[modeller_usage] ligand modeling in binding site

[mahendra awale <>]

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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