Thanks a lot Jason.
On Wed, Apr 1, 2015 at 5:49 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Apr 1, 2015 at 10:42 AM, Kshatresh Dutta Dubey <
> kshatresh.gmail.com>
> wrote:
>
> > 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?
> >
>
> You should be able to do this all within the same cpptraj run. The
> dihedral command creates a data set for the dihedral you measured. The
> distance command also creates a data set. (You are free to name any of
> these data sets.)
>
> Then specify the names of those two data sets to the corr command.
>
> Alternatively, you can create the data sets via the "readdata" command in
> cpptraj if you do not want to re-run the calculation, and use the "corr"
> command on those data sets. Or, of course, you can write a script to
> compute the cross-correlation function between the data sets yourself
> (using numpy, for instance).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
--
With best regards
************************************************************************************************
Kshatresh Dutta Dubey
Post Doctoral Researcher,
Lise Meitner Center for Computational Quantum Chemistry
Hebrew University of Jerusalem Israel
Jerusalem, Israel
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Received on Wed Apr 01 2015 - 08:00:07 PDT
