Thank you for your response but I want to use modeller for the minimization of the energy

I dont know there is any script in modeller does EM. well you can use advance modelling to refine your loop https://salilab.org/modeller/tutorial/advanced.html.

otherwise you have to do EM of your modelled protein by using Gromacs or some available web sever http://www.yasara.org/minimizationserver.htm  

Thank you so much Navneet Chaturvedi 

Syntax use for loop refining or optimization

# Loop refinement of an existing model

from modeller import *

from modeller.automodel import *

log.verbose()

env = environ()

# directories for input atom files

env.io.atom_files_directory = './:../atom_files'

# Create a new class based on 'loopmodel' so that we can redefine

# select_loop_atoms (necessary)

class MyLoop(loopmodel):

# This routine picks the residues to be refined by loop modeling

def select_loop_atoms(self):

# 10 residue insertion

return selection(self.residue_range('273', '283'))

m = MyLoop(env,

inimodel='TvLDH-mult.pdb', # initial model of the target

sequence='TvLDH') # code of the target

m.loop.starting_model= 1 # index of the first loop model

m.loop.ending_model = 10 # index of the last loop model

m.loop.md_level = refine.very_fast # loop refinement method; this yields

# models quickly but of low quality;

# use refine.slow for better models

m.make()