Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program.

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.