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[modeller_usage] CHARMM atom type is out of range



Hellow everyone,
 I am learning how to use Modeller. It gives me the following infor
in the log file:
.....

preppdf_203E> CHARMM atom type is out of range;
             Probably because model.generate_topology() was not called.
             Atom index, atom type:        0

Summary of failed models:
hgl.B99990001.pdb         preppdf_203E> CHARMM atom type is out of
range; Probably because model.generate_topology() was not called. Atom
index, atom type:        0


Dynamically allocated memory at          finish [B,kB,MB]:
4148015    4050.796     3.956
Starting time                                            : 2006/08/28
16:17:29.348
Closing time                                             : 2006/08/28
16:17:48.589
Total CPU time [seconds]                                 :      17.68

I believe my alignment is ok. Here's my script:
# Modeling using a provided initial structure file (inifile)

from modeller.automodel import *    # Load the automodel class

log.verbose()
env = environ()

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

a = automodel(env,
             alnfile  = 'alignment.ali',     # alignment filename
             knowns   = 'mgl',              # codes of the templates
             sequence = 'hgl',              # code of the target
             inifile  = 'mgl.pdb')    # use 'my' initial structure
a.starting_model= 1                 # index of the first model
a.ending_model  = 1                 # index of the last model
                                   # (determines how many models to calculate)
a.make()                            # do homology modelling

Can somebody give me a hint?
Thanks alot.
JOE



--
_________________________________________
Joe (zhaocai) Zhou
Department of Pathology & Laboratory Medicine
University of Pennsylvania, School of Medicine
252 John Morgan Building
36th Street & Hamilton Walk
Philadelphia, PA 19104-6082
Tel: 215-898-2870
Fax:215-898-2401
Cell:781-330-2409
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