Good day,
I created a grid using the Autodock tools and then using those coordinates and size I created a configuration file for Vina. But in the results, the location of the ligand do not match the specified coordinates and size. I used the PyMol for visualization, but the ligand is not placed within the previously selected coordinates.
Thank you for help.
There can be 2-3 reasons for this. The main reason might be the gridbox not matching with the configuration file.
1. The parameters(center_x, center_y, center_z) in the config file not matching the coordinates set in the grid box - For this you can open the grid.txt file you had prepared and copy the last lines as dimensions for x, y and z in the config file . This will ensure that both the coordinates are matching.
2. Size of parameters in the config file might be incorrect from what is specified by you in the grid - We can set it correctly by opening the grid file and then setting the size in the config file.
Let me know if that works !
Pls don't hesitate to ping me if the problem persists :)
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