@inbook{1d10fe24efb44a1aaafec59c442881d5,
title = "Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen",
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",
author = "Chen, {Yu Wai} and Yong Wang and Leung, {Yun Chung} and Wong, {Kwok Yin}",
note = "Funding Information: We acknowledge support from the Innovation and Technology Commission of Hong Kong, the Hong Kong Polytechnic University and the Life Science Area of Strategic Fund 1-ZVH9. Publisher Copyright: {\textcopyright} 2021, Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2021",
month = oct,
day = "31",
doi = "10.1007/978-1-0716-0892-0_16",
language = "English",
volume = "2199",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "277--288",
booktitle = "Methods in Molecular Biology",
}