[gmx-users] secondary structure query
jalemkul at vt.edu
Tue Jun 12 16:23:23 CEST 2018
On 6/12/18 9:31 AM, SHAHEE ISLAM wrote:
> i am following this tutorial
> 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
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.
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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