Energy minimization

[zaidi AT prochem.khi.sdnpk.undp.org (Prof. Zafar H. Zaidi)]

Hi Andrej
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.
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.
Advise please.
Regards
Kamran Azim