I’m just following up to note that this issue with the namelist and the script was resolved in another thread where it was also raised. There is a typographical error in the released script where the namelist is automatically generated. I inadvertently introduced the error into the script for MCIPv5.0 when I removed the processing for MM5 and changed the name of the namelist variable from “file_ter” to “file_geo”.
The solution is to modify your script to replace “file_ter” with “file_geo” where the namelist is generated. This has been corrected in MCIPv5.1 (released with CMAQv5.3.1).