[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, 

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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