Hi Gerardo - 

Something based on distance alone (and not e.g. H-bonding network) could be done in a straightforward fashion in PyMOL:

    select close_wats, (object1 and solvent) within 1 of (object2 and solvent)

    hide everything, solvent

    as nb_spheres, close_wats

This would give you only the waters in object 1, but you could expand this logic and include the object2 waters as well.

    select close_wats, close_wats or ((object2 and solvent) within 1 of (object1 and solvent))

Hope that helps.

Cheers,

Jared

On Jun 6, 2017, at 7:30 PM, gerardo andres <[log in to unmask]> wrote:

Hi everyone, does anyone know any strategy or program (besides pywater) to identify conserved waters in a protein?

Thanks, 

Gerardo