# Determination of ligand and individual residue (of protein) interaction energy

**URL:** <https://gromacs.bioexcel.eu/t/determination-of-ligand-and-individual-residue-of-protein-interaction-energy/232>\
**Category:** User discussions\
**Created:** [June 2, 2020, 6:04pm UTC](https://gromacs.bioexcel.eu/t/determination-of-ligand-and-individual-residue-of-protein-interaction-energy/232 "2020-06-02T18:04:35Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ashish](https://avatars.discourse-cdn.com/v4/letter/a/ea666f/32.png) [@ashish](https://gromacs.bioexcel.eu/u/ashish)\
**Post date:** [June 2, 2020, 6:04pm UTC](https://gromacs.bioexcel.eu/t/determination-of-ligand-and-individual-residue-of-protein-interaction-energy/232/1 "2020-06-02T18:04:35Z")

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GROMACS version: 2020.1  
GROMACS modification: No  
Here post your question

Dear Justin, I have run a protein-ligand MD using CHARMM36 force field. Now I want to determine the interaction energy (LJ-SR and Coul-SR) of ligand with the individual residue / amino acid (of protein) present in the radius of 4 A distance from ligand.

I want to know the interaction energy with each amino acid involved in the selected radius.  
Do I need to make multiple indexes considering each amino acid and ligand or something else?

Please suggest.

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [June 5, 2020, 12:14pm UTC](https://gromacs.bioexcel.eu/t/determination-of-ligand-and-individual-residue-of-protein-interaction-energy/232/2 "2020-06-05T12:14:09Z")

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Each residue or ligand needs to be its own index group. You can then get the full interaction energy matrix (some terms will not be of interest) via

`energygrps = res1 res2 res3 ... lig`