[gmx-users] dssp in gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jul 10 08:31:03 CEST 2007

taveechai taveecharoenkool wrote:
> Dear all,
>  i have a problem with do_dssp in gromacs. I had
> downloaded the dssp program and did  as manual said
> setenv DSSP /usr/.../../dssp
> When i typed do_dssp -f xx.xtc -s xx.tpr -o xx.xpm,
> the program didn't seem to end.

You're running DSSP on every frame in your trajectory, and that probably 
takes a while. Read "do_dssp -h" and work out how to use fewer 
trajectory frames.

> i also went to the dssp directory..
>  typed >> ./dsspcmbi xx.pdb xxx.??? it gave me
> something which is not in xpm format.. 
> i don't know now. 

You should read the DSSP documentation for this...


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