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
