Fluorescent proteins (FPs) have had an enormous impact
on molecular
and cellular biology and are employed in a wide range of studies of
molecular structure and dynamics. Yet, only a modest number of papers
have published molecular dynamics (MD) parameters describing FPs.
And despite the development of a wide range of FPs, there has been
no careful development of MD parameters across a series of FPs. In
this work, we present MD parameters describing six fluorescent protein
chromophores (EGFP, EBFP, EYFP, ECFP, mCherry, and DsRed) for use
with the Cornellet al. (J. Am. Chem. Soc.1995,117,5179−5197) family of AMBER force fields, including ff14SB and ff19SB.
We explore a wide range of solvent dielectric constants for determining
the chromophore equilibrium geometry and evaluate the impact of the
modeled solvent on the final atomic charges. We also present our methodological
approach in which we considered all six chromophores together with
a focus on modularity, transferability, and balance with existing
force fields. The parameters given here make it easy to employ MD
simulations to study any of the six systems, whereas the methodology
makes it easy for anyone to extend this work to develop consistent
parameters for additional fluorescent proteins. The results of our
own MD simulations are presented, showing that the classical MD parameters
yield chromophore structural distributions that compare well with
QM/MM simulations.