Dear
I am trying to do energy minimization step by running optimize.py script file but it does not execute every time i tried to run and got the following error, i will be thankful if you help me get this problem resolved.
IOError: pdbnam_____E> Filename for PDB code not found: hGLR Directories: ../atom_files Extensions : :.atm:.pdb:.ent:.crd (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, .7z, .xz, and trying PDB-style subdirectories - e.g. ab for pdb1abc.ent)
# Example for: conjugate_gradients(), molecular_dynamics(), model.switch_trace()
# This will optimize stereochemistry of a given model, including # non-bonded contacts.
# non-bonded contacts.
from modeller import * from modeller.scripts import complete_pdb from modeller.optimizers import conjugate_gradients, molecular_dynamics, actions
env = environ() env.io.atom_files_directory = ['../atom_files'] env.edat.dynamic_sphere = True
env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib')
code = '*hGLR*' mdl = complete_pdb(env, code) mdl.write(file=code+'.ini')
# Select all atoms: atmsel = selection(mdl)
# Generate the restraints: mdl.restraints.make(atmsel, restraint_type='stereo', spline_on_site=False) mdl.restraints.write(file=code+'.rsr')
mpdf = atmsel.energy()
# Create optimizer objects and set defaults for all further optimizations cg = conjugate_gradients(output='REPORT') md = molecular_dynamics(output='REPORT')
# Open a file to get basic stats on each optimization trcfil = file(code+'.D00000001', 'w')
# Run CG on the all-atom selection; write stats every 5 steps cg.optimize(atmsel, max_iterations=20, actions=actions.trace(5, trcfil)) # Run MD; write out a PDB structure (called '1fas.D9999xxxx.pdb') every # 10 steps during the run, and write stats every 10 steps md.optimize(atmsel, temperature=300, max_iterations=50, actions=[actions.write_structure(10, code+'.D9999%04d.pdb'), actions.trace(10, trcfil)]) # Finish off with some more CG, and write stats every 5 steps cg.optimize(atmsel, max_iterations=20, actions=[actions.trace(5, trcfil)])
mpdf = atmsel.energy()
mdl.write(file=code+'.B')
I am trying to give the code which i have got after my pdb files are dveveloped.