NDLI: GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates

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GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates

Content Provider	PubMed Central
Author	Kirschner, Karl N. Yongye, Austin B. Tschampel, Sarah M. Jorge, GonzÁlez-outeiriÑo Daniels, Charlisa R. Foley, B. Lachele Woods, Robert J.
Copyright Year	2007
Abstract	A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both α- and β-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies.
Related Links	http://dx.doi.org/10.1002/jcc.20820
Ending Page	655
Page Count	34
Starting Page	622
File Format	PDF
ISSN	01928651
e-ISSN	1096987X
Journal	Journal of computational chemistry
Issue Number	4
Volume Number	29
Language	English
Publisher Date	2008-03-01
Access Restriction	Open
Subject Keyword	Chemistry(all) Computational Mathematics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Chemistry Computational Mathematics

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