From: Faisal, H M Nasrullah (hmnasrullah.faisal_at_ndsu.edu)
Date: Tue Dec 22 2020 - 20:52:34 CST
Thanks for your kind reply. I totally overlooked that matter.
From: Gumbart, JC <gumbart_at_physics.gatech.edu>
Sent: Tuesday, December 22, 2020 8:43 PM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>; Faisal, H M Nasrullah <hmnasrullah.faisal_at_ndsu.edu>
Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>; owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial
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.
On Dec 22, 2020, at 3:39 PM, Faisal, H M Nasrullah <hmnasrullah.faisal_at_ndsu.edu<mailto:hmnasrullah.faisal_at_ndsu.edu>> wrote:
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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