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Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

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Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
Cite this: J. Chem. Inf. Model. 2012, 52, 12, 3155–3168
Publication Date (Web):November 12, 2012
https://doi.org/10.1021/ci3003649
Copyright © 2012 American Chemical Society

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    Abstract

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    Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug candidates interacting with biological systems. In these simulations, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and partial atomic charges is required. In the present article, algorithms for the assignment of parameters and charges for the CHARMM General Force Field (CGenFF) are presented. These algorithms rely on the existing parameters and charges that were determined as part of the parametrization of the force field. Bonded parameters are assigned based on the similarity between the atom types that define said parameters, while charges are determined using an extended bond-charge increment scheme. Charge increments were optimized to reproduce the charges on model compounds that were part of the parametrization of the force field. A “penalty score” is returned for every bonded parameter and charge, allowing the user to quickly and conveniently assess the quality of the force field representation of different parts of the compound of interest. Case studies are presented to clarify the functioning of the algorithms and the significance of their output data.

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    A list of bond, angle, and dihedral charge increments that were constrained during the charge increment optimization. Toppar stream files for the case studies as generated by the CGenFF program. A table with minimized bond length and angles for N-benzylacetamide (3), analogous to Table 2. This material is available free of charge via the Internet at http://pubs.acs.org .

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