[gmx-users] Removing molecules around protein

[Leandro Bortot]

Hi,

     You can do this by using g_select to create an index file containing
the group you are interested in, i.e. the system without a "shell" of
molecules around the protein. Then you can use trjconv to get a .pdb/.gro
file with these coordinates.
     Note that g_select itself has a very good built-in help documentation.
It will certainly help you finding the specific selection string for your
system. Just use g_select and type "help" when asked for your selection.

     I hope it helps.


Leandro.

On Thu, Mar 5, 2015 at 6:05 AM, Todor Antonijevic <t_antoni at uncg.edu> wrote:

> Hi,
>
> How to delete/remove molecules that overlap with my protein or that are ~5A
> around it?
>
> Thank you
> --
> 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-request at gromacs.org.
>