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

From: Daniel Roe <>
Date: Wed, 20 May 2020 12:20:05 -0400


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...


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 - 09:30:04 PDT
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