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Dear Mr./Mrs.
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:
DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4DGlcpNS[3S]a1-4LIdopA[2S]a1-4-OH
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.
Javi