[MMTK] MMTK beguinner

Matias Saavedra matomatias at hotmail.com
Tue Apr 19 15:29:14 CEST 2005


Ok i get the idea. So i think that deformation energy is the usefull 
magnitude for the analysis i want to carry out. I want to determine the 
flexibility in the active site of several proteins.

So a simple question arises:

The problem of the scaling factor for the results of fluctuations applies to 
energy deformations as well? Or the energy deformations magnitudes 
calculated with the CalphaForceField can be used directly?

Another question:
The simplification of the system by considering only Calpha carbons is 
sensible enough to detect changes in flexibility produced by point (single) 
mutations? or should i use for that purpose the complete Amber94 analysis?


Thanks a lot for your concern.

Matias.

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