Interacting Residues

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1

GROMACS version: 2018.3
GROMACS modification: Yes/No
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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.

2

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
regards

3

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)
Regards