How to make index group for backbone atoms of a protein chain

User discussions
1

GROMACS version: 2024.4
GROMACS modification: Yes/No

I have a protein complex consists of 2 chains. I want to make a index group for backbone atoms for both chains respectively. I’m aware of making index file by using ‘gmx make_ndx’ and by selecting atom/residue of interest to make a index file, but how to find and select backbone atoms in the .gro file?

2

I am not completely sure of what you want to do specifically, but if you know how to generate the index file of the backbone and you want to extract only those atoms then you can just use trjconv tool and select the corresponding entry in the index file. If you just want to read quickly which atoms are these you can grep them, something like grep 'CA' yourfile.gro.

1 Like
3

Thanks I think I have figured it out.
For example my protein consists of 10000 atoms. Chain A consists of 6000 atoms. To make index group for backbone atoms of chain A:

gmx make_ndx -f myfile.gro -o index.ndx
…

> a 1-6000
> name 17 chain-A
> 17 & a N
> 17 & a CA
> 17 & a C
> 18 | 19 | 20
> name 21 chain-A_backbone

Is this method feasible or is there other way around?

4

This seems okay, depending on the atom names.

However, I would rather use the tpr file where the topology information is stored properly, something like

gmx make_ndx -f myfile.tpr -o index.ndx

If Group 1 is Protein, as usual, then you can do

splitch 1

and then something like

alpha & beta

where alpha is the number of the group generated by splitch that contains your protein of interest and beta is the one that contains the backbone atoms of whole system.