A Guide to the Continuous Constant PH Molecular Dynamics Methods in Amber and CHARMM [Article V1.0]

Overview

Journal Living J Comput Mol Sci

Date 2023 Feb 13

PMID 36776714

Authors

Jack A Henderson

Ruibin Liu

Julie A Harris

Yandong Huang

Vinicius Martins de Oliveira

Jana Shen

Affiliations

Soon will be listed here.

Abstract

Like temperature and pressure, solution pH is an important environmental variable in biomolecular simulations. Virtually all proteins depend on pH to maintain their structure and function. In conventional molecular dynamics (MD) simulations of proteins, pH is implicitly accounted for by assigning and fixing protonation states of titratable sidechains. This is a significant limitation, as the assigned protonation states may be wrong and they may change during dynamics. In this tutorial, we guide the reader in learning and using the various continuous constant pH MD methods in Amber and CHARMM packages, which have been applied to predict p values and elucidate proton-coupled conformational dynamics of a variety of proteins including enzymes and membrane transporters.

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