This Title All WIREs
How to cite this WIREs title:
WIREs Comput Mol Sci
Impact Factor: 16.778

Recent developments and applications of the CHARMM force fields

Full article on Wiley Online Library:   HTML PDF

Can't access this content? Tell your librarian.

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.

[ Normal View | Magnified View ]

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.

[ Normal View | Magnified View ]

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

[ Normal View | Magnified View ]

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.

[ Normal View | Magnified View ]

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.

[ Normal View | Magnified View ]

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.

[ Normal View | Magnified View ]

A simplified parametrization flow chart.

[ Normal View | Magnified View ]

Browse by Topic

Molecular and Statistical Mechanics > Molecular Mechanics

Access to this WIREs title is by subscription only.

Recommend to Your
Librarian Now!

The latest WIREs articles in your inbox

Sign Up for Article Alerts