đŸŽ¯ Ligand-Centric Grid Box Calculator

Instantly generate precise grid parameters centered on a co-crystallized ligand

Configuration

Distance added to all sides of the ligand to form the binding box

ℹī¸ How It Works

Redocking experiments or screening against a known binding pocket shouldn't require manual measurement in PyMOL. This tool automatically calculates the optimal docking grid based directly on the spatial coordinates of a co-crystallized ligand.

1

Upload Complex

Provide your complete protein-ligand structure in PDB format.

2

Auto-Detection

Our custom text parser instantly locates the non-standard ligand molecule, ignoring waters and ions.

3

Bounding Box

The tool extracts all ligand coordinates to calculate its mathematical center and extremities.

4

Format Output

Coordinates are expanded by your padding and formatted for Vina & AD4 config files.

When to Use This Tool

  • Redocking Protocol Validation: When you need to perfectly encompass the native ligand to validate your docking software's accuracy.
  • Known Binding Sites: When running a virtual screen against a previously established active pocket.
  • Blind Docking Alternative: Highly effective for small proteins where calculating the entire surface area is computationally expensive.

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 standard 0.4 Å spacing

Tips

  • There is no need to strip waters (`HOH`) or standard ions before uploading; the tool automatically filters them out.
  • This tool ignores strict PDB `MODEL` formatting, making it immune to errors caused by multi-model files.

Citation

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