i am trying to show the van der waals interactions between a drug and its active site in pymol. i am able to display polar interactions such as hydrogen bonds, how ever i do not know how to display van der waals interactions. can someone please explain to me how this done?
Van der Waals interactions occur when adjacent atoms come close enough that their outer electron clouds just barely touch.
You can use the "within" selection ( https://pymolwiki.org/index.php/Selection_Algebra ) to select all atoms within a given distance of a selection of atoms. VdW forces are repulsive at distances less than the sum of the VdW radii of the atoms, attractive at slightly longer distances, but fall off very quickly at higher distances, as they are proportional to 1/r to the seventh power.
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