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CCP4BB  March 2012

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Subject:

Re: van der Waals distances

From:

Michael Schnieders <[log in to unmask]>

Reply-To:

Michael Schnieders <[log in to unmask]>

Date:

Wed, 21 Mar 2012 10:36:15 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (71 lines)

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
>

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