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Theory and implementation
This analysis is based on an analytical relationship for the estimation of the generalized order parameter
(see Section 4.2.7.1) of N-H vectors of the protein backbone. It related
of the N-H vector of residue
i to close contact experienced by the H atom and the carbonyl oxygen of the preceeding residue i-1
with heavy atoms k using the formula:
 |
(4.199) |
where
is the distance between the carbonyl oxygen of residue i-1 and heavy atom k and
is
the distance between the amide proton of residue i and heavy atom k. The parameter b is set to -0.1 which takes into account that order
parameters of rigid protein regions typically lie around 0.9. The sum ranges over all heavy atoms k that do not belong to amino
acids i and i-1. For more details about this method, please refer to Ref. [73]
Beside the time-dependent
defined in Eq; 4.199, nMOLDYN also provide a time-averaged
defined as:
 |
(4.200) |
where
is the number of selected frames for the analysis.
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pellegrini eric
2009-10-06