diff --git a/python/ctsm/site_and_regional/tower_site.py b/python/ctsm/site_and_regional/tower_site.py
index 1679df83e9..1f0bb93b24 100644
--- a/python/ctsm/site_and_regional/tower_site.py
+++ b/python/ctsm/site_and_regional/tower_site.py
@@ -391,11 +391,13 @@ def run_case(
                 case.set_value("RUN_TYPE", "hybrid")
 
             if run_type == "postad":
+                case.case_setup()
                 self.set_ref_case(case)
                 case.set_value("STOP_N", run_length)
 
             # For transient cases STOP will be set in the user_mod_directory
             if run_type == "transient":
+                case.case_setup()
                 if self.finidat:
                     case.set_value("RUN_TYPE", "startup")
                 else: