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@salilab.org - WWW/URL: http://salilab.org/~azat