Amber Archive Nov 2023: by date

Tuesday, 31 October 2023
- [AMBER] reference potential alchemical calculation Pietro Vidossich via AMBER
Wednesday, 1 November 2023
- [AMBER] Query regarding pi-pi stacking interaction Sourav Bhowmik via AMBER
- [AMBER] Regarding lie command- linear interaction energy Jenny 148 via AMBER
- [AMBER] CpHMD question Matthew Guberman-Pfeffer via AMBER
- [AMBER] Bug in savepdb command Ye Mei via AMBER
Thursday, 2 November 2023
- [AMBER] 回复: Query regarding pi-pi stacking interaction 郭家藩 via AMBER
- [AMBER] Continuous constant pH MD Skanda Sastry via AMBER
- [AMBER] Error during re weighting in GaMD Munazzah Fatima Ansari via AMBER
- [AMBER] Error during re weighting in GaMD Skanda Sastry via AMBER
- [AMBER] RESP charge fitting error in MCPB.py Kandhan, Palanisamy via AMBER
- [AMBER] Model a protein with Tyrosine anion Xiangwei Zhu via AMBER
- Re: [AMBER] Model a protein with Tyrosine anion Todd Minehardt via AMBER
- [AMBER] Cucurbituril tutorial Hugo Yuset Samayoa Oviedo via AMBER
Friday, 3 November 2023
- [AMBER] amber trajectory visualization issue: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Model a protein with Tyrosine anion Dr. Anselm Horn via AMBER
- Re: [AMBER] Cucurbituril tutorial Dr. Anselm Horn via AMBER
- Re: [AMBER] amber trajectory visualization issue: Dr. Anselm Horn via AMBER
- Re: [AMBER] Model a protein with Tyrosine anion Carlos Simmerling via AMBER
- Re: [AMBER] Query regarding pi-pi stacking interaction David A Case via AMBER
- [AMBER] Amber22/AmberTools23 install issues with pmemd.cuda Ravi Abrol via AMBER
- [AMBER] Modifying a bias .nc file for ABMD Michael Bruist via AMBER
Sunday, 5 November 2023
- [AMBER] cpptraj mask : Kankana Bhattacharjee via AMBER
- Re: [AMBER] cpptraj mask : Daniel Roe via AMBER
- [AMBER] Rdf calculation: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Rdf calculation: SATYAJIT KHATUA via AMBER
- Re: [AMBER] Rdf calculation: SATYAJIT KHATUA via AMBER
- Re: [AMBER] Rdf calculation: SATYAJIT KHATUA via AMBER
- Re: [AMBER] Rdf calculation: SATYAJIT KHATUA via AMBER
- Re: [AMBER] Rdf calculation: SATYAJIT KHATUA via AMBER
- Re: [AMBER] Rdf calculation: SATYAJIT KHATUA via AMBER
- Re: [AMBER] Rdf calculation: SATYAJIT KHATUA via AMBER
- Re: [AMBER] Rdf calculation: SATYAJIT KHATUA via AMBER
Monday, 6 November 2023
- [AMBER] Rdf calculation Jenny 148 via AMBER
- Re: [AMBER] Rdf calculation: SATYAJIT KHATUA via AMBER
- [AMBER] Thioester Bond Parameters Shah, Tejas V. via AMBER
- Re: [AMBER] Thioester Bond Parameters Dr. Anselm Horn via AMBER
- Re: [AMBER] Model a protein with Tyrosine anion Xiangwei Zhu via AMBER
Tuesday, 7 November 2023
- Re: [AMBER] questions about AmberTools installation from source Damas Joao CHST via AMBER
- [AMBER] Holding Host-Guest COM constant during binding enthalpy MD Meyer, Olivia \(meyerok\) via AMBER
- [AMBER] help with parallel GPUs for GaMD Martinez Noa, Yisel via AMBER
- Re: [AMBER] Holding Host-Guest COM constant during binding enthalpy MD Carlos Simmerling via AMBER
- Re: [AMBER] Holding Host-Guest COM constant during binding enthalpy MD Gert Kruger via AMBER
Wednesday, 8 November 2023
- [AMBER] MMPBSA mask VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] Model a protein with Tyrosine anion Carlos Simmerling via AMBER
- Re: [AMBER] MMPBSA mask Bill Miller III via AMBER
- Re: [AMBER] Model a protein with Tyrosine anion Xiangwei Zhu via AMBER
- [AMBER] Compilation Failures? Jones De Andrade via AMBER
Thursday, 9 November 2023
- Re: [AMBER] Model a protein with Tyrosine anion Carlos Simmerling via AMBER
- Re: [AMBER] problem about pmemd.cuda.MPI PUJAN AJMERA via AMBER
- [AMBER] problem about pmemd.cuda.MPI ning via AMBER
- Re: [AMBER] problem about pmemd.cuda.MPI ning via AMBER
- [AMBER] Alcohol and water binary mixture system Singh,Ravi via AMBER
Friday, 10 November 2023
- Re: [AMBER] problem about pmemd.cuda.MPI Dr. Anselm Horn via AMBER
- [AMBER] Boost parameters for Accelerated MD Enrico Martinez via AMBER
- [AMBER] CUDA version for AMBER22 Mingxuan Jiang via AMBER
- Re: [AMBER] CUDA version for AMBER22 Renato Araujo via AMBER
- [AMBER] Regarding maximum molecular system size Singh,Ravi via AMBER
- [AMBER] Comparing FF Energies: 99SB/14SB/19SB translated with parmed to Gromacs Albert Gauss via AMBER
- Re: [AMBER] CUDA version for AMBER22 Todd Minehardt via AMBER
- Re: [AMBER] Comparing FF Energies: 99SB/14SB/19SB translated with parmed to Gromacs Carlos Simmerling via AMBER
- [AMBER] Command 'combine' in 'tleap' Introducing 'TER' Between Residues Yu Chen via AMBER
- [AMBER] Enquiry about the Best way to Simulate Phosphorylated Tyrosines Mingxuan Jiang via AMBER
- Re: [AMBER] Regarding maximum molecular system size David A Case via AMBER
- Re: [AMBER] Regarding maximum molecular system size Todd Minehardt via AMBER
Saturday, 11 November 2023
- Re: [AMBER] Enquiry about the Best way to Simulate Phosphorylated Tyrosines Dr. Anselm Horn via AMBER
- Re: [AMBER] Command 'combine' in 'tleap' Introducing 'TER' Between Residues David A Case via AMBER
- Re: [AMBER] Command 'combine' in 'tleap' Introducing 'TER' Between Residues David Case via AMBER
- Re: [AMBER] fcc_metals.lib not found Setyanto Md via AMBER
- Re: [AMBER] Regarding maximum molecular system size Singh,Ravi via AMBER
Sunday, 12 November 2023
- Re: [AMBER] CUDA version for AMBER22 Jones De Andrade via AMBER
- [AMBER] In which order do dihedral types override in main parameter sets? He, Amy via AMBER
- [AMBER] Split a .nc file Singh,Ravi via AMBER
- Re: [AMBER] Regarding maximum molecular system size Carlos Simmerling via AMBER
- Re: [AMBER] Split a .nc file Carlos Simmerling via AMBER
- Re: [AMBER] Comparing FF Energies: 99SB/14SB/19SB translated with parmed to Gromacs Albert Gauss via AMBER
- [AMBER] Problem in Conversion from .nc to mdcrd file Singh,Ravi via AMBER
- Re: [AMBER] Problem in Conversion from .nc to mdcrd file Todd Minehardt via AMBER
- Re: [AMBER] Comparing FF Energies: 99SB/14SB/19SB translated with parmed to Gromacs Carlos Simmerling via AMBER
- Re: [AMBER] Problem in Conversion from .nc to mdcrd file Carlos Simmerling via AMBER
- [AMBER] Polarizabilitiy Calculations Gillispie, Nathan via AMBER
Monday, 13 November 2023
- [AMBER] cyclic peptide in water box Sepideh Jafari via AMBER
- Re: [AMBER] cyclic peptide in water box Dr. Anselm Horn via AMBER
- [AMBER] Extracting MD snaphots: Kankana Bhattacharjee via AMBER
- Re: [AMBER] [Sender Not Verified] Extracting MD snaphots: Steinbrecher, Thomas via AMBER
- Re: [AMBER] Model a protein with Tyrosine anion Xiangwei Zhu via AMBER
- Re: [AMBER] Regarding maximum molecular system size David A Case via AMBER
- Re: [AMBER] CUDA version for AMBER22 David A Case via AMBER
- Re: [AMBER] Polarizabilitiy Calculations David A Case via AMBER
- Re: [AMBER] In which order do dihedral types override in main parameter sets? David A Case via AMBER
- Re: [AMBER] CUDA version for AMBER22 Jones De Andrade via AMBER
Tuesday, 14 November 2023
- [AMBER] Use of IPolQ scheme for macromolecular complexes Jakub Jakubec via AMBER
- Re: [AMBER] CUDA version for AMBER22 David A Case via AMBER
- [AMBER] MMGBSA descomposition VERONICA MARTIN HERNANDEZ via AMBER
- [AMBER] Error: Incompatible CUDA and GNU versions Info via AMBER
- Re: [AMBER] [EXTERNAL] Error: Incompatible CUDA and GNU versions Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER
- [AMBER] Compilation Question Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] [EXTERNAL] Error: Incompatible CUDA and GNU versions Scott Brozell via AMBER
- [AMBER] Residue type in input pdb Prithviraj Nandigrami via AMBER
- Re: [AMBER] Compilation Question David A Case via AMBER
Wednesday, 15 November 2023
- Re: [AMBER] [EXTERNAL] Error: Incompatible CUDA and GNU versions Info via AMBER
- [AMBER] Error in MMPBSA VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] Error in MMPBSA Bill Miller III via AMBER
- Re: [AMBER] Error in MMPBSA Pedro Guillem via AMBER
- Re: [AMBER] [EXTERNAL] Error: Incompatible CUDA and GNU versions Info via AMBER
- Re: [AMBER] [EXTERNAL] Error: Incompatible CUDA and GNU versions David A Case via AMBER
- [AMBER] Updated Benchmarks including new ADA series GPUs Ross Walker via AMBER
- [AMBER] PBSA error Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] PBSA error Ray Luo via AMBER
- Re: [AMBER] PBSA error Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] PBSA error Ray Luo via AMBER
- Re: [AMBER] PBSA error Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] PBSA error Ray Luo via AMBER
Thursday, 16 November 2023
- [AMBER] Issues in Modified nucleotide parametrization using Antechamber and Parmchk2 Priyasha Majee via AMBER
- Re: [AMBER] MMGBSA descomposition Pedro Guillem via AMBER
- [AMBER] No build when downloading amber22 Johannes Loeffler via AMBER
- Re: [AMBER] No build when downloading amber22 Daniel Roe via AMBER
- [AMBER] Announcement: Release of DOCK 6.11 Scott Brozell via AMBER
- Re: [AMBER] Issues in Modified nucleotide parametrization using Antechamber and Parmchk2 He, Amy via AMBER
Friday, 17 November 2023
- [AMBER] RESP fitting in solvent Jakub Jakubec via AMBER
- Re: [AMBER] MCPB, negative force constant? Pengfei Li via AMBER
Sunday, 19 November 2023
- Re: [AMBER] R: Inquiry about PMEMD.CUDA availability in non-commercial license David A Case via AMBER
Wednesday, 29 November 2023
- [AMBER] antechamber error-- QMMM: System specified with odd number of electrons Yang, Li-Yen via AMBER
- [AMBER] amber 20 installing error on Rocky linux 9.1 东不拉 via AMBER
Thursday, 30 November 2023
- [AMBER] Looking for a force field with ester linkages between protein chains permitted. David Cowburn via AMBER
- Re: [AMBER] antechamber error-- QMMM: System specified with odd number of electrons Todd Minehardt via AMBER
Wednesday, 29 November 2023
- [AMBER] Fwd: pocket volume calculation Sruthi Sudhakar via AMBER
Tuesday, 28 November 2023
- Re: [AMBER] RESP fitting in solvent FyD via AMBER
Thursday, 30 November 2023
- Re: [AMBER] amber 20 installing error on Rocky linux 9.1 David A Case via AMBER
- Re: [AMBER] Looking for a force field with ester linkages between protein chains permitted. David A Case via AMBER
Tuesday, 28 November 2023
- [AMBER] pocket volume calculation Sruthi Sudhakar via AMBER
Thursday, 30 November 2023
- [AMBER] Would AMBER suit my purpose? Mignolet, Alex via AMBER
- Re: [AMBER] Reproduce a Simulation Skanda Sastry via AMBER
- Re: [AMBER] Reproduce a Simulation Skanda Sastry via AMBER

Last message date: Thu Nov 30 2023 - 20:30:02 PST
Archived on: Wed Nov 20 2024 - 05:56:05 PST

Amber Archive Nov 2023 by date