First of all try to post to the same thread. There are people like you who might seek the same information and will find it helpful.
> > I tried following ur procedure but I am getting the following error :- > > "Sequence Difference between alignment and pdb residues" > > What I did is, I deleted the sequence of loop from the pdb file also .. > Now its giving the error "No. of residues in the alignment and the pdb file > are different" > >
You might find this helpful:
http://www.salilab.org/modeller/FAQ.html#17
Look at you .pdb and .log files and THINK. I model missing loops all the time.
I have a doubt regarding this procedure , since the sequence of loop present > in the target doesnot match with that of template , then how the structure > will be modelled ?? ... As Homology modeling relies completely on copying > the backbone of template sequence and then model the structure accordingly > for the target ... > >
Loop modeling is designed for cases where you have not template - it wont use any information from .pdb files. I asked you something last time, to search the mailing list as this question has been answered in the past. Just before your post someone asked about loop refinement and I posted a link to the manual (in fact you could find that section of the Manual by yourself if you had searched properly) which describes the loop modeling method:
http://www.salilab.org/modeller/manual/node452.html#SECTION:loopmethod
loopmodel.loop.md_level controls the refinement level, I recommend setting it to refine.very_slow and create as much loop models as possible. The refinement procedure encompasses MD with Simulated Annealing.
Next time search the mailing list and the manual thoroughly before you ask something that has been answered before.
Thomas