[gmx-users] Ligand molecule occupancy

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Wed Sep 25 11:46:39 CEST 2019


I have multiple ligand molecules of the same type in my system. If I wanted to monitor the Cartesian coordinates of each individual ligand during a simulation, is there a Gromacs tool to do that? or do I have write a custom script?

Some background:
My purpose is to look at binding/unbinding events for each ligand individually. I have calculated the minimum distance between protein residues and ligands in my system, but this does not give the identity of the ligand (e.g. resid or atom number) within a particular cut-off. I used the gmx pairdist module in Gromacs to calculate the minimum distance.

Any guidance will be much appreciated.

Best wishes,


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