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Subject:
Simulating cyanogenic glucoside
From:
Senal Dinuka <[log in to unmask]>
Reply To:
Users of GLYCAM & GLYCAM-Web <[log in to unmask]>
Date:
Fri, 19 Oct 2018 00:43:57 -0400
Content-Type:
text/plain
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text/plain (6 lines) 
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

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