[EMBOSS] How to modify a program?

[Tao Song]

Hi,

     I am new to Unix system, so sorry if it is a too simple question.
I need to modify the DIGEST  program (\EMBOSS-4.0.0\emboss\digest)
to change some rules for trypsin digestion. The part of the program that
I need to modify is in another program (EMBOSS-4.0.0\nucleus\embprop.c).
After modify the embprop program I compiled with gcc and got a embprop.o
file. But when I ran the DIGEST program it still give the same results and 
didn't
change. Are there some steps that I missed?

     Thanks a lot for your help!

     Regards,

     Tao