This DS 3.0P/P8CU2  protocol takes a complete molecule as input then calcuates the energy  (standard energy calculation options are available) the results are returned color coded by the sum of forces experienced by each atom.  This is a convenient way to visualize any "hot spots" that might need further optimization.

Installation:  Download the protocol then add to DS  In Discovery Studio   go to the Protocol Explorer, right-click on the folder you want to add the protocol to, choose Import..., navigate to the location of the this protocol file and enter it then click  "Open".  After this step the protocol will be available from either Pipeline Pilot or Discovery Studio.  Because of the visual nature of this protocol it is expected to be of most use when run from Discovery Studio.  However, the output structure file from running this script will have the "Isotropic Displacement" atom property replaced with the "force-on-atom" values.