Hi i am doing ligand modeling in binding site of protein i am using ligand/model-multiple-hetero.py script file but geting errors it is say that alignment sequence not found in pdb file the outpu after running script shown below File "ligand.txt", line 17, in ? a.make() File "/usr/local/modeller8v2/modlib/modeller/automodel/automodel.py", line 100, in make self.homcsr(exit_stage) File "/usr/local/modeller8v2/modlib/modeller/automodel/automodel.py", line 318, in homcsr aln = self.read_alignment() File "/usr/local/modeller8v2/modlib/modeller/automodel/automodel.py", line 312, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/usr/local/modeller8v2/modlib/modeller/alignment.py", line 36, in append return self.__int_append('alignment.append', io, libs, vars) File "/usr/local/modeller8v2/modlib/modeller/alignment.py", line 68, in __int_append libs=libs.modpt, **vars) File "/usr/local/modeller8v2/modlib/modeller/util/top.py", line 33, in read_alignment return _modeller.read_alignment(aln, io, libs, *args) _modeller.error: rdpir___648E> Alignment sequence not found in PDB file: 2 1xxx.pdb the log.file out put shown below rdpir___377W> Too many fields ( 11 - should be 10) in the second line of the sequence entry (fields are separated by a colon, :) structure:1GZ8.pdb::::::::0.00:00 rdpir___648E> Alignment sequence not found in PDB file: 2 1GZ8.pdb thank u
Mahendra Eknath Awale Institute Scholar M. S. (Pharm.) Dept.of Pharmacoinformatics National Institute of Pharmaceutical Education and Research NIPER S.A.S.Nagar, Mohali, Punjab-160062 INDIA. Institute Web http://www.niper.gov.in/
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