Dear All: I am a new user of MODELLER 9. I got an appreciable model using modeller and I would like to evaluate the model by the model.energy(). But I got an error like,

runcmd______> topology.append(file='$(LIB)/top_heav.lib') read_to_681_> topology.submodel read from topology file: 3 runcmd______> parameters.append(file='$(LIB)/par.lib') runcmd______> model.read(file='nitro.B99990066', (def)model_format='PDB', (def)model_segment=('FIRST:@', 'LAST:')) runcmd______> alignment.append_model(atom_files='nitro.B99990066', align_codes='nitro.B99990066') runcmd______> alignment.append_model(atom_files='nitro.B99990066.ini', align_codes='nitro.B99990066-ini') runcmd______> model.generate_topology((def)patch_default=True)

getf_______W> RTF restraint not found in the atoms list: residue type, indices: 11 120 atom names : C +N atom indices : 880 0

getf_______W> RTF restraint not found in the atoms list: residue type, indices: 11 120 atom names : C CA +N O atom indices : 880 875 0 881

runcmd______> model.transfer_xyz((def)cluster_cut=-1.0, (def)cluster_method='RMSD') transfe_507E> Number of residues in alignment different from that in MODEL: 60 120 (Did you call clear_topology() before generate_topology() ?)

The top file is,

# Example for: model.energy()

# This will calculate the stereochemical energy (bonds, # angles, dihedrals, impropers) for a given model.

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

aln = alignment(env) code = "nitro.B99990066" mdl = model(env, file=code) aln.append_model(mdl, atom_files=code, align_codes=code) aln.append_model(mdl, atom_files=code+'.ini', align_codes=code+'-ini')

mdl.generate_topology(aln[code+'-ini'])

mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')

mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False) molpdf = mdl.energy(edat=energy_data(dynamic_sphere=True))

Could any body help me with this? I used PROCHECK and found 90% of residue resides in core area ie most favoured.

Thank you in advance

Cheers J.Prabha