Free energy calculation of protein ligand system

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Dear all,
I want to run a protein-ligand system in water and calculate its free binding energy. I saw the tutorial but it only uses the methanol or ethanol molecule in water. The mdp files confuse me. the system to decouple is methanol or ethanol only. but for me it is a protein-ligand complex. to do the decoupling, should i create an index file for the complex and water and ions? then can run the index file as the decoupled system.
next question is that since i have to find the free binding energy of the complex, should i run two md simulations; one with the complex and another with ligand only? that would really be a waste of time.

I have looked at the possibility of converting the topologies to amber but no avail there are a lot of parmed errors and the files are nor recognised.Since i have ambertools18 that cannot be upgraded to AmberTools 20, i cannot use the GMXPBSA function nor can i use the g_mmpbsa asit is only compatible with the older versions.

Please give suggestions as i am running out time for a paper submission.

thank you