[gmx-users] do we still have a do_dssp and dssp compatibility issue? thread: do_dssp failed to execute

[César Ávila]

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.pk at 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
>
>
>
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