[gmx-users] charting Ligand's movement in the binding pocket

[Prasanth G, Research Scholar]

Dear All,

I am interested in charting the trajectory of the ligand with respect to
the residues of the binding pocket, during the simulation.
May be representing the center of mass of the ligand as a dot at each
frame, would help us see the path traced by the ligand in the pocket,
during the simulation. Is there a possibility to do this during the
trajectory analysis period / post production..?
I was wondering if we could perform PCA and impose the ligand's trajectory
on the bound complex and visualize only the ligand's movement with respect
to the amino acid residues of the binding pocket. But this would not give a
clear idea as the residues in binding pocket also move during the course of
simulation.
Hoping that i was able to explain it well enough..
Thank you in advance.

-- 
Regards,
Prasanth.