[gmx-users] Regarding creating indexing with atoms having same labelling in different molecules
tasneemkausar12 at gmail.com
Tue Jul 11 09:13:24 CEST 2017
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>
> 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
> 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,
> Ph.D Student
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