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

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