Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization.
Esther Heid, Markus Fleck, Payal Chatterjee, Christian Schröder, Alexander D MacKerell
Author Information
Esther Heid: Department of Computational Biological Chemistry , University of Vienna, Faculty of Chemistry , Währingerstraße 17 , A-1090 Vienna , Austria. ORCID
Markus Fleck: Department of Computational Biological Chemistry , University of Vienna, Faculty of Chemistry , Währingerstraße 17 , A-1090 Vienna , Austria.
Payal Chatterjee: Department of Pharmaceutical Sciences, School of Pharmacy , University of Maryland , Baltimore , Maryland 21201 , United States.
Christian Schröder: Department of Computational Biological Chemistry , University of Vienna, Faculty of Chemistry , Währingerstraße 17 , A-1090 Vienna , Austria. ORCID
Alexander D MacKerell: Department of Pharmaceutical Sciences, School of Pharmacy , University of Maryland , Baltimore , Maryland 21201 , United States. ORCID
The derivation of atomic polarizabilities for polarizable force field development has been a long-standing problem. Atomic polarizabilities were often refined manually starting from tabulated values, rendering an automated assignment of parameters difficult and hampering reproducibility and transferability of the obtained values. To overcome this, we trained both a linear increment scheme and a multilayer perceptron neural network on a large number of high-quality quantum mechanical atomic polarizabilities and partial atomic charges, where only the type of each atom and its connectivity were used as input. The predicted atomic polarizabilities and charges had average errors of 0.023 Å and 0.019 e using the neural net and 0.063 Å and 0.069 e using the simple increment scheme. As the algorithm relies only on the connectivities of the atoms within a molecule, thus omitting dependencies on the three-dimensional conformation, the approach naturally assigns like charges and polarizabilities to symmetrical groups. Accordingly, a convenient utility is presented for generating the partial atomic charges and atomic polarizabilities for organic molecules as needed in polarizable force field development.
References
Nature. 2000 Jun 22;405(6789):947-51
[PMID: 10879535]
