[gmx-users] do_dssp Segmentation fault

João Henriques joao.henriques.32353 at gmail.com
Mon Nov 12 10:55:44 CET 2012


do_dssp (4.5.5) is broken. There are two possible answers you're gonna get

1) Use old dssp, which you are using.
2) You're an idiot, which are not.

What I did to solve the problem was, download gmx from git, and substitute
the /src/tools/do_dssp.c of gmx 4.5.5 with the one from the git version.
Re-compile it and voila! This do_dssp version accepts both old and new dssp
and you have to specify which version with the flag -ver if I remember

This worked perfectly for me. I hope it helps you as well.

All the best,
João Henriques

On Mon, Nov 12, 2012 at 8:38 AM, mshappy1986 <mshappy1986 at 126.com> wrote:

> Hi all,
>    I am meeting the following error in Gromacs 4.5.5 with do_dssp
>    Here is the command
>        do_dssp -f md.xtc -s md.tpr -o dssp.xpm
>   give me the following error
>    segmentation fault
>   I have downloaded the executable DSSP form
> http://swift.cmbi.ru.nl/gv/dssp/ and set the environment variable, but
> do_dssp did not work.
>   How can I fix it?
>   Thanks a lot
> --
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João Henriques

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