Hi sxn, What do you mean with reverse coarse graining? You can specify the secondary structure also as string, which is doable if the peptide is not too long, e.g. using -ss HHHHHHHLLLLLLL. Otherwise, you can put the secondary structure you want in a simple file, and pass that with the option -ss.
Cheers, Tsjerk On Fri, May 1, 2015 at 4:24 PM, shivangi nangia <shivangi.nan...@gmail.com> wrote: > Hello, > > I wish to turn off the secondary structure restraint in half of the peptide > while using martinze.py. > > Is there any way in which this can be done. > > I have tried to delete the columns in .dssp file which tell about the > structure and character of the peptide but I still get a completely helical > peptide on reverse coarse graining. > > Thanks in advance. > > Best, > sxn > -- > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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.
