On 2/13/18 7:30 AM, email@example.com wrote: > I have been testing whether I could use Modeller to minimize a > protein-protein complex.
Modeller's strength is satisfying a bunch of distance restraints. It's not a great general purpose dynamics package - for that you'd be better off using something like CHARMM or GROMACS. Your script looks fine but you haven't given Modeller any restraints between the receptor and ligand, so there's nothing to pull them together. In a regular MD package you might expect solvent, dispersion, or electrostatics to do this, but Modeller doesn't model any of those interactions.
Ben Webb, Modeller Caretaker