MCPB.py: A Python Based Metal Center Parameter Builder

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• 作者：Pengfei Li ; Kenneth M. Merz Jr.
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2016
• 出版时间：April 25, 2016
• 年：2016
• 卷：56
• 期：4
• 页码：599-604
• 全文大小：378K
• 年卷期：0
• ISSN：1549-960X

文摘

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.