[modeller_usage] model.energy()

["Jayapal, Prabha" <>]

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