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Re: Energy minimization

Dear Kamran!

Replying to your question:...

> We have docked a small peptide on the active site of protease
> molecule, now want to perform structural refinement and energy
> minimization. Can OPTIMIZE command of modeller do that or
> implementation of any energy minimizer is needed.

Yes, as soon as you build an initial model, you can OPTIMIZE it with
available scoring functions (make sure you set DYNAMIC_LENNARD = ON, and
others - OFF).

> Kindly note, OPTIMIZE successfully eliminate all short non-bonded
> contacts and improved stereochemical parameters of the initial
> enz-inhibitor complex..
> Secondly, is it obligatory to use minimizer during these type of
> work.

By default, OPTIMIZE uses minimizer or MD, depending on

OPTIMIZATION_METHOD  = 1 selects a conjugate gradients optimization
method. 
OPTIMIZATION_METHOD  = 3 selects a molecular dynamics optimization at a
fixed temperature. 

Please read more about in in the manual.

Thank you for choosing MODELLER not only as a comparative modelling
tool, but also as a general refinement engine.

Yours,

Azat.

> Advise please.
> Regards
> Kamran Azim

--
- Dr. Azat Badretdinov 
- The Rockefeller Univ, Box 270 
- 1230 York Ave, New York NY 10021, USA
- Phone: (212) 327 7206
- Fax: (212) 327 7540
- E-mail: azat AT salilab.org
- WWW/URL: http://salilab.org/~azat