Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

• DOI: 10.1021/acs.jctc.1c00571
• Publication Date: 2021-09-22T22:14:40Z
• Authors: Yudong Qiu; Daniel G. A. Smith; Simon Boothroyd; Hyesu Jang; David F. Hahn; Jeffrey Wagner; Caitlin C. Bannan; Trevor Gokey; Victoria T. Lim; Chaya D. Stern; Andrea Rizzi; Bryon Tjanaka; Gary Tresadern; Xavier Lucas; Michael R. Shirts; Michael K. Gilson; John D. Chodera; Christopher I. Bayly; David L. Mobley; Lee-Ping Wang
• Keywords: Chemical Physics; Molecular Conformation; Ligands; 530; Computer Software; Medicinal and Biomolecular Chemistry; Benchmarking; Networking and Information Technology R&D (NITRD); Physical chemistry; Theoretical and Computational Chemistry; Theoretical and computational chemistry; Chemical Sciences; Humans; Petroselinum; Biochemistry and Cell Biology; Ecosystem

We present a methodology for defining and optimizing a general force field for classical molecular simulations, and we describe its use to derive the Open Force Field 1.0.0 small-molecule force field, codenamed Parsley. Rather than using traditional atom typing, our approach is built on the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism, which handles increases in the diversity and specificity of the force field definition without needlessly increasing the complexity of the specification. Parameters are optimized with the ForceBalance tool, based on reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These quantum reference data are computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. In this initial application of the method, we present essentially a full optimization of all valence parameters and report tests of the resulting force field against compounds and data types outside the training set. These tests show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields, as is accuracy on binding free energies. We find that this initial Parsley force field affords accuracy similar to that of other general force fields when used to calculate relative binding free energies spanning 199 protein-ligand systems. Additionally, the resulting infrastructure allows us to rapidly optimize an entirely new force field with minimal human intervention.