Add support for Amber prmtop files with NBFIX

As of AmberTools 12, tleap has had the ability to implement specific pairwise Lennard Jones parameters, which is used by the new ff14ipq force field.  Also using ParmEd, off-diagonal elements of the LJ matrix can be obtained as well (and such an approach is used to implement the new Chen-Garcia RNA force field which seems promising).

Previous behavior was to ignore off-diagonal elements, and the existence of off-diagonal elements did not result in any kind of error.

The typical `NonbondedForce` object is still used to account for 1-4 exceptions and is used for the Lennard-Jones interactions when no off-diagonal elements are detected.

The `CustomNonbondedForce` implemented here uses the A- and B-coefficient formulation of the LJ potential which allows slightly more flexibility in the functional potential by allowing purely-repulsive or purely-attractive potentials to be used (although no FFs that I'm aware of utilize this).
> Even if the forces of individual atoms are not entirely negligible (which it usually is), as long as particle density is mostly isotropic past the cutoff the net force on any single particle should average out to zero, anyway..
> 

Good thing we're never simulating anisotropic systems where solute diameters are greater than the cutoff (often 9A), like proteins or anything...

Joking aside, this can actually be a significant problem for both energy conservation and it's fluctuations, especially if one tried to use a metropolized form of any integrator to sample from the actual Boltzmann distribution.  Codes like Amber often use thermostats that simply mask the issues that arise from omitting cutoffs from Lennard jones interactions.  Don't forget the surface of the sphere goes as r^2 and its integral as r^3, so the error falls off much more slowly than r^-6.  And the integrators we use are only valid in the case where we have twice differentiable potentials, which is violated as soon as you use a cutoff like this.