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Hi Andrew,

It is very strange that we have 0YN, but not 6YN.  I have put this request on the list, for our next update of GLYCAM force field.

If you need to build the 1-6 linkage GlcNH2 now, you can modify the 0YN through tLEaP.

Several steps to do that through tLEaP:

  1. remove H6O.
  2. change atom type of O6 from Oh to Os.
  3. connect O6 with C1 in other sugar with bond command.
  4. Alter the charge on O6 in 0YN.  (charge value of O6 + charge value of H6O - 0.194)

Feel free to let me know if you have further questions.

Best,

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 Andrew Guy <[log in to unmask]>
Sent: Sunday, September 23, 2018 10:10:54 PM
To: [log in to unmask]
Subject: Beta 1-6 linkage for GlcNH2
 
Hi all,

I was wondering if anyone had a prep file for the b1-6 linkage form of the GlcNH2 residue (i.e. 6YN)? The prep files supplied through GlycamWeb only have 0YN/n topologies.

Kind regards,

Andrew