Hello everyone. I have completed MD simulation for a macromolecule with 130 residues. after completion of the process, I found most of the residues of protein remain below 2.4 A. so can I say that most of my protein residues are stable within the simulation. here I attached the figure of my protein rmsf with ligand contacts. can anybody help me to interpret the results
Hi Rohit Pritam Das
I have seen your RMSF result most probability the residues of protein less fluctuate throughout simulation and formed many hydrogen bond with ligands so ligand quite stable with protein.
RMSF of the given picture indicate that the RMSF of your protein amino acids are not so high. If, it is the RMSF of protein-ligand complex, ligand is stable in the protein cavity.
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