Hi All,

Finally, I have modified and it  works fine for me.

I made the changes part in bold

import sys

import os

from modeller import *

from modeller.optimizers import molecular_dynamics, conjugate_gradients

from modeller.automodel import autosched

def optimize(atmsel, sched):

for step in sched:

step.optimize(atmsel, max_iterations=200, min_atom_shift=0.001)

refine(atmsel)

cg = conjugate_gradients()

cg.optimize(atmsel, max_iterations=200, min_atom_shift=0.001)

def refine(atmsel):

md = molecular_dynamics(cap_atom_shift=0.39, md_time_step=4.0,

md_return='FINAL')

init_vel = True

for (its, equil, temps) in ((200, 20, (150.0, 250.0, 400.0, 700.0, 1000.0)),

(200, 600,

(1000.0, 800.0, 600.0, 500.0, 400.0, 300.0))):

for temp in temps:

md.optimize(atmsel, init_velocities=init_vel, temperature=temp,

max_iterations=its, equilibrate=equil)

init_vel = False

def make_restraints(mdl1, aln):

rsr = mdl1.restraints

rsr.clear()

s = selection(mdl1)

for typ in ('stereo', 'phi-psi_binormal'):

rsr.make(s, restraint_type=typ, aln=aln, spline_on_site=True)

for typ in ('omega', 'chi1', 'chi2', 'chi3', 'chi4'):

rsr.make(s, restraint_type=typ+'_dihedral', spline_range=4.0,

spline_dx=0.3, spline_min_points = 5, aln=aln,

spline_on_site=True)

modelname, respos1, restyp1,respos2, restyp2, chain,pdb_filename, out_name = sys.argv[1:]#change

log.verbose()

env = environ(rand_seed=-49837)

env.io.hetatm = True

env.edat.dynamic_sphere=False

env.edat.dynamic_lennard=True

env.edat.contact_shell = 4.0

env.edat.update_dynamic = 0.39

env.libs.topology.read(file='$(LIB)/top_heav.lib')

env.libs.parameters.read(file='$(LIB)/par.lib')

mdl1 = model(env, file=pdb_filename)

ali = alignment(env)

ali.append_model(mdl1, atom_files=pdb_filename, align_codes=modelname)

#ResiduePositionMutationSelection

s = selection(mdl1.chains[chain].residues[respos1],mdl1.chains[chain].residues[respos2])#change

s.mutate(residue_type=restyp1)#change

s.mutate(residue_type=restyp2)#change

ali.append_model(mdl1, align_codes=modelname)

mdl1.clear_topology()

mdl1.generate_topology(ali[-1])

mdl1.transfer_xyz(ali)

mdl1.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')

mdl2 = model(env, file=pdb_filename)

mdl1.res_num_from(mdl2,ali)

#WriteAndReadMutation

mdl1.write(file=modelname+restyp1+respos1+restyp2+respos2+chain+'.tmp')#change

mdl1.read(file=modelname+restyp1+respos1+restyp2+respos2+chain+'.tmp')#change

make_restraints(mdl1, ali)

mdl1.env.edat.nonbonded_sel_atoms=1

sched = autosched.loop.make_for_model(mdl1)

#MutationOptimization

s = selection(mdl1.atoms['CA:'+respos1+':'+chain].select_sphere(5),mdl1.atoms['CA:'+respos2+':'+chain].select_sphere(5))#change

mdl1.restraints.unpick_all()

mdl1.restraints.pick(s)

s.energy()

s.randomize_xyz(deviation=4.0)

mdl1.env.edat.nonbonded_sel_atoms=2

optimize(s,sched)

mdl1.env.edat.nonbonded_sel_atoms=1

optimize(s,sched)

s.energy()

mdl1.write(file=out_name)

os.remove(modelname+restyp1+respos1+restyp2+respos2+chain+'.tmp')