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Re: [modeller_usage] CHARMM atom type is out of range



zzj wrote:
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?

Your script looks OK. Send your alignment, initial model (mgl.pdb) and any template PDBs, so that we can reproduce your problem. See http://salilab.org/modeller/manual/node11.html

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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