I guess you have the mutation at the interface of the PPI , so what I would do is to take only the interface of the wild type and extract only the interface of the mutant, then run a normal mode analysis, for the NMA, you could use this server http://biosig.unimelb.edu.au/dynamut2/.

I'd advise you do use alchemical free energy simulations.

Didier Barradas : If using NMA, why would you cut parts of the proteins? Wouldn't it change completely the results? Was it ever tested?

Isaure Chauvot de Beauchêne I'm assuming the mutation is at the interface, usually, interfaces are flat and not very extensive ,I know some attempts to use the complete Protein complex and run MD simulations , and the energy calculation gets overtaken by other factors. some other attempts use other software such al FoldX but then the size of the complex becomes the limiting factor. Using the interface is not a bad idea as it should have symmetry complementary. Was it ever test it the way I proposed? Not really, but depends on the user and the end scope, What if they do not know any knowledge of alchemical free energy simulations or just need something just descriptive, yes, it is circumstantial and this is just an option