[gmx-users] Regarding getting the coordinates within certain region of amino-acid
Dilip.H.N
cy16f01.dilip at nitk.edu.in
Thu Apr 12 10:04:29 CEST 2018
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.
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---
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&>
> > > > --
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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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