[chimerax-users] Compound Docking in UCSF Chimera

[Elaine Meng]

Hi Ayush Patel,
You do not need a surface to use Autodock Vina.  It uses atom positions, not surfaces.

So yes, ChimeraX can show a surface (e.g. command "surface" after you open your structure) when Chimera fails, but as far as I know, that does not have any connection with ligand-receptor docking with Autodock Vina.

Chimera has a tool (menu: Tools... Surface/Binding Analysis... Autodock Vina) that is just a graphical interface to your already installed Autodock Vina.  You have to enter the location of your Autodock Vina executable into the interface so that it knows what to use.  However, that graphical interface only allows a very low amount of sampling and is not suitable for most research purposes, as explained here:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

ChimeraX does not have this tool.  Chimera has a ViewDock tool for looking at docking results, and ChimeraX has a ViewDockX tool for looking at docking results, but it does not run the docking.  Instead you use the docking program separately and then open the output file in Chimera or ChimeraX.

Viewdock
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>
ViewDockX
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>

Currently we recommend using Autodock Vina directly, not from Chimera or ChimeraX.  You can find documentation and tutorials on the Autodock Vina website:
<http://vina.scripps.edu/>

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

> On Sep 25, 2021, at 7:11 AM, Ayush Patel via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Sir or Madam;
> 
> Recently, I was having issues with docking a ligand into a receptor due to surface calculation failures. A quick search told me to use ChimeraX. However, I am not sure how to carry out docking in ChimeraX. Could you please explain how to do this?
> 
> As a side note, I do currently have AutoDock Vina.
> 
> Thank you so much,
> Ayush Patel