[gmx-users] index two groups for the distance calculation

[MD]

Hi Mark,
They have the correct number in the .gro file. Chain A has residues from 6
to 330 which contains my residue 159, chain B has residues from 1 to 30
which contains my residue 15. So if I select "r 15" when indexing there
will be two residue 15 selected, one from chain A and one from chain B. Is
there a way to specifically select residue 15 from chain B?
Thank you,
Ming

On Wed, May 2, 2018 at 9:17 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Look at the contents of the .gro file with the "less" tool and see what the
> numbering is :-)
>
> Mark
>
> On Wed, May 2, 2018 at 3:07 PM MD <refmac5 at gmail.com> wrote:
>
> > Hi Gromacs,
> >
> > I was trying to index two amino acids to two groups and calculate the
> > distance between them.
> >
> > I used the command
> >
> > "gmx make_ndx -f md.gro -o index.ndx"
> >
> > and tried to select residue 159 from chain A (group of r_159) and residue
> > 15 from chain B. However, when I used the  "l" function to list all the
> > residues I was not able to find the residue 15 from chain B. I was able
> to
> > find it based on the sequence but it has a different number 372, instead
> of
> > 15 in its original structure of chain B. I think gromacs renumbered the
> > whole sequence and combined chain A and B? When I select r 372, i was
> told
> > it is an empty group.
> >
> > Can someone help me here, please?
> >
> > Thanks in advance,
> >
> > Ming
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