First of all Happy New Year to everyone. Second, Justin I admire you. You keep this forum alive and very well tended. Great job.Third, Parisa, try running do_dssp with the flag -dt and pick an interval one or two orders of magnitude smaller than the length of your simulation. That should do it. Best regards.
> Message: 7 > Date: Tue, 1 Jan 2013 22:47:39 +0330 > From: Parisa Rahmani <rahmani.p...@gmail.com> > Subject: Re: [gmx-users] secondary structure analyze > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <caac4-tstt+pgwo04avj64hflvkz8mnsqrf-uugykbuxcs5r...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Thanks Justin for the reply, > how i can sure that it uses the DSSP package correctly , > it seems that it just uses the gromacs code : > ( > Opening library file /home/parisa/parisa/share/gromacs/top/phbres.dat > Opening library file /home/parisa/parisa/share/gromacs/top/aminoacids.dat > Opening library file /home/parisa/parisa/share/**gromacs/top/ss.map > ) > for some reasons I use gromacs 3.3.3. -- 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