Entering edit mode
7 weeks ago
Sky
•
0
Hello everyone, I have a question regarding RMSD value. I have made a graph of ligand and backbone protein but the RMSD value of my compound is above the value of the backbone protein (Black: ligand, Red: Backbone protein). I would like to know if the protein is considered stable or not. I am new to bioinformatics I am confused about the results as in the research papers I have seen RMSD values usually under the backbone protein or Apo protein. But my ligand-complex graph is above the backbone. Please help me regarding this. I have also attached image (Black: ligand, Red: Backbone protein). Thank you in advance.
As per this graph, the protein (red) is very stable,while the ligand seems not so stable.
If the black line represent the ligand only, then you should dig deeper, and see what is wrong? And if the black line represent the complex (protein+ligand), then I think you added the whole protein including H-atoms and ligand. Just create a new group that contains backbond or Ca atoms from protein and ligand atoms and recalculate the RMSD.
It is often a good thing to extract the trajectory in PDB and visually inspect the coordinates. This will give you an idea whether your simulation is stable or not.