[AMBER] Individual water lifetimes within a distance cutoff?

From: Kenneth Huang <kennethneltharion.gmail.com>
Date: Mon, 8 Jun 2020 19:18:17 -0400

Hi all,

A slightly open ended question- does anyone have a good way for calculating
the individual lifetimes for water within a distance cutoff? Ie, how long
is any given water within X distance of a residue present in consecutive
frames? So if water 100 was there for n=1 till n=100, it'd register as 100
frames, and if that water ever came back after, it'd reset the counter

I've managed to get a working script using a combination of
watershell+closest to fetch water IDs meeting some distance criteria, but
am running into issues with getting the lifetimes. My first instinct was to
try to brute force it by measuring distance of water as-

distance x :waterID :resID

And then parse that output with awk, but then I realized I'd have to do
that for ~17,000 distinct water IDs, which seems very cost prohibitive. It
seems like there should be something I could possibly use from the output
of closest, but I haven't been able to find anything so far.

The solution I tried was to then grab the output from closest, and run it
through an R script that's able to determine how many frames it takes for
every water to migrate away from some inital point. However,trying to track
individual water lifetimes, I'm running into similar issues with just the
sheer time/memory cost.



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Received on Mon Jun 08 2020 - 16:30:01 PDT
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