[Chimera-users] Autodock Vina

[Kate Wegener]

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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