Abstract
A general purpose force field such as MMFF94/MMFF94s, which can properly deal with a wide range of diverse structures, is very valuable in the context of a cheminformatics toolkit. Herein we present an open-source implementation of this force field within the RDKit. The new MMFF functionality can be accessed through a C++/C#/Python/Java application programming interface (API) developed along the lines of the one already available for UFF in the RDKit. Our implementation was fully validated against the official validation suite provided by the MMFF authors. All energies and gradients were correctly computed; moreover, atom type and force constants were correctly assigned for 3D molecules built from SMILES strings. To provide full flexibility, the available API provides direct access to include/exclude individual terms from the MMFF energy expression and to carry out constrained geometry optimizations. The availability of a MMFF-capable molecular mechanics engine coupled with the rest of the RDKit functionality and covered by the BSD license is appealing to researchers operating in both academia and industry.
Highlights
Molecular mechanics force fields are the workhorse of computational chemists for molecular simulations, owing to their low computational demands compared to CPU-intensive quantum mechanical methods
We present an implementation of MMFF within the open-source cheminformatics toolkit RDKit [15]; MMFF functionality can be accessed through C++, C#, Python and Java application programming interfaces (APIs)
The validation suites include a detailed log file generated by OPTIMOL, a molecular-mechanics program developed at Merck where the force field was first implemented, which lists for each molecule the MMFF atom types and charges and the overall potential energy, decomposed into the seven energy terms which appear in Equation 1
Summary
Molecular mechanics force fields are the workhorse of computational chemists for molecular simulations, owing to their low computational demands compared to CPU-intensive quantum mechanical methods. The MMFF formal charge paradigm is based on resonant charges distributed over heteroatoms of the respective functional groups, which is different to the one implemented in the RDKit. In the API, atom types and charges are assigned upon construction of an instance of the MMFFMolProperties class. In the API, atom types and charges are assigned upon construction of an instance of the MMFFMolProperties class This class includes methods to choose between the MMFF94/MMFF94s variants, to access atom types and partial charges, to set the dielectric model (constant or distance-dependent) and the dielectric constant, or to exclude selected terms from the energy expression (Equation 1), respectively. A few examples of simple and constrained geometry optimizations and potential energy calculations are available as Additional files 1, 2 and 3; more examples can be found in the RDKit test suite (both C++ and Python)
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