Determining residues within a certain distance

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Hello all

I saw that a paper I’m recreating calculated RMSD’s of the heavy atoms between ligand and binding sites and that they used all the residues within 5.0 angstroms (0.5 nm). My question is, is there a way to determine what residues are within a 5.0 angstrom radius of the ligand? I imagine it’s simply done but I’m confusing the functions of gmx distance/mindist/select and I’m not sure how to do this. Sorry if this has been answered before.

Thank you in advance
Sam

2

Hi,
see gmx select ( see gmx select — GROMACS 2021 documentation) also see the dynamic selection (implement in some gromacs tools)
here example and syntax here:
Selection syntax and usage — GROMACS 2021 documentation
Best
Alessandra