AMBER-DYES in AMBER: Implementation of fluorophore and linker parameters into AmberTools

The Journal of Chemical Physics
Bastian Schepers, Holger Gohlke

Abstract

Molecular dynamics (MD) simulations of explicit representations of fluorescent dyes attached via a linker to a protein allow, e.g., probing commonly used approximations for dye localization and/or orientation or modeling Förster resonance energy transfer. However, setting up and performing such MD simulations with the AMBER suite of biomolecular simulation programs has remained challenging due to the unavailability of an easy-to-use set of parameters within AMBER. Here, we adapted the AMBER-DYES parameter set derived by Graen et al. [J. Chem. Theory Comput. 10, 5505 (2014)] into "AMBER-DYES in AMBER" to generate a force field applicable within AMBER for commonly used fluorescent dyes and linkers attached to a protein. In particular, the computationally efficient graphics processing unit (GPU) implementation of the AMBER MD engine can now be exploited to overcome sampling issues of dye movements. The implementation is compatible with state-of-the-art force fields such as GAFF, GAFF2, ff99SB, ff14SB, lipid17, and GLYCAM_06j, which allows simulating post-translationally modified proteins and/or protein-ligand complexes and/or proteins in membrane environments. It is applicable with frequently used water models such as TIP3P, TIP4P...Continue Reading

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Citations

Mar 17, 2021·The Journal of Chemical Physics·Charles L BrooksEmad Tajkhorshid
Jun 3, 2021·Antioxidants·Chanchao LorthongpanichSurapol Issaragrisil
Jun 24, 2021·Nucleic Acids Research·Jose A NakamotoPohl Milón
Nov 24, 2020·Journal of Chemical Theory and Computation·Robert A ShawJ Grant Hill
Jan 12, 2022·Journal of Chemical Information and Modeling·Sorin MuraruMariana Ionita

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