MCPB.py: A Python Based Metal Center Parameter Builder

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.