[gmx-users] Protein-ligand binding Cut-offs

[Pandya, Akash]

Hi all,

I have ran a simulation with a protein and multiple ligand molecules inserted randomly inside a box. I want to isolate those ligand molecules that are closest to the protein by a cut-off of four angstroms or so. Is there a command I could use to do this for me or would I have to use a molecular visualizer software for this?

Thanks,

Akash