Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation

From: Faisal, H M Nasrullah (hmnasrullah.faisal_at_ndsu.edu)
Date: Thu Sep 17 2020 - 10:07:35 CDT

Hi All,

I am going over the tutorial of protein-ligand binding free energy calculation using the alchemical route. Double annihilation of ligand using fep was understandable to me. But I cannot understand the simulation output of harmonic restraints' effect on free energy using colvars module. I ran the input files of 'tutorial-protein-ligand\Archives\AlchemicalRoute\Restraints%3ABound' this folder and the output files were .dcd, .log and .colvars.sate file. No .pmf file was generated. Then How can I calculate the free energy due to harmonic restraints? Any advice will be highly appreciated.


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