[gmx-users] secondary structure query

Justin Lemkul jalemkul at vt.edu
Tue Jun 12 16:23:23 CEST 2018

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 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


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