Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 31, Issue 4, Pages 671-690Publisher
WILEY
DOI: 10.1002/jcc.21367
Keywords
empirical force field; drug design; computational chemistry; medicinal chemistry; molecular modeling; molecular dynamics; computer aided drug design
Categories
Funding
- NIH [GM51501, GM070855, CA107331, CA120215, HL082670]
- NSF [CHE-0823198]
- Direct For Mathematical & Physical Scien
- Division Of Chemistry [0823198] Funding Source: National Science Foundation
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The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform all-CHARMM simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 31: 671-690, 2010
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