PBSA calculations
- Marcelo Andrade Chagas via AMBER (Thu Sep 22 2022 - 10:20:39 PDT)
[AMBER] MMPBSA.py.MPI not bulit in Amber20
- Yoshitaka Moriwaki via AMBER (Tue Sep 20 2022 - 22:04:42 PDT)
- Adrian Roitberg via AMBER (Mon Sep 19 2022 - 10:55:14 PDT)
- amirhossein taghavi via AMBER (Sun Sep 18 2022 - 11:43:07 PDT)
[AMBER] Modifying Parameters in parm7
- David A Case via AMBER (Fri Sep 30 2022 - 17:52:40 PDT)
- Collin Nisler via AMBER (Fri Sep 30 2022 - 13:27:38 PDT)
[AMBER] Nanodisk preparation with Packmol-memgen?
- Gustavo Seabra via AMBER (Fri Sep 02 2022 - 09:44:19 PDT)
[AMBER] Normal mode analysis for entropy calculation in MM/GBSA
- David A Case via AMBER (Sat Sep 24 2022 - 06:23:16 PDT)
- He, Amy via AMBER (Fri Sep 16 2022 - 06:04:36 PDT)
[AMBER] NUMEXTRA Error
- David A Case via AMBER (Fri Sep 30 2022 - 08:14:33 PDT)
- Qi Wang via AMBER (Thu Sep 29 2022 - 13:19:37 PDT)
[AMBER] On the skipping of first frames in mmpbsa calculations
- Enrico Martinez via AMBER (Mon Sep 12 2022 - 05:25:53 PDT)
[AMBER] paramfit and EQM - EVDW-ELE(MM) energy difference
- Cenk Andac via AMBER (Wed Sep 07 2022 - 11:55:07 PDT)
- Cenk Andac via AMBER (Wed Sep 07 2022 - 05:38:01 PDT)
- Cenk Andac via AMBER (Tue Sep 06 2022 - 08:11:40 PDT)
[AMBER] Possible memory leaks in Amber22
- Franz Waibl via AMBER (Tue Sep 20 2022 - 05:44:47 PDT)
[AMBER] problem of the protonation of the ligand
- Enrico Martinez via AMBER (Tue Sep 06 2022 - 09:25:43 PDT)
- sribone via AMBER (Tue Sep 06 2022 - 08:58:02 PDT)
- Enrico Martinez via AMBER (Tue Sep 06 2022 - 08:46:04 PDT)
- Enrico Martinez via AMBER (Mon Sep 05 2022 - 02:38:12 PDT)
- Enrico Martinez via AMBER (Mon Sep 05 2022 - 00:43:32 PDT)
- Enrico Martinez via AMBER (Fri Sep 02 2022 - 09:57:33 PDT)
[AMBER] Problem with TI minimization
- David Case via AMBER (Fri Sep 02 2022 - 13:24:55 PDT)
- David A Case via AMBER (Fri Sep 02 2022 - 13:17:12 PDT)
- Matthew Guberman-Pfeffer via AMBER (Thu Sep 01 2022 - 20:03:20 PDT)
[AMBER] problems in using autoimage
- Giulia Sormani via AMBER (Wed Sep 28 2022 - 05:08:51 PDT)
- David A Case via AMBER (Fri Sep 23 2022 - 09:26:45 PDT)
- Daniel Roe via AMBER (Thu Sep 22 2022 - 06:53:54 PDT)
- David A Case via AMBER (Wed Sep 21 2022 - 18:08:07 PDT)
- Daniel Roe via AMBER (Wed Sep 21 2022 - 11:49:00 PDT)
- Giulia Sormani via AMBER (Wed Sep 21 2022 - 09:04:04 PDT)
[AMBER] Question about NAB package usage in AMBER
- David A Case via AMBER (Thu Sep 01 2022 - 12:42:08 PDT)
[AMBER] Raw RDF exceeds total number of waters?
- Daniel Roe via AMBER (Thu Sep 08 2022 - 12:59:39 PDT)
- Matthew Guberman-Pfeffer via AMBER (Thu Sep 08 2022 - 11:54:44 PDT)
[AMBER] Segmentation fault when starting parmchk2 for an artificial nucleotide
- Jiaan Zhu via AMBER (Sun Sep 25 2022 - 13:31:44 PDT)
- Jiaan Zhu via AMBER (Sat Sep 24 2022 - 18:55:06 PDT)
- David A Case via AMBER (Sat Sep 24 2022 - 06:30:54 PDT)
- Jiaan Zhu via AMBER (Thu Sep 22 2022 - 07:27:02 PDT)
- Jiaan Zhu via AMBER (Sun Sep 04 2022 - 13:18:13 PDT)
- David A Case via AMBER (Sun Sep 04 2022 - 06:04:25 PDT)
- Jiaan Zhu via AMBER (Sun Sep 04 2022 - 03:46:32 PDT)
[AMBER] Test result of amber22 installation
- Yeng-Tseng Wang via AMBER (Thu Sep 08 2022 - 05:15:47 PDT)
- Yeng-Tseng Wang via AMBER (Tue Sep 06 2022 - 17:11:48 PDT)
- David A Case via AMBER (Tue Sep 06 2022 - 12:17:35 PDT)
- Dulal Mondal via AMBER (Mon Sep 05 2022 - 06:08:06 PDT)
[AMBER] Unwrapping in MSD calculations with pytraj/cpptraj
- Daniel Roe via AMBER (Mon Sep 12 2022 - 15:38:52 PDT)
- Daniel Roe via AMBER (Fri Sep 09 2022 - 12:56:28 PDT)
- Daniel Roe via AMBER (Tue Sep 06 2022 - 07:45:43 PDT)
[AMBER] Use of parmed to generate modified prmtop file
- Sruthi Sudhakar via AMBER (Fri Sep 23 2022 - 23:08:38 PDT)
[AMBER] Using CHARMM-GUI FF Convert from CHARMM to Amber With Ligand
- Collin Nisler via AMBER (Mon Sep 26 2022 - 07:41:32 PDT)
- David A Case via AMBER (Mon Sep 26 2022 - 05:45:51 PDT)
[AMBER] Warning in free energy output file
- Carlos Simmerling via AMBER (Wed Sep 28 2022 - 08:56:13 PDT)
- Sayan Poddar via AMBER (Wed Sep 28 2022 - 08:47:58 PDT)
[AMBER] What to use to build nanodisc system?
- Gustavo Seabra via AMBER (Mon Sep 19 2022 - 13:15:50 PDT)
[AMBER] Which molecule should the environment feel, in TI simulations?
- David A Case via AMBER (Thu Sep 29 2022 - 06:47:56 PDT)
- Liao via AMBER (Wed Sep 28 2022 - 15:39:14 PDT)
Problem with TI minimization
- Matthew Guberman-Pfeffer via AMBER (Fri Sep 02 2022 - 20:39:58 PDT)
Raw RDF exceeds total number of waters?
- Daniel Roe via AMBER (Tue Sep 13 2022 - 05:21:54 PDT)

Amber Archive Sep 2022 by subject