[gmx-users] Regarding getting the coordinates within certain region of amino-acid

[Joe Jordan]

You need -on for gmx select to write out the index file.

On Thu, Apr 12, 2018 at 8:48 AM, Dilip.H.N <cy16f01.dilip at nitk.edu.in>
wrote:

> I tried the following two ways ie., with gmx select and with gmx trjorder
>
> 1) when i give the command :-
> gmx trjorder -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -o order.gro -nshell
> -r 0.35
>
> i got an output file, it has all the water molecules (i have 511 water
> molecules in my system) for each time frame but it has arranged according
> to the smallest distance to atoms in the reference group. (but i want only
> those water molecules within 0.35nm of nitrogen of glycine molecule.)
>
> 2) in this command:-
> gmx select -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -oi -select '"close to
> name N" resname SOL and within 0.35 of group protein'
>
> i am getting an .dat file which has only the coordinates and the format on
> as in index file format.
>
> Actually, i wanted the format in which the gmx trjorder output gives (as in
> my case, order.gro), but i want only those water molecules which are within
> 3.5 nm of the nitrogen atom of glycine molecule for each time frame.
>
> Any suggestions are appreciated.
>
> Thank you.
>
> ‌
> <https://mailtrack.io/> Sent with Mailtrack
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>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
>
> On Wed, Apr 11, 2018 at 6:23 PM, Marc Hoemberger <hoemberg at brandeis.edu>
> wrote:
>
> > You can use either gmx trjorder with the nshell parameter (if it is as
> > simple as within Xnm of Y, use nshell parameter, see manual) or gmx
> select
> > (if you need some more complex selection).
> >
> > On Wed, Apr 11, 2018 at 3:54 AM, Dilip.H.N <cy16f01.dilip at nitk.edu.in>
> > wrote:
> >
> > > Hello all,
> > >
> > > I want to get the water molecules which are at a certain distance (say
> > all
> > > the water molecules which are within 0.35nm of the Nitrogen atom of
> > glycine
> > > molecule). How can i get this all the coordinates.?
> > >
> > > Any specific commands..??
> > >
> > >
> > > Thank you.
> > >
> > > ---
> > > With Best Regards,
> > >
> > > Dilip.H.N
> > > PhD Student.
> > > <https://mailtrack.io/> Sent with Mailtrack
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> > signature&utm_campaign=
> > > signaturevirality&>
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> >
> > --
> > Marc Hoemberger
> > Ph.D. Candidate, Biochemistry and Biophysics,
> > Laboratory of Dorothee Kern
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> > Brandeis University
> > Waltham, MA, 02453
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-- 
Joe Jordan