[gmx-users] dssp in gromacs

[Mark Abraham]

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...


Mark