Question about generating *.box.pdb with mk_prepare_receptor.py

[sasaju]

I noticed that when calculating the coordinates of the box's vertices, int() is used instead of float(). Could this lead to discrepancies with the actual box calculation?

Meeko/meeko/gridbox.py

Line 55 in 07a38f8

def box_to_pdb_string(box_center, npts, spacing=0.375):

Meeko/meeko/gridbox.py

Line 67 in 07a38f8

step_x = int(npts[0] / 2.0) * spacing

[rwxayheee]

Hi @sasaju
This function is only used to produce the output (box.pdb) to visualize the box. It will not change how the size of the box is determined. Calculation of the box size (calc_box) was done before this function is called in mk_prepare_receptor.py) and written by a different function box_to_vina_string to box.txt which is the config file for Vina.

But you're likely right that the int can cause a discrepancy between numbers in box.pdb and box.txt. Not very sure wether and why this was done intentionally. This function currently produces the boundary of the integer (with spacing = 1.0) grids given a specific center.

[diogomart]

The actual grids will have a discrete number of points, both in autogrid and in vina. Autogrid even forces an odd number of grid points in each dimension (I don't know why). I don't remember why I wrote that exact equation.

[sasaju]

Thanks for your response! 😁