[gmx-users] Re: A problem with do_dssp command

Justin Lemkul jalemkul at vt.edu
Wed May 8 21:27:34 CEST 2013

On 5/8/13 3:25 PM, zugunder wrote:
> OK, thanks a lot, got it.
> But suddenly I got an unexpected error executing do_dssp:
> Program g_do_dssp, VERSION 4.5.7
> Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/tools/do_dssp.c,
> line: 572
> Fatal error:
> Failed to execute command: /usr/local/bin/dssp -na ddKypQH4 ddgk6w8G >
> /dev/null 2> /dev/null
> And it gives me a whole bunch of empty or very small files with irregular
> names (as those above).
> What could this be?

Is the DSSP executable actually located in /usr/local/bin/dssp?  If not, you 
need to set the DSSP environment variable to its actual location (please see the 
Gromacs website where all of this is described).



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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