<div dir="ltr">Dear Kate<div>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</div><div>Regards </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El mar., 28 abr. 2020 a las 2:05, Kate Wegener (<<a href="mailto:kate.wegener@adelaide.edu.au">kate.wegener@adelaide.edu.au</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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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="gmail-m_4085016803789847926divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>><br>
<b>Sent:</b> Tuesday, 28 April 2020 12:21 AM<br>
<b>To:</b> Kate Wegener <<a href="mailto:kate.wegener@adelaide.edu.au" target="_blank">kate.wegener@adelaide.edu.au</a>><br>
<b>Cc:</b> <a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a> <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>><br>
<b>Subject:</b> Re: [Chimera-users] Autodock Vina</font>
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<div>Hi Kate,<br>
Sorry, there are no plans on our part. <br>
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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/" target="_blank">http://vina.scripps.edu/</a>><br>
<<a href="http://dock.compbio.ucsf.edu/index.html" target="_blank">http://dock.compbio.ucsf.edu/index.html</a>><br>
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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/" target="_blank">http://blaster.docking.org/</a>><br>
<<a href="http://www.swissdock.ch/" target="_blank">http://www.swissdock.ch/</a>><br>
<<a href="https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiAutoDock" target="_blank">https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiAutoDock</a>><br>
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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>
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> On Apr 26, 2020, at 11:48 PM, Kate Wegener <<a href="mailto:kate.wegener@adelaide.edu.au" target="_blank">kate.wegener@adelaide.edu.au</a>> 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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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><font face="trebuchet ms, sans-serif"><b>Julio Román Maza</b></font><div><font face="trebuchet ms, sans-serif"><i>Docente T.C.O.</i></font></div><div><font face="trebuchet ms, sans-serif"><b><i>Programa de Química</i></b></font></div><div><font face="trebuchet ms, sans-serif"><b>Universidad del Atlántico</b></font></div></div></div>