If you are using pytraj, you could make use of the scipy.spatial.Delaunay
to compute a convex hull for the protein. With a bit of legwork, you can
use the result as a way to test which waters are inside or outside of that
hull.
It could also work well with volume map based approach as well.
I've seen a handful of specialized analysis programs that take this kind of
approach to define binding pockets and solvent channels. E.g. CASTp
http://sts.bioe.uic.edu/castp/background.html and MOLE2
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765717/ although there are
literally dozens of others.
Many seem to work either on a grid / voxel approach, or a
vornoi tesselation / delaunay triangulation approach, or some combination
of the two.
On Wed, May 20, 2020 at 9:22 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Short answer is unfortunately no. The 'watershell' command (or really
> any other command in cpptraj) doesn't have a concept of "inside" a
> protein. It works by counting waters that are within certain distance
> cutoffs from each atom. I suppose if your protein were roughly
> spherical you could pick 1 atom or residue near the center of the
> protein, choose a short first cutoff, then a second cutoff that's
> roughly the radius of your protein, but that seems pretty problematic.
> Would be interesting in the future to implement a command with concept
> of "inside" a protein, but I don't see myself getting to it anytime
> soon unfortunately...
>
> -Dan
>
> On Wed, May 6, 2020 at 9:18 AM 石娜 <shina14.mails.jlu.edu.cn> wrote:
> >
> >
> > Dear amber developers:
> >
> > In the process of analyse the trajectory, I need to calculate the
> number of
> > water molecules inside the protein in each snapshot. Can watershell
> achieve
> > this goal? If not, can you recommend a better method. I am looking
> forward
> > to your reply! Thanks very much!
> > Yours sincerely!
> >
> > Na Shi
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>
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Received on Wed May 20 2020 - 10:00:03 PDT
