ADL: Help

Diogo Martins diogo.stmart at
Wed Sep 9 23:34:42 PDT 2020

Hi Shabnam,

The help pages cover the topics of your questions, I recommend going
through them:

Best regards,

On Wed, 9 Sep 2020 at 20:45, sarah sarahii <shabnamn2001 at> wrote:

> Dear Researchers
> Hello,
> I have a question about the interpretation of AutoDock(4) docking results.
> I got the docking results with high RMSD. However, I even performed another
> docking with the ligand, which was existed in the basic file of the protein
> (mofegiline with one subunite of 2vz2), but I again found a high RMSD. I
> want to ask you please help me about the questions:
> 1. How should I define the "reference structure" to obtain the result with
> low RMSD.
> 2. Is it necessary to have low RMSD in result of docking or not?
> 3. Please mention the steps in details to define the "reference structure"
> in the related file (or files) to reach the perfect and correct results of
> docking (with Autodock 4) in accompany with low RMSD.
> I thank you
> Sincerely Yours,
> Shabnam
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