I am having a hard time being a beginner to docking simulations. I can run successful docking with proteins without having a cofactor using tutorials and guides. Now I have a heme protein with heme bound in the active centre and a Mg ion in there as well. If I manually remove heme and Mg from the protein and prepare the protein pdbqt for docking, it works fine. But if I leave heme in there, I get errors. Can someone please give a step by step instructions how to prepare the heme proteins (with bound heme and Mg in there) for docking with a substrate/ligand.

Thanks