New QM/MM implementation of the MOPAC2012 in the GROMACS

Abstract

Hybrid QM/MM simulations augmented with enhanced sampling techniques proved to be advantageous in different usage scenarios, from studies of biological systems to drug and enzyme design. However, there are several factors that limit the applicability of the approach. First, typical biologically relevant systems are too large and hence computationally expensive for many QM methods. Second, a majority of fast non ab initio QM methods contain parameters for a very limited set of elements, which restrains their usage for applications involving radionuclides and other unusual compounds. Therefore, there is an incessant need for new tools which will expand both type and size of simulated objects. Here we present a novel combination of widely accepted molecular modelling packages GROMACS and MOPAC2012 and demonstrate its applicability for design of a catalytic antibody capable of organophosphorus compound hydrolysis.