HADDOCK run failed due to topology file


I’m trying to dock a small peptide and a small polysaccharide. Using the Guru interface as I have NOE distance restraints.

The pdb files imported were for the peptide just a pdb ID and pointing to the right chain, and for the polysaccharide I have extracted it from a pdb structure and added the hydrogens in Pymol (probably not very legant way of doing it). Unfortunately Acpype doesn’t seem to like my ligand and PRDRG doens’t deal with hydrogens (meaning is not great for NOE restraints). Does anyone have a tip on how to get correct topology files?

Best wishes

Define your noes to the heavy atoms for the Oligosaccharides- only option for the server

Thanks, will give it another try (TBH your warned before).

Another option could be to use of old, never published server to build oligosaccharide topologies for CNS:


It comes without warranty :slight_smile:

You would have to use those in a local version of HADDOCK, basically manually adding the PDB files and correspond files (file.cns…) in the begin dir.

And specifying the proper parameter file for the oligosaccharide in run.cns

I considered that this morning, unfortunately the saccharide has some sulphation patterns and I don’t think the available building blocks will allow me.to get it.

Thanks for he feedback though.

Best wishes