diff --git a/rmgpy/rmg/input.py b/rmgpy/rmg/input.py
index 6fe74c9ed3..4824f4331e 100644
--- a/rmgpy/rmg/input.py
+++ b/rmgpy/rmg/input.py
@@ -92,9 +92,12 @@ def database(
 def species(label, structure, reactive=True):
     logging.debug('Found {0} species "{1}" ({2})'.format('reactive' if reactive else 'nonreactive', label, structure.toSMILES()))
     spec, isNew = rmg.reactionModel.makeNewSpecies(structure, label=label, reactive=reactive)
-    assert isNew, "Species {0} is a duplicate of {1}. Species in input file must be unique".format(label,spec.label)
-    rmg.initialSpecies.append(spec)
-    speciesDict[label] = spec
+    #assert isNew, "Species {0} is a duplicate of {1}. Species in input file must be unique".format(label,spec.label)
+    if isNew:
+    	rmg.initialSpecies.append(spec)
+    	speciesDict[label] = spec
+    else:
+	logging.info("Species {0} is a duplicate of {1}. Avoid it and continue calculation ...".format(label,spec.label))
     
 def SMARTS(string):
     return Molecule().fromSMARTS(string)