Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial

From: Faisal, H M Nasrullah (hmnasrullah.faisal_at_ndsu.edu)
Date: Tue Dec 22 2020 - 14:39:15 CST

Dear all,

I am trying to go through the tutorial of Standard Binding Free Energies between protein and Ligand. I am a bit confused regarding the 'bound.fep' file from 'Restraints%3ABound' directory under the 'AlchemicalRoute' archives. My question is why the protein was being decoupled from the system instead of the ligand (the beta column of protein is tagged with -1)? Can anybody please give me some insight?

Thanks in advance.


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