Li Pengfei, Merz Kenneth M
Department of Chemistry, Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States.
J Chem Inf Model. 2016 Apr 25;56(4):599-604. doi: 10.1021/acs.jcim.5b00674. Epub 2016 Mar 23.
MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach. It has an optimized code structure, with far fewer required steps than the previous developed MCPB program. It supports various AMBER force fields and more than 80 metal ions. A series of parametrization schemes to derive force constants and charge parameters are available within the program. We give two examples (one metalloprotein example and one organometallic compound example), indicating the program's ability to build reliable force fields for different metal ion containing complexes. The original version was released with AmberTools15. It is provided via the GNU General Public License v3.0 (GNU_GPL_v3) agreement and is free to download and distribute. MCPB.py provides a bridge between quantum mechanical calculations and molecular dynamics simulation software packages thereby enabling the modeling of metal ion centers. It offers an entry into simulating metal ions in a number of situations by providing an efficient way for researchers to handle the vagaries and difficulties associated with metal ion modeling.
MCPB.py是一个基于Python的金属中心参数构建器，已被开发用于采用键合模型方法构建用于模拟金属配合物的力场。它具有优化的代码结构，所需步骤比先前开发的MCPB程序少得多。它支持各种AMBER力场和80多种金属离子。程序中提供了一系列用于推导力常数和电荷参数的参数化方案。我们给出两个例子（一个金属蛋白例子和一个有机金属化合物例子），表明该程序能够为不同的含金属离子配合物构建可靠的力场。原始版本随AmberTools15一起发布。它是根据GNU通用公共许可证v3.0（GNU_GPL_v3）协议提供的，可免费下载和分发。MCPB.py在量子力学计算和分子动力学模拟软件包之间架起了一座桥梁，从而能够对金属离子中心进行建模。它通过为研究人员提供一种有效方式来处理与金属离子建模相关的变幻莫测和困难，为在多种情况下模拟金属离子提供了一条途径。
