Dear All,

I have tried generate a models for single point mutation along with optimization and refinement on the selected region of atoms but I am getting bad DOPE score(lesser negative value -11k) for optimized models compared to unoptimized automodels DOPE score(-36K).

Also, I observed that DOPE score get increase when I increase the number of atoms for optimization but at same time this leads to bad models.

May I know what is the reason for this issue? because when I do the same thing with mutate_model.py I got the same DOPE score as automodels.

Here, I am giving the MyModel class where I define my own optimization,refinement and restraints criteria (same as mutate_model.py):

class MyModel(automodel):

def select_atoms(self): # a non-bonded pair has to have at least as many selected atoms self.env.edat.nonbonded_sel_atoms = 1 sched = autosched.loop.make_for_model(self) s=selection( self.atoms['CA:'+'102'+':'+'A'].select_sphere(20)).by_residue() self.restraints.unpick_all() self.restraints.pick(s) s.energy() #s.randomize_xyz(deviation=-4) s.energy() return s

def optimize(s, sched): # conjugate gradient for step in sched: step.optimize(s, max_iterations=200, min_atom_shift=0.001) # md refine(s) cg = conjugate_gradients() cg.optimize(s, max_iterations=200, min_atom_shift=0.001)

def refine(self,atmsel,actions): # at T=1000, max_atom_shift for 4fs is cca 0.15 A. 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 special_restraints(self, aln): rsr = self.restraints rsr.clear() s = selection(self) 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)

Thanking you in advance

With Regards Mahesh V