Article ID: 1271 - Last Modified: April 18, 2011
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.
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