[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
> > > > >
> > > > > * 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
More information about the gromacs.org_gmx-users
mailing list