Missing centre grid co-ordinates and size_x, size_y and size_z value in 140 complex dataset to apply for Autodock Vina

[srilekha1993]

As vina need the center grid co-ordinates and size_x,size_y,size_z values but the dataset only contains grid maps. Is there any way to evaluate these co-ordinates?

[rwxayheee]

Hi @srilekha1993, what kind of grid map files do you have access to? You can get the center coordinates and the dimensions from both the .map and .fld files generated from autogrid, if that helps. Open them in a text editor and you should be able to find them at the beginning of these files

[srilekha1993]

@rwxayheee Thanks a lot for this information

[srilekha1993]

@rwxayheee I have tried with few of the ligands for Vina GPU not able to run any of the example using the given co-ordinates and dimensions The map file looks like below

The config file looks like below

After running Autodock vina its showing the following error

Please have a look and let me know how to resolve it

[rwxayheee]

@srilekha1993 size_x size_y size_z are lengths (in Å), so their values = NELEMENTS SPACING = 50 0.375 = 18.75 could you try that?

18x18x18 can create a box for the ligand in 5WLO if centered at the binding site. 50x50x50 can be enough to encompass the entire protein (which may or may not be what you want)

[srilekha1993]

Thanks a lot @rwxayheee. It worked now