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

宋青 chingsong962005 at sas.ustb.edu.cn
Fri Oct 10 23:41:26 PDT 2014


Dear Elaine,

Thank you for your help!  I was able to dock a sugar with the FAD in situ, but only under following conditions: (1) change names of hydrogen atoms of the hydroxy groups of FAD from HOx to HxO; (2) for dockprep, calculate charges of FAD using method of Gasteiger instead of AM1-BCC.  Hope the information is useful as user feedback.
Best regards,
Ching
--
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
> -----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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