[Chimera-users] Autodock Vina

[JULIO MAZA VILLEGAS]

Dear Kate
The pdbqt (pdb+charges+torsions) file that VINA (an webina) produces are
the poses of the ligand within the search area defined in the receptor. You
could try to open this file extension in UCSF Chimera with the Tools >
Surface/Binding Alaysis > ViewDock menu, it enables to open the pdbqt file
extension. You need to load the receptor as well in order to give a glance
of the docking results
Regards

El mar., 28 abr. 2020 a las 2:05, Kate Wegener (<
kate.wegener at adelaide.edu.au>) escribió:

>
> Thanks Elaine. I have also found a web-server that runs Autodock Vina
> called Webina that I'm trialling. It creates an output file with extension
> *.pdbqt, but I can't work out how to open that in Chimera. Should it be
> possible? It asks me to select what type of file it is from an extensive
> list, but I don't see anything there that corresponds to Vina output. Any
> ideas?
>
> kind regards,
> Kate
>
> <http://researchers.adelaide.edu.au/profile/kate.wegener>
>
>
>
> ------------------------------
> *From:* Elaine Meng <meng at cgl.ucsf.edu>
> *Sent:* Tuesday, 28 April 2020 12:21 AM
> *To:* Kate Wegener <kate.wegener at adelaide.edu.au>
> *Cc:* chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> *Subject:* Re: [Chimera-users] Autodock Vina
>
> Hi Kate,
> Sorry, there are no plans on our part.
>
> Autodock Vina (and many other docking programs, DOCK etc.) are available
> for download and installation for running directly.
> <http://vina.scripps.edu/>
> <http://dock.compbio.ucsf.edu/index.html>
>
> Or if you wish to avoid installing any docking program yourself, there are
> at least a few docking web servers you could also run directly (independent
> of Chimera).  I can't make a recommendation, but to mention a few:  Dock
> Blaster, SwissDock, MTiAutoDock ...
> <http://blaster.docking.org/>
> <http://www.swissdock.ch/>
> <
> https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiAutoDock
> >
>
> I hope this helps,
> ELaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Apr 26, 2020, at 11:48 PM, Kate Wegener <kate.wegener at adelaide.edu.au>
> wrote:
> >
> > I'm new to this list, but I saw in the archives that there was a thread
> on the shutdown of the Opal2 server. I wondered if there were any plans to
> make Autodock Vina available on alternate servers? Or if anyone knows of
> another way to access an Autodock Vina server? I have been using this
> server in a class for the past 5 or 6 years, so I'm keen to find an
> alternative option.
> > kind regards,
> > Kate
>
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-- 
*Julio Román Maza*
*Docente T.C.O.*
*Programa de Química*
*Universidad del Atlántico*
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