The input for this protocol is a trajectory from a molecular dynamics simulation which was performed on
some complex (i.e. a protein-ligand complex or a protein-protein complex). This protocol then performs three single energy calculations:
(a) on the complex
(b) on one body/part of the complex
(c) on the remaining part of the complex
The following energy is calculated for each frame:
Gbinding = G(a) - G(b) - G(c)
Then the average of Gbinding is calculated over all frames and reported as the DeltaG_Average.
The user specifies whether to use an Implicit Solvent Model and other forcefield simulation parameters. The system you specify as the 'Input Typed Molecule' should NOT contain solvent.
Note, this protocol will only run on Windows with DS 1.7 (not Linux)