All-atom molecular dynamics (MD) simulations are a powerful approach to studying the structure and dynamics of proteins related to health and disease. Advances in the MD field allow modeling proteins with high accuracy. However, modeling metal ions and their interactions with proteins is still challenging for MD simulations. Over one-third of known protein structures bind metal ions and have various cellular functions, such as structural stability, catalysis, and regulation. NPL4 is a zinc-binding protein and works as a cofactor for p97, and together they regulate protein homeostasis. NPL4 is also of biomedical importance and has been proposed as the target of Antabuse, a drug recently repurposed for drug cancer treatment. Recent experimental studies have proposed that the Antabuse metabolites, bis-(diethyldithiocarbamate)-copper (CuET) and cupric ions released from CuET, induce NPL4 misfolding and consequent aggregation. However, the molecular details of the mechanisms of interactions of Antabuse metabolites with NPL4 and the consequent structural effects are still elusive. In this context, biomolecular simulations can help to shed light on the related structural details. To apply MD simulations to NPL4 and its interaction with copper or Antabuse metabolites the first important step is identifying a suitable force field to describe the protein in its zinc-bound states. A challenge is that we cannot rely on bonded parameters that could help to stabilize the interaction between the protein and zinc, overcoming the limitations of non-bonded parameters. This is due to the fact that, if we want to study the misfolding mechanism, we cannot rule out that the zinc ion may detach from the protein structure during the process and copper replaces it in the metal binding site. In light of the above observations, we compared different MD force fields, including non-bonded zinc and copper parameters, on different protein constructs. At first, we investigated the force-field ability to model the coordination geometry of the metal ions. To this goal, we compared the results from MD simulations with optimized geometries from quantum mechanics calculations using a model system of the zinc coordination site for Npl4.