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

[Reeki Emrizal]

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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