Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen

Yu Wai Chen, Yong Wang, Yun Chung Leung, Kwok Yin Wong

Research output: Chapter in book / Conference proceedingChapter in an edited book (as author)Academic researchpeer-review

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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages277-288
Number of pages12
DOIs
Publication statusPublished - 31 Oct 2021

Publication series

NameMethods in Molecular Biology
Volume2199
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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