Fix very subtle bug in Amber prmtop with NBFIX

Some topology files have some of the nonbonded pairs in the Lennard-Jones matrix
pointing to a 0 entry in the HBOND_ACOEF and HBOND_BCOEF arrays. This commit
simply skips over those entries, having previously checked that all entries in
the 10-12 sections are 0.  There is actually an example of this already in the
test suite (see ff14ipq.parm7), but this fortuitously did not cause any
difference in those test results.

The reason this bug is not evident in that test case is because the A- and
B-coefficients pulled when the index was -1 (later decremented to -2) was also
coincidentally 0. However, if this was not the case (as it does not *have* to
be), then who knows what could happen.

This also adds more of a check against 10-12 topology files. ParmEd actually
supports using the 10-12 potential in OpenMM when specified in the Amber prmtop,
but it is sufficiently rare that it is not worth porting to OpenMM, IMO.

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py

@@ -305,6 +305,10 @@ class PrmtopLoader(object):
             return self._nonbondTerms
         except AttributeError:
             pass
+        # Check if there are any non-zero HBOND terms
+        for x, y in zip(self._raw_data['HBOND_ACOEF'], self._raw_data['HBOND_BCOEF']):
+            if float(x) or float(y):
+                raise Exception('10-12 interactions are not supported')
         self._nonbondTerms=[]
         lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer)
         energyConversionFactor = units.kilocalorie_per_mole.conversion_factor_to(units.kilojoule_per_mole)
@@ -333,6 +337,7 @@ class PrmtopLoader(object):
         for i in range(numTypes):
             for j in range(numTypes):
                 index = int(self._raw_data['NONBONDED_PARM_INDEX'][numTypes*i+j]) - 1
+                if index < 0: continue
                 rij = type_parameters[i][0] + type_parameters[j][0]
                 wdij = sqrt(type_parameters[i][1] * type_parameters[j][1])
                 a = float(self._raw_data['LENNARD_JONES_ACOEF'][index])
@@ -477,6 +482,7 @@ class PrmtopLoader(object):
                     typ1 = atomTypeIndexes[iAtom] - 1
                     typ2 = atomTypeIndexes[lAtom] - 1
                     idx = nbidx[numTypes*typ1+typ2] - 1
+                    if idx < 0: continue
                     a = parm_acoef[idx]
                     b = parm_bcoef[idx]
                     try:
@@ -870,6 +876,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
         for i in range(numTypes):
             for j in range(numTypes):
                 idx = nbidx[numTypes*i+j] - 1
+                if idx < 0: continue
                 acoef[i+numTypes*j] = sqrt(parm_acoef[idx]) * afac
                 bcoef[i+numTypes*j] = parm_bcoef[idx] * bfac
         if has_1264:
@@ -878,6 +885,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
             for i in range(numTypes):
                 for j in range(numTypes):
                     idx = nbidx[numTypes*i+j] - 1
+                    if idx < 0: continue
                     ccoef[i+numTypes*j] = parm_ccoef[idx] * cfac
             cforce = mm.CustomNonbondedForce('(a/r6)^2-b/r6-c/r^4; r6=r^6;'
                                              'a=acoef(type1, type2);'
@@ -911,6 +919,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
             for i in range(numTypes):
                 for j in range(numTypes):
                     idx = nbidx[numTypes*i+j] - 1
+                    if idx < 0: continue
                     ccoef[i+numTypes*j] = parm_ccoef[idx] * cfac
             cforce = mm.CustomNonbondedForce('-c/r^4; c=ccoef(type1, type2)')
             cforce.addTabulatedFunction('ccoef',