Amber Archive Nov 2023: by subject

[AMBER] [EXTERNAL] Error: Incompatible CUDA and GNU versions
- David A Case via AMBER (Wed Nov 15 2023 - 07:37:12 PST)
- Info via AMBER (Wed Nov 15 2023 - 05:36:40 PST)
- Info via AMBER (Wed Nov 15 2023 - 00:20:56 PST)
- Scott Brozell via AMBER (Tue Nov 14 2023 - 12:43:07 PST)
- Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER (Tue Nov 14 2023 - 07:49:17 PST)
[AMBER] [Sender Not Verified] Extracting MD snaphots:
- Steinbrecher, Thomas via AMBER (Mon Nov 13 2023 - 03:13:35 PST)
[AMBER] Alcohol and water binary mixture system
- Singh,Ravi via AMBER (Thu Nov 09 2023 - 22:00:41 PST)
[AMBER] amber 20 installing error on Rocky linux 9.1
- David A Case via AMBER (Thu Nov 30 2023 - 13:21:55 PST)
- 东不拉 via AMBER (Wed Nov 29 2023 - 22:43:44 PST)
[AMBER] amber trajectory visualization issue:
- Dr. Anselm Horn via AMBER (Fri Nov 03 2023 - 04:27:37 PDT)
- Kankana Bhattacharjee via AMBER (Fri Nov 03 2023 - 01:39:24 PDT)
[AMBER] Amber22/AmberTools23 install issues with pmemd.cuda
- Ravi Abrol via AMBER (Fri Nov 03 2023 - 15:54:45 PDT)
[AMBER] Announcement: Release of DOCK 6.11
- Scott Brozell via AMBER (Thu Nov 16 2023 - 12:03:40 PST)
[AMBER] antechamber error-- QMMM: System specified with odd number of electrons
- Todd Minehardt via AMBER (Thu Nov 30 2023 - 10:16:58 PST)
- Yang, Li-Yen via AMBER (Wed Nov 29 2023 - 15:24:34 PST)
[AMBER] Boost parameters for Accelerated MD
- Enrico Martinez via AMBER (Fri Nov 10 2023 - 01:28:06 PST)
[AMBER] Bug in savepdb command
- Ye Mei via AMBER (Wed Nov 01 2023 - 18:59:05 PDT)
[AMBER] Command 'combine' in 'tleap' Introducing 'TER' Between Residues
- David Case via AMBER (Sat Nov 11 2023 - 15:05:44 PST)
- David A Case via AMBER (Sat Nov 11 2023 - 09:52:07 PST)
- Yu Chen via AMBER (Fri Nov 10 2023 - 10:23:02 PST)
[AMBER] Comparing FF Energies: 99SB/14SB/19SB translated with parmed to Gromacs
- Carlos Simmerling via AMBER (Sun Nov 12 2023 - 14:24:36 PST)
- Albert Gauss via AMBER (Sun Nov 12 2023 - 13:11:37 PST)
- Carlos Simmerling via AMBER (Fri Nov 10 2023 - 08:04:26 PST)
- Albert Gauss via AMBER (Fri Nov 10 2023 - 03:30:29 PST)
[AMBER] Compilation Failures?
- Jones De Andrade via AMBER (Wed Nov 08 2023 - 18:47:00 PST)
[AMBER] Compilation Question
- David A Case via AMBER (Tue Nov 14 2023 - 20:10:49 PST)
- Matthew Guberman-Pfeffer via AMBER (Tue Nov 14 2023 - 10:52:07 PST)
[AMBER] Continuous constant pH MD
- Skanda Sastry via AMBER (Thu Nov 02 2023 - 00:31:27 PDT)
[AMBER] CpHMD question
- Matthew Guberman-Pfeffer via AMBER (Wed Nov 01 2023 - 17:32:02 PDT)
[AMBER] cpptraj mask :
- Daniel Roe via AMBER (Sun Nov 05 2023 - 11:13:00 PST)
- Kankana Bhattacharjee via AMBER (Sun Nov 05 2023 - 10:35:00 PST)
[AMBER] Cucurbituril tutorial
- Dr. Anselm Horn via AMBER (Fri Nov 03 2023 - 04:16:05 PDT)
- Hugo Yuset Samayoa Oviedo via AMBER (Thu Nov 02 2023 - 16:19:20 PDT)
[AMBER] CUDA version for AMBER22
- David A Case via AMBER (Tue Nov 14 2023 - 07:26:04 PST)
- Jones De Andrade via AMBER (Mon Nov 13 2023 - 19:49:48 PST)
- David A Case via AMBER (Mon Nov 13 2023 - 08:10:54 PST)
- Jones De Andrade via AMBER (Sun Nov 12 2023 - 01:14:01 PST)
- Todd Minehardt via AMBER (Fri Nov 10 2023 - 05:59:36 PST)
- Renato Araujo via AMBER (Fri Nov 10 2023 - 02:25:54 PST)
- Mingxuan Jiang via AMBER (Fri Nov 10 2023 - 01:52:55 PST)
[AMBER] cyclic peptide in water box
- Dr. Anselm Horn via AMBER (Mon Nov 13 2023 - 01:05:39 PST)
- Sepideh Jafari via AMBER (Mon Nov 13 2023 - 00:29:35 PST)
[AMBER] Enquiry about the Best way to Simulate Phosphorylated Tyrosines
- Dr. Anselm Horn via AMBER (Sat Nov 11 2023 - 00:06:08 PST)
- Mingxuan Jiang via AMBER (Fri Nov 10 2023 - 11:31:46 PST)
[AMBER] Error during re weighting in GaMD
- Skanda Sastry via AMBER (Thu Nov 02 2023 - 09:01:21 PDT)
- Munazzah Fatima Ansari via AMBER (Thu Nov 02 2023 - 02:36:26 PDT)
[AMBER] Error in MMPBSA
- Pedro Guillem via AMBER (Wed Nov 15 2023 - 04:31:08 PST)
- Bill Miller III via AMBER (Wed Nov 15 2023 - 04:28:50 PST)
- VERONICA MARTIN HERNANDEZ via AMBER (Wed Nov 15 2023 - 04:10:27 PST)
[AMBER] Error: Incompatible CUDA and GNU versions
- Info via AMBER (Tue Nov 14 2023 - 07:39:37 PST)
[AMBER] Extracting MD snaphots:
- Kankana Bhattacharjee via AMBER (Mon Nov 13 2023 - 01:34:29 PST)
[AMBER] fcc_metals.lib not found
- Setyanto Md via AMBER (Sat Nov 11 2023 - 18:33:09 PST)
[AMBER] Fwd: pocket volume calculation
- Sruthi Sudhakar via AMBER (Wed Nov 29 2023 - 07:18:13 PST)
[AMBER] help with parallel GPUs for GaMD
- Martinez Noa, Yisel via AMBER (Tue Nov 07 2023 - 15:40:22 PST)
[AMBER] Holding Host-Guest COM constant during binding enthalpy MD
- Gert Kruger via AMBER (Tue Nov 07 2023 - 21:44:15 PST)
- Carlos Simmerling via AMBER (Tue Nov 07 2023 - 15:49:50 PST)
- Meyer, Olivia \(meyerok\) via AMBER (Tue Nov 07 2023 - 11:00:49 PST)
[AMBER] In which order do dihedral types override in main parameter sets?
- David A Case via AMBER (Mon Nov 13 2023 - 08:39:00 PST)
- He, Amy via AMBER (Sun Nov 12 2023 - 01:46:26 PST)
[AMBER] Issues in Modified nucleotide parametrization using Antechamber and Parmchk2
- He, Amy via AMBER (Thu Nov 16 2023 - 20:05:54 PST)
- Priyasha Majee via AMBER (Thu Nov 16 2023 - 05:24:08 PST)
[AMBER] Looking for a force field with ester linkages between protein chains permitted.
- David A Case via AMBER (Thu Nov 30 2023 - 13:24:53 PST)
- David Cowburn via AMBER (Thu Nov 30 2023 - 10:13:35 PST)
[AMBER] MCPB, negative force constant?
- Pengfei Li via AMBER (Fri Nov 17 2023 - 12:07:34 PST)
[AMBER] MMGBSA descomposition
- Pedro Guillem via AMBER (Thu Nov 16 2023 - 06:52:47 PST)
- VERONICA MARTIN HERNANDEZ via AMBER (Tue Nov 14 2023 - 07:24:56 PST)
[AMBER] MMPBSA mask
- Bill Miller III via AMBER (Wed Nov 08 2023 - 09:12:52 PST)
- VERONICA MARTIN HERNANDEZ via AMBER (Wed Nov 08 2023 - 07:45:12 PST)
[AMBER] Model a protein with Tyrosine anion
- Xiangwei Zhu via AMBER (Mon Nov 13 2023 - 07:21:53 PST)
- Carlos Simmerling via AMBER (Thu Nov 09 2023 - 12:08:50 PST)
- Xiangwei Zhu via AMBER (Wed Nov 08 2023 - 14:20:37 PST)
- Carlos Simmerling via AMBER (Wed Nov 08 2023 - 08:55:16 PST)
- Xiangwei Zhu via AMBER (Mon Nov 06 2023 - 12:48:30 PST)
- Carlos Simmerling via AMBER (Fri Nov 03 2023 - 04:39:01 PDT)
- Dr. Anselm Horn via AMBER (Fri Nov 03 2023 - 04:11:18 PDT)
- Todd Minehardt via AMBER (Thu Nov 02 2023 - 15:11:21 PDT)
- Xiangwei Zhu via AMBER (Thu Nov 02 2023 - 13:34:48 PDT)
[AMBER] Modifying a bias .nc file for ABMD
- Michael Bruist via AMBER (Fri Nov 03 2023 - 18:45:17 PDT)
[AMBER] No build when downloading amber22
- Daniel Roe via AMBER (Thu Nov 16 2023 - 07:41:16 PST)
- Johannes Loeffler via AMBER (Thu Nov 16 2023 - 07:21:00 PST)
[AMBER] PBSA error
- Ray Luo via AMBER (Wed Nov 15 2023 - 18:35:47 PST)
- Matthew Guberman-Pfeffer via AMBER (Wed Nov 15 2023 - 18:02:03 PST)
- Ray Luo via AMBER (Wed Nov 15 2023 - 17:52:33 PST)
- Matthew Guberman-Pfeffer via AMBER (Wed Nov 15 2023 - 16:11:40 PST)
- Ray Luo via AMBER (Wed Nov 15 2023 - 15:29:59 PST)
- Matthew Guberman-Pfeffer via AMBER (Wed Nov 15 2023 - 12:43:23 PST)
[AMBER] pocket volume calculation
- Sruthi Sudhakar via AMBER (Tue Nov 28 2023 - 05:14:22 PST)
[AMBER] Polarizabilitiy Calculations
- David A Case via AMBER (Mon Nov 13 2023 - 08:35:13 PST)
- Gillispie, Nathan via AMBER (Sun Nov 12 2023 - 15:27:05 PST)
[AMBER] problem about pmemd.cuda.MPI
- Dr. Anselm Horn via AMBER (Fri Nov 10 2023 - 01:16:07 PST)
- ning via AMBER (Thu Nov 09 2023 - 17:03:34 PST)
- ning via AMBER (Thu Nov 09 2023 - 16:45:59 PST)
- PUJAN AJMERA via AMBER (Thu Nov 09 2023 - 16:54:24 PST)
[AMBER] Problem in Conversion from .nc to mdcrd file
- Carlos Simmerling via AMBER (Sun Nov 12 2023 - 14:27:10 PST)
- Todd Minehardt via AMBER (Sun Nov 12 2023 - 14:18:39 PST)
- Singh,Ravi via AMBER (Sun Nov 12 2023 - 14:11:59 PST)
[AMBER] Query regarding pi-pi stacking interaction
- David A Case via AMBER (Fri Nov 03 2023 - 07:35:24 PDT)
- Sourav Bhowmik via AMBER (Wed Nov 01 2023 - 00:41:17 PDT)
[AMBER] questions about AmberTools installation from source
- Damas Joao CHST via AMBER (Tue Nov 07 2023 - 04:27:10 PST)
[AMBER] R: Inquiry about PMEMD.CUDA availability in non-commercial license
- David A Case via AMBER (Sun Nov 19 2023 - 10:16:40 PST)
[AMBER] Rdf calculation
- Jenny 148 via AMBER (Mon Nov 06 2023 - 00:26:40 PST)
[AMBER] Rdf calculation:
- SATYAJIT KHATUA via AMBER (Mon Nov 06 2023 - 00:33:06 PST)
- SATYAJIT KHATUA via AMBER (Sun Nov 05 2023 - 23:59:13 PST)
- SATYAJIT KHATUA via AMBER (Sun Nov 05 2023 - 23:54:19 PST)
- SATYAJIT KHATUA via AMBER (Sun Nov 05 2023 - 23:44:29 PST)
- SATYAJIT KHATUA via AMBER (Sun Nov 05 2023 - 23:42:23 PST)
- SATYAJIT KHATUA via AMBER (Sun Nov 05 2023 - 23:18:01 PST)
- SATYAJIT KHATUA via AMBER (Sun Nov 05 2023 - 23:02:55 PST)
- SATYAJIT KHATUA via AMBER (Sun Nov 05 2023 - 22:53:50 PST)
- SATYAJIT KHATUA via AMBER (Sun Nov 05 2023 - 22:42:58 PST)
- Kankana Bhattacharjee via AMBER (Sun Nov 05 2023 - 22:18:23 PST)
[AMBER] reference potential alchemical calculation
- Pietro Vidossich via AMBER (Tue Oct 31 2023 - 18:34:42 PDT)
[AMBER] Regarding lie command- linear interaction energy
- Jenny 148 via AMBER (Wed Nov 01 2023 - 02:03:46 PDT)
[AMBER] Regarding maximum molecular system size
- David A Case via AMBER (Mon Nov 13 2023 - 08:06:57 PST)
- Carlos Simmerling via AMBER (Sun Nov 12 2023 - 03:40:23 PST)
- Singh,Ravi via AMBER (Sat Nov 11 2023 - 22:40:26 PST)
- Todd Minehardt via AMBER (Fri Nov 10 2023 - 14:40:21 PST)
- David A Case via AMBER (Fri Nov 10 2023 - 12:42:16 PST)
- Singh,Ravi via AMBER (Fri Nov 10 2023 - 03:09:07 PST)
[AMBER] Reproduce a Simulation
- Skanda Sastry via AMBER (Thu Nov 30 2023 - 20:17:52 PST)
- Skanda Sastry via AMBER (Thu Nov 30 2023 - 20:16:02 PST)
[AMBER] Residue type in input pdb
- Prithviraj Nandigrami via AMBER (Tue Nov 14 2023 - 13:46:27 PST)
[AMBER] RESP charge fitting error in MCPB.py
- Kandhan, Palanisamy via AMBER (Thu Nov 02 2023 - 10:54:46 PDT)
[AMBER] RESP fitting in solvent
- FyD via AMBER (Tue Nov 28 2023 - 09:35:55 PST)
- Jakub Jakubec via AMBER (Fri Nov 17 2023 - 07:30:06 PST)
[AMBER] Split a .nc file
- Carlos Simmerling via AMBER (Sun Nov 12 2023 - 03:38:11 PST)
- Singh,Ravi via AMBER (Sun Nov 12 2023 - 03:20:54 PST)
[AMBER] Thioester Bond Parameters
- Dr. Anselm Horn via AMBER (Mon Nov 06 2023 - 09:46:29 PST)
- Shah, Tejas V. via AMBER (Mon Nov 06 2023 - 08:44:02 PST)
[AMBER] Updated Benchmarks including new ADA series GPUs
- Ross Walker via AMBER (Wed Nov 15 2023 - 08:44:20 PST)
[AMBER] Use of IPolQ scheme for macromolecular complexes
- Jakub Jakubec via AMBER (Tue Nov 14 2023 - 02:16:20 PST)
[AMBER] Would AMBER suit my purpose?
- Mignolet, Alex via AMBER (Thu Nov 30 2023 - 13:51:23 PST)
[AMBER] 回复: Query regarding pi-pi stacking interaction
- 郭家藩 via AMBER (Thu Nov 02 2023 - 00:10:06 PDT)

Amber Archive Nov 2023 by subject