Eur. Phys. J. D (2016) 70: 12
https://doi.org/10.1140/epjd/e2015-60424-9

Regular Article

Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology^*

¹ Goethe-Universität Frankfurt am Main, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
² MBN Research Center, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
³ University of Southern Denmark (SDU), Campusvej 55, 5230 Odense M, Denmark
⁴ A.F. Ioffe Physical-Technical Institute, Polytekhnicheskaya ul. 26, 194021 St. Petersburg, Russia
⁵ Bogolyubov Institute for Theoretical Physics, Metrolohichna str. 14-b, Kiev, 03680, Ukraine

^a e-mail: solovyov@mbnresearch.com

Received: 20 July 2015
Received in final form: 17 November 2015
Published online: 19 January 2016

Abstract

The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, we provide several illustrative case studies where dynamical topology is necessary. In particular, it is shown that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems.