[gmx-users] resolution influence on simulations

[David van der Spoel]

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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