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From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Tue Dec 22 2020 - 20:43:36 CST

Good question. In fact, that file (bound.fep) is not used at all from what I can tell. For determining the role of the restraints, the alchemical route uses thermodynamic integration through colvars.

Best,
JC

On Dec 22, 2020, at 3:39 PM, Faisal, H M Nasrullah <hmnasrullah.faisal_at_ndsu.edu<mailto:hmnasrullah.faisal_at_ndsu.edu>> wrote:

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.

Faisal