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 <borregu...@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. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
