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

[Elaine Meng]

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.
Best,
Elaine
----------
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