RUS  ENG
Full version
JOURNALS // Matematicheskaya Biologiya i Bioinformatika // Archive

Mat. Biolog. Bioinform., 2015 Volume 10, Issue 2, Pages 580–592 (Mi mbb246)

Mathematical Modeling

Inclusion of the most important multi-particle interactions in the AMBER force field and optimization of energy parameters of the revised force field

S. A. Garbuzinskiya, B. T. Matkarimovb, A. V. Finkelsteina

a Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia
b National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan

Abstract: A new functional form for force field of non-covalent interactions is developed. Besides traditional members, it involves induced (by partial charges) polarization of all atoms as well as three-particle dispersion interactions of atoms with covalent bonds. The corresponding new members are added to a standard AMBER force field. Within this unified functional form of the force field, parameters of all types of non-covalent interactions are optimized using data on molecular crystals. A noticeable increase in correlation coefficient between calculated and experimental energy of cohesion of molecules in molecular crystals is shown.

Key words: non-covalent atom-atom interactions, three-particle interactions, polarizability, partial charges, “atom-covalent bond” interaction, molecular crystals, energy of cohesion.

UDC: 577.1, 577.3, 54.03

Received 08.12.2015, Published 24.12.2015

DOI: 10.17537/2015.10.580



© Steklov Math. Inst. of RAS, 2024