You could use this simple cpptraj script;
#######################
parm protein.top
trajin trajectory.traj
secstruct :1-55 out dssp.gnu sumout dssp.agr
#######################
Then plot data using command;
gnuplot dssp.gnu
Thanks and Regards,
---------------------------------------------
Dr. Prajwal P. Nandekar
Postdoc, Molecular and Cellular Modeling
HITS gGmbH, Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg
Mobile: +49-151-71660851
Website: http://www.h-its.org/en/research/mcm/dr-prajwal-nandekar/
<
http://www.h-its.org/de/research/mcm/people/>
On Thu, Aug 11, 2016 at 6:26 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> I am not sure what you did in cpptraj, but I do not see a gnu file as
> output there.
>
> Anyways, the file you sent with extension .gnu is NOT a gnuplot file, is
> is a regular data file with no gnuplot commands. That is why you got an
> error
>
> adrian
>
>
>
> On 8/11/16 12:16 PM, Parviz Seifpanahi Shabane wrote:
> > Sure, Thank you for your help, I will be grateful if you help me about my
> > second question too.
> > secondarystructuer-folded-ff10.gnu
> > <https://drive.google.com/a/vt.edu/file/d/0BwxMdQ596dWgdndfN0dVZ0ZXSlE/
> view?usp=drive_web>
> >
> >
> > On Thu, Aug 11, 2016 at 12:05 PM, Adrian Roitberg <roitberg.ufl.edu>
> wrote:
> >
> >> Dear Parviz.
> >>
> >> First, that seems like a gnuplot question, not amber. Second, can you
> >> attach the .gnu file so we can see what is happening ?
> >>
> >> Thanks
> >>
> >>
> >>
> >> On 8/11/16 12:03 PM, Parviz Seifpanahi Shabane wrote:
> >>> Dear Amber User,
> >>> I need to calculate the secondary structure(Para+Anti+Alpha+3-10+Pi)
> of
> >> my
> >>> protein vs time.I used this script (below).
> >>> parm 1WJB-OPC-FF10-folded.top
> >>> trajin 1WJB-OPC-FF10-folded.prod1.traj
> >>> secstruct :1-55 secstr-folded-ff10.dat out
> >>> secondarystructuer-folded-ff10.dat sumout average-folded-ff10.dat
> >> assignout
> >>> overall-folded-ff10.dat
> >>> and I got the file (secondarystructuer-folded-ff10.gnu), in this file
> >> each
> >>> kind of secondary structuer show with the number, I used the " gnuplot
> >>> secondarystructuer-folded-ff10.gnu" to see the graph and I got this
> >> error
> >>> "secondarystructuer-folded-ff10.gnu", line 2: invalid command".
> >>> dose any one knows what is the problem?
> >>> and how to get the graph (secondary structure(Para+Anti+Alpha+3-10+Pi)
> >> vs
> >>> time)?
> >>> Best Regrads
> >>> Parviz
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >> --
> >> Dr. Adrian E. Roitberg
> >> University of Florida Research Foundation Professor.
> >> Department of Chemistry
> >> University of Florida
> >> roitberg.ufl.edu
> >> 352-392-6972
> >>
> >>
> >> _______________________________________________
> >> 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
>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Aug 12 2016 - 02:00:03 PDT
