[gmx-users] Simulated annealing

[Osmany Guirola Cruz]

I don't have NMR information i am trying to predict the structure of my 
peptdide from scratch
, like Marc Ceruso says in another mail.



Kay Gottschalk wrote:

> 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.
>
> On Thursday, July 31, 2003, at 01:15 AM, Osmany Guirola Cruz wrote:
>
>     my peptide have 11 aminoacids and it is cyclic.
>
>     Marc Ceruso wrote:
>
>     On Wed, 30 Jul 2003, Osmany Guirola Cruz wrote:
>
>
>
>     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
>
>
>     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.
>
>
>
>
>
>     :-( . 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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>
>
>
> 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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