Hello @munshimdrasel ,
In this other thread where @tlspero helped you troubleshoot an MCIP issue, you mentioned that you had previously run CMAQ successfully for the entire U.S. but now you have rerun WRF for a smaller domain and reprocessed those new WRF fields through MCIP.
Are you trying to use these new MCIP files for the CMAQ run you are asking about here? If yes, did you also reprocess all other gridded input files (emissions, etc.) for this new domain? In your run script, did you update the grid name and GRIDDESC file to use the one generated by MCIP for your new domain rather than the one you had used in your CMAQ run for the entire U.S.?