Current Status of the AMOEBA Polarizable Force Field

By Jay W. Ponder, Chuanjie Wu, Pengyu Y. Ren, Vijay S. Pande, John D. Chodera, Michael J. Schnieders, I. Haque, David L. Mobley, D. Lambrecht, Robert A. Distasio Jr. and 4 more. Journal of Physical Chemistry B, 2010

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Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models towards more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.

Subfields: Atomic and Molecular Physics, and Optics, Physical and Theoretical Chemistry

View Paper: https://www.semanticscholar.org/paper/2e4e2fb0d08e93ee597381b3c7225a0f49c18ec1

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In Atomic and Molecular Physics, and Optics

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Citations in the corpus

FreeSolv: A database of experimental and calculated hydration free energies, with input files (2014, neutral): “While other methods such as implicit-solvent calculations [33, 40, 45, 50] and MD simulations based on polarizable force fields [42, 43] or QM-MM approaches [60] are also of considerable interest, this has not been a major emphasis of our work.”
The future of molecular dynamics simulations in drug discovery (2011, background): “The more advanced force ﬁelds of today appear to work well in limited cases [67, 70], but their generality, especially in protein–ligand binding, remains unproven.”
The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling (2011, methodology): “36 An alternative is to use an empirical functional form to enforce hydrogen bond angles and distances, fitting to experimental PDB data.”
Collective many-body van der Waals interactions in molecular systems (2012, background): “Almost all of these interatomic potentials utilize an effective interatomic pairwise approximation to account for nonbonded interactions, the notable exception being polarizable force fields, which treat induction (static) effects using mutually interacting sites (3, 4).”