Re: [AMBER] CPPTRAJ: Cluster structures keeping only one water, by position?

--
Gustavo Seabra.
On Fri, Oct 9, 2020 at 5:42 PM Niel Henriksen <shireham.gmail.com> wrote:
> Check out the closest command:
> https://amber-md.github.io/cpptraj/CPPTRAJ.xhtml#toc-Subsection-11.15
>
> https://amber-md.github.io/pytraj/latest/analysis.html?highlight=closest#pytraj.closest
>
> I've done a similar thing before ... use closest command to write a
> trajectory with the specified number of waters that are closest to an atom
> mask.  you can also write out a corresponding prmtop that has the same
> number of waters along with your solute. You can then use that
> prmtop/trajectory in subsequent analysis.
>
> Best,
> --Niel
>
> On Fri, Oct 9, 2020 at 11:15 AM Gustavo Seabra <gustavo.seabra.gmail.com>
> wrote:
>
> > Hi all,
> >
> > I have the MD of a system that now I'd like to cluster and obtain the
> > representative structures of each cluster. As it happens, this system has
> > exactly one *very* conserved water, that I'd like it to be in the
> > structures. However, although there is always *some* water molecule at
> this
> > position, the specific water molecule at the position changes during the
> > MD.
> >
> > Is there anyway I can do a cluster analysis that will print the final
> > structures with only this specific water? Or any way I can strip all
> waters
> > BUT for this one before clustering? (It would have to be by position, not
> > residue number.)
> >
> > I appreciate any ideas. Thanks a lot!
> > --
> > Gustavo Seabra.
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> >
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