[gmx-users] Help with gmx make_ndx

[Quyen V. Vu]

Dear gromacs user,
my system contain such groups:

  0 System              : 943920 atoms
  1 DNA                 :  3198 atoms
  2 LA                  :    76 atoms
  3 CL                  :   130 atoms
  4 Water               : 940516 atoms
  5 SOL                 : 940516 atoms
  6 non-Water           :  3404 atoms
  7 Other               :    76 atoms
  8 LA                  :    76 atoms
  9 CL                  :   130 atoms
 10 Ion                 :   130 atoms
 11 LA                  :    76 atoms
 12 CL                  :   130 atoms
 13 Water_and_ions      : 940646 atoms

Now, I want to get index of La and CL ions then I type:
       gmx make_ndx -f em.gro -o index.ndx
at the make_ndx prompt I type: "8|9"
then in my index.ndx I get group [LA_CL], also get [system] group ( too
much index)
How can I use correct make_ndx?
Thank you.