Re: [AMBER] can i analysis number of water molecules in protein by watershell

From: Wesley Michael Botello-Smith <>
Date: Wed, 20 May 2020 09:39:46 -0700

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
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 and MOLE2 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 <> 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 <> 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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Received on Wed May 20 2020 - 10:00:03 PDT
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