dear all
I have tried to run MD using namd and visualization with vmd. for practicing, I run 1 ns of simulation and I got rmsd result as well as rmsf for the protein and complex. from the result that I got, can I conclude that the attachment of ligand gives some conformational change to the protein as the rmsd value decreases? and after I calculate the RMSF value, seems that complex increases the RMSF value. To see the flexibility of protein which value I should consider? RMSF or RMSD?
Hello,
RMSF calculates deviation between the position of Residues. So you can compare the flexibilities of parts of the proteins
Comparison between two proteins can be made by taking other measures in to account like radius of gyration, RMSD.
thank you very much for your answer, really appreciate it. does ligand attachment to protein, usually increase the RMSF value of protein? can I say the RMSF value indicates the flexibility of each amino acid rsidue?
Generally (at least from what I saw until now) a protein tends to stabilize with the ligand. So, you'll see a lower RMSD for the complex than for Apo system. The RMSF, specially in the residues within active site, can increase in the complex, since there will be other interactions than the Apo system. The RMSD and RMSF are very important in such studies. As Rezvan Marjani stated, with the RMSF you can compare flexibilities of some parts of the protein, but if you really want to talk about flexibility, you need more simulation time.
Best,
Lorenzo
- Badges
- Science topic
- Similar topics
- Filing