[gmx-users] resolution influence on simulations
Ruben Martinez Buey
ruben at akilonia.cib.csic.es
Thu Nov 28 21:33:17 CET 2002
Hi everybody,
Thanks a lot for your help.
Anyway, the lower is the resolution, the more is the r.m.s deviation after the run??
I mean you can use a cut-off to check which changes are really significatives
[r.m.s.d Vs residue number], and this cut-off can be the r.m.s.d of the last step in
the simulation plus the averaged r.m.s.d. of all the residue`s rmsd at the end of the
run. Is it right??
Thanks a lot,
cheers,
Ruben
Daan Virtual wrote:
> 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
> > >
> > > 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
> > >
> > > _______________________________________________
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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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>
> ##############################################################################
>
> 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
>
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--
___________________________________________
Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144 28006 MADRID
Tlf: +34-91-561 18 00 ext. 4380
___________________________________________
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