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Prediction of octanol-water partition coefficients for the SAMPL6-[Formula:  see text] molecules using molecular dynamics simulations with OPLS-AA,  AMBER and CHARMM force fields. - Abstract - Europe PMC
Prediction of octanol-water partition coefficients for the SAMPL6-[Formula: see text] molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields. - Abstract - Europe PMC

molecular dynamics - Alternative to CGenFF for generating large ligand  topology - Matter Modeling Stack Exchange
molecular dynamics - Alternative to CGenFF for generating large ligand topology - Matter Modeling Stack Exchange

Molecules | Free Full-Text | Drug Repurposing for Influenza Virus  Polymerase Acidic (PA) Endonuclease Inhibitor | HTML
Molecules | Free Full-Text | Drug Repurposing for Influenza Virus Polymerase Acidic (PA) Endonuclease Inhibitor | HTML

Converting CGenFF generated parameters (.str & .mol2) to gromacs topology ·  Issue #1062 · ParmEd/ParmEd · GitHub
Converting CGenFF generated parameters (.str & .mol2) to gromacs topology · Issue #1062 · ParmEd/ParmEd · GitHub

Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS —  Bioinformatics Review
Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS — Bioinformatics Review

Frontiers | Computational Characterizations of the Interactions Between the  Pontacyl Violet 6R and Exoribonuclease as a Potential Drug Target Against  SARS-CoV-2 | Chemistry
Frontiers | Computational Characterizations of the Interactions Between the Pontacyl Violet 6R and Exoribonuclease as a Potential Drug Target Against SARS-CoV-2 | Chemistry

parameters for pyridoxal-5'-phosphate (PLP)-serine - CHARMM forums
parameters for pyridoxal-5'-phosphate (PLP)-serine - CHARMM forums

How to overcome the error: "CGenFF versions are not equivalent!" in running  Gromacs?
How to overcome the error: "CGenFF versions are not equivalent!" in running Gromacs?

Precise force-field-based calculations of octanol-water partition  coefficients for the SAMPL7 molecules | SpringerLink
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules | SpringerLink

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception  and Atom Typing | Semantic Scholar
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing | Semantic Scholar

NAMD QM/MM (CGenFF) - Adrea's Notebook and Journal
NAMD QM/MM (CGenFF) - Adrea's Notebook and Journal

Protein-Ligand Simulation Using GROMACS - 作业部落 Cmd Markdown 编辑阅读器
Protein-Ligand Simulation Using GROMACS - 作业部落 Cmd Markdown 编辑阅读器

Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM,  OPLS, AMBER, and OpenFF families against experimental cross-solvation free  ener ... - Physical Chemistry Chemical Physics (RSC Publishing)  DOI:10.1039/D1CP00215E
Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM, OPLS, AMBER, and OpenFF families against experimental cross-solvation free ener ... - Physical Chemistry Chemical Physics (RSC Publishing) DOI:10.1039/D1CP00215E

RESNAME error while using cgenff python script - User discussions - GROMACS  forums
RESNAME error while using cgenff python script - User discussions - GROMACS forums

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception  and Atom Typing | Semantic Scholar
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing | Semantic Scholar

Large scale relative protein ligand binding affinities using  non-equilibrium alchemy - Chemical Science (RSC Publishing)  DOI:10.1039/C9SC03754C
Large scale relative protein ligand binding affinities using non-equilibrium alchemy - Chemical Science (RSC Publishing) DOI:10.1039/C9SC03754C

Additive CHARMM force field for naturally occurring modified  ribonucleotides - Xu - 2016 - Journal of Computational Chemistry - Wiley  Online Library
Additive CHARMM force field for naturally occurring modified ribonucleotides - Xu - 2016 - Journal of Computational Chemistry - Wiley Online Library

CHARMM force field parameters for 2′-hydroxybiphenyl-2-sulfinate,  2-hydroxybiphenyl, and related analogs - ScienceDirect
CHARMM force field parameters for 2′-hydroxybiphenyl-2-sulfinate, 2-hydroxybiphenyl, and related analogs - ScienceDirect

How to generate topology of small molecules & ligands for MD Simulation? —  Bioinformatics Review
How to generate topology of small molecules & ligands for MD Simulation? — Bioinformatics Review

How to generate CHARMM force field for GROMACS using CGenFF?
How to generate CHARMM force field for GROMACS using CGenFF?

Graphical User Interface Quickstart — SilcsBio User Guide
Graphical User Interface Quickstart — SilcsBio User Guide

In silico characterization and homology modeling of cytosolic APX gene  predicts novel glycine residue modulating waterlogging stress response in  pigeon pea [PeerJ]
In silico characterization and homology modeling of cytosolic APX gene predicts novel glycine residue modulating waterlogging stress response in pigeon pea [PeerJ]

Department of Computational Biological Chemistry
Department of Computational Biological Chemistry

GitHub - jandom/paramchem: Python scrapper for paramche/cgenff server,  small molecule parametrization
GitHub - jandom/paramchem: Python scrapper for paramche/cgenff server, small molecule parametrization

How to generate CHARMM force field for GROMACS using CGenFF?
How to generate CHARMM force field for GROMACS using CGenFF?

Protein-Ligand Complex
Protein-Ligand Complex

Molefacture Plugin, Version 2.0
Molefacture Plugin, Version 2.0