Re: [AMBER] Amber DSSP : Secondary structure

From: Daniel Roe <>
Date: Wed, 6 Jun 2018 13:07:01 -0400


On Wed, Jun 6, 2018 at 7:17 AM, Garima Singh <> wrote:
> Hello Amber user,
> In cpptraj command "Secstruct" has been used. Which uses dssp to calculate
> secondary structure and plot were generated through gnuplot. I got this
> kind of plot attached below ?
> How to plot dssp.gnu visualise in ns and residue label clearly? What does

You can convert to 'ns' and change the X axis label with the 'time'
and 'xlabel' keywords of the 'datafile' command, e.g.

datafile dssp.gnu time <factor> xlabel "ns"

where <factor> is the conversion factor from frames to ns for your
trajectory (for example if you wrote 1 frame every ps the factor would
be 0.001 to convert to ns).

> this black color represents (none) means? how to interpret it? Have you got
> any idea of how to overcome this problem.

None means that the DSSP algorithm did not assign any structure.


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Received on Wed Jun 06 2018 - 10:30:02 PDT
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