Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions.

ABSTRACT: Modeling metalloproteins often requires classical molecular dynamics (MD) simulations in order to capture their relevant motions, which in turn necessitates reliable descriptions of the metal centers involved. One of the most successful approaches to date is provided by the "cationic dummy model", where the positive charge of the metal ion is transferred toward dummy particles that are bonded to the central metal ion in a predefined coordination geometry. While this approach allows for ligand exchange, and captures the correct electrostatics as demonstrated for different divalent metal ions, current dummy models neglect ion-induced dipole interactions. In the present work, we resolve this weakness by taking advantage of the recently introduced 12-6-4 type Lennard-Jones potential to include

SUBMITTER: Liao Q 

PROVIDER: S-EPMC5672556 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature