Dear Amber community,
I am trying to count the number of waters inside a buried pocket of a protein for each frame of my simulation. I have tried using the "closest" command on cpptraj and then apply a cut-off on the distance between the waters and a specific mask, but unfortunately waters inside and outside the pocket have the same distance to my mask.
Any ideas or suggestions are appreciated!
Best wishes,
Marion.
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Received on Mon May 08 2023 - 10:00:02 PDT
