[MMTK] Normal mode analysis problem (model = calpha,cutoff=2.5)

qiancheng shen qianchengshen at gmail.com
Wed Mar 28 07:17:42 UTC 2012


Hello All,
         I'm new to MMTK and I'm not familiar with Normal Mode Analysis.
         I tried a tiny protein with only two residues(LYS and VAL). And
the coordinate of Calpha atom is [0.102,0.9618,0.9045] and
[0.1236,1.2954,0.7236].
         I think the energy equation should be E = 1/2*C*[(x1-x2)**2].
          But I can not understand the force constants matrix given by MMTK
         It looks like:
         [[[   287.14341492   4474.65154911  -2404.82609992]
           [  -287.14341492  -4474.65154911   2404.82609992]]

           [[  4474.65154911  69729.98664023 -37475.20672376]
           [ -4474.65154911 -69729.98664023  37475.20672376]]

           [[ -2404.82609992 -37475.20672376  20140.41858683]
            [  2404.82609992  37475.20672376 -20140.41858683]]]
     .....................
        Could any one explain me how the matrix was generated? E.g. How to
get the first element 287.1434..?


Thanks in advance.

Shen
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