Reconciling MA'AT and molecular dynamics models of linkage conformation in oligosaccharides.

Abstract

MA'AT conformational models of the phi torsion angles of O-glycosidic linkages differ from those obtained from MD simulation. To determine the source of the discrepancy, MA'AT analyses were performed using DFT-derived equations obtained with and without psi constraints. The resulting phi models were essentially the same, indicating a force-field problem. Circular standard deviations (CSDs) were found to provide reliable estimates of torsional averaging.