[gmx-users] do_dssp file format

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Thu Jan 10 12:43:46 CET 2008

> Hi gromacs users
> For my work I have performed some simulations of a protein in water with an other MD software not compatible with >GROMACS. And I would like to compute the time evolution of the secondary structure of my protein, I know that the >with >the xpm2ps tool give in gromacs. Is it possible to have an (small) exemple of an .xpm file generated by the do_dssp >tools

Just run a 10-step MD simulation and generate one yourself. Or convert
your other trajectories into .pdb format and use that as input to
do_dssp. You do not necessarily need a .tpr file for do_dssp, see "man
do_dssp" under the "-s" flag.


Thanks Mark for your suggestions but it is not working for me So i have tested an other approach with VMD to obtain the secondary structure time series for my protein. The ouput graph obtained is not pretty, so i would like to make for a paper a same graph that i found in some gromacs papers. For this i need to convert the output datas file of VMD to gromacs xpm file obtained with do_dssp with a script and convert it to ps with the xpm2ps tool. In gromacs documentation i can not find an exemple of xpm file generated with do_dssp. So it is possible to obtain from the gromacs users a small exemple of this file to see how the datas are arranged

Thank you very much


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