Dear Sachin

If you have prime Module of Schrodinger, then you can remodel the protein and minimize it in Schrodinger.

Otherwise you have to remodel the protein using Either Modeller or SwissModeller or any other software and then Minimize the protein in Schrodinger.

Or you can also use Chimera to minimize protein using Conjugate and Steepest Descent Minimization.

You need to have Prime license to run the protein minimization.