We are investigating the impact of DNA methylation on the transcription factor interaction using MD simulation cascade. One of the complex is already available in pdb (PDB ID:5T00). The major issue is the selection of appropriate forcefield to handle protein and methylated DNA complex. In the literature, some researchers have already used CHARMm36 forcefield for methylated DNA. When we typed the complex with this forcefield, no matching template were found for the methylated bases. Can anybody guide me in detail on how to type this complex properly? Also there are Zn metal ions in the complex. Is it possible to perform the simulation along with the Zn metal ions?

Below is the screenshot of methylated bases for which no matching template found while using CHARMm36 forcefield