I was dealing with the same situation. I am using the latest version of DSSP (April 2011). Neither gromacs 4.5.3 or 4.5.4 would work. <br>After applying Pradip's patch, do_dssp worked for me. <br><br>I would say that the change in flags is related to the fact that "<font><font face="Arial">In 2011 Maarten Hekkelman has written new software" (as stated on DSSP homepage). </font></font><br>
<br>Thanks :D.<br> <br><br><div class="gmail_quote">2011/8/6 Pradip Biswas <span dir="ltr"><<a href="mailto:biswas.pk@gmail.com">biswas.pk@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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 style="font-family:monospace;font-size:medium;white-space:pre-wrap"><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 style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span> dptr,bDoAccSurf?"":"-i",pdbfile,"-o",tmpfile,bVerbose?"":"2> /dev/null");</div>
</div><div><br></div><font color="#888888"><div>-pb<br><br><br>
</div></font></div>
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