Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates |
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Authors: | Eklund Robert Widmalm Göran |
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Affiliation: | Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden. |
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Abstract: | Parameterization of the phi and omega torsion angles in pyranosidic saccharides was performed based on density functional theory calculations. The modified CHARMM force field, which is referred to as PARM22/SU01, was tested on a glucosyl trisaccharide. A molecular dynamics simulation of the oligosaccharide with explicit water as solvent was performed to investigate the conformational flexibility. Protonz.sbnd;proton distances and heteronuclear spin-spin coupling constants were calculated from the trajectories and showed good agreement to those previously determined by NMR spectroscopy. |
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Keywords: | Molecular mechanics smallcaps" >charmm Conformation Density functional theory NMR |
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