If you want the residues in a particular secondary structure, you can use do_dssp, see http://manual.gromacs.org/current/online/do_dssp.html . g_hbonds can calculate hydrogen bonds. To separate the h-bonds by secondary structure, I suppose some scripting is needed.
2013/8/16 balu <balu2...@vit.ac.in> > > <http://gromacs.5086.x6.nabble.com/file/n5010545/ss.png> > Can anyone suggest me to calculate the number of alpha-, 3-10, pi-helical > hydrogen bonds in protein using gromacs. > Is there any particular commands in gromacs, please let me know... > Thank you... > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Hai-friends-tp5010545.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