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

宋青 chingsong962005 at sas.ustb.edu.cn
Thu Oct 9 19:49:28 PDT 2014


We will try it again. Thanks a lot!
Ching


> -----原始邮件-----
> 发件人: "Elaine Meng" <meng at cgl.ucsf.edu>
> 发送时间: 2014-10-10 02:41:12 (星期五)
> 收件人: "宋青" <chingsong962005 at sas.ustb.edu.cn>
> 抄送: chimera-users at cgl.ucsf.edu
> 主题: Re: [Chimera-users] co-factor FAD in autodock-vina
> 
> 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
> 



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