[gmx-users] Query regarding do_dssp program

[Justin Lemkul]

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.
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