<div dir="auto">I also used downloded autodook vina in chimera</div><div class="gmail_extra"><br><div class="gmail_quote">On 27 Aug 2020 8:04 p.m., "Elaine Meng" <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Muhammad,<br>
The web service that was used by the "Autodock Vina" tool in Chimera is no longer available. To use this tool in Chimera, now you have to download and install Autodock Vina on your own computer, as explained in the help page:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/<wbr>chimera/docs/<wbr>ContributedSoftware/vina/vina.<wbr>html</a>><br>
<br>
Or, you could use some other docking program or web service (not in Chimera). There are many good docking programs developed by other groups, including:<br>
<br>
Autodock Vina  <<a href="http://vina.scripps.edu/" rel="noreferrer" target="_blank">http://vina.scripps.edu/</a>><br>
DOCK  <<a href="http://dock.compbio.ucsf.edu/index.html" rel="noreferrer" target="_blank">http://dock.compbio.ucsf.edu/<wbr>index.html</a>><br>
<br>
Web services:<br>
<br>
Swissdock <<a href="http://www.swissdock.ch/" rel="noreferrer" target="_blank">http://www.swissdock.ch/</a>><br>
Webina <<a href="https://durrantlab.pitt.edu/webina/" rel="noreferrer" target="_blank">https://durrantlab.pitt.edu/<wbr>webina/</a>><br>
For virtual screening, DOCK Blaster: <<a href="https://blaster.docking.org/" rel="noreferrer" target="_blank">https://blaster.docking.org/</a>><br>
<br>
After you do the docking separately from Chimera, you could still use the ViewDock tool in Chimera to analyze the output files.<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/<wbr>chimera/docs/<wbr>ContributedSoftware/viewdock/<wbr>framevd.html</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 Aug 26, 2020, at 9:12 PM, MUHAMMAD FURQAN AKBER <<a href="mailto:f2018140043@umt.edu.pk">f2018140043@umt.edu.pk</a>> wrote:<br>
> <br>
> Hi hope you are fine?<br>
> I cant find out the final result by protein ligand docking by chimera. This shows the error with pdb receptor. <br>
> What can i do ?<br>
<br>
</blockquote></div></div>