On 05/26/2012 07:16 AM, M wrote: > I have a problem concerning the step of evaluating my model. I'm > using the whatif server > (http://swift.cmbi.ru.nl/servers/html/index.html). Most of the scores > are fine, but there are many abnormally short interatomic distances > according to whatif. The problem doesn't result from the alignment. > Is it possible that it is a result of different parametrization used > by modeller (or by the implemented CHARMM force field)?
The CHARMM force field in Modeller is fundamentally the same as in CHARMM 22 itself, so this is unlikely to be the problem. The other terms in the force field derive from the alignment, so if your model is poor either the problem really is in the alignment or the optimizer failed to satisfy all the restraints. The latter problem is generally solved by building a larger number of models.
Ben Webb, Modeller Caretaker