# Interacting Residues

**URL:** <https://gromacs.bioexcel.eu/t/interacting-residues/614>\
**Category:** User discussions\
**Created:** [August 3, 2020, 7:15am UTC](https://gromacs.bioexcel.eu/t/interacting-residues/614 "2020-08-03T07:15:40Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![tofadare](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/tofadare/32/271_2.png) [@tofadare](https://gromacs.bioexcel.eu/u/tofadare)\
**Post date:** [August 3, 2020, 7:15am UTC](https://gromacs.bioexcel.eu/t/interacting-residues/614/1 "2020-08-03T07:15:40Z")

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GROMACS version: 2018.3  
GROMACS modification: Yes/No  
Here post your question  
Please, I need someone to explain to me how I can determine the amino acid residues that interact closely with my ligand during my protein-ligand simulation. I have completed the 50ns simulation and I have determined rmsd, rmsf, RoG, SASA and Hbonds but I need to know the residues that interacted specifically with the ligand during the course of the simulation.

I would be glad if anyone can help me out with that.

Thank you.

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [August 3, 2020, 3:01pm UTC](https://gromacs.bioexcel.eu/t/interacting-residues/614/2 "2020-08-03T15:01:53Z")

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HI,  
you could have a look at the contacts between the ligand and the protein using for example gmx mindist  
[http://manual.gromacs.org/current/onlinehelp/gmx-mindist.html?highlight=contact](http://manual.gromacs.org/current/onlinehelp/gmx-mindist.html?highlight=contact)  
regards

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**Author:** ![Abhijit](https://avatars.discourse-cdn.com/v4/letter/a/46a35a/32.png) [@Abhijit](https://gromacs.bioexcel.eu/u/Abhijit)\
**Post date:** [August 21, 2020, 4:09am UTC](https://gromacs.bioexcel.eu/t/interacting-residues/614/3 "2020-08-21T04:09:05Z")

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Hi,  
To do the contact score analysis, I wrote a vmd tcl script that can do the job.  
Contact me personally, I will share the script with you. (email: [abhijitchemiitd@gmail.com](mailto:abhijitchemiitd@gmail.com))  
Regards