Hi, I'd start by checking if that last residue is a normal one...
Mark On Sat, Aug 5, 2017 at 2:02 PM YanhuaOuyang <15901283...@163.com> wrote: > > > Dear Mark, > > Thank you, I have figure out the problem, but to my surprise, the > output xpm file lack the information of the last residue for the CHARMM27 > force file (charmm's trajectory is good), but not for other force field. I > wonder whether the DSSP program in the gromacs ignore the last residue of > structures generated by CHARMM27 force field. > > Best regards, > Ouyang > > > > > > > > > At 2017-08-04 22:32:25, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: > >Hi, > > > >Isn't that figure what is in the xpm file? > > > >Mark > > > >On Fri, Aug 4, 2017 at 4:20 PM YanhuaOuyang <15901283...@163.com> wrote: > > > >> Hi, > >> I have run a MD simulation and used gmx do_dssp to calculate the > >> secondary structure content. The output files are md_dssp.xpm and > >> scount.xvg. I want to know that each residue belongs to what kind of > >> secondary structure for each frame. But the scount.xvg output file only > >> have the number of residues with each secondary structure and the total > >> secondary structure count as a function of time. So, can I get the > >> information on "each residue belongs to which kind of secondary > structure > >> for each frame" to draw a figure of " amino acid vs secondary > structure" ? > >> > >> Best regards, > >> Ouyang > >> -- > >> 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. > -- 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.