Dear Dr. Arvind and Dr. Webb

Thank you very much for your help. The problem as you point out was the
lacking of the cystein's chain identification.

Below I paste the corrected script (in case other people look up this kind of errors in the list):

# Homology modeling by the automodel class
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

# Redefine the special_patches routine to include the additional disulfides
# (this routine is empty by default):
class MyModel(automodel):
    def special_patches(self, aln):
        # A disulfide between residues 345 and 668:
        self.patch(residue_type='DISU', residues=(self.residues['345:A'],
                                                  self.residues['668:A']))

log.verbose()    # request verbose output
env = environ() # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = './:../atom_files'

# Read in HETATM records from template PDBs
env.io.hetatm = True

a = MyModel(env,
            alnfile = 'alignment.ali', # alignment filename
            knowns   = ('2ioaB_amidase', '2vobB', '2ioaB_sinthetase'), # codes of the templates
            sequence = 'tcruzi')              # code of the target
a.starting_model= 3                 # index of the first model
a.ending_model = 3                 # index of the last model
                                        # (determines how many models to calculate)
a.make()                            # do the actual homology modeling

--
Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221