diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst
index 5d1e7c872c..f0dc857dcd 100644
--- a/doc/src/create_atoms.rst
+++ b/doc/src/create_atoms.rst
@@ -536,6 +536,11 @@ command.
 A rotation vector specified for a single molecule must be in
 the z-direction for a 2d model.
 
+For :doc:`molecule templates <molecule>` that are created from multiple
+files, i.e. contain multiple molecule *sets*, only the first set is
+used.  To create multiple molecules the files currently need to be
+merged and different molecule IDs assigned with a Molecules section.
+
 Related commands
 """"""""""""""""
 
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index 75c30bd0b8..8e21c19c9a 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -179,7 +179,8 @@ void CreateAtoms::command(int narg, char **arg)
       if (imol == -1)
         error->all(FLERR, "Molecule template ID {} for create_atoms does not exist", arg[iarg + 1]);
       if ((atom->molecules[imol]->nset > 1) && (comm->me == 0))
-        error->warning(FLERR, "Molecule template for create_atoms has multiple molecules");
+        error->warning(FLERR, "Molecule template for create_atoms has multiple molecule sets. "
+                       "Only the first set will be used.");
       mode = MOLECULE;
       onemol = atom->molecules[imol];
       molseed = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);