Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen.

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.

Citation

Yu Wai Chen, Yong Wang, Yun-Chung Leung, Kwok-Yin Wong. Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen. Methods in molecular biology (Clifton, N.J.). 2021;2199:277-288

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PMID: 33125656

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