charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS.
charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS.
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DOI：
10.1021/acs.jcim.3c00860
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发表时间：
2023-07-24
影响因子：
5.6
通讯作者：
Lemkul, Justin A.
中科院分区：
文献类型：
--
作者：
Wacha, Andras F.;Lemkul, Justin A.
CHARMM是应用最广泛的生物分子力场之一。尽管它是与同名的专用分子模拟引擎紧密结合开发的，但它也可以与其他代码一起使用。GROMACS是一款成熟的、高度优化的、多用途的分子动力学软件，具有足够的通用性，足以适应许多不同的力场势函数和相关算法。由于与软件设计相关的概念差异，以及残基拓扑和参数集固有的大量数字数据，从一种软件格式到另一种软件格式的转换并不简单。在这里，我们提供了一种自动且经过验证的方法，将CHARMM力场移植为GROMACS引擎可以读取的格式，以一种自我记录和可重现的方式协调两个代码的不同功能，所需的用户交互最少。与以前解决相同问题的尝试不同，本方法完全基于上游数据文件，不涉及任何硬编码数据。用于感知局部内部几何的启发式方法直接适用于其他力场的类似变换。
CHARMM is one of the most widely used biomolecular force fields. Although developed in close connection with a dedicated molecular simulation engine of the same name, it is also usable with other codes. GROMACS is a well-established, highly optimized, and multipurpose software for molecular dynamics, versatile enough to accommodate many different force field potential functions and the associated algorithms. Due to conceptional differences related to software design and the large amount of numeric data inherent to residue topologies and parameter sets, conversion from one software format to another is not straightforward. Here, we present an automated and validated means to port the CHARMM force field to a format read by the GROMACS engine, harmonizing the different capabilities of the two codes in a self-documenting and reproducible way with a bare minimum of user interaction required. Being based entirely on the upstream data files, the presented approach does not involve any hard-coded data, in contrast with previous attempts to solve the same problem. The heuristic approach used for perceiving the local internal geometry is directly applicable for analogous transformations of other force fields.
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影响因子：
3.3
作者：
Klauda, Jeffery B.;Venable, Richard M.;Freites, J. Alfredo;O'Connor, Joseph W.;Tobias, Douglas J.;Mondragon-Ramirez, Carlos;Vorobyov, Igor;MacKerell, Alexander D., Jr.;Pastor, Richard W.
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影响因子：
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通讯作者：
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影响因子：
5.5
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Best, Robert B.;Zhu, Xiao;Shim, Jihyun;Lopes, Pedro E. M.;Mittal, Jeetain;Feig, Michael;MacKerell, Alexander D., Jr.
通讯作者：
MacKerell, Alexander D., Jr.
影响因子：
3
作者：
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通讯作者：
Mackerell, Alexander D., Jr.