diff --git a/rmgpy/data/base.py b/rmgpy/data/base.py
index 860a5c6254..42b34ee471 100644
--- a/rmgpy/data/base.py
+++ b/rmgpy/data/base.py
@@ -371,9 +371,9 @@ def loadOldDictionary(self, path, pattern):
                     self.entries[label].item = makeLogicNode(' '.join(lines[1:]) )
                 # Otherwise convert adjacency list to molecule or pattern
                 elif pattern:
-                    self.entries[label].item = Group().fromAdjacencyList(record)
+                    self.entries[label].item = Group().fromAdjacencyList(record,saturateH=True)
                 else:
-                    self.entries[label].item = Molecule().fromAdjacencyList(record)
+                    self.entries[label].item = Molecule().fromAdjacencyList(record,saturateH=True)
         except InvalidAdjacencyListError, e:
             logging.error('Error while loading old-style dictionary "{0}"'.format(path))
             logging.error('Error occurred while parsing adjacency list "{0}"'.format(label))
diff --git a/rmgpy/data/kinetics/family.py b/rmgpy/data/kinetics/family.py
index bdf154f492..b5db0c6cda 100644
--- a/rmgpy/data/kinetics/family.py
+++ b/rmgpy/data/kinetics/family.py
@@ -1168,7 +1168,7 @@ def __generateProductStructures(self, reactantStructures, maps, forward, **optio
             radical1 = atom1.radicalElectrons
             spin1 = atom1.spinMultiplicity
             
-            if radical1 > 1 and radical1 < 4:
+            if atom1.label != '' and radical1 > 1 and radical1 < 4:
                 
                 if radical1 == 2 and spin1 == 3:
                     atom1.setSpinMultiplicity(1)
@@ -1245,7 +1245,7 @@ def __generateProductStructures(self, reactantStructures, maps, forward, **optio
                 radical2 = atom2.radicalElectrons
                 spin2 = atom2.spinMultiplicity
             
-                if radical2 > 1 and radical2 < 4:
+                if atom2.label != '' and radical2 > 1 and radical2 < 4:
                     
                     if radical2 == 2 and spin2 == 3:
                         atom2.setSpinMultiplicity(1)
diff --git a/rmgpy/rmg/model.py b/rmgpy/rmg/model.py
index 36c0bcffa4..5d6679086e 100644
--- a/rmgpy/rmg/model.py
+++ b/rmgpy/rmg/model.py
@@ -1040,7 +1040,6 @@ def prune(self, reactionSystems, fluxToleranceKeepInEdge, maximumEdgeSpecies):
 
         numCoreSpecies = len(self.core.species)
         numEdgeSpecies = len(self.edge.species)
-        numPdepNetworks = self.networkCount
 
         # All edge species that have not existed for more than two enlarge
         # iterations are ineligible for pruning
@@ -1057,7 +1056,7 @@ def prune(self, reactionSystems, fluxToleranceKeepInEdge, maximumEdgeSpecies):
                 if maxEdgeSpeciesRates[i] < rate:
                     maxEdgeSpeciesRates[i] = rate
 
-            for i in range(numPdepNetworks):
+            for i in range(len(self.networkList)):
                 network = self.networkList[i]
                 rate = reactionSystem.maxNetworkLeakRates[i]
                 # Add the fraction of the network leak rate contributed by