[gmx-users] Regarding creating indexing with atoms having same labelling in different molecules

[Dilip H N]

Hello,
I am having problems during creating the indexes for atoms which have same
atom labelling for the two/three different molecules in the system (say
nitrogen atom that is labelled as N in both the molecules).
 whn i gave the command:-
gmx make_ndx -f md.gro -o a.ndx
i am getting the prompt as :-
Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:     1    Protein residues
There are:    10      Other residues
There are:   200      Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...

  0 System               :  750 atoms
  1 Protein                :    10 atoms
  2 Protein-H            :     5 atoms
  3 C-alpha              :     1 atoms
  4 Backbone           :     3 atoms
  5 MainChain          :     3 atoms
  6 MainChain+Cb   :     3 atoms
  7 MainChain+H     :     6 atoms
  8 SideChain          :     4 atoms
  9 SideChain-H      :     2 atoms
 10 Prot-Masses     :    10 atoms
 11 non-Protein       :  890 atoms
 12 Other                :   140 atoms
 13 TMAO              :   140 atoms
 14 Water               :   600 atoms
 15 SOL                 :   600 atoms
 16 non-Water       :   374 atoms

Here i need say the nitrogen present in protein (1 protein: 10 atoms) index
and the nitrogen's present in tmao (13 TMAO: 140 atoms) in the .ndx file.ie.,
i need the nitrogen present in protein and nitrogen's present in tmao in
the index file..
How can i get this..?? wht will be the commands for this... i tried with
various commands but in vain....


Thank you...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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