Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates

Parameterization of the φ and ω 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. Protonproton distances and heteronuclear spin–spin coupling constants were calculated from the trajectories and showed good agreement to those previously determined by NMR spectroscopy.