Dear Modeller users, I created several mutants of my protein (which is a homodimeric protein) using the script mutate_model.py.and all has gone perfectly, but I have a problem in introducing a mutation.

I want to introduce mutation in position 321 of both chains. So, I started introducing mutation in chain A using the command: mod9.11 - myprot 321 TYR A <mutate_model.py> myprotTYR321.log and all went OK. When I introduced the mutation in chain B starting from the mutant obtained in the previous step, using the command: mod9.11 - myprotTYR321 321 TYR B <mutate_model.py> myprotTYR321TYR321.log MODELLER gave me the following error message: OverflowError:check_inf__E> Atom 5347 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated.

The strange thing is that if I start introducing the mutation from chain B using the command: mod9.11 - myprot 321 TYR B <mutate_model.py> myprotTYR321-B.log MODELLER stops with the following error: OverflowError:check_inf__E> Atom 5345 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated.

I had a look at the original structure; atoms 5345 and 5347 are, respectively, atoms CB and O of the residue preceding the mutant one, and no apparent problems are present in the protein structure (no distortions, no aberrant structures - the residue is inserted into a beta sheet). But assuming that I have a problem on my structure, why the problem is not in the same atom when I start mutating from chain A or from chain B, considering that the procedure involves exactly the same residue?

Thanks a lot for your help, best regards Anna