使用 LigParGen 对 Gromacs 分子动力学模拟进行大配体的参数化。

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

机构信息

Department 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.

出版信息

Methods Mol Biol. 2021;2199:277-288. doi: 10.1007/978-1-0716-0892-0_16.

DOI:10.1007/978-1-0716-0892-0_16

PMID:33125656

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.

摘要

分子动力学（MD）模拟是研究分子间相互作用的一种强大方法。定义所有相关成分的力学性能和拓扑结构至关重要。虽然蛋白质的参数已经得到很好的确立，但对于广泛的配体和底物，情况并非如此。在这里，我们引入了一个非常有用的服务，专为小分子设计。我们描述了一个协议，将这个工具扩展到超出其当前大小（200 个原子）和形式电荷（2+ 到 2-）限制。