Index file generation

User discussions
1

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
Stefano

2

Hi,
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
    Alessandra
3

Thanks for suggestions.
Stefano