phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids

Phosphorylated amino acids are involved
in many cell
regulatory
networks; proteins containing these post-translational modifications
are widely studied both experimentally and computationally. Simulations
are used to investigate a wide range of structural and dynamic properties
of biomolecules, such as ligand binding, enzyme-reaction mechanisms,
and protein folding. However, the development of force field parameters
for the simulation of proteins containing phosphorylated amino acids
using the Amber program has not kept pace with the development of
parameters for standard amino acids, and it is challenging to model
these modified amino acids with accuracy comparable to proteins containing
only standard amino acids. In particular, the popular ff14SB and ff19SB
models do not contain parameters for phosphorylated amino acids. Here,
the dihedral parameters for the side chains of the most common phosphorylated
amino acids are trained against reference data from QM calculations
adopting the ff14SB approach, followed by validation against experimental
data. Library files and corresponding parameter files are provided,
with versions that are compatible with both ff14SB and ff19SB.