[Chimera-users] Chimera autodock vina for ligand docking on RNA

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 3 18:27:06 PDT 2020

Hi Reeki,
I thought you were using the Autodock Vina tool dialog, sorry.  Here is the page for the Chimera "vina" command that does the same stuff, including prep options.

However, if you are just using Chimera for the prep step, the prep scripts for vina originally came from Autodock and maybe you just want to use them directly instead of through Chimera.


Chimera also has a Dock Prep tool that you can run separately, but that one is not used automatically by the Autodock Vina tool (or "vina" command) in Chimera.

Again, however, I do not know if Autodock Vina is appropriate for docking to RNA.  You might want to check on that and/or take a look at other docking programs.

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

> On Sep 3, 2020, at 6:16 PM, Reeki Emrizal <reeki at mfrlab.org> wrote:
> Hi Elaine,
> Sorry about the subject. Just realised I forgot to add one after I hit send.
> I’ve tried autodock vina (not through chimera) and it works. However, I would like to automate both the receptor and ligand preparation steps and docking process and it seems to me that chimera is capable of it.
> Is there a help page that contains the command to turn off those options (Ignore chains of non-standard residues and Ignore all non-standard residues). The help page you provide doesn’t seem to provide a command that I can used in a docking script.
> Thanks for your help
> On Thursday, September 3, 2020, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Reeki,
> I changed the subject line to something useful.
> The "Autodock Vina" tool in Chimera is just an interface that calls Autodock Vina as a separate program.  You should check the "receptor options" in this tool:  there are two options to ignore residues that are not standard amino acids.  I assume you should change those options to "false".  The options are explained in the Help page, which you can see by clicking the Help button, or view the copy on our website here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> However, even if you change these options to false and the docking calculation finishes, I do not know whether Autodock Vina is expected to give good results for docking to RNA.  Also, the tool in Chimera does not allow very much sampling with Autodock Vina; for more thorough sampling of space, you may want to use Autodock Vina directly (not from Chimera).
> The Chimera developers are not the developers of the Autodock Vina program, so I am not an expert on this topic.  Maybe you would find more information about whether Autodock Vina is meant to work for RNA receptors at 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 2, 2020, at 5:02 PM, Reeki Emrizal <reeki at mfrlab.org> wrote:
> > 
> > Dear Chimera team,
> > 
> > I'm attempting to dock small molecule ligand on a RNA molecule using chimera autodock vina. However, the docking process ended prematurely after the receptor.pdb (the RNA molecule) file is made. Please find attached a screenshot of the reply log. I'm suspecting the error comes from the receptor.pdb file made by chimera. Please find attached the screenshots of receptor.pdb files for a RNA molecule and a protein molecule. The receptor.pdb for protein has the column for residue names parsed correctly (e.g. "THR") but not for the receptor.pdb for RNA (e.g. "G" which I believed should be "  G").
> > 
> > My questions are: (1) Is chimera allows docking of small molecule ligand on RNA molecule and (2) Is the a parameter that I've overlooked to allow this?
> > 
> > Kind Regards
> > <receptor.pdb protein.png><reply log.png><receptor.pdb rna.png>

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