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

Mark Abraham mark.j.abraham at gmail.com
Wed May 2 15:18:06 CEST 2018


Look at the contents of the .gro file with the "less" tool and see what the
numbering is :-)


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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