Dear all,
 
Let's say that I have two pdb files of protein A and protein B and that approximate interactions of the two proteins are known. Then can I get a complex structure using MODELLER by restraining the distances of two or three interactions between A and B in the top file with the following type of alignment file?
 
>P1;A
structureX:A
--AAAAA--/------------*
>P1;B
structureX:B
-------------/--BBBBB--*
>P1;AB
sequence:AB
--AAAAA--/--BBBBB--*
 
Cheers,
Han