thank you sir,for your suggestion.yes the error was because of version mismatch.
On 6/12/18, Justin Lemkul <jalem...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.