The following script optimize.py is not working for me. It is giving an error in the line: is giving an error in this line:
mdl.generate_topology<aln, sequence=code+'ini'>
Please suggest.
Script
env = environ() env.edat.dynamic_sphere = True
env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib')
code = 'unbound-scrwl' aln = alignment(env) mdl = model(env, file=code) aln.append_model(mdl, align_codes=code, atom_files=code) aln.append_model(mdl, align_codes=code+'-ini', atom_files=code+'.ini') mdl.generate_topology(aln, sequence=code+'-ini') mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl.write(file=code+'.ini')
# Generate the restraints: mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False) mdl.restraints.write(file=code+'.rsr')
mpdf = mdl.energy() mdl.switch_trace(file=code+'.trc') mdl.optimize(optimization_method=1, max_iterations=20, output='REPORT', trace_output=1) mdl.optimize(optimization_method=3, temperature=300, max_iterations=50, output='REPORT', trace_output=1) mdl.optimize(optimization_method=1, max_iterations=20, output='REPORT', trace_output=1) mpdf = mdl.energy()
mdl.write(file=code+'.B')
Dr. Jayashree RamanaLecturer, Department of Biotechnology and Bioinformatics Jaypee University of Information Technology Waknaghat, Solan Himachal Pradesh-173234
http://www.juit.ac.in/Department/bio/faculty_bio.php?faculty_id=118