How to make specific index in gromacs?

Hello Dears

I would like to make specific indexes in Gromacs. There is a polymer chain (PPO) with side chains (attached bellow). I’d like to make indexes of C (carbon) just for the benzene ring, not the side chain. How can I do that?
I tried gmx make_ndx and selected atom C . But it selects all Carbons in-ring and side chain. Could you, please, help me with That?

Thanks a lot


Do make_ndx and give specific atomnames that represent the benzene ring C1,C6 or whichever that is.
eg: gmx make_ndx -f filename.gro

a atomname

Dear struc_bio

I tried

gmx make_ndx

but all Carbons in the polymer chain is named as “C” and there is no difference. And there are lots of rings and alkyle side chains! This is my main problem


Please let us know how does your gro file look?
Paste some contents here.

You need distinct atom names in your structure, otherwise you’ll never be able to do any kind of sensible analysis. Many programs will write coordinate files with junk atom names like this. You need to fix it before trying to move forward with anything.

Dear @struc_bio

I found the problem and fixed it.

Thanks a lot

1 Like

Dear @jalemkul

Thanks for your help. I fixed the problem.