Department of Chemistry, Yale University, New Haven, CT, USA.
Department of Chemistry, Michigan State University, East Lansing, MI, USA.
Methods Mol Biol. 2021;2199:257-275. doi: 10.1007/978-1-0716-0892-0_15.
The MCPB.py program greatly facilitates force field parameterization for metal sites in metalloproteins and organometallic compounds. Herein we present an example of MCPB.py to the parameterization of the dioxygen binding metal site of peptidylglycine-alphahydroxylating monooxygenase (PHM), which contains a copper ion. In this example, we also extend the functionality of MCPB.py to support molecular dynamics (MD) simulations in GROMACS through a python script. Illustrative MD simulations were performed using GROMACS and the results were analyzed. Notes about the program were also provided in this chapter, to assist MCPB.py users for metal site parameterizations.
MCPB.py 程序极大地方便了金属蛋白和金属有机化合物中金属位点的力场参数化。在此，我们提供了一个 MCPB.py 用于多肽基甘氨酸-α-羟化单加氧酶 (PHM) 的双氧结合金属位点参数化的示例，其中包含一个铜离子。在这个例子中，我们还通过一个 Python 脚本扩展了 MCPB.py 的功能，以支持 GROMACS 中的分子动力学 (MD) 模拟。使用 GROMACS 进行了说明性的 MD 模拟，并对结果进行了分析。本章还提供了有关该程序的说明，以帮助 MCPB.py 用户进行金属位点参数化。
