Hi,
It's still not clear to me what you do want, and/or why all the advice
provided so far did not work for you. Could you provide more details please
(exact commands used etc).
Thanks,
-Dan
On Monday, August 15, 2016, Parviz Seifpanahi Shabane <sparviz.vt.edu>
wrote:
> 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 <javascript:;>
> > 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
> <javascript:;>> 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
> <javascript:;>>
> > > 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 <javascript:;>
> > > >>> 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 <javascript:;>
> > > >> 352-392-6972
> > > >>
> > > >>
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org <javascript:;>
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > > _______________________________________________
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> > > > 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 <javascript:;>
> > > 352-392-6972
> > >
> > >
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Mon Aug 15 2016 - 14:30:02 PDT
