I'm trying to predict where a small molecule ligand will dock to a dimer protein and am trying to do a completely blind search. To do so, I use the start from mover to place the ligand at the center of my protein and then the initial perturb option in the Transform mover to randomly move it outside the protein. Since the protein is not circular, depending on which direction the ligand goes, it can end up pretty far from the protein. If this is wrong, or there is a better way to do it, feel free to let me know.
As for my main question, I was wondering if there was a way to either filter out structures in which the ligand was not in contact with the protein or a way to constrain the ligand to the surface of the protein during the initial perturb move.
I have currently tried using DSasa as an indirect way of filtering, but it doesn't appear to be working. I did notice that there is ligand_is_touching_X field in the scorefile but have no idea where that originates from and so cannot figure out how to incorporate that into a filter.