ADL: regarding active site

Oleg Trott trott at
Wed Jun 17 19:53:29 PDT 2009

On Wed, Jun 17, 2009 at 7:12 PM, Davide
Mercadante<dmer018 at> wrote:
> Hi Oleg,!
> I tried the running of Vina as you showed on the tutorial and you were
> alright, I solved the problem. Vina doesn't allow the ligand to jump the
> site where I placed the grid. The calculations are really fast compared to
> Autodock and I advice everyone from my own experimence to use Vina.
> However, I have two questions:
> the flag "all" in the parameter file doesn't seem to be recognized and Vina
> (on an ubuntu machine) gives you an error. Without the flag is all fine. In
> this case the output is written to an output file that starts with the name
> of the ligand pdbqt file.

This is explained on top of the tutorial page, above the video.

> I have visualized this output (using a text editor) and it shows all the
> conformations in the pdbqt file.

I take it that you are trying to say that there is more than one model
in the PDBQT?

> I have opened the file using pymol but the
> software is able to visualize only the first conformation I think and
> doesn't show all the conformers:
> 1) I need to modify the pdqt file and save it in some other format to
> visualize all the conformers? If yes, how?

The version I have has no problems there. Try "->" key. Failing that,
post a screenshot and your output file.

> 2) there is an option to cluster the conformations as in autodock and to
> have the graphs of rmsd Vs the number of conformations fo r an rmsd given
> value?

Vina does "clustering", i.e. avoiding redundancies automatically
without asking. Please read the paper if you need to know more.

Best of luck,
Oleg Trott, Ph.D. (Columbia University)

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