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Hi Senal,

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.

Best regards,

Xiao


Xiaocong Wang
Complex Carbohydrate Research Center
The University of Georgia
315 Riverbend Road,
Athens, GA, 30602
Tel: (706) 254-7958
E-mail: [log in to unmask]

From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Senal Dinuka <[log in to unmask]>
Sent: Friday, October 19, 2018 12:43:57 AM
To: [log in to unmask]
Subject: Simulating cyanogenic glucoside
 
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

Thank you