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