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