You need more prep files. Go to the site below and look in the "Special Releases" section. You need the GlcNS prep file. Load that in your leap session.
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 GYS residue is unknown):
Warning: Unknown residue: 6YS number:2 type: Terminal/beginning…
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.
Athens, GA USA