Amber Archive Mar 2023: by subject

[AMBER] [Sender Not Verified] CPPTRAJ, mindset xyz components
- Steinbrecher, Thomas via AMBER (Fri Mar 10 2023 - 01:37:36 PST)
[AMBER] [Sender Not Verified] Problem with Zn2+ ion in a pdb file for a receptor-ligand complex
- Siavoush Dastmalchi via AMBER (Fri Mar 10 2023 - 23:38:28 PST)
- Steinbrecher, Thomas via AMBER (Tue Mar 07 2023 - 03:32:30 PST)
[AMBER] Adding organic molecules to the water box
- Carlos Simmerling via AMBER (Wed Mar 01 2023 - 04:52:01 PST)
- Dhanush Ramesh Anitha via AMBER (Wed Mar 01 2023 - 04:44:36 PST)
[AMBER] Address the nonphysical coordination bond between Zn and the other atoms in the active site while using MCPB.py
- Deepthi Jose via AMBER (Tue Mar 14 2023 - 21:51:01 PDT)
[AMBER] Amber 22 Nvidia GPU Benchmarks
- Vincenzo Maria D'Amore via AMBER (Tue Mar 21 2023 - 13:23:02 PDT)
- Ross Walker via AMBER (Tue Mar 21 2023 - 13:12:41 PDT)
- Ross Walker via AMBER (Fri Mar 17 2023 - 08:03:11 PDT)
- Vincenzo D'Amore via AMBER (Fri Mar 17 2023 - 03:45:01 PDT)
[AMBER] AMBER Parameters for LYS-GLY Isopeptide bond
- Robin Betz via AMBER (Wed Mar 15 2023 - 21:24:47 PDT)
- Shah, Tejas V. via AMBER (Wed Mar 15 2023 - 20:50:17 PDT)
[AMBER] AMBER18 pmemd.cuda installation on NVIDIA 3080
- Daniel Hall via AMBER (Thu Mar 23 2023 - 07:42:52 PDT)
- Ross Walker via AMBER (Thu Mar 23 2023 - 07:37:49 PDT)
- Ross Walker via AMBER (Thu Mar 23 2023 - 07:22:01 PDT)
- Daniel Hall via AMBER (Thu Mar 23 2023 - 07:26:58 PDT)
- Daniel Hall via AMBER (Thu Mar 23 2023 - 07:16:09 PDT)
[AMBER] Amber21 help!
- David A Case via AMBER (Wed Mar 22 2023 - 08:02:38 PDT)
- Monsurat M. Lawal via AMBER (Tue Mar 21 2023 - 17:40:56 PDT)
- Ramírez, Gustavo via AMBER (Tue Mar 21 2023 - 16:10:27 PDT)
[AMBER] amber22 installation error cusparse_LinearSolvers.cu
- ABDELATIF MESSAOUDI via AMBER (Mon Mar 06 2023 - 13:16:51 PST)
- David A Case via AMBER (Mon Mar 06 2023 - 10:35:57 PST)
- Madhavan Jayaraman via AMBER (Fri Mar 03 2023 - 21:54:34 PST)
[AMBER] Amber22 installation on Ubuntu 22.04
- David A Case via AMBER (Wed Mar 15 2023 - 07:11:55 PDT)
- Bansal, Prateek Dinesh via AMBER (Fri Mar 10 2023 - 08:00:07 PST)
[AMBER] ambpdb -c flag is unknown
- David Case via AMBER (Sat Mar 11 2023 - 05:47:38 PST)
- SATYAJIT KHATUA via AMBER (Sat Mar 11 2023 - 01:19:46 PST)
- Siavoush Dastmalchi via AMBER (Sat Mar 11 2023 - 01:00:29 PST)
[AMBER] An update on Folding at Work-From-Home and Fast AF MD
- Jason Swails via AMBER (Fri Mar 31 2023 - 05:33:21 PDT)
[AMBER] Antechamber preparation of the system docked to two identical ligands
- Enrico Martinez via AMBER (Thu Mar 23 2023 - 05:17:05 PDT)
- Dr. Anselm Horn via AMBER (Tue Mar 21 2023 - 09:27:41 PDT)
- Enrico Martinez via AMBER (Tue Mar 21 2023 - 09:00:10 PDT)
[AMBER] ATP parameters for simulation compatible with Amber19SB force field?
- Gustavo Seabra via AMBER (Mon Mar 06 2023 - 09:35:05 PST)
[AMBER] auto-correlation using cpptraj
- Daniel Roe via AMBER (Sun Mar 12 2023 - 07:47:17 PDT)
- Dulal Mondal via AMBER (Sat Mar 11 2023 - 07:16:24 PST)
[AMBER] CIC Annual Meeting during WiFo 2023 – Call for Papers – Deadline extended to 16.03.
- Guessregen, Stefan /DE via AMBER (Tue Mar 07 2023 - 07:40:23 PST)
[AMBER] Constant pH MD simulation of non-protein systems
- Vinicius Wilian Cruzeiro via AMBER (Tue Mar 07 2023 - 10:37:00 PST)
- MADHUSMITA DEVI via AMBER (Tue Mar 07 2023 - 10:33:07 PST)
[AMBER] Constant pH pair list overflow. Increase MAX_TITR_RES in constantph.F90; recompile
- X (Mon Mar 13 2023 - 04:23:33 PDT)
[AMBER] CPPTRAJ, mindset xyz components
- Daniel Roe via AMBER (Thu Mar 09 2023 - 11:11:21 PST)
- Matthew Guberman-Pfeffer via AMBER (Thu Mar 09 2023 - 10:20:29 PST)
[AMBER] Distance between residues: Too many iteration in routine
- He, Amy via AMBER (Thu Mar 02 2023 - 10:29:28 PST)
- Hocine EL KHAOUDI ENYOURY via AMBER (Thu Mar 02 2023 - 10:26:45 PST)
- Hocine EL KHAOUDI ENYOURY via AMBER (Thu Mar 02 2023 - 10:19:13 PST)
- He, Amy via AMBER (Thu Mar 02 2023 - 10:22:55 PST)
[AMBER] Distance matrix
- Dulal Mondal via AMBER (Sat Mar 04 2023 - 21:02:56 PST)
[AMBER] Electrostatic Energy !
- angad sharma via AMBER (Thu Mar 02 2023 - 03:22:14 PST)
[AMBER] Error in running nmode showing ZeroDivisionError: division by zero
- Jason Swails via AMBER (Fri Mar 31 2023 - 05:36:35 PDT)
- Nishad Ankita Rudal via AMBER (Fri Mar 31 2023 - 03:29:30 PDT)
[AMBER] Error on tiMerge in parmed
- Osman, Roman via AMBER (Fri Mar 03 2023 - 09:35:42 PST)
[AMBER] Error when running Amber on GPU: cudaIpcOpenMemHandle failed on gpu->pbPeerAccumulator Handle invalid argument
- Siwakorn Sukharom via AMBER (Sat Mar 04 2023 - 22:42:26 PST)
[AMBER] Extended ZN force field (EZAFF)?
- Kenneth Huang via AMBER (Wed Mar 08 2023 - 13:18:45 PST)
[AMBER] ff19SB + OPC3 water model
- Carlos Simmerling via AMBER (Mon Mar 27 2023 - 07:08:01 PDT)
- Vlad Cojocaru via AMBER (Mon Mar 27 2023 - 07:00:39 PDT)
[AMBER] Free energy simulation with the MMPBSA
- SATYAJIT KHATUA via AMBER (Thu Mar 02 2023 - 19:59:25 PST)
- ABDELATIF MESSAOUDI via AMBER (Thu Mar 02 2023 - 15:03:36 PST)
[AMBER] Fwd: Distance matrix
- Carlos Simmerling via AMBER (Tue Mar 07 2023 - 03:53:19 PST)
- Dulal Mondal via AMBER (Mon Mar 06 2023 - 20:50:22 PST)
[AMBER] H++ server got hacker attack.
- Setyanto Md via AMBER (Sat Mar 25 2023 - 08:49:34 PDT)
[AMBER] Half-harmonic restraint
- Carlos Simmerling via AMBER (Tue Mar 21 2023 - 14:11:39 PDT)
- Carlos Simmerling via AMBER (Tue Mar 21 2023 - 11:59:12 PDT)
- Jose Luis Guerra via AMBER (Tue Mar 21 2023 - 11:09:40 PDT)
[AMBER] Help needed with thermodynamic integration: Collision of cations in binding energy calculation
- David A Case via AMBER (Mon Mar 20 2023 - 10:36:41 PDT)
- He, Amy via AMBER (Sun Mar 19 2023 - 07:25:01 PDT)
- Kevin Mei via AMBER (Thu Mar 16 2023 - 20:28:57 PDT)
- He, Amy via AMBER (Thu Mar 16 2023 - 09:27:06 PDT)
- Mei Kevin via AMBER (Thu Mar 16 2023 - 09:06:15 PDT)
[AMBER] How to shield charged side chain from ion binding / would you transform a counterion in TI simulations?
- Carlos Simmerling via AMBER (Tue Mar 07 2023 - 15:20:37 PST)
- Carlos Simmerling via AMBER (Tue Mar 07 2023 - 15:06:45 PST)
- Carlos Simmerling via AMBER (Tue Mar 07 2023 - 12:39:42 PST)
- He, Amy via AMBER (Tue Mar 07 2023 - 10:46:01 PST)
[AMBER] Implementing string method in AMBER
- Jose Luis Guerra via AMBER (Sat Mar 25 2023 - 17:40:44 PDT)
- Souvik Dey via AMBER (Thu Mar 23 2023 - 09:09:27 PDT)
- David A Case via AMBER (Wed Mar 22 2023 - 07:56:58 PDT)
- Souvik Dey via AMBER (Tue Mar 21 2023 - 09:36:38 PDT)
[AMBER] Implicit solvent MD for membrane proteins
- Ravi Abrol via AMBER (Fri Mar 24 2023 - 23:42:56 PDT)
- Ravi Abrol via AMBER (Tue Mar 07 2023 - 18:45:47 PST)
[AMBER] Is it Ok to upgrade NVidia driver
- David A Case via AMBER (Mon Mar 06 2023 - 10:31:18 PST)
- Broto Santoso via AMBER (Fri Mar 03 2023 - 18:12:42 PST)
[AMBER] Is Potential ABMD Memory Leak Fixed In AMBER22?
- Owen O'Reilly via AMBER (Wed Mar 22 2023 - 20:20:08 PDT)
[AMBER] Issues with simulating 5'-phosphorylated RNA strands
- Maria Nagan via AMBER (Tue Mar 21 2023 - 17:13:44 PDT)
- Harvey Dale via AMBER (Tue Mar 21 2023 - 16:28:05 PDT)
[AMBER] life time calculation
- Daniel Roe via AMBER (Mon Mar 20 2023 - 12:00:50 PDT)
- Dulal Mondal via AMBER (Mon Mar 20 2023 - 11:44:12 PDT)
[AMBER] MCPB.py step 2 KeyError with crystal water
- Jasmin Güven via AMBER (Tue Mar 28 2023 - 06:45:44 PDT)
[AMBER] MMPBSA problem
- Bill Miller III via AMBER (Wed Mar 01 2023 - 12:01:23 PST)
- Bill Miller III via AMBER (Wed Mar 01 2023 - 07:50:50 PST)
[AMBER] Net charge of a POPC molecule is not zero
- Kosuke Tachibana via AMBER (Sat Mar 18 2023 - 01:45:28 PDT)
- Dickson, Callum via AMBER (Wed Mar 15 2023 - 07:22:59 PDT)
- Kosuke Tachibana via AMBER (Mon Mar 13 2023 - 10:27:59 PDT)
[AMBER] Nonphysical coordination bond between Zn and the other atoms in the active site while using MCPB.py
- SHAHID P via AMBER (Fri Mar 17 2023 - 05:03:47 PDT)
[AMBER] ParmEd problem: LJ12_6_4 +pTYR. Error: Could not find parameters for ATOM_TYPE CG
- Jason Swails via AMBER (Mon Mar 20 2023 - 13:26:45 PDT)
- Paiardi, Giulia via AMBER (Fri Mar 17 2023 - 04:56:09 PDT)
[AMBER] PCA warning
- Daniel Roe via AMBER (Wed Mar 15 2023 - 07:02:29 PDT)
- Sayan Poddar via AMBER (Wed Mar 15 2023 - 06:53:54 PDT)
[AMBER] pmemd.cuda test possible failure
- Freddy Bernal via AMBER (Wed Mar 01 2023 - 03:34:28 PST)
[AMBER] Problem loading pdb4amber in Amber 20
- Joanna Michelle E. Chua via AMBER (Tue Mar 21 2023 - 06:36:49 PDT)
- David A Case via AMBER (Tue Mar 21 2023 - 06:21:39 PDT)
- Hai Nguyen via AMBER (Fri Mar 17 2023 - 15:16:25 PDT)
- Hai Nguyen via AMBER (Fri Mar 17 2023 - 14:35:21 PDT)
- Joanna Michelle E. Chua via AMBER (Fri Mar 17 2023 - 09:16:55 PDT)
[AMBER] problem with MMPBSA.py
- Siavoush Dastmalchi via AMBER (Wed Mar 15 2023 - 03:35:37 PDT)
- Siavoush Dastmalchi via AMBER (Wed Mar 15 2023 - 00:22:33 PDT)
[AMBER] Problem with running production with pmemd.cuda
- Carlos Simmerling via AMBER (Mon Mar 20 2023 - 16:14:14 PDT)
- Joanna Michelle E. Chua via AMBER (Mon Mar 20 2023 - 15:47:43 PDT)
[AMBER] Problem with Zn ion a protein-ligand complex
- Siavoush Dastmalchi via AMBER (Mon Mar 06 2023 - 21:59:44 PST)
- Siavoush Dastmalchi via AMBER (Mon Mar 06 2023 - 11:04:38 PST)
[AMBER] Problem with Zn ion in pdb file
- Siavoush Dastmalchi via AMBER (Mon Mar 06 2023 - 01:48:20 PST)
[AMBER] Problem with Zn2+ ion in a pdb file for a receptor-ligand complex
- Siavoush Dastmalchi via AMBER (Tue Mar 07 2023 - 02:31:56 PST)
[AMBER] Query regarding distance calculation
- Daniel Roe via AMBER (Tue Mar 21 2023 - 18:30:51 PDT)
- Saikat Pal via AMBER (Tue Mar 21 2023 - 09:04:21 PDT)
[AMBER] Query regarding restarting the replica exchange molecular dynamics simulation
- Munazzah Fatima Ansari via AMBER (Wed Mar 22 2023 - 05:21:02 PDT)
[AMBER] Request for Assistance with AMBER Output File for RMSF Analysis
- Daniel Roe via AMBER (Wed Mar 15 2023 - 07:00:06 PDT)
- Daniel Roe via AMBER (Sun Mar 12 2023 - 06:25:37 PDT)
- Daniel Roe via AMBER (Fri Mar 10 2023 - 12:26:38 PST)
- Roy, Rajarshi via AMBER (Fri Mar 10 2023 - 12:20:57 PST)
[AMBER] RTX6000-ADA Benchmarks
- Ross Walker via AMBER (Tue Mar 21 2023 - 13:09:21 PDT)
[AMBER] Running QM/MM in parallel; multi-sander
- Vilhelm Ekberg via AMBER (Wed Mar 08 2023 - 05:54:38 PST)
[AMBER] RuntimeError in Pytraj
- Hai Nguyen via AMBER (Wed Mar 08 2023 - 09:54:11 PST)
- Hai Nguyen via AMBER (Thu Mar 02 2023 - 11:13:44 PST)
- maryam ghorbaninia via AMBER (Thu Mar 02 2023 - 11:04:26 PST)
[AMBER] Segmentation fault when running pmemd.cuda.MPI in Amber22 with plumed 2.8.2
- Tien Phan via AMBER (Wed Mar 29 2023 - 14:38:13 PDT)
[AMBER] Significant slow down with NMR restraints
- Kenneth Huang via AMBER (Thu Mar 16 2023 - 10:49:30 PDT)
- Carlos Simmerling via AMBER (Thu Mar 16 2023 - 10:57:16 PDT)
- Ava Waggett via AMBER (Thu Mar 16 2023 - 10:09:20 PDT)
[AMBER] steered MD of anion transporters through membrane
- Jordi Bujons via AMBER (Wed Mar 01 2023 - 03:01:38 PST)
[AMBER] Terminal phosphates with RNA
- Piia Bartos via AMBER (Wed Mar 01 2023 - 02:12:12 PST)
[AMBER] The latest version of miniconda3-py3.10 cannot successfully install amber20 with cmake
- wangjianing_mail via AMBER (Wed Mar 08 2023 - 08:39:00 PST)
[AMBER] Thermodynamic Integration DV/DL output
- Songyan Xia \(LHS, 118010341\) via AMBER (Sun Mar 26 2023 - 20:01:39 PDT)
- David A Case via AMBER (Sun Mar 26 2023 - 05:26:48 PDT)
- Songyan Xia \(LHS, 118010341\) via AMBER (Fri Mar 24 2023 - 18:37:44 PDT)
- David A Case via AMBER (Fri Mar 24 2023 - 18:24:22 PDT)
- Songyan Xia \(LHS, 118010341\) via AMBER (Thu Mar 23 2023 - 02:47:00 PDT)
[AMBER] TI calculation regarding charge change in TI region.
- Fanyu Zhao via AMBER (Mon Mar 27 2023 - 01:13:24 PDT)
[AMBER] time correlation
- David A Case via AMBER (Tue Mar 21 2023 - 06:17:44 PDT)
- Dulal Mondal via AMBER (Mon Mar 20 2023 - 23:08:19 PDT)
[AMBER] Updates for sander python interface?
- Brian Radak via AMBER (Tue Mar 21 2023 - 11:02:52 PDT)
[AMBER] Volmap using cpptraj
- Hai Nguyen via AMBER (Fri Mar 31 2023 - 07:21:53 PDT)
- Dulal Mondal via AMBER (Fri Mar 31 2023 - 07:19:10 PDT)
[AMBER] Water Survival Probability
- Daniel Roe via AMBER (Sun Mar 12 2023 - 07:50:39 PDT)
- ABDUL BASIT via AMBER (Fri Mar 10 2023 - 20:28:11 PST)
[AMBER] Wrong distance calculation with cpptraj
- Daniel Roe via AMBER (Tue Mar 14 2023 - 10:55:29 PDT)
- Azurmendi, Hugo via AMBER (Tue Mar 14 2023 - 08:12:51 PDT)
[AMBER] 回复: Free energy simulation with the MMPBSA
- Huang ZiJian via AMBER (Thu Mar 02 2023 - 20:17:52 PST)
[AMBER] 回复: MCPB.py step 2 KeyError with crystal water
- Huang ZiJian via AMBER (Tue Mar 28 2023 - 19:52:25 PDT)
[AMBER] 回复: 回复: Electrostatic Energy !
- Huang ZiJian via AMBER (Thu Mar 02 2023 - 22:14:35 PST)
Antechamber preparation of the system docked to two identical ligands
- Enrico Martinez via AMBER (Tue Mar 28 2023 - 06:47:40 PDT)
- Enrico Martinez via AMBER (Tue Mar 28 2023 - 03:02:11 PDT)
- Enrico Martinez via AMBER (Tue Mar 28 2023 - 02:52:15 PDT)
- Enrico Martinez via AMBER (Mon Mar 27 2023 - 09:58:33 PDT)
- Enrico Martinez via AMBER (Mon Mar 27 2023 - 09:12:54 PDT)
- Enrico Martinez via AMBER (Mon Mar 27 2023 - 09:01:43 PDT)
- Enrico Martinez via AMBER (Mon Mar 27 2023 - 06:28:21 PDT)
- Enrico Martinez via AMBER (Fri Mar 24 2023 - 04:37:33 PDT)
- Enrico Martinez via AMBER (Fri Mar 24 2023 - 02:21:00 PDT)
CPPTRAJ, mindist xyz components
- Daniel Roe via AMBER (Fri Mar 10 2023 - 06:10:59 PST)
Issues with simulating 5'-phosphorylated RNA strands
- Harvey Dale via AMBER (Thu Mar 23 2023 - 07:57:12 PDT)
- David A Case via AMBER (Wed Mar 22 2023 - 08:07:02 PDT)
Running QM/MM in parallel; multi-sander
- David A Case via AMBER (Wed Mar 15 2023 - 07:07:08 PDT)

Amber Archive Mar 2023 by subject