Current Status of the AMOEBA Polarizable Force Field

Current Status of the AMOEBA Polarizable Force Field

2010 March 4 | Jay W. Ponder, Chuanjie Wu, Pengyu Ren, Vijay S. Pande, John D. Chodera, Michael J. Schnieders, Imran Haque, David L. Mobley, Daniel S. Lambrecht, Robert A. DiStasio Jr., Martin Head-Gordon, Gary N. I. Clark, Margaret E. Johnson, Teresa Head-Gordon
The AMOEBA polarizable force field is a next-generation model that improves upon fixed charge models by incorporating polarization effects, allowing more accurate molecular property descriptions. This study evaluates AMOEBA's performance against electronic structure calculations and experimental data, showing it excels in predicting structural and thermodynamic properties of small molecules and proteins. AMOEBA is particularly effective in protein-ligand binding and computational X-ray crystallography, where polarization and accurate electrostatics are critical. It also performs well in predicting solvation free energies of drug-like molecules and in modeling water dynamics near protein surfaces. The AMOEBA model includes a detailed treatment of polarization effects, using atomic multipoles and explicit dipole polarization to respond to changing environments. It has been validated against a wide range of systems, including alanine tetrapeptide conformational energies, water clusters, and solvation free energies of small molecules. AMOEBA's performance is comparable to advanced quantum mechanical methods, with a chemical accuracy of 0.5 kcal/mol or better for small molecule and protein-ligand interactions. The model's ability to accurately reproduce molecular polarizabilities and electrostatic potentials makes it a valuable tool for molecular simulations. AMOEBA has been tested in the 2009 OpenEye SAMPL competition, where it performed well, especially for highly soluble molecules. The study highlights AMOEBA's potential as a reliable and accurate force field for molecular simulations, particularly in complex biological systems.The AMOEBA polarizable force field is a next-generation model that improves upon fixed charge models by incorporating polarization effects, allowing more accurate molecular property descriptions. This study evaluates AMOEBA's performance against electronic structure calculations and experimental data, showing it excels in predicting structural and thermodynamic properties of small molecules and proteins. AMOEBA is particularly effective in protein-ligand binding and computational X-ray crystallography, where polarization and accurate electrostatics are critical. It also performs well in predicting solvation free energies of drug-like molecules and in modeling water dynamics near protein surfaces. The AMOEBA model includes a detailed treatment of polarization effects, using atomic multipoles and explicit dipole polarization to respond to changing environments. It has been validated against a wide range of systems, including alanine tetrapeptide conformational energies, water clusters, and solvation free energies of small molecules. AMOEBA's performance is comparable to advanced quantum mechanical methods, with a chemical accuracy of 0.5 kcal/mol or better for small molecule and protein-ligand interactions. The model's ability to accurately reproduce molecular polarizabilities and electrostatic potentials makes it a valuable tool for molecular simulations. AMOEBA has been tested in the 2009 OpenEye SAMPL competition, where it performed well, especially for highly soluble molecules. The study highlights AMOEBA's potential as a reliable and accurate force field for molecular simulations, particularly in complex biological systems.
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