[Chimera-users] in the docking process this message appear and does not continue, opal:vina_1.1.2 unavailable what i should do

Don Gabo gabrielsrbio at gmail.com
Mon May 4 08:29:48 PDT 2020

Thank you.

Was investigating and I solved the problem by the following way:

Download and install the AutoDock Vina app from this website:
http://vina.scripps.edu/download.html , then go to Tools-> Surface/Binding
Analysis->AutoDock Vina, click on it, then go to "Executable Location",
click on "Local", then in "Browse" and look for the executable file
"vina.exe" of the recently installed AutoDock Vina (I found it
on C:\Program Files (x86)\The Scripps Research Institute\Vina\vina.exe),
click on it and then "Ok" in the AutoDock Vina window of Chimera.

I got to use the AutoDock Vina function as it was with the website, no
changes in performance and no need for uploading receptor/ligands
nor downloading docking files.

Best regards!

On Thu, Apr 30, 2020 at 10:11 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Sorry, the Autodock Vina web service is no longer available.
> This was already discussed on the mailing list
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016738.html>
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016752.html>
> and is also shown on the Help page for this tool:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> Somebody on the mailing list mentioned that there is another Autodock Vina
> web server called Webina
> <https://durrantlab.pitt.edu/webina/>
> ...that you may be able to use directly (not in Chimera).  I have not
> tried it myself, but according to others, after you get the output file
> from Webina you may be able to open and view it with the ViewDock tool in
> Chimera as described in the second message below:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016762.html>
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016764.html>
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Apr 30, 2020, at 6:37 AM, Ahmed Tawfeek <ahmed_tawfeek83 at yahoo.com>
> wrote:
> >
> > Dear Professors and Doctors,
> > I need the help
> > I am trying to learn the work on chimera for the purpose of checking my
> compounds as organic chemist but i could not continue, because at the
> docking stage, the autodock vina does not work and this message appear,
> >
> > the message " opal:vina_1.1.2 unavailable"
> >
> > what is the solution
> >
> > Best Regards
> >
> > Ahmed Tawfik
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M.C Gabriel Salazar Robles
Estudiante de Doctorado en Biotecnología en la UPAEP
Profesor de asignatura en la Universidad Politécnica Metropolitana de puebla
Cel/WhatsApp: 2228 33 54 58
Email: gabrielsrbio at gmail.com
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