I encountered the exact same error with Gromacs-4.5 as posted by Sunita Patel back in October 2010 and could not find any solution in the gmx_thread. The error was:<div><span class="Apple-style-span" style="font-family: monospace; font-size: medium; white-space: pre; "><br>
</span></div>Failed to execute command: /home/path-to-dssp -na dd3sOJn3 ddZl9dcf > /dev/null 2> /dev/null<div><br>I found that the do_dssp fails to fork dssp as the latter does not recognize the flag "-na" defined in do_dssp. The dssp code that I downloaded recently, recognizes the only flags "-i", "-o", "-v", "-d" and "-h".<br>
<br></div><div>So, I just tweaked the "-na" flag in the do_dssp source code as follows and the do_dssp and dssp combination worked fine for me.</div><div><br></div><div>original:</div><div><div>sprintf(dssp,"%s %s %s %s > /dev/null %s",</div>
<div><span class="Apple-tab-span" style="white-space:pre">        </span> dptr,bDoAccSurf?"":"-na",pdbfile,tmpfile,bVerbose?"":"2> /dev/null");</div><div><br></div><div>replaced by:</div>
<div><div>sprintf(dssp,"%s %s %s %s > /dev/null %s",</div><div><span class="Apple-tab-span" style="white-space: pre; ">        </span> dptr,bDoAccSurf?"":"-i",pdbfile,"-o",tmpfile,bVerbose?"":"2> /dev/null");</div>
</div><div><br></div><div>-pb<br><br><br>
</div></div>