[Chimera-users] AutoDock Vina Help

[Elaine Meng]

Hi Ali,
There are a huge number of docking programs: Autodock Vina, UCSF DOCK and many others. However, I don't know which can be used for RNA-protein docking vs. small molecule-protein or protein-protein docking, so you may need to investigate or literature-search that yourself.  I should also mention that the sampling that was allowed by the Autodock Vina web service was extremely unlikely to be sufficient for something as flexible and big as RNA, so I don't think that would have been the right tool for your question anyway.  You may have gotten a result but it wouldn't be a reliable indicator of reality.

<http://vina.scripps.edu/>
<http://dock.compbio.ucsf.edu/>

You would need to obtain and use the docking program directly (not through a Chimera interface).  Then you may be able to look at the output using the ViewDock tool in Chimera. Not sure why  you mentioned PDB2PQR... I don't think that has anything to do with Autodock Vina.
 
If you want the ease of a web server (nothing to install yourself) a few are listed below.  However, again I do not know if they are intended or can be used for RNA-protein docking.

SwissDock  <http://www.swissdock.ch/>
Webina   <https://durrantlab.pitt.edu/webina/>
DOCK Blaster <http://blaster.docking.org/>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 23, 2020, at 8:46 AM, Ali <alikiyaei at gmail.com> wrote:
> 
> Hi Everyone,
> 
> As of the end of April 2020, the webserver to opal is no longer working. I have tried to build the PDB2PQR programme locally but have been struggling.
> 
> Basically, need to align a RNA molecule to a sight within the pdb. If anyone can help, please assist.
> 
> Thank you,
> 
> Ali from Cape Town