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