Re: [AMBER] Individual water lifetimes within a distance cutoff?

From: Markowska <>
Date: Tue, 9 Jun 2020 14:49:16 +0200

Hi Kenneth!

Are the water molecules which you want to measure the lifetime are within
the protein's interior or on the surface?
If they are located within the protein's interior, then I think AQUA-DUCT,
a software that me and my group have developed, might help you in that and
provide you much much more info!
If you're interested please check the AQUA-DUCT website:

Best regards,
Karolina Mitusińska

wt., 9 cze 2020 o 01:19 Kenneth Huang <>

> 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
> again.
> 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.
> Best,
> Kenneth
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
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Received on Tue Jun 09 2020 - 06:00:03 PDT
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