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
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()
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