Reply To: PDB HETATM

[Anonymous]

I found a related post in the rosetta++ forum that appears I need to pull the ligand out of the PDB file as if I was doing a Protein-ligand docking. The ligand in my particular example is required for the protein to dock with a different protein which also requires a different ligand.

If I have two PDB files that I want to do Protein-Protein docking where each has a ligand what steps do I need to go through to make sure the ligands are considered in the overall best docking model for the lowest score.