[modeller_usage] align sequences

Hi, I have several proteins (AA sequences) that I would like to  
compare for possible interactions but I do not know where they will  
bind.  I looked at the example:
proteinA; AAAAAAAAAAAAA------------
proteinB; -------------BBBBBBBBBBBB
chimera;  AAAAAAAAAAAAABBBBBBBBBBBB

but this didn't help as I don't know where they will interact/bind.   
I've tried a few times to enter the sequences, but obviously am  
getting error messages for incorrect format.  Wondering if anyone knew  
how to solve this???
Thanks for your help, rgerber