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?