On 13/11/12 14:18, David A Case wrote:
> 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?
I get a good correlation between calculated S2 and the experimental S2.
>> ****************************************
>> - 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?
I'm still waiting for the other experimental result, R1 and R2.
My hope was that with a long simulation to get better NOE value with
this method.
thanks a lot
max
> ....dac
>
>
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Received on Tue Nov 13 2012 - 08:30:02 PST
