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:
- remove H6O.
- change atom type of O6 from Oh to Os.
- connect O6 with C1 in other sugar with bond command.
- 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.
Complex Carbohydrate Research Center
The University of Georgia
315 Riverbend Road,
Athens, GA, 30602
Tel: (706) 254-7958
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.