[gmx-users] secondary structure analyze

Parisa Rahmani rahmani.prs2 at gmail.com
Tue Jan 1 20:06:52 CET 2013

Hi gmx users

I want to do secondary structure analyze for my trajectory of protein.
I've downloaded DSSP packages from "
and put it in /usr/local/bin , and rename the folder to dssp.
when i run "do_dssp -f rmsd.pdb -s protein.tpr -sc scount.xvg -o ss.xpm"

the following appears,

Opening library file /home/parisa/parisa/share/gromacs/top/phbres.dat
Opening library file /home/parisa/parisa/share/gromacs/top/aminoacids.dat
Group     0 (      System) has   420 elements
Group     1 (     Protein) has   420 elements
Group     2 (   Protein-H) has   322 elements
Group     3 (     C-alpha) has    43 elements
Group     4 (    Backbone) has   128 elements
Group     5 (   MainChain) has   171 elements
Group     6 (MainChain+Cb) has   208 elements
Group     7 ( MainChain+H) has   214 elements
Group     8 (   SideChain) has   206 elements
Group     9 ( SideChain-H) has   150 elements
Select a group: 1
Selected 1: 'Protein'
There are 43 residues in your selected group
Opening library file /home/parisa/parisa/share/gromacs/top/ss.map
Reading frame       0 time    1.000
Back Off! I just backed up dd35REJx to ./#dd35REJx.1#

and the program is continuously running without .xpm and xvg outputs.

i searched the mailing list, but I couldn't find  the solution (because
many of them was about the old DSSP version , that is not available now)

any suggestion would be greatly appreciated.

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