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WIREs Comput Mol Sci
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Recent developments and applications of the CHARMM force fields

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Abstract Empirical force fields (FFs) commonly used to describe the condensed‐phase properties of complex systems such as biological macromolecules are continuously being updated. Improvements in quantum mechanical methods used to generate target data, availability of new experimental target data, incorporation of new classes of compounds, and new theoretical developments (e.g., polarizable methods) make FF development a dynamic domain of research. Accordingly, a number of improvements and extensions of the Chemistry at HARvard Molecular Mechanics (CHARMM) FFs have occurred over the years. The objective of the present review is to provide an up‐to‐date overview of the CHARMM FFs. A limited presentation on the historical aspects of FFs will be given, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development. This is followed by information on the CHARMM additive and polarizable FFs, including examples of recent applications of those FFs. © 2011 John Wiley & Sons, Ltd. This article is categorized under: Molecular and Statistical Mechanics > Molecular Mechanics

Schematic representation of how atomic polarizability is treated in the CHARMM polarizable force field using methanol as an example. Drude oscillators (or particles) (blue, ‘D’) are attached to non‐hydrogen parent atoms through harmonic bonds (dashed lines). Oxygen lone pairs (green, ‘LP’) are connected with constrained bonds, angles, and dihedrals relative to the COH plane. Hydrogens are not considered as polarizable entities in this model.

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Flowchart for the determination of parameters for drug‐like molecules as described in Ref 16. 3‐phenoxymethylpyrrolidine is assembled from two of its constituents, ethoxybenzene and 3‐hydroxymethyltetrahydrofuran, available from the CGenFF. Parameters were identified for the pyrrolidine group by analogy. Optimization of the dihedrals I, II, and III is required to produce an accurate computational model for this molecule.

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Cyclic hexopyranose and furanose compounds parametrized for the CHARMM carbohydrate force field.

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The anisotropic nature of polarizability for a sulfur atom in ethylmethylsulfide is probed using +0.5e point charges placed on two perpendicular arcs (inset). Differences between QM perturbed and unperturbed electrostatic potentials are used to determine polarization response as a function of orientation. Polarizability anisotropy parameters are fitted to reproduce relative response curves obtained through quantum mechanical calculations.

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Orientation of test water molecules around the polarizable atom of interest exemplified through ethanethiol. Carbon is in cyan, sulfur in yellow, and LP in blue. ‘120’ is probing for interactions along the S‐LP axis. ‘180’ is oriented toward the CS bond. ‘BIS’ water points at the bisection of the CSH valence angle. ‘PR’ is pointed directly at the sulfur proton and along the SH bond.

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Illustration of model compounds used in the parametrization of the CHARMM additive protein force field. (a) N‐methyl acetamide is used to model the peptide bond; (b) side chains, such as in PHE, are modeled by analogous compounds that include terminating methyl or ethyl groups; (c) alanine dipeptide is the model compound for optimization of the φ/ψ torsional parameters, including CMAP corrections.

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A simplified parametrization flow chart.

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