Dear All,
I hope you all know that default mutate_model.py script works only for single mutation but I want to make it for double and combination of mutation and I beleive this would be possible by callling mutate() function twice but I got stuct in between. So, If anyone one has idea about how to modify then kindly write me here.
Thanking you in advance
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')
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