[gmx-users] how to set system for absolute free enegy calculation of ligand in protein

[Sadaf Rani]

Dear Gromacs users
I need your suggestions regarding the calculation of free energy of binding
in of ligand protein-ligand complex in setting up the system.
I am performing binding free energy calculation following alchemical free
energy path. I added a single molecule type in topology for both protein
and ligand in order to add distance restraints between ligand and protein
atoms however for decoupling ligand from protein I need a separate molecule
type for the ligand.
How should I set the system to avoid this problem?

Thanks in advance.

Sadaf