We introduce a toolset of program libraries collectively titled multipurpose atom-typer for CHARMM (MATCH) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. A general chemical pattern-matching engine achieves assignment of atom types, charges and force field parameters through comparison against a customizable list of chemical fragments. To demonstrate the accuracy of parameters constructed by MATCH, each molecule within each force field included in CHARMM36 will have its parameters generated by every other force field in an exhaustive manner. These cross validation studies illustrate that bond increment rules derived from one force field can be transferred to another. Finally, the chemical-space coverage offered by the recent CHARMM general force field will be demonstrated by generating the force field parameters of one million molecules from the PubChem database of small molecules.

MATCH: An atom-typing toolset for molecular mechanics force fields

243rd National Meeting (2012)

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