ADL: Vina result confusion

kanika sharma ksharma997 at gmail.com
Mon Jun 29 06:01:54 PDT 2015


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,



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?

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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