SimTk/openmm — pull request #524 by swails (2014-07-11 19:51:57+00:00)
Title: 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).