How can we build a multidomain protein from smaller fragments

Hi
I have a multidomain protein of more than 2000 residues..I have generated the fragments (domains) with I-tasser and tried to connect by giving them as templates for a new I-tasser run. But it seems that I need to stick with the below 1500 limit that I-tasser can accept, which is not possible as my protein is larger. .is there is a turn around this problem or I need to connect them manually..Thanks in advance