On Mon, Mar 30, 2015 at 3:44 PM, Kshatresh Dutta Dubey <kshatresh.gmail.com>
wrote:
> Dear Users,
>
> I have MD trajectories of a protein-ligand complex. During closer
> inspection of MD movie, I found that the rotation of one of phenyl ring of
> Phe causes ligand dynamics. It is quite obvious in MD movies. However, I am
> unable to show this correlated motion in 2D picture. The calculation of
> Chi2 dihedral clearly shows the rotation of phenyl ring but I have no idea
> to show the dynamics of ligand during MD.
>
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?
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".
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).
The exact cpptraj command you'll need to use will depend on the analysis
you choose to do to define ligand dynamics.
> I will be very thankful if someone can suggest me the appropriate type
> of analysis using cpptraj such that this correlated motion between rotation
> of phenyl ring and ligand dynamics can be pictorially represented.
>
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 01 2015 - 06:30:02 PDT
