I am working on loading 4c55 into tleap. Some glycan residues can not be recognizable by the force field. So I am trying to build part of glycan with Carbohydrate Builder at http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=1. I want to find the correct residue name of these residues in GLYCAM force field.
But I always forget how to tell α- and β- Glycoside bond and conformation. The following figure is pretty clear to illustrate this (cited from http://chemistry.tutorvista.com/organic-chemistry/glycosidic-linkage.html). If the CH2OH was at the same direction with O in glycoside bond, it’s β, or it’s α.