Next Article in Journal
Combined Machine Learning and Molecular Modelling Workflow for the Recognition of Potentially Novel Fungicides
Previous Article in Journal
Marine Cyanobacteria: A Source of Lead Compounds and their Clinically-Relevant Molecular Targets
Article

Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation

by 1,* and 2
1
Institute of Science, Department of Chemistry, Dicle University, 21280 Diyarbakir, Turkey
2
Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Dicle University, 21280 Diyarbakir Turkey
*
Author to whom correspondence should be addressed.
Molecules 2020, 25(9), 2196; https://doi.org/10.3390/molecules25092196
Received: 24 March 2020 / Revised: 5 May 2020 / Accepted: 6 May 2020 / Published: 8 May 2020
(This article belongs to the Section Computational and Theoretical Chemistry)
Boric acid, borate esters, and hydroxy derivatives are biologically active molecules. Thus, performing molecular dynamics simulations of these molecules is vital in terms of drug design, but it is difficult to find directly generated Amber parameters based on an ab initio method for these kinds of molecules in the literature. In this study, Amber parameters for such molecules containing boron were generated based on ab initio calculations using the paramfit program, which applies a combination of genetic and simplex algorithms, and the Visual Force Field Derivation Toolkit (VFFDT) program containing the Seminario method. The minimized structure, after obtaining novel parameters and using the sander program, was compared with the experimental crystallographic structures, and it was observed that the root-mean-square deviation (RMSD) value between the experimental structure and minimized structure agreed reasonably well. In addition, the molecule was heated, and the molecular dynamics simulation was successfully obtained with the novel parameters. View Full-Text
Keywords: Amber; force field; parameterization; boron Amber; force field; parameterization; boron
Show Figures

Figure 1

MDPI and ACS Style

Kurt, B.; Temel, H. Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation. Molecules 2020, 25, 2196. https://doi.org/10.3390/molecules25092196

AMA Style

Kurt B, Temel H. Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation. Molecules. 2020; 25(9):2196. https://doi.org/10.3390/molecules25092196

Chicago/Turabian Style

Kurt, Barış, and Hamdi Temel. 2020. "Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation" Molecules 25, no. 9: 2196. https://doi.org/10.3390/molecules25092196

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop