Dear modellers
i am trying to build models for a single missing loop on a known xtal structure and i have a couple of questions
1) can modeller introduce hydrogen bonds in loop modelling (is it true that all-hydrogen models are not fully implemented for loop modelling)?
2) is it true that modeller does not include hydrophobic packing factors? i currently have models with fully exposed hydrophobics that have similar 'modeller objective function' to those with more buried hydrophobic sidechains.
i'm a modeller newbie, and above is based on my understanding (i.e. likely flawed) of the mail archives and docs. perhaps i should be introducing some 'artificial' distance restraints to mimic the effects of the above interactions?
any advice greatly received.
cheers dave gell