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

MD refmac5 at gmail.com
Wed May 2 15:07:42 CEST 2018

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,


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