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

2017-07-11 Thread 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 
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 
> 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: 1Protein 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
> >
> >
> >
> >  Sent with Mailtrack
> >  > referral=cy16f01.di...@nitk.edu.in=22>
> > --
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> >
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Re: [gmx-users] Regarding creating indexing with atoms having same labelling in different molecules

2017-07-11 Thread 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 
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: 1Protein 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
>
>
>
>  Sent with Mailtrack
>  referral=cy16f01.di...@nitk.edu.in=22>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Regarding creating indexing with atoms having same labelling in different molecules

2017-07-11 Thread 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: 1Protein 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



 Sent with Mailtrack

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