How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

[alevilla]

Hi,
a variety of tools are available in GROMACS to calculate distance.
Maybe you can find some help from this conversation

What is the difference between gmx distance, gmx mindist and gmx pairdist?

Hi, I am trying to compute distance between four residues of a protein involved in active site. I am getting confused in mindist, pairdist and gmx distance. What are the limits and differences in three? Which analysis can be helpful in plotting distance between A-B, B-C, C-D and D-A residues over time, where ABCD are 4 residues forming bottleneck for ligand entry.

Or other in the forum.
Best regards
Alessandra