[MMTK] MMTK-questions about normal modes analysis

Ma Yong ymaz at essex.ac.uk
Wed Feb 20 17:46:33 UTC 2008



I have some question about the normal modes analysis


1) Is it suitable to use calpha mode to approximate this protein (pdb file-
1LN6, Metarhodopsin)? Compared with the standard calculation , what will be
lost by using approximation method?

   If I use standard calculation based on MMTK, what is minimum requirements
for the computer and how long will the calculation take ( say it the number
of atoms is 5000)?



2) How to calculate the absorption spectra based on the Normal modes
analysis using MMTK? For example, I ran the examples in the manual-
deformation_modes.py, I can get the frequency for each mode, how to get the
normalised intensity absorption spectrum based on these information? 







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