Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

ABSTRACT: Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, 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 charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such a

SUBMITTER: Vanommeslaeghe K 

PROVIDER: S-EPMC3528824 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature