Knowledge Base

Article ID: 1271 - Last Modified:

How do I freeze the receptor in an Embrace calculation?

In a typical Embrace calculation, all of the ligands and the entire receptor are minimized. However, it is possible to set up either an energy difference or an interaction energy calculation, where the receptor is constrained, but each ligand is minimized.

In the Embrace context, Atoms for Substructure are not required to use shells of fixed or frozen atoms. To set up an Embrace calculation with a fixed or frozen receptor, in the Substructure tab, create a new shell, enter the molecule number (or numbers) of the receptor, and finally set the constraining force constant or freeze the atoms. No Substructure definitions are required, as each ligand is automatically included into the set of atoms minimized with the native force field potential.

For example, assuming the receptor to be frozen is the first molecule in the Workspace, click New in the Shells section of the Substructure tab, enter mol.n 1 in the ASL text box for Additional atoms for shell, then select Freeze atoms. The atoms in the receptor are highlighted with orange markers.

The MacroModel Quick Start Guide has more examples of calculations using substructures and shells.

Keywords: MacroModel

Back to Search Results

Was this information helpful?

What can we do to improve this information?

To ask a question or get help, please submit a support ticket or email us at
Knowledge Base Search

Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles