[gmx-users] How to parameterize the volume occupied by a protein?

[Jose Borreguero]

Dear all,

I have superimposed a protein onto a silica block (see picture in
https://goo.gl/ZS9xVm).

Now I need to remove the silica atoms overlapping the protein. This
requires parameterization of the volume occupied by the protein in a way
that will let me query whether a point in space is inside the volume.

Does anyone know how to parameterize the volume occupied by a protein?

Best,
Jose Borreguero.