Reconciling MA′AT and molecular dynamics models of linkage conformation in oligosaccharides
Reagan J. Meredith, Robert J. Woods, Ian Carmichael, Anthony S. Serianni
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.
Topics & Concepts
Linkage (software)Molecular dynamicsDynamics (music)ChemistryComputational biologyBiologyPhysicsComputational chemistryBiochemistryGeneAcousticsGlycosylation and Glycoproteins ResearchMicrobial Metabolites in Food BiotechnologyPolysaccharides and Plant Cell Walls