[Chimera-users] co-factor FAD in autodock-vina

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 9 11:41:12 PDT 2014

Dear Ching Song,
I didn't know the answer, so I just tried it, and it worked fine in Chimera 1.8.  

I opened 2vfs and deleted everything except the protein and FAD  (deleted solvent, ions, and XYL).  So that's the receptor, #0.

Then I opened some other small molecule structure to use as ligand, #1.

Then I started Autodock Vina, created the search box, entered name for output, and chose receptor #0 and ligand #1.  Looked in the "Receptor options" to make sure that "Ignore all non-standard residues" was "false".  Clicked Apply, and the job ran successfully.

I had a problem in Chimera 1.9, which I will report as a bug, but if you stick with Chimera 1.8 it apparently works.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 8, 2014, at 8:27 PM, 宋青 <chingsong962005 at sas.ustb.edu.cn> wrote:

> Dear Chimera Design Team,
> We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ.  Thank you for your help.
> --
> Ching Song, Ph.D.
> Department of Biological Science and Engineering
> School of Chemistry and Biological Engineering
> University og Science and Technology Beijing
> Xue Yuan Lu 30, Li Hua Lou Room 111
> Hai Dian District
> Beijing 100083, P. R. China
> 86-10-62334497

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