[gmx-users] do_dssp file format

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 9 00:05:11 CET 2008

ABEL Stephane 175950 wrote:
> 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 do_dssp tool in GROMACS is made for this. This tools also plot the results in .xpm matrix file which can be convert 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.


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