Hi! I ran MD Simulations of protein structure through SCHRODINGER software. The protein of interest has a lot of loops. I am getting very high RMSD of protein after simulations. How to solve this problem? Is the high RMSD really due to alot of loops?
I am attaching RMSD images and the image of protein structure.
The different RMSDs are of different pdb structures of same protein.
Hi Alina Rahman ,
Loop regions are usually more dynamic. A protein structure with a lot of loops is expected to have larger RMSD compared to a protein that has less loops (i.e. more secondary structure). So, this isn't necessarily a problem. The important thing to generally check in RMSD plots is whether your curve is stable before the end of the simulation time (X axis). In your case, they do seem to stabilize, which is good.
Although, one of your plots has a Y axis of upto 36 angstroms. You may have to correct the PBC issue in this trajectory and re-plot the RMSD.
Thank you Dheeraj Prakaash for the answer. The thing is I am aiming to do binding free energy calculations for the protein. And according to my supervisor, RMSD greater than 2 Angstrom is not reliable to do binding free energy calculations. Is this really a thing or I can carry on my research with this high RMSD?
Hi Alina Rahman,
To check this, you could exclude the loops from your RMSD calculations, or better yet plot the RMSD of the ligand only (maybe with some key binding site residues).
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