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

[Modeller Caretaker <modeller-care@ucsf.edu>]

On Mon, Jul 05, 2004 at 03:00:34PM +0530, Himanshu Grover wrote:
>    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??

Sure, you can do that - see question 12 in the FAQ:
http://salilab.org/modeller/FAQ.html#12

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

You can use whichever restraints you choose. You can add your own
restraints, or override the default restraints with your own restraints
file if you like - this is also in the FAQ.

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

That depends on whether your template gives you enough information to
generate all the restraints you need - it depends on your system.

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

It's not necessary to use homology-derived restraints; Modeller can use
the CHARMM 22 force field and do standard MD if you like (although if
you want to go down this road, you're probably better off using a
dedicated MD package like CHARMM or GROMOS, and bear in mind that with
MM force fields, such 'refinement' without template information is
likely to lead to a worse structure). If you have a template, you
probably want to use it.

	Ben Webb, Modeller Caretaker
-- 
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