I want to perform a molecular dynamics simulation of a protein that has several PTMs in order to find possible ligand pockets that might not be present in a simulation of that protein without PTMs.

The problem is that there are several pools of this protein, and each pool has its own PTMs. It's not known which PTMs are constitutional (present in all pool). What PTMs should I take into account when performing molecular dynamics?

I was thinking of taking into account the portion of the protein with fewer PTMs simply because it has fewer variables (PTMs). Perform simulations with various combinations of PTMs and stick with the ligand pocket present in most simulations. Should I use the entire protein or just the portion with PTMs?

Thank you.