[gmx-users] Query regarding do_dssp program

[Sundari]

Yes, Sir,  I  made the gro file for a particular time by using "gmx
trjconv" command ( also checked with -pbc mol, whole, no_jump options )
but every time the 2ndary structure visualization in vmd is different from
dssp sequence of residues in gromacs. Fox example in my protein dssp shows
8 residues making beta-sheets but when I load that particular time frame in
vmd for visualizing the structure,  these 8 residues showing 5-helix
structure.

Please suggest something.

On Mon, Jan 13, 2020 at 7:01 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/13/20 7:22 AM, Sundari wrote:
> > 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.
>
> Are you sure you're looking at the same snapshots? Those are wildly
> different structures. I have had VMD show coils for helices and strands
> before, but never any disagreement to this extent.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
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