Calculation of different types of contacts in gromacs

[Nik]

GROMACS version: 2023.3
GROMACS modification: No
Is it possible to use gmx mindist to calculate non-polar contacts between two proteins (or protein any ligand)? What index groups should be use for such purposes (protein without hydrogens or something else)?
I looked through some previous topics:

Which tools for calculation of number of nonpolar contacts?

Hi. Thanks Alessandra. I used this command: gmx mindist -f md.xtc -s md.tpr -n index.ndx -d 0.6 -group And I selected two groups. But I obtained only 1 output file (mindist.xvg) containing distance info and without info about number of contacts. In the online manual, I saw: gmx mindist computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from the respective groups) and the number of contacts within a given distance are wri…

Number of contacts between ligand and enzyme - hydrogens yes or no?

GROMACS version: 2020 GROMACS modification: Yes Hello, I’ve seen examples where the number of contacts between a ligand and enzyme is determined. Is this calculated with or without hydrogens typically? I’ve seen examples where the average # of contacts per ligand heavy atom is quoted, which implies without. I was curious if anyone here knows which is more common (if one is) Thanks in advance Sam

But I still would be grateful for some advice on the index groups selection.