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

[Mark Abraham]

Hi,

You sound like you want a selection of all silica atoms within a distance
of any protein atom, which eg gmx select does. But gmx solvate is built for
the job of removing such atoms - here you are "solvating" with silica. You
may need to teach the tool about suitable atomic radii. See the the help
text.

Mark

On Sat, 17 Jun 2017 02:05 Jose Borreguero <borreguero at gmail.com> wrote:

> 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.
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