Take a look at one of the processor-specific log files, e.g., CTM_LOG_000. Look for the section where emissions are being read, and check to see if the model reports that key species are not found. What mechanism did you use in compiling the model, and does that match your emissions species?
If this does not help, provide more details, including model version and log files. Please also see the “PLEASE READ before posting” message.