Why did some carbon atom names change in the Neu5Ac units ?
ANSWER The atom names of the two first carbons (and of the atoms linked to these two carbons) were changed in the Neu5Ac units (“4sa.prep” and “sa.prep” GLYCAM files) as it follows: GLYCAM atom names Accelrys atom names (new USER FRAGMENT and RESIDUE libraries) C1 C2 O1A O2A O1B O2B C2 C1 => used in glycosidic linkage H2 H1 In the new Accelrys USER FRAGMENT and RESIDUE libraries we built, each glycosidic linkage between two monosaccharides is realized between the C1 atom of the first sugar and an oxygen (position 2, 3, 4 or 6, for instance) of the second sugar. In Sialic acid (Neu5Ac) units, the C2 atom is the one that is implied in the glycosidic linkage. In order, to keep homogeneous rules between the diFFerent sugars (Glc, Gal, Man and Neu5Ac) which allow compatibility and recognition between the USER FRAGMENT and RESIDUE libraries, the atom name of the C1 and C2 atoms were interchanged for the “SA4” and “SA0” Accelrys units.
