• RE: distance constraint from fixed cofactor to substrate (ligand to be docked)

    Ilenia,

    The cofactor we include in the protein's PDB file is defined as just a group of HETATM:

        HETATM15065  O1  COF Z   1      11.702  15.566  16.752  1.00  0.00           O 

        …

        TER        

    Is there something else we may need to specify or any special formatting requirements for Gold?

    Hector

     

  • RE: distance constraint from fixed cofactor to substrate (ligand to be docked)

    Ilenia,

    I took your code above and replaced the protein and ligand file names (also changed the atom labels to search for) and I get the same error message - RuntimeError('Cannot find appropriate protein.'). I tried using a mol2 file for the protein (instead of the PDB just in case) but it did not make any difference. As I previously mentioned, if I use a protein atom instead then I can set the distance constraint just fine and I am also using a substructure constraint that works properly. Let me know if you have any other suggestions.

    FYI, I'm using the 2018 CSD API downloaded about a month ago.

    Thanks,

    Hector

     

  • distance constraint from fixed cofactor to substrate (ligand to be docked)

    I have a working docking setup with a substructure constraint between a protein residue atom and the substrate to be docked. However, I need to add a distance constraint between the cofactor (see below) and the same substrate. Attempts to do this result in a runtime error of 'Cannot find appropriate protein.' The code is based on the CCDC docking sample and works properly w/o the distance constraint.

    Information:

     * the 'fixed' cofactor is part of the protein PDB file (Z:COF1)

     * the substrate is the ligand to be docked and is in a separate mol2 file

     * I get the cofactor atom using 

        cofactor_atom = [a for a in self.protein.ligands[0].atoms if a.label=="H24"][0]

      * I get the substrate atom using (after reading the mol2 file it into self.substrate - same approach used for the substructure constraint that works)

        substrate_atom = [a for a in self.substrate.atoms if a.label=="O1"][0]

      * I then try calling the add constraint function which fails (both atoms used are previously found properly)

        self.settings.add_constraint(self.settings.DistanceConstraint(cofactor_atom, substrate_atom))

     

    It looks like the issue is with the cofactor atom being in the protein ligands (if I use a protein residue atom then I can add the constraint). Is there a proper way to define a distance constraint between a cofactor, that is part of the protein pdb file, and the ligand to be docked?

     

    Thanks,

    Hector