A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0]

Jack A. Henderson, Ruibin Lui, Julie A. Harris, Yandong Huang, Vinicius M. de Oliviera, Jana Shen
2022 Living journal of computational molecular science  
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
more » ... the reader in learning and using the various continuous constant pH MD methods in Amber and CHARMM packages, which have been applied to predict pK a values and elucidate proton-coupled conformational dynamics of a variety of proteins including enzymes and membrane transporters.
doi:10.33011/livecoms.4.1.1563 pmid:36776714 pmcid:PMC9910290 fatcat:socrgdwcsndqjj47ymthfz4hi4