On Mon, Apr 01, 2024, Kankana Bhattacharjee via AMBER wrote:
>
>I performed the MD simulation of a protein-ligand complex, now I would like
>to visualize the MD trajectory to understand the ligand binding pose etc. I
>want to collect representative snapshots from the MD trajectory.
>How can I achieve this job using cpptraj tool ? Kindly help me with this.
To add to Carlos' suggestion of clustering: it depends on what you mean by
"representative". For visualizing the trajectory, you may just need to (a) do
nothing; or (b) look at the arguments to "trajout" to, say, select every
n-th snapshot.
I'd definitely recommend doing this visualization first, then proceed to
clustering.
....dac
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Received on Mon Apr 01 2024 - 09:00:03 PDT
