Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen

Yu Wai Chen; Yong Wang; Yun-Chung Leung; Kwok-Yin Wong

doi:10.1007/978-1-0716-0892-0_16

Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen

Methods Mol Biol. 2021:2199:277-288. doi: 10.1007/978-1-0716-0892-0_16.

Authors

Yu Wai Chen¹, Yong Wang², Yun-Chung Leung², Kwok-Yin Wong²

Affiliations

¹ Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Hong Kong. yu-wai.chen@polyu.edu.hk.
² Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Hong Kong.

PMID: 33125656
DOI: 10.1007/978-1-0716-0892-0_16

Abstract

Molecular dynamics (MD) simulation is a powerful method of investigating the interaction between molecular species. Defining the mechanical properties and topologies for all components involved is critical. While parameters for proteins are well established, those for the wide range of ligands and substrates are not. Here we introduce a very useful service which is designed for small organic molecules. We describe a protocol to extend this tool to beyond its current size (200 atoms) and formal charge (2+ to 2-) limits.

Keywords: Fluorescein; Gromacs; Ligand parameters; Moenomycin A; Molecular dynamics (MD) simulation; OPLS-AA/L forcefield; Peptidoglycan glycosyltransferase; Protein-ligand complex.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Ligands
Molecular Dynamics Simulation*
Proteins / chemistry*
Software*

Substances

Ligands
Proteins