Hi Karolina and Daniel,
Thanks for the suggestions! The water in question is currently interfacial
between protein/DNA, though it is good to know there's a tool to look for
water internal of a protein. I'll take a look at the lifetime command, and
see if I can't get it to do something similar to what I want- thanks again!
Best,
Kenneth
On Tue, Jun 9, 2020 at 11:01 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> 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
> run
> 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
>
> Run2:
> 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!
>
> -Dan
>
> On Mon, Jun 8, 2020 at 7:19 PM Kenneth Huang
> <kennethneltharion.gmail.com> 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 - 21:00:03 PDT
