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

[Jose Borreguero]

Hi Mark,

I decided to write my own script, which computes distances between silica
and protein atoms as you suggested. Removing the silica is not trivial
because one must remove SiO2 molecules but there is no unique way to
partition a silica block into SiO2 molecules.

.Jose

On Fri, Jun 16, 2017 at 8:54 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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