[gmx-users] conformational change

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Dec 14 09:50:28 CET 2012

Hey Julio, Shine,

I would like to see the 'here' and 'here'. Pymol has two routines for
determining secondary structure, one of which uses the same approach as
dssp to classify helices and sheets. A relevant question is, what is a
helix? Is a helix a stretch of residues that is defined by dssp as helix?
That is also just a heuristic.
Justin is quite right that what is observed is largely the consequence of
the force field and settings. Make sure that the force field and settings
you use reproduce proper behaviour. The structure will not just change
because of the placement of waters, or that shouldn't be a persistent
And why would it be a helix for all of the residues for all of the time?
Because the crystal structure shows it's a helix? Maybe it's more flexible
in solution and only a helix for a given proportion of time. If you're
afraid to see (temporary) loss of structure, then it may be better not to
simulate at all.



On Fri, Dec 14, 2012 at 6:32 AM, Julio Dominguez <acheron24 at hotmail.com>wrote:

> Hello Shine,
> Besides what Justin mentioned you have to be careful of what you consider
> a helix or a loop. Pymol is note very accurate when it assigns secondary
> structure. I recommend you install dssp within Pymol (see here and here)
> and double check you secondary structure. Odds are that it still is a helix.
> Best regards.
> > Message: 4
> > Date: Thu, 13 Dec 2012 22:53:30 +0530
> > From: Shine A <shine.a at iisertvm.ac.in>
> > Subject: [gmx-users] conformational change
> > To: gmx-users at gromacs.org
> > Message-ID:
> >       <CAEUDBJr1nBB2We-rJzg0H9er9Bf0cEgqn4mgwratJyPff=A0=
> g at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Sir,
> >
> >         I am studying the dynamics of a beta barrel shaped membrane
> > protein. The starting end of the barrel is a helix which is inside the
> > barrel. During salvation with genbox some water molecules entered inside
> > the barrel.Then I did the 20 ns dynamics.After dynamics more number of
> > water molecules trapped inside the barrel. I convert the output gro file
> > into pdb and viewed using pymol. Then I noticed that the starting helix
> > part is changed in to loop.Then I calculated the rmsd deviation and
> radius
> > of gyration, it not showing any characteristic deviation.Is water
> molecule
> > change the conformation of helix inside the barrel? Is it necessary to
> > delete all the water molecules inside the barrel before dynamics? then
> > how?
> >
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4

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