[gmx-users] resolution influence on simulations

[Daan Virtual]

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".

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
>
>
>
>


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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

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