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

From: Daniel Roe <>
Date: Tue, 9 Jun 2020 11:01:09 -0400


I would probably use the 'hbond' command and select the residue of
interest to get hydrogen bonds between that residue and waters (you
can omit the angle criterion if you just want a distance criterion),
make sure I save the time series, then run lifetime analysis on that.
Something like:

hbond HB <residue mask> solventdonor :WAT solventacceptor :WAT.O series
lifetime HB[solventhb] out solvent.lifetime.dat

If you want to play around with the 'lifetime' analysis it might be
better to write the hbond data to a file with the 'uvseries' keyword,
then read that data back in, e.g.

Run 1:
hbond HB <residue mask> solventdonor :WAT solventacceptor :WAT.O
series uvseries uv.dat

readdata uv.dat name UV
runanalysis UV out solvent.lifetime.dat

See the manual for full details on the keywords available for 'hbond'
and 'lifetime'.

Hope this helps!


On Mon, Jun 8, 2020 at 7:19 PM Kenneth Huang
<> wrote:
> 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 - 08:30:04 PDT
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