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. After applying Pradip's patch, do_dssp worked for me.
I would say that the change in flags is related to the fact that "In 2011 Maarten Hekkelman has written new software" (as stated on DSSP homepage). Thanks :D. 2011/8/6 Pradip Biswas <biswas...@gmail.com> > 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: > > Failed to execute command: /home/path-to-dssp -na dd3sOJn3 ddZl9dcf > > /dev/null 2> /dev/null > > 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". > > 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. > > original: > sprintf(dssp,"%s %s %s %s > /dev/null %s", > dptr,bDoAccSurf?"":"-na",pdbfile,tmpfile,bVerbose?"":"2> /dev/null"); > > replaced by: > sprintf(dssp,"%s %s %s %s > /dev/null %s", > dptr,bDoAccSurf?"":"-i",pdbfile,"-o",tmpfile,bVerbose?"":"2> /dev/null"); > > -pb > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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