We are trying to build “heparin sulfate octasaccharide” using its GLYCAM website (GAG builder Heparin/Heparan sulfate) and use it with AMBER-16 and xleap; but by the moment, this is impossible.
Exactly, we are using the next sequence:
The problem is in the residue DGlcpNS[3S]a1 (named by GLYCAM builder as ‘6YS’), which is not detected in xleap and the following message appears (The YS residue is unknown):
Warning: Unknown residue: 6YS number: 2 type: terminal/beginning
... relaxing end constraints to try for a dbase match
Warning: -no luck
Warning: one sided connection. Residue (default_name) missing connect1 atom.
Can you help us?
If you need anything else, please let me know.
Kind regards and have a good day.