diff --git a/src/molecule.cpp b/src/molecule.cpp
index 090ce9e77f..c9155adc7e 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -634,6 +634,10 @@ void Molecule::read(int flag)
       error->all(FLERR,"Molecule file has no Body Integers section");
     if (bodyflag && ndbody && dbodyflag == 0)
       error->all(FLERR,"Molecule file has no Body Doubles section");
+    if (nmolecules > 0 && !moleculeflag)
+      error->all(FLERR,"Molecule file has no Molecules section");
+    if (nfragments > 0 && !fragmentsflag)
+      error->all(FLERR,"Molecule file has no Fragments section");
   }
 
   // auto-generate special bonds if needed and not in file