title: MCPB.py: A Python Based Metal Center Parameter Builder.
abstract: 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.
authors.affiliation: Department of Chemistry, Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Li
authors.affiliation: Department of Chemistry, Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States.
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Merz
mesh_terms: D008667:Metalloproteins / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009942:Organometallic Compounds / Q000737:chemistry*; D011381:Programming Languages; D011487:Protein Conformation; D011789:Quantum Theory
chemical_list: D008667:Metalloproteins; D009942:Organometallic Compounds