Molecular Mechanics Parameterization of Anesthetic Molecules

Abstract

Anesthetic drug molecules are being increasingly studied through the use of computational methods such as molecular dynamics (MD). Molecular mechanics force fields require the investigator to supply parameters for the force field equation, which are not available for novel molecules. Careful selection of these parameters is critical for simulations to produce meaningful results. Therefore, this chapter presents a state-of-the-art method for determining these parameters by comparison to quantum mechanics calculations and experimental quantities. Ketamine is used as an example to demonstrate the process.

Ketamine Metabolite (2R,6R)-Hydroxynorketamine Interacts with μ and κ Opioid Receptors

“…Therefore, we manually refined those parameters. We employed QM methods, following the Force Field Took Kit workflow 41 with modifications, 42 including dihedral interaction corrections as necessary.…”

Development of CHARMM compatible force field parameters and molecular dynamics simulations for the pesticide flupyradifurone

“…There is no gold standard method that is universally accepted to validate newly designed parameters. 25 However, since the end goal of the latter is to predict real life events, one sensible approach is to compute physical properties with MD simulations and compare the corresponding results to experiments. For FLU, available experimental data are scarce.…”