I am running SMOKE for three mechanisms CB05, RACM2 and SAPRC07 using the same emissions input files. The merge files it produces (CMAQ input files) for RACM2 and SAPRC07 runs does not contain NO or NO2 species. CB05 output does contain NO and NO2. Any clue what is the problem here?
Check how you have configured your inventory table (INVTABLE) and the speciation profiles you are using for each mechanism and compare them.