[gmx-users] do_dssp file format

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 10 19:03:30 CET 2008

Quoting ABEL Stephane 175950 <Stephane.ABEL at cea.fr>:

> > 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.
> Mark
> 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

What exactly is "not working?"  As in, what commands are you issuing?  Did the
MD fail, or the analysis of the trajectory?  If you provide this type of
information, we may be able to help you better.


> Thank you very much
> Stefane
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list