Hi, Exactly what dssp command worked? Your use of do_dssp must be consistent with that. You must be making a specific error, so general descriptions of your actions are likely to be counterproductive. :-) Please don't filter things through your head, because that assumes you are doing the right things, and the evidence is against that! :-)
Mark On Feb 17, 2015 1:14 AM, "HANNIBAL LECTER" <hanniballecte...@gmail.com> wrote: > > Yes, the binary is working on a single pdb file. > > On Mon, Feb 16, 2015 at 7:06 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 2/16/15 6:55 PM, HANNIBAL LECTER wrote: > > > >> 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. > >> > >> > > Does the dssp binary work when you run it on a single .pdb file (as it's > > designed to do)? If not, then the binary is (somehow) incompatible with > > your machine. Compiling from source would fix that. > > > > -Justin > > > > 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. > >>> > >>> > > -- > > ================================================== > > > > 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. -- 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.