Modeling Chemical Reactions and Equilibria in Amber
TUTORIAL A18: Constant pH
Molecular Dynamics Example - Calculating pKas for titratable
side chains in HEWL
In this tutorial we will learn how to use the AMBER software to perform
molecular dynamics simulations at constant pH (CpHMD), one of the most
important chemical equilibria in biology. Solution pH affects titratable
side chains in proteins (and, on occasion, ribozymes), which can have a
dramatic impact on the function, structure, and stability of large
biomolecules. CpHMD is a method that uses a hybrid molecular dynamics/Monte
Carlo approach to sample conformations and protonation states of various
titratable residues in biomolecules. This method can help capture the
coupling between protein structure and pH.
TUTORIAL A2: A simple coupled
potential QM/MM/MD simulation.
In most simulations, the classical amber force field is the preferred method
for defining and navigating an energy surface. Since AMBER 9, however, we
have offered the capability to simulate coupled quantum mechanical and
Newtonian mechanical (QM/MM) systems. This tutorial demonstrates how to set
up a simple QM/MM MD simulation of NMA in solution.