Protein-ligand affinity

From: James Starlight (
Date: Mon Oct 14 2013 - 13:20:17 CDT

Dear NAMD users,

I have trajectory of the protein complexed with the ligand (burried in the
protrein interiour from the start of simulation). Now I want to find out
how I can calculate affinity of my ligand to the protein. The one possible
way of do such task is the interaction energy estimation of my complex
(based on the occurence of the non-covalent contacts between both partners
during production run). Could someone provide me with some tutorial or
explain me how I could perform such analysis with the VMD tools ?

Thanks for help,


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