loop modeling

Hi all, I whuld like your advice: I build a model of a membrane protein and I want now to do "loop modeling" to few extra cellular and intra-cellular loops. I wonder if this protocol of modeller is the right choice since the model doesn't contain the membrane and I actually ignore the influence of the polar heads. thank's Moshe Amity.

-------------------------------------- Moshe Amity amitaym@mail.biu.ac.il Dep. of Chemistry Bar Ilan University Israel.