Hi Wu,
Not sure if it helps you or not, but what I am doing in same situation is
trying to define the required modifications as different treatments
(if possible) just in one FILEX, doesnot take that much time to run
all the treatments through DSSAT shell, then I open the output file
(e.g. Overview.out) in Excel, afterwards, a piece of VB codes in its Macro
can do magic and you may do anything you want with model's output data.
Regards
Mohammad