ADL: regarding active site

Davide Mercadante dmer018 at
Wed Jun 17 19:12:47 PDT 2009

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

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

Thanks infinitely for your help I appreciate much the usage of vina.


2009/6/17 Oleg Trott <trott at>

> On Tue, Jun 16, 2009 at 10:22 PM, Davide
> Mercadante<dmer018 at> wrote:
> > can I just go through
> > the installation of autodock-vina without removing autodock4?
> Yes
> --
> Oleg Trott, Ph.D. (Columbia University)
> ________________________________________________
> --- ADL: AutoDock List  --- ---

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