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Hi David, Perhaps the most accurate inter- and intramolecular forces available for macromolecular X-ray crystallography refinement are currently based on the polarizable multipole AMOEBA force field. AMOEBA includes explicit support for the interactions you mentioned: 1.) repulsion-dispersion (Pauli repulsion and London dispersion forces) 2.) permanent multipole - permanent multipole (including permanent dipole - permanent dipole) 3.) permanent multipole - induced dipole (including permanent dipole - induced dipole) 4.) induced dipole - induced dipole (many-body polarization) Secondary quantum mechanical effects are either implicitly accounted for in the model when the repulsion-dispersion term is fit to experimental thermodynamics (liquid densities and heats of vaporization) or are simply neglected. Although AMOEBA is more expensive than traditional chemical restraints used for refinement, we've shown it's fast enough for any data set in the Protein Databank (i.e. even Ribosomes with 2 million atoms in the unit cell). The inter- and intramolecular distances achieved by AMOEBA-assisted X-ray refinement have been shown to be very accurate. For example, in a recent study of 17 macromolecular datasets we achieved an average MolProbity score in the 95th percentile (see the reference below and citations within for more details). AMOEBA-assisted X-ray refinement is implemented in a free, open source (GPL v.3) program called "Force Field X". The FFX engine could be included in existing refinement programs if there is interest and we are open to considering an alternative license as necessary. http://ffx.kenai.com Best Wishes, Mike Fenn, T. D. and M. J. Schnieders, Polarizable atomic multipole X-ray refinement: Weighting schemes for macromolecular diffraction, Acta Crystallographica Section D 2011 67, (11), 957-65. http://dx.doi.org/10.1107/S0907444911039060 On 3/20/12 9:41 AM, "David Mueller" <[log in to unmask]> wrote: >van der Waals distancesDear Crystallographers: > >I am mapping out van der Waals contacts between a small molecule and a >protein. What are the generally accepted limits for positive van der >Waals interactions? I am defining van der Waals interactions as the >energy of interaction between permanent dipoles, plus the energy of >interaction between permanent dipoles and dipoles induced by them, plus >the energy of interaction between neutral atoms. Is this complete? >Accurate? > > >Is there an associated reference? > >Cheers > > >David M. Mueller >Biochemistry and Molecular Biology >The Chicago Medical School >Rosalind Franklin University of Medicine and Science >