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

Dilip.H.N cy16f01.dilip at nitk.edu.in
Fri Apr 20 09:38:44 CEST 2018 

Any suggestions as to how to write the script.? or on feeding the index
file to trjconv manually...??

Thank you.



[image: Mailtrack]
<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality3&>
Sender
notified by
Mailtrack
<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality3&>

---
With Best Regards,

Dilip.H.N
PhD Student.

On Thu, Apr 12, 2018 at 1:48 PM, Joe Jordan <e.jjordan12 at gmail.com> wrote:

> 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
> > > > > >
> > > > > > * 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-request at gromacs.org.
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Marc Hoemberger
> > > > > Ph.D. Candidate, Biochemistry and Biophysics,
> > > > > Laboratory of Dorothee Kern
> > > > > MS-009, 415 South St.
> > > > > Brandeis University
> > > > > Waltham, MA, 02453
> > > > > --
> > > > > 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-request at gromacs.org.
> > > > >
> > > > --
> > > > 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-request at gromacs.org.
> > >
> > >
> > >
> > >
> > > --
> > > Joe Jordan
> > > --
> > > 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-request at gromacs.org.
> > >
> > --
> > 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-request at gromacs.org.
>
>
>
>
> --
> Joe Jordan
> --
> 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-request at gromacs.org.
>

More information about the gromacs.org_gmx-users mailing list