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FFParam:用于小分子 CHARMM 加性和 Drude 极化力场参数化的独立软件包。

FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules.

机构信息

Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.

出版信息

J Comput Chem. 2020 Apr 5;41(9):958-970. doi: 10.1002/jcc.26138. Epub 2019 Dec 30.

DOI:10.1002/jcc.26138
PMID:31886576
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7323454/
Abstract

Accurate force-field (FF) parameters are key to reliable prediction of properties obtained from molecular modeling (MM) and molecular dynamics (MD) simulations. With ever-widening applicability of MD simulations, robust parameters need to be generated for a wider range of chemical species. The CHARMM General Force Field program (CGenFF, https://cgenff.umaryland.edu/) is a tool for obtaining initial parameters for a given small molecule based on analogy with the available CGenFF parameters. However, improvement of these parameters is often required and performing their optimization remains tedious and time consuming. In addition, tools for optimization of small molecule parameters in the context of the Drude polarizable FF are not yet available. To overcome these issues, the FFParam package has been designed to facilitate the parametrization process. The package includes a graphical user interface (GUI) created using Qt libraries. FFParam supports Gaussian and Psi4 for performing quantum mechanical calculations and CHARMM and OpenMM for MM calculations. A Monte Carlo simulated annealing (MCSA) algorithm has been implemented for automated fitting of partial atomic charge, atomic polarizabilities and Thole scale parameters. The LSFITPAR program is called for automated fitting of bonded parameters. Accordingly, FFParam provides all the features required for generation and analysis of CHARMM and Drude FF parameters for small molecules. FFParam-GUI includes a text editor, graph plotter, molecular visualization, and text to table converter to meet various requirements of the parametrization process. It is anticipated that FFParam will facilitate wider use of CGenFF as well as promote future use of the Drude polarizable FF.

摘要

准确的力场 (FF) 参数是从分子建模 (MM) 和分子动力学 (MD) 模拟中获得可靠预测性质的关键。随着 MD 模拟的应用范围不断扩大,需要为更广泛的化学物质生成更强大的参数。CHARMM 通用力场程序 (CGenFF,https://cgenff.umaryland.edu/) 是一种基于与可用的 CGenFF 参数类比,为给定小分子获得初始参数的工具。然而,通常需要改进这些参数,并且执行它们的优化仍然繁琐且耗时。此外,在 Drude 极化 FF 上下文中优化小分子参数的工具尚不可用。为了克服这些问题,FFParam 包被设计用于促进参数化过程。该包包括使用 Qt 库创建的图形用户界面 (GUI)。FFParam 支持 Gaussian 和 Psi4 进行量子力学计算,以及 CHARMM 和 OpenMM 进行 MM 计算。已经实现了蒙特卡罗模拟退火 (MCSA) 算法,用于自动拟合部分原子电荷、原子极化率和 Thole 标度参数。LSFITPAR 程序用于自动拟合键参数。因此,FFParam 为生成和分析小分子的 CHARMM 和 Drude FF 参数提供了所需的所有功能。FFParam-GUI 包括文本编辑器、图形绘图器、分子可视化和文本到表格转换器,以满足参数化过程的各种要求。预计 FFParam 将促进 CGenFF 的更广泛使用,并推动未来使用 Drude 极化 FF。

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2
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