[modeller_usage] modeller as an optimizer, not as a modeller??

["Himanshu Grover" <>]

hellow,
   i wish to know whether modeller can be used as a general optimization
tool. I have a structure of my protein... also know its binding site to
another protein (its a protein-protein complex). i just want to apply
simulated annealing to the binding site of my model, to find the best
binding conformation... can modeller do that for me??

   regarding the same, please apprise me of some details...

firstly, do i need to use the restraints generated by modeller... if yes,
which ones??

secondly, what new restraints, if at all, should be applied(as a part of
special restraints).

thirdly,is it necessary to use homology basis, the alignment, templates,
and homology derived restraints...??

if anyone could give me a sample top script as to how the problem can be
tackled, it would be a great help... moreover, any other
nuances/suggestions in the approach would be appreciated...

thanks very much,

sincerely,
himanshu