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
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
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
