ADL: autodock Digest, Vol 93, Issue 5

Julio Dominguez acheron24 at
Thu May 10 15:03:09 PDT 2012

Dear Mary,

About your second question, well, it is really a question? Are you asking with program is correct, either autodock or dock6? Both results should be treated as predictions. Are you expecting the correct answer to be the one with the ligand at the interface because of experimental evidence? If so, you should follow the results that match the experimental data. 

Best regards.

> Message: 1
> Date: Thu, 10 May 2012 16:42:26 +0530
> From: Mary Varughese <maryvj1985 at>
> Subject: ADL: no effective docking
> To: autodock at
> Message-ID:
> 	<CAAjRZU3LgAiPRpa+swvgS9h52Lk4Q_gf=NDnKj6+UpCeSuFDMQ at>
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> Hi,
> I am a beginner in autodock4 with ADT.
> In the tutorial they talk about merging non-polar hydrogens. I didnt
> understand its purpose.what the difference of doing it or not?
> I am trying to dock (almost blind dock )a ligand into the interphase
> between a dimer protein. The grid box covers the interphase region abt 80
> 90 60 with centre at the geometry centre of the dimer by default. when view
> both protein and ligand in the viewer the ligand is far from protein (since
> its not an available complex). I have done the same with dock6. So i  was
> expecting that on running autodock the ligand will find a suitable position
> in the interphase between the dimer within the grid box. although the
> autodock and autogrid runs succesfully i didnt get any conformation within
> the interphase.
> -- 
> Mary Varughese
> Research Scholar
> School of Pure and Applied Physics
> Mahatma Gandhi University
> India

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