Re: [AMBER] how to interprete file

From: Daniel Roe <>
Date: Wed, 15 Jun 2011 12:52:22 -0400


If I remember correctly, the 2 output files for the ptraj secstruct
command have formats:

Time Res1 Res2 ... ResN
Where each "ResX" column has a letter corresponding to a secondary
structure type (H for helix, B for anti-parallel beta, etc - see the
ptraj section of the AmberTools manual for the complete list).

<file>.sum has the average secondary structure for each residue.

In order to view <file> in xmgrace you'll probably have to write a
script that will process it. However, the overall SS averages in
<file>.sum file should be easy to view in xmgrace.

As a secondary note, if you use cpptraj you can output the SS averages
directly to xmgrace format, e.g. for the first 10 residues:

secstruct :1-10 out dssp.dat sumout dssp.sum.agr

"dssp.sum.agr" will contain the averages and can be read by xmgrace.


On Wed, Jun 15, 2011 at 4:27 AM, fatahiya <> wrote:
> i'm done in running secstruct analysis using ptraj.
>  after that i have got my output file, but know i don't know how to interpret my
> output file.
> for example my output file is and
> i was used command xmgrace but the graph is weird.
> can anybody help me or give me a link that i can learn more how to interpret my
> data.
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Jun 15 2011 - 10:00:04 PDT
Custom Search