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

宋青 chingsong962005 at sas.ustb.edu.cn
Tue Oct 14 00:50:02 PDT 2014


Thanks for your continuous support! We will keep you posted of our Chimera experience! Ching


> -----原始邮件-----
> 发件人: "Elaine Meng" <meng at cgl.ucsf.edu>
> 发送时间: 2014-10-14 08:51:13 (星期二)
> 收件人: "宋青" <chingsong962005 at sas.ustb.edu.cn>
> 抄送: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> 主题: Re: [Chimera-users] co-factor FAD in autodock-vina
> 
> Dear Ching,
> Thanks for the information — sorry that you found problems!
> 
> From your description, it sounds like the Vina prep scripts don’t like the Chimera-generated hydrogen names for the nonstandard residue (FAD).  When I tested with FAD after your first question, I didn’t add hydrogens in Chimera, and in our earlier tests of Vina with Chimera hydrogen addition, we hadn’t tried structures with FAD.
> 
> I’m not sure what exactly was the problem with AM1-BCC, but we have noticed before that this method can have problems with residues with highly charged parts like the phosphates of FAD.
> 
> Best regards,
> 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 10, 2014, at 11:41 PM, 宋青 <chingsong962005 at sas.ustb.edu.cn> wrote:
> 
> > 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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> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> > 
> 



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