Energy Scoring Method in Grid

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The general form of energy scoring function:

Energy scoring function

It's easy to see that the Coulumb potential Energy term could be separated into receptor and ligand part. If the Lennard-Jones one could be separated, it will be easy to precalculate the potential of each grid point in docking region and speed up the docking process.

Computational chemist took the assumption that the coefficients for Lennard-Jones part in energy scoring function are also separable.

Lennard-Jones coefficients

The new form of energy scoring function like this:

Energy score function

So each time, when you run the grid calculation, you get the grid value in each grid point

potential energy at each grid point

and save them in your *.nrg file.

In dock process, the program generate the energy of certain ligand atom by statistically summarizing the closest eight gird points' value. The energy score for a ligand will be the total of all its atoms