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Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen

Yu Wai Chen¹, Yong Wang², Yun-Chung Leung²

¹Department 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.

Methods in Molecular Biology (Clifton, N.J.)

|October 30, 2020

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

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