your pdb file name that you write in your alignment file is not equal with your pdb file in atom file folder.
On 22/11/06, Dhananjay dhananjay.c.joshi@gmail.com wrote: > > Hello all, > > I am getting followin error while running mod8v2 model-default.py > > > > > [dhananjay@cdfd-wstn7 automodel] mod8v2 model-default.py > Traceback (most recent call last): > File "model-default.py ", line 18, in ? > a.make() # do the actual homology modelling > File > "/users/dhananjay/bin/modeller8v2/modlib/modeller/automodel/automodel.py", > line 100, in make > self.homcsr (exit_stage) > File > "/users/dhananjay/bin/modeller8v2/modlib/modeller/automodel/automodel.py", > line 318, in homcsr > aln = self.read_alignment() > File > "/users/dhananjay/bin/modeller8v2/modlib/modeller/automodel/automodel.py", > line 312, in read_alignment > aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) > File "/users/dhananjay/bin/modeller8v2/modlib/modeller/alignment.py", > line 36, in append > return self.__int_append('alignment.append ', io, libs, vars) > File "/users/dhananjay/bin/modeller8v2/modlib/modeller/alignment.py", > line 68, in __int_append > libs=libs.modpt, **vars) > File "/users/dhananjay/bin/modeller8v2/modlib/modeller/util/top.py", > line 33, in read_alignment > return _modeller.read_alignment(aln, io, libs, *args) > > > _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not > found in the alignment file; ALIGN_CODES( 1) = 1M1G > > > > I am new to this software. Please tell me whats wrong here > > > Thanking you in advance > > > -- > Dhananjay C Joshi > Project Assistant > LT & LSB, C D F D > ECIL Road, Nacharam > Hyderabad-500 076, INDIA > Tel : +91-40-27151344 > Fax : +91-40-27155610 > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > >