Index file generation

GROMACS version: 2021
GROMACS modification: No
Dear gromacs users,
I am trying to generate an index file containing alfa carbon atoms as starting file for itp; the system I am trying to simulate is composed by two equal chains and a third different one; generating the index file with make_ndx utility, what I get is a sequence of consecutive indexes of all the alfa carbons, and obviously there is no correspondence with the indexes of the top file. While I can work around for the first two chains, I do not know how to get the correct indexes for the third chain in the topology. Does anyone have any suggestions?
Thanks in advance

To get an index group of CA alpha carbon for each chain you can

  1. define a group for each chains
  2. a group of CA (alpha carbon) labelled as C_alpha
  3. using the command for each chain_group
    group_chain & C_alpha
    (e.i group_chainA & C_alpha give you a group having the CA of chain A)
    Note that the atom numbering in the index file corresponds to the numbering you see in the gro file.
    I hope it helps

Thanks for suggestions.