[gmx-users] Query regarding do_dssp program

Sundari sundi6170 at gmail.com
Mon Jan 13 15:15:45 CET 2020


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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list