Specifying a Substructure for Embrace

The use of substructures can dramatically speed up Embrace calculations. Specifying substructures is described in the Embrace help topics (Embrace Minimization Panel, Embrace Conformational Search Panel). Substructures used in Embrace must meet an additional requirement: the receptor atoms must be numbered starting from 1 when constructing the substructure. Below are two simple recipes for setting up substructures. In the first, you can define shells of constrained atoms near the association site in the receptor. In the second, all atoms in the receptor are either fixed or frozen. If you already have a suitable substructure, you can simply read it in by clicking Read .sbc File.