ADL: Vina result confusion

kanika sharma ksharma997 at gmail.com
Tue Jun 30 02:04:16 PDT 2015


Thanks for clearing my doubt Ruth

The config file specifies the 'flex' parameter and I included TRP296 and
ASP202 as flexible residues. While looking at the interactions I wasn't
able to figure out why vina suggests interactions between two residues from
receptor. Is it because they are flexible?

On Mon, Jun 29, 2015 at 7:20 PM, Ruth Huey <rhuey at scripps.edu> wrote:

> ________________________________________
> From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] On
> Behalf Of kanika sharma [ksharma997 at gmail.com]
> Sent: Monday, June 29, 2015 6:01 AM
> To: autodock at scripps.edu
> Subject: ADL: Vina result confusion
>
> Hello everyone
>
>
> I used Vina for docking and I prepared my receptor and ligand files in
> autodock. I visualised the interactions of this docking as it is instructed
> in : http://mgldev.scripps.edu/pipermail/autodock/2014-April/009346.html
>
> Now, I have  a trouble, I saw the "output list of : receptor contacts " in
> python shell and it gives me this :
>
> 1 A:ASP202-> A:ASP202,
> 2 A:TYR299-> A:TRP296,
> 3 A:TYR193->  :LIG1,
> 4 A:PRO287->  :LIG1,
> 5 A:THR286->  :LIG1,
> 6 A:GLY295-> A:TRP296,
> 7 A:ASP279->  :LIG1,
> 8 A:ASP292-> A:TRP296,
> 9 A:LEU297-> A:TRP296,
> 10 A:THR203-> A:ASP202,
> 11 A:MET90-> A:TRP296,
> 12 A:LEU39-> A:TRP296,
> 13 A:LEU201-> A:ASP202,
> 14 A:SER93-> A:TRP296,
> 15 A:TRP198-> A:ASP202,
> 16 A:PHE291->  :LIG1,
> 17 A:TRP296-> A:TRP296,
>
> This output shows that your docked ligand has contacts with 5 chain A
> residues: TYR193, PRO287, THR286, ASP279 and PHE291
> The rest of this output suggests that you included 2 flexible residues in
> your docking: ASP202 TRP 296
>
> In my config file my ligand is cadd.pdbqt. Now I am really confused that
> why in place of cadd, vina thinks my ligand is TRP296 or ASP202?
> ?Does your config file specify a flexible residue pdbqt file using the
> keyword 'flex'?
>
> Another thing, I use the same ligand for 3 more receptors so I just prepare
> the receptor with autodock and use different config file to run vina. I
> hope that's not the problem.
>
> --
> *Regards,*
>
> *Kanika Sharma*
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>



-- 
*Regards,*

*Kanika Sharma*


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