[gmx-users] make index

[farial tavakoli]

Dear GMX users
I am trying to make an index.ndx file of my complex which includes a receptor and a peptide using this command:

  gmx make_ndx -f em.gro -o index.ndx


Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:   330    Protein residues
There are: 15278      Water residues
There are:     7        Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...

  0 System              : 51172 atoms
  1 Protein             :  5331 atoms
  2 Protein-H           :  2659 atoms
  3 C-alpha             :   330 atoms
  4 Backbone            :   990 atoms
  5 MainChain           :  1322 atoms
  6 MainChain+Cb        :  1633 atoms
  7 MainChain+H         :  1639 atoms
  8 SideChain           :  3692 atoms
  9 SideChain-H         :  1337 atoms
 10 Prot-Masses         :  5331 atoms
 11 non-Protein         : 45841 atoms
 12 Water               : 45834 atoms
 13 SOL                 : 45834 atoms
 14 non-Water           :  5338 atoms
 15 Ion                 :     7 atoms
 16 NA                  :     7 atoms
 17 Water_and_ions      : 45841 atoms

 nr : group      '!': not  'name' nr name   'splitch' nr    Enter: list groups
 'a': atom       '&': and  'del' nr         'splitres' nr   'l': list residues
 't': atom type  '|': or   'keep' nr        'splitat' nr    'h': help
 'r': residue              'res' nr         'chain' char
 "name": group             'case': case sensitive           'q': save and quit
 'ri': residue index

> splitch 1

Found 10 chains
1:   189 atoms (1 to 189)
2:   108 atoms (190 to 297)
3:   283 atoms (298 to 580)
4:   130 atoms (581 to 710)
5:   173 atoms (711 to 883)
6:    10 atoms (884 to 893)
7:  4087 atoms (894 to 4980)
8:    99 atoms (4981 to 5079)
9:   125 atoms (5080 to 5204)
10:   127 atoms (5205 to 5331)
I dont know it found 10 chains instead of finding 2 chains ( chain A and chain B).How can I make the desired index file composed of:18 protein chain A19 protein chain B

best regardsFarial