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

Joe Jordan e.jjordan12 at gmail.com
Thu Apr 12 10:21:10 CEST 2018


Since gmx trjconv does not work with dynamic selections, you can either
feed the index file to trjconv and manually pick which frames to dump or
write a script that calls trjconv to dump the atoms you want for each
timestep you want.

On Thu, Apr 12, 2018 at 10:04 AM, Dilip.H.N <cy16f01.dilip at nitk.edu.in>
wrote:

> The -on option too gives the output as in index format, which i don't want.
> I want it in a .gro file and not as in an index file format.In gmx select
> options the output files are written in .xvg/.ndx.dat format only...
> i want the output to be written like the following:-
>
> frame t= 0.000
>  1543
>     1GLY      N    1   1.206   1.052   1.131
>     1GLY     H1    2   1.266   1.070   1.215
>     1GLY     H2    3   1.270   1.019   1.056
>     1GLY     H3    4   1.134   0.981   1.155
>     1GLY     CA    5   1.158   1.191   1.103
>     1GLY    HA1    6   1.086   1.211   1.181
>     1GLY    HA2    7   1.127   1.205   1.001
>     1GLY      C    8   1.276   1.289   1.123
>     1GLY    OT1    9   1.252   1.408   1.108
>     1GLY    OT2   10   1.392   1.257   1.149
>   253SOL     OW  764   1.085   0.998   0.837
>   253SOL    HW1  765   0.998   0.982   0.883
>   253SOL    HW2  766   1.109   0.919   0.781
>   252SOL     OW  761   0.848   1.089   0.990
>   252SOL    HW1  762   0.767   1.098   1.049
>   252SOL    HW2  763   0.881   1.180   0.965
> .
> .
> frame t= 1.000
>  1543
>     1GLY      N    1   1.229   1.032   1.106
>     1GLY     H1    2   1.277   1.040   1.198
>     1GLY     H2    3   1.290   0.979   1.041
>     1GLY     H3    4   1.145   0.976   1.127
>     1GLY     CA    5   1.198   1.175   1.059
>     1GLY    HA1    6   1.128   1.213   1.132
>     1GLY    HA2    7   1.175   1.175   0.953
>     1GLY      C    8   1.309   1.273   1.082
>     1GLY    OT1    9   1.282   1.393   1.056
>     1GLY    OT2   10   1.417   1.237   1.137
>   155SOL     OW  470   1.005   1.448   1.113
>   155SOL    HW1  471   1.103   1.445   1.095
>   155SOL    HW2  472   0.957   1.477   1.030
>   388SOL     OW 1169   1.307   1.001   1.370
>   388SOL    HW1 1170   1.329   1.053   1.452 etc...
>
> Any suggestions are appreciated.
>
> Thank you.
>> <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=
> signaturevirality&>
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
>
> On Thu, Apr 12, 2018 at 1:12 PM, Joe Jordan <e.jjordan12 at gmail.com> wrote:
>
> > 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
> > > <https://mailtrack.io?utm_source=gmail&utm_medium=
> > signature&utm_campaign=
> > > signaturevirality&>
> > >
> > > ---
> > > 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
> > > > > <https://mailtrack.io?utm_source=gmail&utm_medium=
> > > > signature&utm_campaign=
> > > > > signaturevirality&>
> > > > > --
> > > > > Gromacs Users mailing list
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> > > >
> > > >
> > > >
> > > > --
> > > > Marc Hoemberger
> > > > Ph.D. Candidate, Biochemistry and Biophysics,
> > > > Laboratory of Dorothee Kern
> > > > MS-009, 415 South St.
> > > > Brandeis University
> > > > Waltham, MA, 02453
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> >
> > --
> > Joe Jordan
> > --
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-- 
Joe Jordan


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