Development and Validation of the Quantum Mechanical Bespoke Protein Force Field.

ABSTRACT: Molecular mechanics force field parameters for macromolecules, such as proteins, are traditionally fit to reproduce experimental properties of small molecules, and thus, they neglect system-specific polarization. In this paper, we introduce a complete protein force field that is designed to be compatible with the quantum mechanical bespoke (QUBE) force field by deriving nonbonded parameters directly from the electron density of the specific protein under study. The main backbone and sidechain protein torsional parameters are rederived in this work by fitting to quantum mechanical dihedral scans for compatibility with QUBE nonbonded parameters. Software is provided for the preparation of QUBE input files. The accuracy of the new force field, and the derived torsional parameters, is tested b

SUBMITTER: Allen AEA 

PROVIDER: S-EPMC6740169 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature