Okay for what?

@Martin Klvana For knowning the stability of ligand in the pocket. As I was reading many answer and paper where they suggested that the RMSD need to be between 1-2 Angstrom for ligand. So, my is not between 1-2 Angstrom than what to do?

Is it ok to have it or needed to be done something.

Dear Shradheya R.R. Gupta,

I would say that is not about what it should be but rather what is it that you looking for? If your ligand is known to stabilize your protein, then you should expect a lower RMSD. Nevertheless, remember that RMSD only shows the variation the protein undertook taking into consideration its initial state. RMSD alone will not answer you if your ligand destabilized the protein, or negatively affected its overall structure. Thus, it's not about how many Angstroms it should be, but more about "what is the role of my ligand, and what should I expect?".

Cheers.

Thank you sir for clarification. It helped.

Let say I docked a ligand to a protein, and a protein-ligand complex was formed. Then, MD Simulation was done on that protein-ligand complex. RMSD graph was generated as what Shradheya R.R. Gupta attached, which fluctuate about 3 Angstrom. Does it meant that the binding pose obtained from docking is not preserved in MD simulation, since the RMSD is quite high?

I appreciate your help ! :)

Dear Keong Zheng Ng

If your RMSD was done taking into consideration Protein+Ligand, a 3A fluctuation might indicate something. However, RMSD alone will not answer that. RMSD is a simple measure, performed only to see how much your molecule variate from your initial state. It does not necessarily indicate destabilization.

If you really want to see if your ligand is complexed to your protein, I advise measuring the distance between the amino acids that coordinates the binding and your ligand. If they are within your expected distance, then your RMSD is not implying unsuccessful docking, its something else.

If you don`t have previous information indicating the expected distance, I can say that, usually, a complex formed by protein+small molecule ligand is between 1A-4A.

I hope it helps. Cheers!

@Zhaoxi Sun thank you for your explanation. Can you explain more on how secondary structure consideration, RMSF and other calculations are useful in protein ligand simulations.

Zhaoxi Sun , is it possible to obtain 'statistically meaningful data' from molecular dynamics simulations?

i would rather run many short (few nanoseconds) MD simulations than one long (microseconds, milliseconds, seconds . . .).

What if the RMSD value for protein and peptide complex is more around 10A. what does that indicate?

Pooja Dhurjad RMSD is calculated to understand your protein's stability and how it differs when complex with a ligand. You can visualize the binding pocket by dumping at 100 ns and see how it affects the secondary structure of your protein. If your ligand stabilizes your protein, the RMSD value of the complex will be lower than your apo protein. Not just focus on the range of values you are getting but compare to the initial structure what conformational changes obtained.