[AMBER] problem in plotting secondary structure graph

From: Sehrish Naz <mjazse.gmail.com>
Date: Tue, 15 Dec 2015 12:19:32 +0500

 I have done protein-protein simulation studies and I am stuck in the
secondary structure analysis. In this regard, I need a little guidance
about plotting graph for secondary structure. I have used amber for
simulation and perform secondary structure analysis by cpptraj command i.e.

*secstruct : 1-336 out dssp.gnu sumout dssp.agr.sum*

Now problem is that I am unable to plot the generated files. It is not
plotted correctly by gnuplot or xmgrace or may be I don't know the commands
for plotting.Can you please tell me the procedure or commands for these
files.Apart of it, I have also generated files by DSSP software which
generated output files having .dssp extension and similarly I could not
understand how to plot this file because there is no such software which
plot or read these generated files and I am unable to find any script for
plotting this file.So please guide me in this regard.


* Sehrish Naz*

*Jr. Research Fellow,*

*Computational Chemistry Unit.*
*Dr. Panjwani Center for Molecular Medicine and Drug Research,*
*International Center for Chemical and Biological Sciences,*
*University of Karachi, Karachi-75270.*
*E-mail: mjazse.gmail.com <misbah.anwar88.gmail.com>*
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Received on Mon Dec 14 2015 - 23:30:03 PST
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