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.
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References
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Acknowledgments
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.
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Chen, Y.W., Wang, Y., Leung, YC., Wong, KY. (2021). Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen. In: Chen, Y.W., Yiu, CP.B. (eds) Structural Genomics. Methods in Molecular Biology, vol 2199. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0892-0_16
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DOI: https://doi.org/10.1007/978-1-0716-0892-0_16
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Publisher Name: Humana, New York, NY
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Online ISBN: 978-1-0716-0892-0
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