Kindly help me interpreting the graph. I am not sure if the ligand is still intact with protein or it has diffused away.
What's the scale of the y-axis? Anyway, the plot tells you that something's going on around 15 ns. The next step is to visualize the trajectory . . . and ask yourself the same question you are asking here. Do some measurements (distances, angles), define some cut-offs, . . .
What's the scale of the y-axis? Anyway, the plot tells you that something's going on around 15 ns. The next step is to visualize the trajectory . . . and ask yourself the same question you are asking here. Do some measurements (distances, angles), define some cut-offs, . . .
RMSD calculations do not provide any kind of information regarding diffusion of molecules. At most, it will only provide structural information of your ligand or protein while it diffuses.
A good way to check for diffusion is simply watch your trajectory. If you want to quantitative information, define residues of the binding site and calculate separately the distance between them and a given atom of your ligand. Increasing distances suggests diffusion.
Visualization of the trajectory should answer your question. The RMSD plot you provided doesn't change much. Also, a 20ns simulation for a protein-ligand complex doesn't tell you much.
If you are using Schrodinger suite, you can try mm-gbsa in Prime module to quantify the binding affinity at different frames.
Hope this helps.
To know the retention time of ligand in binding cavity or ligand unbinding kinetics, you have to visualize your generated trajectories from MD Simulation in Maestro
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