When setting up the FEP and MSLD simulation protocols, it is necessary to make the window containing the appropriate ligand or complex data active in order for it to be chosen in the protocol parameter. To make it easier to switch between the windows, dock the floating protocol dialog using the minimize icon to the right of the protocol name. The protocol parameter set is added to the bottom right of the client and the different windows can be selected to enter the parameter values.
After filling in the parameters, the protocol can be run with the green run arrow in the toolbar (or by right-clicking in the parameter window). Alternatively if you prefer to run as a floating protocol, you can click on the toggle window docking icon above the parameters next to the pushpin and it will return the parameter set to the floating position.