Re: [AMBER] problem in plotting secondary structure graph

From: Daniel Roe <>
Date: Tue, 15 Dec 2015 09:12:41 -0700


Based on the command that you used, the format of 'dss.agr.sum' will
be a "standard" data format with each data set in a column. Cpptraj
detects data output format by extension, so you need to do to get
grace formatted output is to give your filename a '.agr' or '.xmgr'
extension, e.g.

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

Hope this helps,


On Tue, Dec 15, 2015 at 12:19 AM, Sehrish Naz <> wrote:
> 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.
> *Regards,*
> * 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: <>*
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Dec 15 2015 - 08:30:04 PST
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