I am trying to run Vina-Carb to dock malto-oligosaccharides in enzymes, but the vina-carb does not start correctly and I suspect it is due to the nomenclature in the ligand .pdbqt file.
What is the correct way to prepare carbohydrate ligand files?
So far, I am using this protocol:
1) Build the ligand with Glycam and download the .pdb file.
2) Open the .pdb in AutoDockTools (ADT); this will add hydrogens and torsions. Output it as a .pdbqt file.
3) Run vina-carb with the .pdbqt file.
Thanks, Tjaard Pijning
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