| Autor: |
Yudong Qiu, Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan, Trevor Gokey, Victoria T. Lim, Chaya Stern, Andrea Rizzi, Xavier Lucas, Bryon Tjanaka, Michael R. Shirts, Michael Gilson, John Chodera, Christopher I. Bayly, David Mobley, Lee-Ping Wang |
| Rok vydání: |
2021 |
| Popis: |
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, code-named Parsley. Rather than traditional atom-typing, our approach builds 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 entire new force field with minimal human intervention. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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