[gmx-users] do_dssp question

Kirill Bessonov kbessonov at gmail.com
Wed Sep 9 00:30:55 CEST 2009

I have used do_dssp program to analyze secondary structure during simulation
of DMPC/DMPE. But I am not clear on installation of dssp.

The program seems to work, I have set all the environmental variables so
that dssp binary is seen in /home/DSSP directory, but I am not sure if I
need to download the database of dssp files from the internet to make this
program work.

There are 14 residues in your selected group
Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
trn version: GMX_trn_file (single precision)
Reading frame       0 time   52.000
Back Off! I just backed up ddoSxMLN to ./#ddoSxMLN.1#
Last frame          0 time   52.000


And I get ss.xps file that when I open it in image viewer is just a blue

How should I properly setup the program and whether it will give me %alpha
helicity over the course of the trajectory, thank you
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