[gmx-users] do_dssp Installation instructions in case you have errors

Kirill Bessonov kbessonov at gmail.com
Mon Dec 14 17:48:17 CET 2009

I had seen people having trouble with do_dssp and that Error line 471 error.

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro
/dev/null 2> /dev/null

So I would like to spill some light on the issue and make documentation
better to understand after hours fiddling with source code.

If you have this error this means that dssp executable was not found even
though the PATH was set correctly (i.e. DSSP path variable)

If you look at the source code the fexist funciton checks if there is any
file in directory and returns true, so if you have any file there the code
will run through and fail on line:

sprintf(dssp,"%s %s %s %s > /dev/null %s",
      dptr,bDoAccSurf?"":"-na",pdbfile,tmpfile,bVerbose?"":"2> /dev/null");

where dssp is the buffer of charcters and dptr is the pointer to the dssp
executable file (not the folder!)

And that is the main source of errors, improper definition of directory
pointer to the executable.

Solution: To correct this mistake add to the path the name of the dssp

E.g. if you named it dssp and put it in your home folder. Add to

DSSP=/home/dssp   (where dssp is not a FOLDER but name of executable)

If you named executable dsspmbi

DSSP=/home/dsspmbi   (and again dsspmbi is the name of executable)

This will define the location of dssp executable properly and you would not
see any weird complicated errors coming up.

Hope it helps
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