I am facing an error with the structure I’ve uploaded. Despite uploading .lib and .frcmod files, my ligand is getting discarded.
I have a phosphotyrosine in my structure, and as recommended for AMBER full MD setup, I changed ATOM to HETATM for it. I also changed other parameters as per AMBER (OG to OS etc.). After these changes, my ligand Y1P for phosphotyrosine is still discarded.
I am very new to MD so I may be missing out on something. Please guide me.