Thank you everyone specially Justin. Finally my do_dssp is working. Problem was with the binary file 'dssp-2.0.4-linux-amd64 <ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64>' . Now I have installed 'dssp-2.0.4-linux-i386 <ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386>' and it is working fine.
Cheers!! On Sat, Feb 28, 2015 at 4:03 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/26/15 10:25 PM, Aarti rana wrote: > >> I tried the same on a single frame also. It's been 24 hrs and still >> showing >> running : >> >> > A single frame should be done in about a second. If it's hanging for any > longer than that, something is wrong. Either the binary fails (try running > DSSP directly, not via do_dssp) or something else weird is happening, but > there's really nothing to go on at present. > > -Justin > > > Select a group: 1 >> Selected 1: 'Protein' >> There are 668 residues in your selected group >> dssp cmd='/usr/local/bin/dssp204 -i ddNf0AkV -o ddtcC3SI > /dev/null 2> >> /dev/null' >> Reading frame 0 time 10000.000 >> Back Off! I just backed up ddNf0AkV to ./#ddNf0AkV.1# >> >> >> On Thu, Feb 26, 2015 at 9:44 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 2/25/15 11:10 PM, Aarti rana wrote: >>> >>> As suggested I followed the other threads too. I am writing down my >>>> exact >>>> steps : >>>> >>>> Downloaded the executable from the dssp site (dssp-2.0.4-amd64) >>>> copied to my vaccine folder >>>> renamed the file to dssp204 >>>> >>>> chmod u=rwx dssp204 >>>>> sudo mv dssp204/usr/local/bin/ >>>>> export DSSP=/usr/local/bin/dssp204 >>>>> do_dssp -f next.xtc -s next.tpr -sc scount.xvg -o ss.xpm -ver 2 >>>>> >>>>> >>>> The program started running. But it's been 7 days and it's still >>>> running. >>>> It seems there is some problem with the run. >>>> >>>> >>>> So make a small test case. Run do_dssp on a single structure, then >>> run it >>> on a shorter trajectory, and see if it works. Maybe the process is hung >>> up, and maybe the reason is external to the program itself. Unless your >>> trajectory is TB in size, there's no way it should run for 7 days. >>> >>> -Justin >>> >>> >>> >>> On Tue, Feb 17, 2015 at 6:29 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>> >>>> >>>> >>>>> On 2/16/15 9:49 PM, Aarti rana wrote: >>>>> >>>>> After issuing command as you asked: >>>>> >>>>>> >>>>>> echo $DSSP >>>>>> >>>>>> /usr/local/bin/dssp >>>>>>> >>>>>>> >>>>>>> And yes I downloaded the "dssp-2.0.4-linux-amd64 >>>>>> <ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64>" file >>>>>> from >>>>>> dssp site. >>>>>> >>>>>> >>>>>> Please see the other thread with this exact same issue as we have >>>>>> gone >>>>>> >>>>> through a number of troubleshooting steps. >>>>> >>>>> -Justin >>>>> >>>>> >>>>> >>>>> On Mon, Feb 16, 2015 at 11:52 PM, Justin Lemkul <jalem...@vt.edu> >>>>> >>>>>> wrote: >>>>>> >>>>>> >>>>>> >>>>>> After looking at this a bit more closely for someone else who asked >>>>>>> the >>>>>>> same question, your clue is here: >>>>>>> >>>>>>> dssp cmd='/usr/local/bin/dssp -na dd31ZWbc ddI6at3a > /dev/null 2> >>>>>>> /dev/null' >>>>>>> >>>>>>> For some reason your do_dssp command is triggering version 1 >>>>>>> syntax. A >>>>>>> version 2 command should be something like: >>>>>>> >>>>>>> dssp cmd='/usr/local/bin/dssp -i ddYB5REk -o ddxi1TAx > /dev/null 2> >>>>>>> /dev/null' >>>>>>> >>>>>>> Note the difference in -i/-o vs. -na. This is the nature of the >>>>>>> problem >>>>>>> when dealing with different versions. Somehow there's a disconnect >>>>>>> between >>>>>>> your DSSP version or the command you're telling us you're issuing. >>>>>>> >>>>>>> >>>>>>> -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. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> >>>>> ================================================== >>>>> >>>>> 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. >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>> ================================================== >>> >>> 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. >>> >>> >> >> >> > -- > ================================================== > > 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? 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