Glide is a popular molecular docking program used to predict the binding mode and affinity of ligands with a protein target. However, its default settings and scoring functions are primarily designed for small organic molecules and may not explicitly account for metal ions.

First, we should know that metal ions have a unique coordination geometries and bonding characteristics compared to organic ligands. Their interactions with proteins involve coordination bonds and electrostatic interactions, which requires specialized treatment in docking algorithms.

Secondly, if glide algorithm was used. In some cases, the Glide docking approach may not adequately model the binding of metal ions due to limitations in the force fields or scoring functions used. These computational methods are typically optimized for organic ligands and may not accurately capture the metal-ligand interactions. Consequently, the docking program may fail to recognize or inaccurately consider the presence of metal ions during the docking process, leading to potential errors in the subsequent visualization and analysis of ligand-metal interactions.

Addressing this issues, specialized docking programs or modified protocols can be employed that are specifically designed to handle metal-ligand interactions. These programs may utilize for instance custom force fields, scoring functions, and algorithms build to accurately model the coordination chemistry of metal ions.

You may want to explore Auto-Dock, MOE or GOLD. I hope this would help!!!!!!!!!!!