Hi everybody,
I am trying to build a model of a transmembrane receptor and I get serious problems and obvious steric errors on the loops which connect the TM helices. The alignment is correct on a biological and phylogenetic basis however there are large insertions on the loops. As a result, there are two main errors that appear in the model. First, the loops are modelled as packed between the TM helices and not as free moving segments that can float in the solvent environment and second, in some cases the loops form kind of knots which are obviously wrong. I guess that there must be some kind of parameter within MODELLER that directs the construction towards the maximum intramolecular contact, this is the only way I can explain this wrong output. Does anybody have an idea on the matter?
many thanks,
Vassilis