A quantum mechanically derived all-atom force field for pyranose oligosacchrides. AMBER parameters and free energy simulations

摘要

In this paper we extend our previously reported parameterization of carbohydrates to an all-atom AMBER-like force field suitable for modeling oligosaccharides. Parameters were developed from Ab initio calculations on small model systems having structures characteristic of 1,2-, 1,3-, and 1,4-glycosidic linkages and monosaccharides to give a complete parameter set for pyranose mono- and oligosaccharides. The accuracy of the parameter set was assessed by free energy calculations on various simple sugars and disaccharides.