I am working on docking a glycoprotein with four branched glycan chains linked to protein ASN residues. The docking completes successfully however in the output structures the terminal residue of the glycan, SIA, has become unbonded and wandered away from the glycan chains. In my pre-docking structures the SIAs are in place and bonded. I read that Haddock has recently started supporting glycans and the structures look good aside from this issue; any advice on how to keep the SIA bound to the previous GAL would be appreciated.
Thank you very much,