[gmx-users] do_dssp failed to execute

[Justin A. Lemkul]

Sunita Patel wrote:
> ***
> *Dear Mark,
> 
> On Mon, 11 Oct 2010 22:54:44 +1100, Mark Abraham wrote
>  > ----- Original Message -----
>  > From: Sunita Patel <sunita at mailhost.tifr.res.in>
>  > Date: Monday, October 11, 2010 22:50
>  > Subject: [gmx-users] do_dssp  failed to execute
>  > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>  >
>  > > Dear User,
>  > >
>  > > I set the path for dssp executable in .bashrc file. Still
>  >
>  > dssp in the path is probably not sufficient. See 
> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
>  >
> I already seen this page and the dssp executable file is present in the 
> specified location.
> I surprise why it was not working before. I freshly downloaded the 
> dsspcmbi executable and rename it to dssp and gave executable file 
> permission and it started working.
> 
> I was doing like this earlier also. May be dssp executable was corrupted.

I would suspect something else was going on.  Note from the error message that 
the dssp executable was not even invoked:

Failed to execute command: /home/sunita/soft/bin -na ...

Thus, do_dssp was trying to execute "bin" instead of "dssp."

The DSSP environment variable must point to the dssp executable itself, not the 
PATH to it.  Maybe you've got things working now, but do check to make sure 
you've got your environment properly configured to save yourself headaches later.

-Justin

> Thanks,
> Sunita
> 
>  > Mark
>  >
>  > > getting following
>  > > error. Could anybody suggest what would be the problem.
>  > >
>  > > ********************************error message********
>  > > Select a group: 5
>  > > Selected 5: 'MainChain'
>  > > There are 134 residues in your selected group
>  > > Opening library file
>  > > /home/sunita/soft/gromacs/share/gromacs/top/ss.mapReading
>  > > frame        0
>  > > time    0.000   
>  > > Back Off! I just backed up dd3sOJn3 to ./#dd3sOJn3.1#
>  > >
>  > > -------------------------------------------------------
>  > > Program do_dssp, VERSION 4.0.7
>  > > Source code file: do_dssp.c, line: 471
>  > >
>  > > Fatal error:
>  > > Failed to execute command: /home/sunita/soft/bin -na dd3sOJn3
>  > > ddZl9dcf >
>  > > /dev/null 2> /dev/null
>  > > **********************************
>  > >
>  > > Thanks,
>  > > Sunit
>  > >
>  > >
>  > > -------------
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> 
> 
> Dr. Sunita Patel
> ---------------------------------------------
> Visiting Fellow
> Department of Chemical Sciences
> T.I.F.R., Homi Bhabha Road, Colaba
> Mumbai - 400005
> ---------------------------------------------
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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