Blind Host–Guest Docking Grid Box Calculator

Calculate the recommended cubic AutoDock grid size for blind host–guest docking from the largest measured dimensions of the host and guest structures.

Docking assumption: Semi-flexible docking where the guest (ligand) is flexible and the host (receptor) is treated as rigid.

How to use this tool

In MOE or a similar molecular modeling tool, measure the largest distance across the host structure by clicking one extreme atom and then the opposite extreme atom.
Repeat the same step for the guest structure.
Enter both measured values below in Å.
Enter the grid spacing. A common AutoDock value is 0.375 Å.

Built-in formulas

The calculator applies the following equations for blind host–guest docking:

L = D_host,max + (3/2 × D_guest,max)

n_pts = ⌈ (L / spacing) + 1 ⌉

Notes about the first formula:
- L is the estimated cubic grid-box length for blind host–guest docking.
-

D host,max

and

D guest,max

are the largest measured distances of the host and guest.
- An additional 1.5× guest-size factor is included to provide extra space for guest flexibility during docking.

The final grid size must not exceed

126 \times 126 \times 126

, and

n pts

must be an even integer.

Enter your values

Largest host distance (Å)

Largest guest distance (Å)

Grid spacing (Å)

Recommended AutoDock Output

84 × 84 × 84

The value of

n pts

is first rounded upward with the ceiling function. If that value is odd, it is increased to the next even integer to satisfy the docking constraint.