I tried autodock vina for same protein and ligand keeping the grid points the same, but every time it gives me different results (i.e no. of hydrogen bonds and binding affinity). I am confused about why its happening. Please suggest what to do.
Thanks in Advance
For sure. Autodock vina use a random seed. Thus it is normal to obtain different results each time. However these results has to be consistent over the runs, i.e, more than 1 kcal/mol of difference use to be too much. If you obtain different values but in similar series, maybe you are detecting more than one binding site. On the other hand if the values are changing every time without following any pattern implies that your ligand is not suitable for the binding site of your target protein.
Hi Melchor,
I am getting the differnece of around 0.4 -0.6 kcal/mol difference every time,,so is it feasible?
About the binding site,do vina calculate and analyse the binding site itself or we have to calculate it?
Hi Mayank,
0.5 - 0.6 is feasible. About the binding site, as you know you, have to give the coordinates x,y,z of the center in that has to place the ligand. These coordinates are based on the target you are giving as a receptor, and you have to calculate them by your own. Vina only gives you the binding energy and the pdbqt file of the ligand whith the coordinates that it adopts on the bindign site. To analyze it you have to load, at the same time, this output pdbtq file and the original receptor file, for example with pymol and check it manually to see what happens, the interactions and so on.
Hope it helps. For more info you can check the Autodock manual.
Hi
I have problem like you with vina, the essential keys you must consider its Grid box size and position, so i recommend you that chose correct box and you will see reproducible result.
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