Friends, I am a newbie to modeller. I have the structure of a protein obtained from MD simulation (total 339 residues). I have another sequences of unknown structure ( total 345 residues). I want to model the structure of the later by using the simulated structure as template.

I first aligned the two sequences with clustwal and made the .ali file (pasted below) . The modeller script i used is attached. Kindly write me what is going wrong ?

*The following is the ali file.*

>P1; temp structureM:temp:1 :A:339 :A :::: VVLENVTEHFNMWKNDMVEQMQEDIISLWDQSLKPCVKLTPLCVGAGSCDTSVITQACPK ISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAE EEVVIRSDNFTNNAKTIIVQLKESVEINCTRPNQNTRKSIHI--GPGRAFYTTGEIIGDI RQAHCNISRAKWNDTLKQIVIKLREQF-ENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCN SAQLFNSTWNN---NTEGSNNTEG-NTITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCS SNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIE* >P1; targ sequence:targ:::::::: VVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVGAGSCNTSVITQACPK VSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAE EEVVIRSANFTDNAKTIIVQLNQSVEINCTRPNNNTRKSIRIQRGPGRAFVTIGK-IGNM RQAHCNISRAKWNATLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCN STQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQFINMWQEVGKAMYAPPISGQIRCS SNITGLLLTRDGGNNNNGSEIFRPGGGDMRDNWRSELYKYKVVKIE*

*I get the following error when i run the command mod9v8 model.py*

'import site' failed; use -v for traceback Traceback (most recent call last): File "model.py", line 11, in ? a.make() File "/apps/modeller/9v8//modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/apps/modeller/9v8//modlib/modeller/automodel/automodel.py", line 424, in homcsr self.check_alignment(aln) File "/apps/modeller/9v8//modlib/modeller/automodel/automodel.py", line 406, in check_alignment aln.check() File "/apps/modeller/9v8//modlib/modeller/alignment.py", line 200, in check self.check_structure_structure(io=io) File "/apps/modeller/9v8//modlib/modeller/alignment.py", line 209, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb :

Thanks, Bala