[gmx-users] Query regarding do_dssp program

[Alessandra Villa]

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 <sundi6170 at 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,
> --
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