Net-Q Model with Charge Transfer and Polarization for Molecular Dynamics

The article describes a new method for dynamic correction of the atom charges for molecular dynamics. The proposed method can be regarded as an extension of the QEq, QTPIE and fluq-q methods. The method is based on a graph which represents the molecular system and allows for charges to be transferred along its edges only. An advantage of the method is that its computational complexity is linear, in contrast to a polynomial one of the QEq and QTPIE. The proposed method correctly describes the charge distribution in the dissociation limit. A comparison of docked ligand positions in a number of the protein-ligand complexes with adjusted charges by the net-q model shows that they are less different from the crystallographic positions than those obtained by using fixed charges.