Add options for AMBER TI restraints

[IAlibay]

As a means to test the AMBER GPU-TI code for Boresch restrained TI simulations, it would be useful to use the code to dump out an AMBER topology that has fictitious bonds added via parmed (see the setBond, setAngle and addDihedral + timerge commands). This should allow us to do a set of transformations where we:

A) Transform the system into a bonded one.
B) Do a one or two step charge/vdw perturbation.

Some of the issues here is that the MBAR code may not work properly, but it is worth trying just in case (if anything it'd make a nice tutorial).