[gmx-users] Making group of different atoms

[Mateusz Bieniek]

Hi Chetan,

You might consider also using MDAnalysis which has a nice little tool just
for this. Here is an example I placed on researchgate:

u=MDAnalysis.Universe("filename.gro")
selected = u.select_atoms("resid 10-15")
selected.write("existing.ndx", mode="a", name="ids10to15")

If you don't have your .ndx, you have to switch the mode to ="w".
https://www.researchgate.net/post/Using_Gromacs_to_make_ndx_command_how_do_I_select_a_residue_which_is_labeled_in_a_different_chain_in_my_tpr_file



On Thu, Jul 12, 2018 at 5:15 PM Shrinath Kumar <shrinath.kumar at ucdconnect.ie>
wrote:

> In the index editor of make_ndx does "a 1566 1567 1569 1571 1574 1579" not
> work? Alternatively, you can just manually make the index file as Sohaib
> suggested. An index group is just:
>
> [ name_of_group ]
> ;atomnr of atoms that make up the group eg.
> 1566 1567 1569 1571 1574 1579 etc..
>
> On 12 July 2018 at 16:24, Chetan Puri <chetanpuris at gmail.com> wrote:
>
> > Yes, I have tried but I am having trouble in making a group for atoms
> with
> > different numbers.
> >
> > On Wed, 11 Jul 2018, 22:29 Quyen V. Vu, <vuqv.phys at gmail.com> wrote:
> >
> > > Have you try make_ndx tool of Gromacs?
> > >
> > > On Wed, Jul 11, 2018, 00:09 Chetan Puri <chetanpuris at gmail.com> wrote:
> > >
> > > > Can someone guide me in how to make a group for atoms number 1566,
> > 1567,
> > > > 1569,1571,1574&1579, which all belong to a tyrosine residue number
> 128
> > of
> > > > protein.
> > > >
> > > > Since I need to measure distance between two groups (ligand and
> > protein)
> > > >
> > > >
> > > > Regards,
> > > > Chetan
> > > > --
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