ADL: Autodock failing docking

Davide Mercadante dmer018 at aucklanduni.ac.nz
Mon Jun 1 13:27:05 PDT 2009


Hi,
I tried to dock a small molecule in the active site of an enzyme using
autodock 4.0.
After the repositioning of the small molecule in the binding pocket of the
enzyme I followed the tutorial for autodock 4.0 given on the website.

However, at the end of the calculation with autodock4 all the energies for
each conformation are the same (+0.49 Kcal/mol) and when I try to visualize
the conformations they disappear from the initial position and don't appear
anymore in the active site of the enzyme where I initially positioned them.

Please, can anyone help me to understand why and how I can solve this
problem?

Thanks for any help, it would be really appreciated.

Cheers,
Davide


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