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
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.
© EDP Sciences, Società Italiana di Fisica, Springer-Verlag 2016
