Hi Jason,
Thanks for your reply.
> It's unclear what you mean by "dynamics". There is no single definition
> of what "dynamics" is -- do you mean that this rotation causes particular
> behavior? Like the ligand adjusting its orientation in the binding
> pocket? A different dihedral angle rotating? Does it eject the ligand
> from the binding pocket?
>
Here ligand dynamics means 'transnational motion', it is going out of the
pocket.
>
>
> You need to form a concrete definition of what you mean by "dynamics" --
> one that you can describe using various geometric measurements (mean
> squared displacement, a different torsion angle, COM distance from some
> residue or point in the binding pocket, atomic fluctuations, etc.). Then
> it could be as simple as plotting the time series of the Chi2 dihedral
> angle alongside the time series of whatever measurement you made to
> quantify "ligand dynamics".
>
I have calculated the chi2 dihedral for phenyl ring and variations in COM
for ligand with respect to an almost stationary point in the complex.
> You can also compute a cross-correlation function between the two time
> series if you need a more quantitative measure of the correlated motion
> (rather than just demonstrating that a particular event in one curve
> follows immediately from an event in the other one).
>
Yes, I want to calculate a cross-correlation between these two data sets
(chi2 dihedral and distance change of ligand). I went through the manual
and it seems that 'corr' command will be suitable for it. However, I am not
sure about the dataset1 and dataset2. Should I use cpptraj out files for
dihedral and COM directly as dataset1 and dataset2, directly?
Thanks once again.
Kshatresh
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Received on Wed Apr 01 2015 - 08:00:03 PDT
