Protein-peptide ligand MD


I would like to perform MD of a peptide ligand with a protein using MDWeb but I am a bit confused on some step and I would like to kindly ask for some help.
If the pdb file of the protein I want to use only exist as bound to another ligand (no apo), can I still use it? Do I just select remove it at the stage when I am checking the protein (when it gives errors and warnings)?
Regarding the ligand I want to use in my simulations, how and when do I include it? Do I need to prepare it somehow (it is a peptide)? It has been crystallized with another protein so can I save the ligand (e.g. in pymol; open the structure and save the ligand as pdb?) and include it in the MDWeb somehow?

I would appreciate any help.

Thank you so much.

All the best