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Hi everybody,
<br>Thanks a lot for your help.
<br>Anyway, the lower is the resolution, the more is the r.m.s deviation
after the run??
<br>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??
<p>Thanks a lot,
<br>cheers,
<br>Ruben
<br>
<p>Daan Virtual wrote:
<blockquote TYPE=CITE>David
<p>I completely agree - I was not trying to say all 3-4 A structures are
bad,
<br>but indeed people need to think about what they are doing and realise
such
<br>structures are likely to contain errors - just downloading and pressing
<br>the start MD button is not a good option.
<p>As a crystallographer I have done one 3.25 A structure myself and I
think
<br>it would be a good experience for everybody doing MD to just have a
look
<br>at such a low resolution structure + electron density map - you will
be
<br>shocked at how little information such a map contains (compared to
high
<br>resolution structures).
<p>Daan
<p>On 27 Nov 2002, David van der Spoel wrote:
<p>> On Tue, 2002-11-26 at 14:01, Daan Virtual wrote:
<br>> >
<br>> > Ruben
<br>> >
<br>> > Don't do it!
<br>> >
<br>> > There are several studies out there suggesting that even making
point
<br>> > mutations in proteins can significantly alter the dynamics. So
think about
<br>> > what it means to start from a structure that is highly likely to
contain
<br>> > significant errors not only in the side chains but also in the
backbone.
<br>> > Just have a look at the quality reports linked from the PDB entries
and
<br>> > you will be shocked (when you compare them to higher resolution
<br>> > structures). Clearly this is also true for (homology) models :
MD is
<br>> > already an "in silico" technique and if you then also start from
an "in
<br>> > silico model" I think the results could be called "questionable".
<br>>
<br>> Having just submitted a "questionable" paper, I would like to comment...
<br>>
<br>> X-ray resolution tells you something about the data. At 3 A resolution,
<br>> the error in the coordinates is roughly 1 A. However there are also
<br>> constraints like bonds, angles and packing (i.e. forcefield
<br>> calculations) that are used to derive a model to fit the data. The
<br>> structures you download from the pdb are *models* optimized to fit
the
<br>> data. A wise old crystallographer taught me never to get a structure
<br>> from the pdb without checking the electron density (even hi-res ones).
<br>>
<br>> Apart from resolution you should be looking at other crystallographic
<br>> measures: R-factors, completeness of the data. You should also verify
<br>> your structure for missing sidechains etc. Read the X-ray paper
<br>> carefully.
<br>>
<br>> In conclusion, if you have a very compelling reason to study just
this
<br>> protein, go for it, but be careful: you have to explain all results
and
<br>> discrepancies with experiment.
<br>>
<br>> >
<br>> > cheers
<br>> >
<br>> > Daan
<br>> >
<br>> >
<br>> >
<br>> >
<br>> > On Wed, 27 Nov 2002, Ruben Martinez Buey wrote:
<br>> >
<br>> > > Hi everybody,
<br>> > >
<br>> > > If you try to see a conformational changes induced by a a ligand,
but
<br>> > > the structure have been resolved at
<br>> > > 3.5 - 4 A resolution. Is this resolution good enough for a molecular
<br>> > > dynamics simulation?
<br>> > > When comparing the two simulations (with and without ligand)
from the
<br>> > > same starting structure the errors produced
<br>> > > by this low resolution are similar and can you eliminate them??
<br>> > >
<br>> > > Thanks in advance,
<br>> > > Cheers,
<br>> > > Ruben
<br>> > >
<br>> > >
<br>> > >
<br>> > >
<br>> >
<br>> >
<br>> > ##############################################################################
<br>> >
<br>> > Dr. Daan van Aalten
Wellcome Trust CDA Fellow
<br>> > Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382
344979
<br>> > Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382
345764
<br>> > School of Life Sciences
E-mail: dava@davapc1.bioch.dundee.ac.uk
<br>> > Univ. of Dundee, Dundee DD1 5EH, UK WWW: <a href="http://davapc1.bioch.dundee.ac.uk">http://davapc1.bioch.dundee.ac.uk</a>
<br>> >
<br>> > O
C O
C Visit the PRODRG server
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<br>> --
<br>> Groeten, David.
<br>> ________________________________________________________________________
<br>> Dr. David van der Spoel, Biomedical
center, Dept. of Biochemistry
<br>> Husargatan 3, Box 576,
75123 Uppsala, Sweden
<br>> phone: 46 18 471 4205
fax: 46 18 511 755
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<p>##############################################################################
<p>Dr. Daan van Aalten
Wellcome Trust CDA Fellow
<br>Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979
<br>Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764
<br>School of Life Sciences
E-mail: dava@davapc1.bioch.dundee.ac.uk
<br>Univ. of Dundee, Dundee DD1 5EH, UK WWW: <a href="http://davapc1.bioch.dundee.ac.uk">http://davapc1.bioch.dundee.ac.uk</a>
<p> O
C O
C Visit the PRODRG server
to take
<br> "
| "
| the stress out of your
topologies!
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<br> |
" |
" <a href="http://davapc1.bioch.dundee.ac.uk/">http://davapc1.bioch.dundee.ac.uk/</a>
<br> C-C-O
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<pre>--
___________________________________________
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
___________________________________________</pre>
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