Pubs-Forcefield – TinkerTools.org

Force Field Publications:

Proteins

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins, Y. Shi, Z. Xia, J. Zhang, R. Best, C. Wu, J. W. Ponder and P. Ren, J. Chem. Theory Comput., 9, 4046-4063 (2013)

Nucleic Acids

AMOEBA Polarizable Atomic Multpole Force Field for Nucleic Acids, C. Zhang, C. Lu, Z. Jing, C. Wu, J.-P. Piquemal, J. W. Ponder and P. Ren, J. Chem. Theory. Comput., 14, 2084-2108 (2018)

Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate, C. Zhang, C. Lu, Q. Wang, J. W. Ponder and P. Ren, J. Chem. Theory Comput., 11, 5326-5339 (2015)

Ions

Approaching ab Initio Complete Basis Set Limit and Experimental Accuracy for Ions in the AMOEBA Polarizable Force Field, C. Wu, P. Ren and J. W. Ponder, CCB Report 2010-01, Washington University School of Medicine (2010) [available from https://dasher.wustl.edu/ponder/papers/ccb-report-2010-01.pdf]

Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field, A. Grossfield, P. Ren and J. W. Ponder, J. Am. Chem. Soc., 125, 15671-15682 (2003)

Water

Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential, C. Liu, J.-P. Piquemal, P. Ren, J. Phys. Chem. Lett., 11, 419–426 (2020)

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model, M. L. Laury, L.-P. Wang, V. S. Pande, T. Head-Gordon and J. W. Ponder, J. Phys. Chem. B., 119, 9423-9437 (2015)

Systematic Improvement on the Classical Molecular Model of Water, L.-P. Wang, T. Head-Gordon, J. Ponder, P. Ren, J. Chodera, P. Eastman, T. J. Martinez and V. S. Pande, Biophys. J., 106, A403 (2014)

Temperature and Pressure Dependence of the AMOEBA Water Model, P. Ren and J. W. Ponder, J. Phys. Chem. B, 108, 13427-13437 (2004)

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation, P. Ren and J. W. Ponder, J. Phys. Chem. B, 107, 5933-5947 (2003)

Parameterization

Automation of AMOEBA Polarizable Force Field Parameterization for Small Molecules, J. D. Wu, G. Chattree and P. Ren, Theor. Chem. Acc., 131, 1138 (2012)