[MMTK] Glycine Mutation Potential energy

Matias Saavedra matias_saavedra at yahoo.com
Mon Sep 19 00:43:44 CEST 2005


Hi Konrad.

I did what you suggested to me to mutate any residue
in a protein into glycine.
this is the code:

def mutateResidue(residue, new_residue_type,
atom_mapping):
     if hasattr(residue.peptide, 'H_3'):
        new_residue_type += '_nt'
     elif hasattr(residue.peptide, 'O_2'):
        new_residue_type += '_ct'
     print "Changing %s into %s" % (residue.type.name,
new_residue_type)
     new_residue = Residue(new_residue_type,
residue.model)
     for g in ['peptide', 'sidechain']:
        g_old = getattr(residue, g)
        g_new = getattr(new_residue, g)
        atoms = map(lambda a: a.name, getattr(g_new,
'atoms'))
        for a in atoms:
            an = getattr(g_new, a)
            ao = None
            try:
                ao = getattr(g_old, a)
            except AttributeError:
                if g == 'sidechain':
                    try:
                        a = atom_mapping[a]
                        ao = getattr(g_old, a)
                    except KeyError:
                        pass
            if ao:
                an.setPosition(ao.position())
            else:
                print "No mapping for atom %s.%s" %
(g, a)
     return new_residue

protein = Protein('insulin')

for chain in protein:
     for residue in chain:
        new_residue = mutateResidue(residue,
                                    'glycine',
{'H_alpha_3': 'C_beta'})
        chain.replaceResidue(residue, new_residue)


when i do that to a previously minimized and saved
universe, and i relaunch a minimization, the potential
energy and the gradient norm are still the same
(compared to the saved universe).

It seems that the mutation of all the residues of a
protein to glycine, doesnt affect the potential energy
and the gradient norm of the system!

What could be happenning?

Thanks


--- khinsen at cea.fr wrote:

> On Sep 13, 2005, at 18:07, Matias Saavedra wrote:
> 
> > How can i determine the nature of the mouvements
> > described by each of the lowest normal modes
> > (direction, collective-concerted, iris-like,
> bending,
> > twists, translations, rotations, rigid body
> regions
> > and their concerted mouvements, etc.) ?
> >
> > I have to combine the data from displacements and
> > deformation energy in some way?
> 
> The deformation energy is a global measure of the
> collectiveness of the 
> mode, but it does not describe the nature of the
> motions. For that, you 
> have to look at the displacements.
> 
> Techniques for analyzing the displacements in terms
> of particular 
> motion types are described in
> 
> 	K. Hinsen, G.R. Kneller
> 	Projection methods for the analysis of complex
> motions in 
> macromolecules
> 	Mol. Sim. 23, 275-292 (2000)
> 
> The support code for these techniques is in
> MMTK.Subspace. An 
> illustration can be found in
> Examples/NormalModes/mode_analysis.py.
> 
> Konrad.
> --
>
---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire Léon Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
> Tel.: +33-1 69 08 79 25
> Fax: +33-1 69 08 82 61
> E-Mail: khinsen at cea.fr
>
---------------------------------------------------------------------
> 
> 



		
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