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my peptide have 11 aminoacids and it is cyclic.<br>
<br>
Marc Ceruso wrote:<br>
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cite="midPine.SGI.4.44.0307301503370.1954810-100000@fulcrum.physbio.mssm.edu">
<pre wrap="">On Wed, 30 Jul 2003, Osmany Guirola Cruz wrote:
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<pre wrap="">Thanks again Xavier,
I have this problem:
I have a peptide whit unknown structure, whit "modeler" i get 10
diferents structures of my peptide, and then.....
i use SA whith the ten models to obtain a "superminimized structure" but
my final structures are NOT similar
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<pre wrap=""><!---->How long is the peptide? Why do you think that your structures should be
similar? In any case, if the peptide is small let's say 1-40 amino acids
chances are that its structure in solution is not unique, but in any case
the similiraty within your ensemble will depend on the strength of the
restraints used to generate the structures. If the homology of your
peptide/protein is low the constraints will be loose reflecting the lack
of empirical knowlege regarding your sequence, in others reflecting the
uncertainty in the structure.
</pre>
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<pre wrap="">:-( . i have the idea that my simulations converge to a unique structure
(my SA = "1000K" to 300K) you say 10 000 i will probe
with 10000 to see what happens. ???????
Xavier Periole wrote:
I guess you have been reading papers from NMR procedures to
generate their models corresponding to the data. If that what you
are doing It would be easier to get a program that NMR people
use, is is probably implemented
It seeems difficult to do that automatically in gromacs, at least
for me.
I guess you that could modify the strength of the constant on the
angles
and bonds in the parameter file and do that for each temperature
you
need but that's gonna to be a pain in the ...
I don't know what you are doing but I can assure you that at 10000
K
the system is pretty flexible. Try to simulate it for 10 ps at
10000 K
and look at the trajectory !! It should convice you. But I don't
know if
it is relevant for your problem.
XAvier
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<pre wrap=""><!---->
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