Dear Xuewu,

Not easily, I’m afraid. In theory heparin *could* be handled by the GLYCAM force field ISOLDE uses for glycosylation sites, but its template scheme is entirely different from the residue representation in the PDB - in GLYCAM, each sulfate and the reducing-terminal hydroxyl are treated as extra residues tacked on to the sugars. Would take a bit of careful special-purpose code to support.

If your heparin chain is reasonably short, you might get reasonable results by treating it as a single large residue and parameterising with the “isolde param” command.

All the best,

Tristan