[MMTK] MMTK beguinner

Matias Saavedra matomatias at hotmail.com
Tue Apr 19 11:39:17 CEST 2005


Hi everone. I' am just getting into MMTK and normal modes analysis, and of 
course i have several questions.

I would like to know which is the better method to determine the amplitude 
of the mouvements of selected residus, for example from the active site, 
DEFORMATION ENERGY or FLUCTUATIONS() from NormalModes class.

In this context i used the method fluctuations() to calculate the mouvements 
of residues in a given protein,  with the  simplified model using 
deformation force field and i obtained very low values (around 0,00005).

I would like to know the units of the fluctuations results and if the values 
i get are in the correct range.

Finally i would like to know how many modes i have to consider to make a 
good fluctuation analysis.


Thanks a lot.

Matias Saavedra

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