[gmx-users] the atomic charges in ligand

Ran Friedman r.friedman at bioc.unizh.ch
Wed Jul 11 11:33:35 CEST 2007

Dear Rui,

The atomic charges (and other FF properties) should match as closely as
possible to the way the FF was developed. In AMBER, these were derived
by fitting to a QM calculations IIRC, and in OPLS and CHARMM they're
usually close to what you'd get from quantum chemistry with a medium
basis set (the basis set it should be mentioned in the literature you read).

To get the atomic charges from a QM calculation, you should calculate
the wave function of the molecule using a reasonable basis set (and
usually after optimising the structure, to get you into a minimum). You
can now calculate the average number of electrons associated with each
atom and get a partial charge, but the results will have a strong
dependence on the geometry of your system. Another option is to
calculate the electrostatic potential over the whole molecule, and fit
the atomic charges so that they reproduce this potential. This method is
less sensitive to small changes in the geometry of the molecule, and is
probably what you refer to.


Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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