[gmx-users] how to make a index file

[aixintiankong]

 i want to analyze the change of secondary structure of the mainchian frome residue 20 to residue 60. so i want to make a index file that only contain the maninchian+H from residue 20 to residue 60.  i have inputed the command " make_ndx -f em.pdb -o index.ndx", but i don't kown how to do next . what should i input ? thank you very much!