Hi, It may very well be. Here's the red mine issue http://redmine.gromacs.org/issues/891. If there's a -ver option for do_dssp then it's capable of the new syntax. If not then it assumes the old syntax. If you can't install a newer version of gromacs there is the option to install old_dssp which is available through the dssp webpage.
Erik On 7 Jun 2013, at 10:20, shika <pqah...@gmail.com> wrote: > Hi Eric, > > I'm using gromacs 4.5.5. > Is it the version is different for dssp? > > Thanks > > On Fri, Jun 7, 2013 at 3:41 AM, Erik Marklund [via GROMACS] > <ml-node+s5086n5008885...@n6.nabble.com> wrote: >> HI, >> >> What version of gromacs is this? DSSP changed its syntax a while back and we >> had to adjust do_dssp accordingly. You may have a mismatch between gromacs >> and dssp versions. >> >> Erik >> >> On 7 Jun 2013, at 08:42, Nur Syafiqah Abdul Ghani <[hidden email]> wrote: >> >>> Hi All, >>> >>> I already done the MD production so I want to analyse the helical >>> structure of my protein by using do_dssp program.The command is like >>> below : >>> >>> do_dssp -s md_water50.tpr -f md_water50.trr -n mainchain.ndx -sc >>> dssp_scount.xvg -a dssp_area.xvg -ta dssp_totarea.xvg -aa >>> dssp_averarea.xvg >>> >>> but after i run the command the result show like : >>> >>> Reading file md_water50.tpr, VERSION 4.5.5 (double precision) >>> Reading file md_water50.tpr, VERSION 4.5.5 (double precision) >>> Segmentation fault (core dumped) >>> >>> >>> I already install the dssp program from >>> ftp://ftp.cmbi.ru.nl/pub/software/dssp/ and follow the instruction as >>> shown there but it seems that nothing happened..I already gedit the >>> .bashrc for dssp. >>> >>> -- >>> Best Regards, >>> >>> Nur Syafiqah Abdul Ghani, >>> Theoretical and Computational Chemistry Laboratory, >>> Department of Chemistry, >>> Faculty of Science, >>> Universiti Putra Malaysia, >>> 43400 Serdang, >>> Selangor. >>> alternative email : [hidden email] @ [hidden email] >>> -- >>> gmx-users mailing list [hidden email] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [hidden email]. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> -- >> gmx-users mailing list [hidden email] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [hidden email]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> ________________________________ >> If you reply to this email, your message will be added to the discussion >> below: >> http://gromacs.5086.x6.nabble.com/segemntation-fault-after-run-do-dssp-tp5008883p5008885.html >> To start a new topic under GROMACS Users Forum, email >> ml-node+s5086n4370410...@n6.nabble.com >> To unsubscribe from GROMACS, click here. >> NAML > > > > -- > Best Regards, > > Nur Syafiqah Abdul Ghani, > Theoretical and Computational Chemistry Laboratory, > Department of Chemistry, > Faculty of Science, > Universiti Putra Malaysia, > 43400 Serdang, > Selangor. > alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/segemntation-fault-after-run-do-dssp-tp5008883p5008886.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
