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

[Mark Abraham]

Hi,

That is, Tasneem's recipe will find all atoms that are in group 1 OR group
13, AND whose name is N. If Dilip just wants the atoms in group 1 AND whose
name is N, then e.g.

1 & a N

There are some examples in the interactive help of gmx make_ndx

Mark

On Tue, Jul 11, 2017 at 9:14 AM Tasneem Kausar <tasneemkausar12 at gmail.com>
wrote:

> 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
> >
> >
> >
> > <https://mailtrack.io/> Sent with Mailtrack
> > <https://mailtrack.io/install?source=signature&lang=en&
> > referral=cy16f01.dilip at nitk.edu.in&idSignature=22>
> > --
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