I am using HADDOCK ver 2.4. I would like to dock one pdb file with eight molecules to another pdb file with one molecule. Is it possible?
My second question is that when I tried that, I received a warning about some residues recorded as unknown, UNK. I have no idea how to deal with those residues. How can I know which residue they correspond to? I think I could edit those if I open the pdb file with notepad.
The error message I got is the following:
Error in PDB file.
Issue when parsing the PDB file at line 1722 .
Your PDB contains an unknown residue UNK using ATOM record, please check the HADDOCK library for a list of supported modified residues. Should this be formatted with record HETATM instead?
The pdb file with eight molecules is this one: 5FLC from PDB