On Thu, Feb 19, 2015, Maryam Hamzehee wrote:
> I did MD simulation for my ligand-protein complex in solvated form. I
> would like to do rmsd for my ligand during MD simulation and see the
> conformational changes of my ligand throughout the simulation. How can
> I do this?
See the "mask" argument to the rmsd command in cpptraj. If you specify that
to be the ligand atoms, you will generate a plot of ligand rms vs. time.
> Is it possible to extract the trajectory of the ligand from
> the main trajectory.
See the "strip" command in cpptraj.
....dac
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Received on Thu Feb 19 2015 - 05:00:02 PST
