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:
http://www.aquaduct.pl/
Best regards,
Karolina Mitusińska
wt., 9 cze 2020 o 01:19 Kenneth Huang <kennethneltharion.gmail.com>
napisał(a):
> 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
