[gmx-users] secondary structure query

[SHAHEE ISLAM]

thank you sir,for your suggestion.yes the error was because of version mismatch.

On 6/12/18, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 6/12/18 9:31 AM, SHAHEE ISLAM wrote:
>> hi,
>> i am following this tutorial
>> http://cgmartini.nl/index.php/tutorials-general-introduction/proteins.
>> afrter converting the coarse grained protein to all atom structure by
>> charmm force field,i have gotten the all atom gro file.now i want to
>> analyse the secondary structure of thih gro file.
>> when i am using this command
>> do_dssp -s aa_charmm.gro -n index1.ndx -f dynamic.xtc -sc scount.xvg
>> -o ss.xpm -dt 10
>> the error is
>> Fatal error:
>> Failed to execute command: /usr/local/bin/dssp -na ddVp6nYX ddensUfd >
>> /dev/null 2> /dev/null
>> thanking you
>> shahee
>
> Likely you've got a version mismatch issue. It appears you're using an
> old version of GROMACS, which may or may not be compatible with the
> newer (version 2.x) DSSP binaries that are distributed. First, check to
> make sure you can directly run DSSP (not via do_dssp) on a coordinate
> file, and if that works, then try upgrading GROMACS to the latest
> version, which has the ability to call DSSP via different syntax
> (version 1.x or 2.x).
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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