I am following your suggestions thank you sir. I converted bbhbond.gnu
(hydrogen bond ) script to jpeg file its work and i get image file but when
I tried to get the .gnu script for DSSP like dssp.gnu . I am also
attaching the script kindly guide me. Thanks
gnuplot dsp.gnu (in cpptraj)
it give error like this
set cbtics 0.000 7.000 1.0
^
"ss.gnu", line 10: increment must be positive
Warning: 'gnuplot' returned 256
script is here
set terminal jpeg size 1024,768
set output "ss.gnu.jpg"
set pm3d map corners2color c1
set ytics 1.000, 1.000
set ytics("MET:1" 1.000,"TYR:2
set cbrange [ -0.500: 7.500]
set cbtics 0.000 7.000 1.0
set palette maxcolors 8
set palette defined (0 "#000000",1 "#0000FF",4 "#00FF00",7 "#FF0000")
set cbtics("None" 0.000,"Para" 1.000,"Anti" 2.000,"3-10"
3.000,"Alpha" 4.000,"Pi" 5.000,"Turn" 6.000,"Bend" 7.000)
set xlabel "Frame"
set ylabel ""
set yrange [ 0.000: 191.000]
set xrange [ 0.000:84002.000]
splot "-" with pm3d title "ss.gnu"
best regards
khalid
On Tue, Dec 19, 2017 at 7:23 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> The 'jpeg' keyword doesn't create a JPEG directly. As I indicated
> before (and as the manual states) it creates a gnuplot script that you
> can run with gnuplot to create the jpeg. Also, the keyword is all
> lowercase. I strongly recommend that you read the manual. For this
> cpptraj input:
>
> secstruct :1-22 out dsp.gnu jpeg
>
> you would then run:
>
> gnuplot dsp.gnu
>
> after cpptraj completes to create the jpeg.
>
> -Dan
>
> On Mon, Dec 18, 2017 at 5:36 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
> > Dear Sir I tried this command with jpeg option but no image open ""error
> > message show jpeg not a jpeg file."
> > This command i used
> >
> > secstruct :1-22 out dsp.gnu JPEG
> > secstruct :1-22 out dsp.gnu dsp.jpeg
> >
> > Kindly guide thanks.
> >
> > On Mon, Dec 18, 2017 at 11:52 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> You could use the 'jpeg' option with gnuplot output to generate
> >> gunplot input that will automatically create a JPEG image for you when
> >> run.
> >>
> >> -Dan
> >>
> >> On Mon, Dec 18, 2017 at 6:04 AM, Rana Rehan Khalid <rrkhalid.umich.edu>
> >> wrote:
> >> > I tried it but no data show in xmgrace. Sir
> >> >
> >> > On Mon, Dec 18, 2017 at 3:47 PM, Hai Nguyen <nhai.qn.gmail.com>
> wrote:
> >> >
> >> >> May be changing file extension would help?
> >> >>
> >> >> (.gnu -> .agr)
> >> >>
> >> >> Hai
> >> >>
> >> >> On Mon, Dec 18, 2017 at 4:17 AM Rana Rehan Khalid <
> rrkhalid.umich.edu>
> >> >> wrote:
> >> >>
> >> >> > Dear Amber Users
> >> >> >
> >> >> > I follow the tutorial of Hbond analysis with CPPTRAJ the file
> >> >> bbhbond.gnu
> >> >> > size is 844 mb which is very big file to open in gnuplot. Because i
> >> tried
> >> >> > to open it many time in gnuplot but its not open. Can anyone tell
> me
> >> how
> >> >> I
> >> >> > can open it. or can I convert .gnu to .agr to visualize the plot.
> >> here is
> >> >> > the command I used to get bbhbond.gnu file.
> >> >> >
> >> >> > hbond Backbone :1-189.C,O,N,H avgout BB.avg.dat series uuseries
> >> >> > bbhbond.gnu
> >> >> >
> >> >> > Regards.
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe
> >> Laboratory of Computational Biology
> >> National Institutes of Health, NHLBI
> >> 5635 Fishers Ln, Rm T900
> >> Rockville MD, 20852
> >> https://www.lobos.nih.gov/lcb
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Dec 20 2017 - 08:30:02 PST
