Frcmod should not misapply terms to the new possible combinations

[bieniekmateusz]

Inspired by #71

Read the left.prmtop and right.prmtop and compare it to the morph.prmtop - to ensure that the new forcefield applies them correctly, and does not misapply any of the existing rules.

[bieniekmateusz]

One possible approach might be taking the .prmtop files from each ligand separately and merging them manually, rather than introducing the inbetween step with the .frcmod. Since the assumption is that the original forcefield prmstop is completely correct. This would probably not be easy though.

A good measure for this is to extract the parameters and functions (angles/dihedrals etc) which are applied on each atom and compare them initially and at the end.

[bieniekmateusz]

Most importantly, it would be useful to have a check for this, which should not be too difficult to write. Just so that we do not let the cases where it does not work through.

[bieniekmateusz]

After further thought, this should not be a problem, because NAMD most likely does not respect these terms and ignores them. So it should be all fine - however - saying that, it would be very easy to apply a test for this case. So I might do jus that.

[bieniekmateusz]

So Shunzhou confirmed that NAMD will not respect these values.

Another question in this topic is to ensure that the new term does not misapply. For example, is it possible that to run into two .frcmod lines that apply to the same atom combination, but have different force?