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Thanks Marc<br>
But if i have 10 diferent structures for the same peptide and i heat it
to 1000K and then cool it to 300K<br>
to each one , i supose that my 10 final structures must be similar. My idea
was to find a unique structure for my peptides<br>
an then do MD.<br>
<br>
<br>
Marc Ceruso wrote:<br>
<blockquote type="cite"
cite="midPine.SGI.4.44.0307310901510.2167071-100000@fulcrum.physbio.mssm.edu">
<pre wrap="">Hi-
Your results are not surprizing. But it seems to me that you would be
happier if you had one single structure for you peptide. Even if it were
that the peptide does have a unique stable conformation the search for it
would be to find a protocol/forcefield that would accurately determine the
correct fold of your peptide: protein folding problem. However, small
peptides do not have a unique
structure in solution. Numerous NMR studies on many peptides have shown
that the peptides (in general) are in equilibirium between different
forms. Take a look at the enkephalin (Scheraga) studies, or some of Ernst
(NMR) studies.
If you have experimental data on your peptide, You could run classical
MD simulations (see Daura and van Gunsteren) for a very long time
(tens/hundreds of ns)and evaluate
your computational results against the NMR data. That would be the measure
of convergence.
I hope this helps
Marco
On Thu, 31 Jul 2003, Osmany
Guirola Cruz wrote:
</pre>
<blockquote type="cite">
<pre wrap="">i have 10 simulations , i do g_cluster to each one and then i do g_confrm
whith the most populated clusters
and , these is the table:
1 2 3 4
5 6 7 8
9 10
1 *
2 0.255333 *
3 0.384980 0.268161 *
4 0.363748 0.356637 0.312702 *
5 0.364454 0.291378 0.168395 0.360910 *
6 0.304329 0.362637 0.352839 0.224768 0.350295 *
7 0.395214 0.427625 0.373925 0.340693 0.329041 0.264797 *
8 0.395720 0.347483 0.315446 0.462918 0.295911 0.384215 0.404703
9 ? ? ? ? ? ? ?
10 0.269739 0.224798 0.375789 0.433382 0.349531 0.403248 0.452217
0.382978
Kay Gottschalk wrote:
I'd do much more than ten structures. Do as many as you can
in a reasonable time and afterwards cluster the results! You
cannot expect your system to converge so easily...
On Thursday, July 31, 2003, at 02:00 AM, Osmany Guirola Cruz
wrote:
that was the problem in my simulation at 1000K my
ten final structures are quite diferent after the
SA.
Xavier Periole wrote:
Yop, sorry I meant 1000 K. 10000 K is way too
much.
Marco is right. With 11 residues it is unlikely
that your peptide has a unique
conformation in solvent. It probably explore
different conformations with diffenrent
probabilities.
How did you generate your 10 structures with
Modeler. I thought it needed a
template !! And what isthe point of doing an SA
on a specific conformation ?
You loose it at 1000K anyway !!
I did some thing similar where I generated 100
conf from SA with an implicit
solvent (faster) and after that I made clusters
of them.
XAvier
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Tel: ++972-8-9343639
Herzl St. 1
Rehovot 76100
Israel
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