charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS

CHARMM is one of the most widely used biomolecular force
fields.
Although developed in close connection with a dedicated molecular
simulation engine of the same name, it is also usable with other codes.
GROMACS is a well-established, highly optimized, and multipurpose
software for molecular dynamics, versatile enough to accommodate many
different force field potential functions and the associated algorithms.
Due to conceptional differences related to software design and the
large amount of numeric data inherent to residue topologies and parameter
sets, conversion from one software format to another is not straightforward.
Here, we present an automated and validated means to port the CHARMM
force field to a format read by the GROMACS engine, harmonizing the
different capabilities of the two codes in a self-documenting and
reproducible way with a bare minimum of user interaction required.
Being based entirely on the upstream data files, the presented approach
does not involve any hard-coded data, in contrast with previous attempts
to solve the same problem. The heuristic approach used for perceiving
the local internal geometry is directly applicable for analogous transformations
of other force fields.