Generating CHARMM-compatible force field parameters for atrazine

Ecker, János (2016) Generating CHARMM-compatible force field parameters for atrazine. JOURNAL OF UNIVERSAL SCIENCE ONLINE, 3 (1). pp. 1-8. ISSN 2416-0008

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Abstract

There are many synthetic, drug-like molecules whose interactions with large biomolecules could be partly described by molecular dynamics studies. The parameters necessary to perform an MD simulation are available for biomolecules (proteins, nucleic acids, lipids, carbohydrates) and for many other small chemical compounds with biological relevance. In case of uncharacterized molecules, parameter sets can be calculated using quantummechanical calculations. The optimized geometry, van der Waals, charge, bond, angle and torsion parameters for the photosystem II-inhibitor herbicide, atrazine, were calculated and integrated into a CHARMMcompatible parameter file. The file (.par) is available, along with the coordinates (.pdb), structure (.psf) and topology (.top), and with this four type of data, atrazine may be part of CHARMM-based molecular dynamics simulations, therefore, its interactions with biomolecules can be studied.

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