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?