[gmx-users] Ligand molecule occupancy

Justin Lemkul jalemkul at vt.edu
Wed Sep 25 14:58:37 CEST 2019

On 9/25/19 5:46 AM, Pandya, Akash wrote:
> Hi,
> 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?

You can print coordinates over time using gmx traj.


> 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,
> Akash


Justin A. Lemkul, Ph.D.
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