I don't think GLYCAM has parameters for cyano group. I suggest that you use gaff for cyanogenic moiety. You also need atomic charges for your molecules. Please check GLYCAM06 paper for procedures to derive charges
for molecules in GLYCAM06.
Complex Carbohydrate Research Center
The University of Georgia
315 Riverbend Road,
Athens, GA, 30602
Tel: (706) 254-7958
Dear GLYCAM users,
I have been trying to simulate a cyanogenic glucoside (linamarin) bound protein with AMBER. Since GLYCAM doesn't offer parameters for a cyanogenic moiety I renamed the sugar portion as "0GB" to comply with GLYCAM residue naming and the rest of the ligand "UNK".
But so far I was unable to generate parameters for the entire system successfully. Am I following a correct approach? I appreciate any guidance on handling this matter