A new GROMOS force field for hexopyranose-based carbohydrates

Authors

  • Roberto D. Lins,

    1. École Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, CH-1015 Lausanne, Switzerland
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  • Philippe H. Hünenberger

    Corresponding author
    1. Laboratorium für Physikalische Chemie, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
    • Laboratorium für Physikalische Chemie, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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Abstract

A new parameter set (referred to as 45A4) is developed for the explicit-solvent simulation of hexopyranose-based carbohydrates. This set is compatible with the most recent version of the GROMOS force field for proteins, nucleic acids, and lipids, and the SPC water model. The parametrization procedure relies on: (1) reassigning the atomic partial charges based on a fit to the quantum-mechanical electrostatic potential around a trisaccharide; (2) refining the torsional potential parameters associated with the rotations of the hydroxymethyl, hydroxyl, and anomeric alkoxy groups by fitting to corresponding quantum-mechanical profiles for hexopyranosides; (3) adapting the torsional potential parameters determining the ring conformation so as to stabilize the (experimentally predominant) 4C1 chair conformation. The other (van der Waals and nontorsional covalent) parameters and the rules for third and excluded neighbors are taken directly from the most recent version of the GROMOS force field (except for one additional exclusion). The new set is general enough to define parameters for any (unbranched) hexopyranose-based mono-, di-, oligo- or polysaccharide. In the present article, this force field is validated for a limited set of monosaccharides (α- and β-D-glucose, α- and β-D-galactose) and disaccharides (trehalose, maltose, and cellobiose) in solution, by comparing the results of simulations to available experimental data. More extensive validation will be the scope of a forthcoming article. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1400–1412, 2005

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