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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Received on Fri Oct 09 2020 - 15:00:02 PDT
