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

[Tasneem Kausar]

Try this
1 | 13 & a N
This will select the group 1 and 13 and all the atom having atom ID N.

On Tue, Jul 11, 2017 at 12:19 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> 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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