[MMTK] Coarse Grain Normal Mode analysis

James Starlight jmsstarlight at gmail.com
Thu Nov 3 08:03:55 UTC 2011


Dear Konrad,


Today I've examined NMA options in MMTK by the examination of the script
presented on the MMTK site. I'd like to discuss it because I have some
questions

Firstly

# Construct system
universe = InfiniteUniverse(AnisotropicNetworkForceField(cutoff=1))
universe.protein = Protein('3pqr_a.pdb', model='calpha')


What exsctly MMTK's force field is most suitable for cg NMA? I've found
several CG force fields like AMM ff, C-alpha ff, deformation ff etc. What
force field could be most suitable for the study of biological motions of
globular (enzymes) or membrane proteins ( receptors, channels) ?
In the past I worked only with ANM where I could varry Cutoff distance as
well as Gamma united force constant. I've found how to chanhe cutoff but
how I can define gamma function ?


Then

# Find a reasonable basis set size and cutoff
nbasis = max(10, universe.numberOfAtoms()/5)
cutoff, nbasis = estimateCutoff(universe, nbasis)

I think that the above just for the reduce sample conformation space of the
macromolecule. (reduction number of output modes from 3N-6 to nbasis
based). Does it true? It's not fullyunderstand what exactly is nbasis and
how I can define it. E.g in nbasis = max(10, universe.numberOfAtoms()/5)
what the values 10 and 5 were used ?


So If nbased was defined correctly
    subspace = FourierBasis(universe, cutoff)
    modes = SubspaceNormalModes(universe, subspace,temperature=300.0)
The normal modes would be calculated in the narrow subspace.

Finally about examination of the results. I have problems with the
graphical representation ( I've created about this separate topic). But now
I'd like to plot my results. Resently I've used matlibplot to plot python
data. Does this options supported by the MMTK?
Could you show me simple example how I can plot RMSF of my protein along
desired normal mode or plot correlation map for the residues?

Thank you for help,

James
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