fixed parseElements

wrappers/python/simtk/openmm/app/forcefield.py

@@ -1679,13 +1679,11 @@ class NBFixGenerator(object):
 
     def __init__(self, forcefield):
         self.ff = forcefield
-        self.parmas = ForceField._AtomTypeParameters(forcefield, 'NonbondedForce', 'Atom', ('charge', 'sigma', 'epsilon'))
-        # I don't need charge but if I don't list it I get an error when calling parseDefinitions. ValueError:
-        # NonBondedForce: <UseAttributeFromResidue> specified an invalid attribute: charge
         self.types1 = []
         self.types2 = []
         self.emin = []
         self.rmin = []
+        self.nbfrc = [f for f in forcefield._forces if isinstance(f, NonbondedGenerator)]
 
     def registerNBFix(self, parameters):
         types = self.ff._findAtomTypes(parameters, 2)
@@ -1708,30 +1706,30 @@ class NBFixGenerator(object):
 
         for nbfix in element.findall('NBFix'):
             generator.registerNBFix(nbfix.attrib)
-        generator.params.parseDefinitions(element)
 
-    def createForce(self, sys, data, nonbfrc, nonbondedMethod):
+    def createForce(self, sys, data, nonbondedMethod):
         """
         Parameters
         ----------
         sys
         data
-        nonbfrc: NonbondedForce
-            NonBondedForce for the "standard" nonbonded interactions. This will be modified (specifically, L-J ixns
-            will be zeroed)
         nonbondedMethod: NonbondedMethod (e.g., NoCutoff, PME, etc)
             The nonbonded method to apply here. Ewald and PME will be interpreted as CutoffPeriodic for the
             CustomNonbondedForce
         """
+        # NonBondedForce for 'standard' nonbonded interactions. This will be modified
+        nonbfrc = self.nbfrc[0]
+
         # We need a CustomNonbondedForce to implement the NBFIX functionality.
         # First derive the lookup tables
+
         lj_indx_list = [0 for atom in data.atoms]
         li_radii, lj_depths = [], []
         num_lj_types= 0
         lj_type_list = []
         for i, atom in enumerate(data.atoms):
             atype = data.atomTypes[atom]
-            values = self.params.paramsForType[atype]
+            values = nonbfrc.params.paramsForType[atype]
             if lj_indx_list[i]: continue # already assigned
             num_lj_types += 1
             lj_indx_list[i] = num_lj_types
@@ -1746,7 +1744,7 @@ class NBFixGenerator(object):
                     lj_indx_list[j] = num_lj_types
                 elif not atype in self.types1 or self.types2:
                     # Only non-NBFix atom types can be compressed
-                    values = self.params.paramsForType[atype2]
+                    values = nonbfrc.params.paramsForType[atype2]
                     ljtype2 = (values['sigma'], abs(values['epsilon']))
                     if ljtype == ljtype2:
                         lj_indx_list[j] = num_lj_types