Paper Citing NAMD - Abstract
Pavlova, Anna; Gumbart, James C.
Parametrization of Macrolide Antibiotics Using the Force Field Toolkit
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:2052-2063, OCT 15 2015
Macrolides are an important class of antibiotics that target the bacterial ribosome. Computer simulations of macrolides are limited as specific force field parameters have not been previously developed for them. Here, we determine CHARMMcompatible force field parameters for erythromycin, azithromycin, and telithromycin, using the force field toolkit (ffTK) plugin in VMD. Because of their large size, novel approaches for parametrizing them had to be developed. Two methods for determining partial atomic charges, from interactions with TIP3P water and from the electrostatic potential, as well as several approaches for fitting the dihedral parameters were tested. The performance of the different parameter sets was evaluated by molecular dynamics simulations of the macrolides in ribosome, with a distinct improvement in maintenance of key interactions observed after refinement of the initial parameters. Based on the results of the macrolide tests, recommended procedures for parametrizing very large molecules using ffTK are given. (C) 2015 Wiley Periodicals, Inc.
