[AMBER] Individual bridging water lifetimes by closest?

From: Kenneth Huang <khuang8.student.gsu.edu>
Date: Fri, 29 Jun 2018 19:21:19 +0000

Hi all,

Is there a way to determine the lifetime of each bridging water that's provided by the hbond command? As in, not the cumulative time that there's a bridging water between residues which is provided, but a breakdown of how long each water resides between two residues.

I've tried using closest with something like this-

    closest 1 :47.NZ noimage first center closestout ws_47.dat outprefix ws_47
    closest 1 :55.OE1 noimage first center closestout ws_55a.dat outprefix ws_55a
    closest 1 :55.OE2 noimage first center closestout ws_55b.dat outprefix ws_55b

And while it does work, there's disagreement between how long any given water tends to be there, ie if I check with grep on the output from hbond, the numbers reported there are very different if I check in closest. I realize part of it is that closest applies a simple distance based mask in picking out the single closest water, so it may not be the best tool for this but I couldn't think of anything else.


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Received on Fri Jun 29 2018 - 12:30:02 PDT
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