Hi, 

I followed this modeling template https://salilab.org/modeller/tutorial/basic.html 
is this a correct one ? the script you showed was part of it too 

Bests
Mohammad

On Mon, Jul 23, 2018 at 8:25 PM Modeller Caretaker <modeller-care@salilab.org> wrote:
On 7/20/18 8:59 AM, Mohammad Goodarzi wrote:
> I have a WT protein which I got the structure from the PDB.
> I have a mutation happing on a single point amino acid.
> I want to see how this mutation influence on specific domian. I want to
> know if I am doing it right or not
...
> what step should I follow and or which script should I use ?

This is simple comparative modeling where your target sequence is
identical to your template sequence except for one residue. A script
similar to that at https://salilab.org/modeller/9.20/manual/node16.html
should work just fine. Alternatively, you can try the mutate model
script at https://salilab.org/modeller/wiki/Mutate%20model

        Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage