[gmx-users] SA

[Nuno R. L. Ferreira]

Hi Osmany

I think that the use or not of restraints it depends of what you want.
For instance, if you have build an helical model of a peptide and do not
know the 3D structure of it, then a SA could be used to randomize the a.a.
lateral chains, while restraining the backbone.

If you know the structure, I think you should at least verify if the final
structure is too far from the initial one.
SA is a fine technique for reaching a minimum structure. In my NMR days, I
played awhile with it, but in this case I have restraints that lead to a
ensemble of "final" structures.  If you do not pose any restraints to the
protein, and if the highest temperature is too high, as usually is, then
maybe SA will destroy your "native" structure.

Regards,
Nuno

----- Original Message ----- 
From: "Osmany Guirola Cruz" <osmany.guirola at cigb.edu.cu>
To: <gmx-users at gromacs.org>
Sent: Wednesday, April 28, 2004 3:14 PM
Subject: [gmx-users] SA


I am doing a SA whith gromacs, i read some papers (Journal of peptide
Science Vol 3, 85-92 (1997)) here the authors explain the protocol thah
they use to do the SA. I am doin something similar whit my peptide and
the new options of gromacs (anneling_points, anneling_time ) ,I heat
,cool ,heat, cool, many times ok whith these theres is not problem my
question is about the constrains , when I do SA what should I do whith
the constrains? (all-bonds, none...) I think that if I remove the
constrains my peptide "is more flexible" and more free of movement
What do you think and recommend me?
Thanks


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Nuno Ricardo Santos Loureiro da Silva Ferreira
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra - Portugal
Fax: +351 239 827703  - www.biolchem.qui.uc.pt
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