Thank you Prajwal, I had this script. it is not give me what I want.
On Fri, Aug 12, 2016 at 4:58 AM, Prajwal Nandekar <prajwal.pharm07.gmail.com
> wrote:
> 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
> > >>
> > >>
> > >> _______________________________________________
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> > >>
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> >
> > --
> > 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 Mon Aug 15 2016 - 13:30:02 PDT
