Hi, VMD and dssp may use a slightly different criteria to define a beta sheet. First I will check in literature if the criteria are the same. In some case, it occur that the the atom types (e.i H) are not properly recognized by the software, and thus secondary structure element can not be determined. Best regards Alessandra
On Sat, Jan 11, 2020 at 6:23 PM Sundari <sundi6...@gmail.com> wrote: > Dear Gromacs Users, > > I have a big query regarding the "do_dssp" tool of gromacs-5.1.2. > Whenever I calculate the protein secondary structure by "gmx do_dssp" , it > shows a significant amount of beta sheet structures. But when I load the > same trajectory file in VMD for visualization of the secondary structure it > does not show any beta-sheet structures. > > Please, anyone, clarify the issue. > > Thank you in advance, > -- > 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.