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I don't have NMR information i am trying to predict the structure of my peptdide
from scratch<br>
, like Marc Ceruso says in another mail.<br>
<br>
<br>
<br>
Kay Gottschalk wrote:<br>
<blockquote type="cite"
cite="mid817EA915-C2C3-11D7-9223-000393BB411E@weizmann.ac.il">It might very
well be that your system is way to flexible; you'd need experimental (=NMR)
restraints, I'd guess. Even a cyclic hexapeptide is very flexible and basically
improbable to predict correctly. <br>
<br>
On Thursday, July 31, 2003, at 01:15 AM, Osmany Guirola Cruz wrote: <br>
<br>
<blockquote>my peptide have 11 aminoacids and it is cyclic. <br>
<br>
Marc Ceruso wrote: <br>
<br>
<tt><font size="+1">On Wed, 30 Jul 2003, Osmany Guirola Cruz wrote: <br>
<br>
</font></tt> <br>
<br>
<tt><font size="+1">Thanks again Xavier, <br>
I have this problem: <br>
I have a peptide whit unknown structure, whit "modeler" i get 10 <br>
diferents structures of my peptide, and then..... <br>
i use SA whith the ten models to obtain a "superminimized structure" but <br>
my final structures are NOT similar <br>
</font></tt> <br>
<br>
<tt><font size="+1">How long is the peptide? Why do you think that your
structures should be <br>
similar? In any case, if the peptide is small let's say 1-40 amino acids <br>
chances are that its structure in solution is not unique, but in any case
<br>
the similiraty within your ensemble will depend on the strength of the <br>
restraints used to generate the structures. If the homology of your <br>
peptide/protein is low the constraints will be loose reflecting the lack <br>
of empirical knowlege regarding your sequence, in others reflecting the <br>
uncertainty in the structure. <br>
<br>
<br>
<br>
</font></tt> <br>
<br>
<tt><font size="+1">:-( . i have the idea that my simulations converge
to a unique structure <br>
(my SA = "1000K" to 300K) you say 10 000 i will probe <br>
with 10000 to see what happens. ??????? <br>
<br>
<br>
<br>
Xavier Periole wrote: <br>
<br>
I guess you have been reading papers from NMR procedures to <br>
generate their models corresponding to the data. If that what you <br>
are doing It would be easier to get a program that NMR people <br>
use, is is probably implemented <br>
It seeems difficult to do that automatically in gromacs, at least <br>
for me. <br>
I guess you that could modify the strength of the constant on the <br>
angles <br>
and bonds in the parameter file and do that for each temperature <br>
you <br>
need but that's gonna to be a pain in the ... <br>
I don't know what you are doing but I can assure you that at 10000 <br>
K <br>
the system is pretty flexible. Try to simulate it for 10 ps at <br>
10000 K <br>
and look at the trajectory !! It should convice you. But I don't <br>
know if <br>
it is relevant for your problem. <br>
<br>
XAvier <br>
<br>
<br>
<br>
<br>
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<br>
<br>
<br>
</blockquote>
Dr. Kay-E. Gottschalk <br>
Department of Biological Chemistry <br>
Weizmann Institute of Science <br>
Tel: ++972-8-9343639 <br>
Herzl St. 1 <br>
Rehovot 76100 <br>
Israel <br>
<br>
</blockquote>
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