[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