[AMBER] Tracking lifetime distance by closest of specific water IDs?

From: Kenneth Huang <kennethneltharion.gmail.com>
Date: Tue, 28 Jul 2020 10:28:51 -0400

Hi all,

I have an odd scenerio where I'm trying to track the full distance lifetime
of a subset of waters from an initial time point, ie frame 1, from a group
of bases over 25 ns chunks of time. I'm having an issue in tracking all the
waters though, in that if I use something like

closest 17130 :8-10&!(.H=) noimage first closestout closest_s2_200
outprefix closest_s2

Where I have a total of 17131 waters in my box, but the problem I'm running
into is that a number of those waters move so far away they're the
furtherest water, so aren't recorded.

I tried stripping out the all but the waters I'm interested in, but I ran
into two issue where I couldn't tell if it was actually leaving the right
waters, and my input for closest has it as N=total number of waters in the

If it were just one residue, I'd try something with distance to get the
missing distance like

dist :WATID.O :8.CA out waterid_8ca.out

And just take the min distance of the atoms in the group. But given there's
three bases, the number of atoms to the water gets large. Given that, I
feel like there's a simple solution that I'm just not thinking of?



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Received on Tue Jul 28 2020 - 07:30:04 PDT
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