Hi Justin, Yes, I have checked the env variables and file is also executable. But still giving fatal error and asking me to specify the dssp version.
Aarti On Fri, Feb 13, 2015 at 8:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/13/15 4:41 AM, Aarti rana wrote: > >> Hi, >> >> I am new to gromacs and using gromacs 4.6.5 and dssp-2.0.4. To study the >> secondary structure, when I am running these commands: >> >> export DSSP=/usr/local/bin/dssp do_dssp -s md_0_1.tpr -f md_0_1_noPBC.xtc >> -o dssp.xvg -ver 2 >> >> I am getting this error: >> >> dssp cmd='/usr/local/bin/dssp -na dd31ZWbc ddI6at3a > /dev/null 2> >> /dev/null' Reading frame 0 time 0.000 Back Off! I just backed up dd31ZWbc >> to ./#dd31ZWbc.1# >> >> -------------------------------------------------------Program do_dssp, >> VERSION 4.6.5 Source code file: >> /build/buildd/gromacs-4.6.5/src/tools/gmx_do_dssp.c, line: 669 >> >> Fatal error: Failed to execute command: Try specifying your dssp version >> with the -ver option. >> >> I have already checked many helping sites but couldn't solve it. I have >> also checked the earlier comments posted here. >> >> I don't know how to fix it. Please help me? >> >> > Is your DSSP environment variable the correct location of the dssp binary > and is the dssp binary executable? > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. > -- *Happy and Healthy mantra of life : Enjoy what you have now, stop collecting luxuries of life, because an unsatisfied person cannot relish the precious moments of life, stay happy, stay cool, keep smiling, stay away from arguments and controversies.....* -- 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.
