[gmx-users] Query regarding do_dssp program

[Justin Lemkul]

On 1/13/20 9:15 AM, Sundari wrote:
> 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.

I'm afraid I can't. Those are two completely different hydrogen bonding 
patterns and I can't imagine how the algorithms would differ so 
dramatically. I have seen VMD render coils for helices and sheets but 
never a totally different secondary structure. Be sure you're telling 
VMD to re-compute structures and re-color the secondary structure 
elements at every snapshot for trajectory visualization, otherwise it 
will render everything the same as the initial frame, which will 
obviously be wrong in the case of large structural changes.

-Justin

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Justin A. Lemkul, Ph.D.
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