Sorry, yes, I actually made a copy and pasted in the /usr/bin directory as well. So there IS actually a copy of the same program.
Yes, my system is 64 bit. Just as a test case, I tried with the 32-bit version as well. Same error as above. On Mon, Feb 16, 2015 at 6:45 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/16/15 6:40 PM, HANNIBAL LECTER wrote: > >> Okay. what can be possibly wrong? I mean if someone CAN run Gromacs-5.0.4 >> + >> DSSP 2.0.4, it should be running in other systems as well unless I am >> messing something up. So I list my steps. >> >> 1. Download the executable from >> ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/ (not the source code, >> but >> just the binaries). >> >> 2. rename the file to dssp204 >> 3. chmod +x dssp204 >> 4. sudo mv dssp204 /usr/local/bin/ >> 5. export DSSP=/usr/loca/bin/dssp204 >> 6. do_dssp -f data/xtc/traj.xtc -s data/tpr/topol.tpr -ver 2 >> >> What can be possibly wrong? >> >> > Not sure, because what you're telling us isn't consistent: > > 1. You're not copying and pasting (or you are and you're setting variables > wrong) because step 4 shows "/usr/loca/bin" as the location of the > executable, which in step 3 you (presumably) put in /usr/local/bin (which > actually makes sense). > > 2. That's not what you did because: > > dssp cmd='/usr/bin/dssp20464 -i ddUkWy9e -o dd7htL6i > /dev/null 2> > /dev/null' > > says you have installed something called "dssp20464" in /usr/bin. > > It's hard to troubleshoot something when you're not giving us consistent > information. If the suffix "20464" indicates version "2.0.4" and 64-bit > architecture, is that appropriate for your system? You have a 64-bit > system, not 32-bit? > > -Justin > > >> The output is shown below: >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> *Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 (single >> precision)Reading file data/tpr/gly16_amber03w_nd0.tpr, VERSION 4.5.6 >> (single precision)Group 0 ( System) has 10901 elementsGroup >> 1 ( Protein) has 121 elementsGroup 2 ( Protein-H) has >> 68 elementsGroup 3 ( C-alpha) has 16 elementsGroup 4 >> ( Backbone) has 50 elementsGroup 5 ( MainChain) has >> 67 >> elementsGroup 6 ( MainChain+Cb) has 67 elementsGroup 7 ( >> MainChain+H) has 85 elementsGroup 8 ( SideChain) has 36 >> elementsGroup 9 ( SideChain-H) has 1 elementsGroup 10 ( >> Prot-Masses) has 121 elementsGroup 11 ( non-Protein) has 10780 >> elementsGroup 12 ( Other) has 2320 elementsGroup 13 >> ( RS1) has 2320 elementsGroup 14 ( Water) has >> 8460 >> elementsGroup 15 ( SOL) has 8460 elementsGroup 16 ( >> non-Water) has 2441 elementsSelect a group: 1Selected 1: 'Protein'There >> are 18 residues in your selected groupdssp cmd='/usr/bin/dssp20464 -i >> ddUkWy9e -o dd7htL6i > /dev/null 2> /dev/null'Reading frame 0 time >> 0.000 Back Off! I just backed up ddUkWy9e to >> ./#ddUkWy9e.1#---------------------------------------------- >> ---------Program >> gmx, VERSION 5.0.4Source code file: >> >> /home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, >> line: 670Fatal error:Failed to execute command: Try specifying your dssp >> version with the -ver option.For more information and tips for >> troubleshooting, please check the GROMACSwebsite at >> http://www.gromacs.org/Documentation/Errors >> <http://www.gromacs.org/Documentation/Errors>--------- >> ----------------------------------------------* >> >> >> On Mon, Feb 16, 2015 at 6:25 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 2/16/15 6:20 PM, HANNIBAL LECTER wrote: >>> >>> Okay, so the same errors seem to be persisting. >>>> >>>> I am not sure what can possibly go wrong in this case. The dssp program >>>> seems to be working (just typing dssp in the shell gives information >>>> regarding the versions of dssp that has been used). >>>> >>>> The dsspold program doesn't seem to be doing much. >>>> >>>> >>>> No idea what that means, so I can't help with that. >>> >>> Does anyone know of a version of DSSP executable corresponding to a >>> >>>> working >>>> Gromacs version? >>>> >>>> >>>> DSSP 2.0.4 works with GROMACS 5.0.4 for sure (I ran it just the other >>> day), but in principle any 2.x version should work with GROMACS 4.6 or >>> newer (the issue was closed 3 years ago, with minimal reported issues and >>> no code modifications since). >>> >>> -Justin >>> >>> >>> On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul <jalem...@vt.edu> >>> wrote: >>> >>>> >>>> >>>> >>>>> On 2/16/15 4:07 PM, HANNIBAL LECTER wrote: >>>>> >>>>> Thanks for your reply. Couple of things. >>>>> >>>>>> I don't really know where to get older dssp binaries. I couldn't find >>>>>> them >>>>>> available for download in the dssp website. >>>>>> >>>>>> >>>>>> http://swift.cmbi.ru.nl/gv/dssp/ >>>>>> >>>>> >>>>> Click on "Distributions" and at the bottom of that page, "DSSPold" is >>>>> the >>>>> old version. >>>>> >>>>> I renamed the mkdssp binary to dssp so I am sure nothing is wrong >>>>> out >>>>> >>>>> there >>>>>> when I export the binaries for utilization in gromacs. >>>>>> >>>>>> >>>>>> Aside from the usual advice of making sure the binary is actually >>>>> executable (and actually runs, check with ./dssp -V for instance), >>>>> there's >>>>> little to go on here. >>>>> >>>>> -Justin >>>>> >>>>> >>>>> On Feb 16, 2015 3:45 PM, "Justin Lemkul" <jalem...@vt.edu> wrote: >>>>> >>>>> >>>>>> >>>>>> >>>>>> On 2/16/15 3:15 PM, HANNIBAL LECTER wrote: >>>>>>> >>>>>>> Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and >>>>>>> there >>>>>>> is >>>>>>> >>>>>>> not >>>>>>>> a scope to specify using the -ver command in this particular version >>>>>>>> as >>>>>>>> opposed to the newer versions (5.0.4). >>>>>>>> >>>>>>>> By '....' I meant >>>>>>>> >>>>>>>> do_dssp -f prot.xtc -s prot.tpr. >>>>>>>> >>>>>>>> How do I specify a dssp version in gromacs-4.5.6? >>>>>>>> >>>>>>>> >>>>>>>> I forget when the -ver flag was introduced. Safe bet is if >>>>>>>> you're >>>>>>>> >>>>>>>> using >>>>>>> an ancient GROMACS version, you need a similarly ancient DSSP >>>>>>> (version >>>>>>> 1.0.x). >>>>>>> >>>>>>> Secondly, I did install Gromacs-5.0.4 for comparison, and I am >>>>>>> using >>>>>>> DSSP >>>>>>> >>>>>>> 2.0.4 again. This time I am using >>>>>>> >>>>>>>> >>>>>>>> do_dssp -f prot.xtc -s prot.tpr -ver 2 >>>>>>>> >>>>>>>> The output I am getting is shown below. Not sure what is going on. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> *There are 18 residues in your selected groupdssp >>>>>>>> cmd='/usr/bin/mkdssp >>>>>>>> -i >>>>>>>> ddJszHtZ -o ddRZ5pwg > /dev/null 2> /dev/null'Reading frame 0 >>>>>>>> time >>>>>>>> >>>>>>>> >>>>>>>> My guess is that "mkdssp" is not actually the same thing as >>>>>>>> "dssp" - >>>>>>>> >>>>>>> make >>>>>>> sure you've installed a real, functional dssp binary. >>>>>>> >>>>>>> -Justin >>>>>>> >>>>>>> 0.000 Back Off! I just backed up ddJszHtZ to >>>>>>> >>>>>>> ./#ddJszHtZ.1#---------------------------------------------- >>>>>>> >>>>>>>> ---------Program >>>>>>>> do_dssp, VERSION 5.0.4Source code file: >>>>>>>> /home/apratim/Programs/gromacs-5.0.4/src/gromacs/ >>>>>>>> gmxana/gmx_do_dssp.c, >>>>>>>> >>>>>>>> line: 670Fatal error:Failed to execute command: Try specifying your >>>>>>>> dssp >>>>>>>> version with the -ver option.For more information and tips for >>>>>>>> troubleshooting, please check the GROMACSwebsite at >>>>>>>> http://www.gromacs.org/Documentation/Errors >>>>>>>> <http://www.gromacs.org/Documentation/Errors>--------- >>>>>>>> ----------------------------------------------* >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> ================================================== >>>>>>> >>>>>>> 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? 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.