Hello,
I am attempting to dock a G-protein with a protein that accelerates GTPase activity of the G-protein. I have conducted runs with the GTP and Magnesium-free structure – however I feel that the next step would be to include the ligands. I worry about distortion of the geometry around the magnesium ion and the GTP using a model that lacks these ligands.
Now I could just run with default parameters since I know that the protein ligand does not interact at all with the GTP or the Magnesium (which I have split into different chains) – however, I am hesitant to do so because the GTP and Magnesium should ideally be fixed using restraints. The proper geometry must be preserved in the docking to be as accurate as possible. For the most part, there is no interaction between the side chains of the residues that bind GTP/Magnesium and the protein docking partner (the GTPase accelerating protein).
If I ran HADDOCK such that docking is only conducted on chain A in protein 1 (where chains B and C are GTP and Mg+2, respectively), is there still a chance that the geometry might not be preserved in the final result? I can’t seem to apply restraint files with the entry level access (i.e. not Guru or Expert). Should I request for more privileges?