Hi Partha, Do you want to completely remove the restraints around the active site? You can do that with this block in the parameter file: geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } Where you see None, enter atom selections. The restraints of the given type (angles, dihedrals, etc.) involving the corresponding selected atoms will be removed. You can have multiple lines for each restaint type. You can check the result by inspecting the .geo file. It is a bit big, but the atom labels are formatted exactly the same way as you see them in your pdb file, e.g. angle: (2, 1, 4) " C LEU A 325 " " CA LEU A 325 " " CB LEU A 325 " angle_model: 110.834 angle_ideal: 110.1 weight: 0.277008 you can search for " C LEU A 325 " in your pdb file or vice versa. You could also try diff orig.geo mod.geo to check the effect of your selections. Ralf