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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?</div>
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kind regards,</div>
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Kate</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, 28 April 2020 12:21 AM<br>
<b>To:</b> Kate Wegener <kate.wegener@adelaide.edu.au><br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [Chimera-users] Autodock Vina</font>
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<div class="PlainText">Hi Kate,<br>
Sorry, there are no plans on our part. <br>
<br>
Autodock Vina (and many other docking programs, DOCK etc.) are available for download and installation for running directly.<br>
<<a href="http://vina.scripps.edu/">http://vina.scripps.edu/</a>><br>
<<a href="http://dock.compbio.ucsf.edu/index.html">http://dock.compbio.ucsf.edu/index.html</a>><br>
<br>
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 ...<br>
<<a href="http://blaster.docking.org/">http://blaster.docking.org/</a>><br>
<<a href="http://www.swissdock.ch/">http://www.swissdock.ch/</a>><br>
<<a href="https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiAutoDock">https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiAutoDock</a>><br>
<br>
I hope this helps,<br>
ELaine<br>
----- <br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Apr 26, 2020, at 11:48 PM, Kate Wegener <kate.wegener@adelaide.edu.au> wrote:<br>
> <br>
> 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.<br>
> kind regards,<br>
> Kate<br>
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