diff --git a/src/atom.cpp b/src/atom.cpp
index f30ace174e..08e9639440 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -2129,14 +2129,18 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom, int ilocal, tagint off
 
   // initialize custom per-atom properties to zero if present
 
-  for (int i = 0; i < nivector; ++i) ivector[i][ilocal] = 0;
-  for (int i = 0; i < ndvector; ++i) dvector[i][ilocal] = 0.0;
+  for (int i = 0; i < nivector; ++i)
+    if (ivname[i]) ivector[i][ilocal] = 0;
+  for (int i = 0; i < ndvector; ++i)
+    if (dvname[i]) dvector[i][ilocal] = 0.0;
   for (int i = 0; i < niarray; ++i)
-    for (int j = 0; j < icols[i]; ++j)
-      iarray[i][ilocal][j] = 0;
+    if (ianame[i])
+      for (int j = 0; j < icols[i]; ++j)
+        iarray[i][ilocal][j] = 0;
   for (int i = 0; i < ndarray; ++i)
-    for (int j = 0; j < dcols[i]; ++j)
-      darray[i][ilocal][j] = 0.0;
+    if (daname[i])
+      for (int j = 0; j < dcols[i]; ++j)
+        darray[i][ilocal][j] = 0.0;
 
   if (molecular != Atom::MOLECULAR) return;