[gmx-users] Query regarding do_dssp program

[Sundari]

Hello Dear,

Actually I was thinking the same i.e. gromacs use "dssp" criteria and vmd
use "stride" algorithm for secondary structure determination.
But the expected error in the two algorithms should not be more than 5%
according to the literature. Here, In my case, the structure contains a lot
of beta-sheets by dssp and that sequence in vmd is showing 5-helix instead
of beta-sheets. I am in a confusion now because I want the snapshots of the
structures obtained by gromacs dssp.

Can you please suggest which algorithm should I use for 2ndary structure or
there is any way to animate secondary structure in vmd according to dssp
algorithm.

Best regards,
Sundari

On Mon, Jan 13, 2020 at 1:37 PM Alessandra Villa <
alessandra.villa.biosim at gmail.com> wrote:

> 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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