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Article ID: 778 - Last Modified:

I would like to dock compounds into a large protein, but when I try to generate the receptor grid, I get a message saying that there are too many atoms. How can I prepare a grid for this protein?

If you are running older software, consider updating to Suite 2010 or later, where the atom limit is 90000.

Otherwise (or if the protein is still too big), to generate grids for this receptor, you would have to reduce the number of atoms. Usually, large proteins like this have multiple domains, often with duplicate chains, binding sites, and ligands. In this situation, the extra copies can be removed via the Protein Preparation Wizard, or by deleting molecules or chains manually.

If you have a single chain that is too large, or if the active site is between two chains, you can consider truncating the protein beyond some distance from the active site (e.g. 30 Å). Atoms far away from the binding site are not likely to affect the docking anyway. You can truncate the protein as follows:

  1. Select the ligand or some atoms in the active site of the protein.
  2. Choose Select from the Delete toolbar button, to open the Atom Selection dialog box.
  3. Click Selection.
  4. Click Proximity, and in the Proximity dialog box, set the proximity to Within 30 Angstroms, select Fill: Residues, and click OK.
  5. In the Atom Selection dialog box, click Invert (to select the atoms further than 30 Å).
  6. Click OK to delete the atoms.

Deleting these residues far from the active site will leave some truncated chain ends. You'll have to cap these with hydrogens. If you have not yet prepared this protein, the necessary hydrogen addition will be done in the Preprocess step of the Protein Preparation Wizard. If your receptor is already prepared, you can add hydrogens via the "+H" toolbar button.

Keywords: large receptor structures, too many atoms, receptor grid, Glide, Maestro

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