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New QM/MM Implementation of the MOPAC2012 in the GROMACS

  • Arthur O. ZalevskyEmail author
  • Roman V. Reshetnikov
  • Andrey V. Golovin
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 965)

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.

Keywords

QMMM hpc Molecular modelling Rational design 

Notes

Acknowledgements

Authors are grateful to Dr. J. Stewart for sources of MOPAC2012 and initial hints on implementation. Computational experiments were carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University supported by the project RFMEFI62117X0011. The study was supported by the Russian Ministry of Education and Science grant RFMEFI57617X0095.

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Arthur O. Zalevsky
    • 1
    • 4
    Email author
  • Roman V. Reshetnikov
    • 2
    • 3
    • 4
  • Andrey V. Golovin
    • 1
    • 3
    • 4
  1. 1.Faculty of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
  2. 2.Institute of Gene BiologyRussian Academy of SciencesMoscowRussia
  3. 3.Apto-Pharm LLCMoscowRussia
  4. 4.Sechenov First Moscow State Medical UniversityMoscowRussia

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