Is it possible to get support for glucosamines/chito-oligos in HADDOCK?
Dear Magnus,
Thanks for your interest in using HADDOCK for your research.
Which glucosamine(s) exactly do you want support for ?
You could treat them as small-molecules, and both topology and parameters will be generated for them.
Hi there
We do have N-Acetylglucosamine supported, so it should be straightforward to implement glucosamine.
The current list of supported glycans can be found at:
I will open an issue to capture this request.
I build chitosan oligosaccharides using CHARMM and then I modify the pdb to fit HADDOCK. I would like support for GCS RCSB PDB - GCS Ligand Summary Page, so that HADDOCK doesn’t convert my amine into carbons.
While I can parameterize the entire 14-mer as a single small molecule via ATB/PRODRG, this flattens the glycan into a single residue. Doing so prevents me from using HADDOCK’s advanced sampling features—specifically, defining per-residue flexibility (e.g., setting the core rings as fully flexible and the termini as semi-flexible) and targeting AIRs to specific internal rings, which is crucial for a ligand of DP14, which I know is long.
Thank you!
Could you share one of your PDB file (e.g. the 14mer) so that we can test things?
Yes, but bioexcel tells me that I’m to new a user to upload files.
Can I send by e-mail?
email is fine - you should be able to find my email 
I hope you have received my e-mail?
Yes I did - thanks - but no time yet to check things - sorry.
No worries, I was just worried the e-mail didn’t make it through.