On Tue, Nov 13, 2012, Meli Massimiliano wrote:
>
> I try to calculate generalized order parameters (S2) and NOE of each
> residue (N-H vector) from a molecular dynamics trajectory.
> I'm using the iRED method as described in the manual but i get very
> strange value
> for the NOE instead for S2 i get a very good correlation versus the
> experimental order parameters.
The above sentence is hard to understand. Do you mean that you get a good
correlation for S2 but a bad correlation for the NOE? Or do you mean
something different?
>
> ****************************************
> - Calculated relaxation rates and NOEs -
> ****************************************
>
> vector R1 R2 NOE
> 0 1.07972 1.13005 -2.46742
> 1 1.43791 1.54210 -1.82056
> 2 1.35727 1.44151 -2.00349
Are the R2 values at all like those observed? A common feature of MD
simulations (especially in TIP3P water) is that the rotational diffusion
is too fast, and hence the R2 rates are sytematically wrong. Such errors
will also affect the NOE. Do you have literature examples (or other
proteins you have simulated) where the NOE's calculated by IRED give good
results?
....dac
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Received on Tue Nov 13 2012 - 05:30:04 PST
