[gmx-users] conformational change

Leandro Bortot leandro.obt at gmail.com
Fri Dec 14 19:02:51 CET 2012

Hi all,

     I've had problems before with waters placed within a beta-sandwich
protein by genbox. Although it is theoretically a matter of running the
simulation and waiting for the waters to "come out", in practice this took
about 30 ns and destroyed a considerable amount of the beta-strands.

     The solution I found at the time was to use a bigger box and to remove
a shell of waters which were at a distance of 5 or less angstroms from the
protein. Then I did a very short (~100ps) NPT equilibration with position
restraints applied to the protein atoms. During this "solvation simulation"
the waters solvated the protein, the box shrank and the density increased
to the "normal" averages. I found that by doing this the waters enter the
cavities in a much more "natural" way.
     So, Shine, maybe doing this can help you, if the inner waters are
related to the helix destabilization. I used VMD to get the residue numbers
of the waters from the .gro file of the whole system (there were some
issues with pymol), then I removed such residues from the .gro file of the
box and adjusted the topology accordingly.

I hope it helps,
Leandro Bortot

2012/12/14 Julio Dominguez <acheron24 at hotmail.com>

> Morning Shine and Tsjerk,
> Sorry for the missing links (here and here), I was refering to PyMol
> wiki's and a blog:
> http://macosxpostdoc.blogspot.mx/2012/04/dssp-through-pymol.html
> http://www.pymolwiki.org/index.php/DSSP_Stride
> But what Tsjerk mentions is far more relevant, I was thinking statically
> last night. First off, PyMol automatic secondary structure detection is
> spotty. Second, the command dss within PyMol does a better job. Third, the
> most systematic way to visualize secondary structure  within Pymol would be
> to use DSSP (or Stride) within PyMol.
> Thinking dynamically, you could run do_dssp, part of Gromacs, and check
> the time course of the whole secondary structure during your simulation.
> There is also g_helix, which can output the % of time a structure spends as
> a helix.
> As everybody has pointed out, the forcefield is the most probable cause.
> Be sure to check recent literature to make sure the ff you are using is not
> biased against (or in favor) of helical structures.
> Best regards.
> >
> > Message: 4
> > Date: Fri, 14 Dec 2012 09:50:28 +0100
> > From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> > Subject: Re: [gmx-users] conformational change
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID:
> >       <CABzE1Sh7pr6yYhQfn2ghhdKAcpW2Q_KRgEzrPjNJD=
> QjJnM5zA at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > 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
> > effect.
> > 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.
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