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