I have been trying to use Join Models to make a C-N bond between the globular domain of a protein and a region of it (a C-terminal tail) whose structure I simulated using MD.

However, when I do the joining with Join Models C-N bond option, I get some serious steric clashes. I have tried to resolve them by hand by adjusting the bond's torsion and angles but it is too complicated.

Other than trying to use other software to minimize clashes, I think I might have to use a brute force method and try a bunch of the structures my MD generated until one of them works.

So what I am trying to do now is write a script to do the model joining automatically with many different structures that I generated, and return the one with the least number of clashes.

But I haven't been able to find a command line equivalent of the Join Models window.. I was wondering if you know if such a command exists, if not what combination of commands would work? (for repositioning the models and forming the bond)

Thanks!