Making an index group for the backbone of a single chain

User discussions
1

GROMACS version: 2020.4
GROMACS modification: No

Hi everyone,

I am wondering, does anyone know a way to make an index group of the backbone atoms of a single chain?

I have conducted an MD simulation of a dimer, and am looking to calculate the RMSD of the backbones of each individual subunit to compare between the two.

Any advice is appreciated!

Josh

2

If you supply make_ndx with a .pdb or .tpr file with chain information, it’s as simple as:

> 4 & ch A

Otherwise, select based on residue number.