[modeller_usage] Mutate and refine residue placement

Hello Modeller.

Having successfully install the newest version of Modeller on my new machine (I ran some test cases), I would like to attempt the construction of a mutant of my protein using the tutorial: http://salilab.org/modeller/wiki/Mutate%20model. However, my protein has metal and DNA with it and, so, I am not sure how Modeller will deal with this. Can you inform me? I am worried that Modeller will simple fail with the error that it can not recognize certain atoms. If it does, is there away I can get around this? Could I do only a local (around the mutated site) minimization only, ignoring the rest of the protein?

I tried to investigate this in the archives but didn't find it. Sorry if this is a repeat.

Thanks ,Steve