Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.

ABSTRACT: The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein struc

SUBMITTER: Moriarty NW 

PROVIDER: S-EPMC6939439 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature