On Wed, 2012-03-21 at 10:16 +0100, Rubén Sánchez Eugenia wrote: > In Physical Chemistry Van der Waals interacions are defined as all > type of forces between molecules (or parts of them) excluding covalent > bonds and electrostatic interactions. So, you are right that the most > common forces included into Van Der Waals are: interaction between > permanent dipoles, interaction > between permanent dipoles and dipoles induced by them, and interaction > between apolar groups due to their polarizability.
But the dipole-related interactions are electrostatic! The full quote is > The attractive or repulsive forces between molecular entities (or between > groups within the > same molecular entity) other than those due to bond formation or to the > electrostatic inter- > action of ions or of ionic groups with one another or with neutral molecules. > The term includes: > dipole-dipole, dipole-induced dipole and London (instantaneous induced > dipole-induced dipole) > forces. It also says > The term is sometimes used loosely for the totality of nonspecific attractive > or repulsive > intermolecular forces. which is, indeed, a loose (and vague) definition (what is meant by nonspecific?). The van der Waals forces arise, imho, from an attempt to break the overall of electrostatic interactions into manageable components. This neglects higher terms in multipole expansion. Difficulty is that it also includes contact repulsion. To answer the original question, you may find the following threads useful http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19876.html http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19861.html Ligplot is an excellent reference point, and it traces back to the hbplus which you can use to output the list of non-bonded interactions. There is als the ligand explorer in the PDB which you probably can use with your own model. Normally, van der Waals contact distances are defined as the sum of the van der Waals radii of the contacting atoms, so it's not a single number. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
