đŸ§Ŧ AutoDock Grid Box Calculator

Fast, automated grid parameters for site-specific molecular docking

Configuration

Enter residue numbers separated by commas
Distance around residues for grid box

ℹī¸ How It Works

This tool calculates AutoDock grid parameters from your selected binding site residues:

1

Upload PDB File

Provide your protein structure in PDB format

2

Specify Residues

Enter the residue numbers that define your binding site (e.g., 45, 46, 89)

3

Set Padding

Choose buffer distance around residues (default 5.0 Å)

4

Get Grid Parameters

Receive coordinates optimized for both AutoDock Vina and AutoDock 4

When to Use This Tool

  • Site-specific docking: When you know the binding site residues, and would like to get Grid parameters accurately to perform Docking.

Output Parameters

  • AutoDock Vina: Uses center (X, Y, Z) and size (size_x, size_y, size_z) coordinates

  • AutoDock 4: Uses grid center coordinates and number of points (npts) per axis with 0.4 Å spacing

Tips

  • Use comma-separated residue numbers: 45, 46, 89
  • Residue numbers must exist in your PDB file

Citation

  • Biopython: Cock, P. J., et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422-1423.