Dual topology description

Figure 3 Mutation of a ligand Asp into Asn in solution and bound to a protein, (a) Thermodynamic cycle, (b) Dual topology description a hybrid ligand with two side chains. Blocks are used to define the hybrid energy function [Eq. (14)]. Only the ligand is shown the environment is either solvent or the solvated protein, (c) Single-topology description.

The creation or annihilation of atoms in a molecular system (e.g., in the dual topology description just discussed) is frequently applied in free energy difference calculations. Although such a process is conceptually identical to other mutations, in practice the treatment of dummy atoms in a free energy difference calculation necessitates further approximations, which cause additional problems. 

When large conformational differences are expected between initial and final states of the system, a dual topology file description of the mutation may be useful. When a dual set of coordinates is present, the conformation of the final structure is not determined by the conformation of the initial structure. 

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