Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates.
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.
Eklund
Robert
R
Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden.
Widmalm
Göran
G
D002236:Carbohydrate Conformation; D009682:Magnetic Resonance Spectroscopy; D019563:Mechanics; D009844:Oligosaccharides / Q000737:chemistry*
D009844:Oligosaccharides