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22 Appendix XII: MolDock Score [Grid]
'MolDock Score [Grid]' is a grid based version of the MolDock Score function.
It precalculates potential-energy values on an evenly spaced cubic grid in order
to speed up calculations. Notice that unlike the standard MolDock Score, the
grid version does not take hydrogen bond directionality into account (hydrogen
bonding is determined solely on distance and hydrogen bonding capabilities).
The energy potential is evaluated by using tri-linear interpolation between
relevant grid points. The rest of the terms in the MolDock Score [Grid] version
(i.e. internal ligand energy contributions and constraint penalties) are identical
to the standard version of the scoring function.
Grids are not stored permanently - they are calculated when needed. (Grid
generation is relatively fast. Typically ~15 seconds for the standard settings).
Grids will automatically be reused while running docking scripts as long as the
target protein does not change.
Notice that large energy grids with high resolution can consume a lot of
memory. Grid resolutions of 0.3 Å -0.4 Å will be adequate in most cases. Look
out for the estimated memory usage in the Docking Wizard. As a rule of thumb
it should never exceed more than half of the physical memory available in the
computer. Also notice that if several instances (processes) of MVD is running,
each process will need to generate its own grid.
Usage From GUI
In order to use the MolDockScore grid version, select it as the evaluation
function in the Docking Wizard ('Scoring Function -> Score -> MolDock
Score [GRID]').
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