[gmx-users] resolution influence on simulations

[Daan Virtual]

David

I completely agree - I was not trying to say all 3-4 A structures are bad,
but indeed people need to think about what they are doing and realise such
structures are likely to contain errors - just downloading and pressing
the start MD button is not a good option.

As a crystallographer I have done one 3.25 A structure myself and I think
it would be a good experience for everybody doing MD to just have a look
at such a low resolution structure + electron density map - you will be
shocked at how little information such a map contains (compared to high
resolution structures).

Daan

On 27 Nov 2002, David van der Spoel wrote:

> On Tue, 2002-11-26 at 14:01, Daan Virtual wrote:
> >
> > Ruben
> >
> > Don't do it!
> >
> > There are several studies out there suggesting that even making point
> > mutations in proteins can significantly alter the dynamics. So think about
> > what it means to start from a structure that is highly likely to contain
> > significant errors not only in the side chains but also in the backbone.
> > Just have a look at the quality reports linked from the PDB entries and
> > you will be shocked (when you compare them to higher resolution
> > structures). Clearly this is also true for (homology) models : MD is
> > already an "in silico" technique and if you then also start from an "in
> > silico model" I think the results could be called "questionable".
>
> Having just submitted a "questionable" paper, I would like to comment...
>
> X-ray resolution tells you something about the data. At 3 A resolution,
> the error in the coordinates is roughly 1 A. However there are also
> constraints like bonds, angles and packing (i.e. forcefield
> calculations) that are used to derive a model to fit the data. The
> structures you download from the pdb are *models* optimized to fit the
> data. A wise old crystallographer taught me never to get a structure
> from the pdb without checking the electron density (even hi-res ones).
>
> Apart from resolution you should be looking at other crystallographic
> measures: R-factors, completeness of the data. You should also verify
> your structure for missing sidechains etc. Read the X-ray paper
> carefully.
>
> In conclusion, if you have a very compelling reason to study just this
> protein, go for it, but be careful: you have to explain all results and
> discrepancies with experiment.
>
> >
> > cheers
> >
> > Daan
> >
> >
> >
> >
> > On Wed, 27 Nov 2002, Ruben Martinez Buey wrote:
> >
> > > Hi everybody,
> > >
> > > If you try to see a conformational changes induced by a a ligand, but
> > > the structure have been resolved at
> > > 3.5 - 4 A resolution. Is this resolution good enough for a molecular
> > > dynamics simulation?
> > > When comparing the two simulations (with and without ligand) from the
> > > same starting structure the errors produced
> > > by this low resolution are similar and can you eliminate them??
> > >
> > > Thanks in advance,
> > > Cheers,
> > > Ruben
> > >
> > >
> > >
> > >
> >
> >
> > ##############################################################################
> >
> > Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
> > Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
> > Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
> > School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
> > Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk
> >
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> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O