I run the simulation through NAMD and analyzed it by using VMD. I have chose the best position of protein-ligand docking. However, the RMSD graph of wild-type is higher compared to mutant. Is it normal or abnormal?
It can occur, if the mutant is more stable than the wild type. But, it would be more interesting to know the stability of the residue/residues which is/are being mutated.
Try to make an index file of the residues of interest and see the RMSD values compared to the wild type.
Also, the RMSF and free energy calculations can be helpful for a meaningful understanding of the effect of mutations after MD.
It is not uncommon, you just need to understand the effect of the mutation. As suggested by Tanuj, I would check the RMSF and compare the residues/domains to understand this effect.
Article Understanding the role of R266K mutation in cystathionine β-...
As Tanuj Sharma and Lorenzo Briganti suggested, Understand the mutation effect in your protein.
Please look into the article. you check the neighboring residues in the mutated site. Analyze your dynamics using cross-correlation or network analysis find the mutant side and check which residue have high correlation with your mutation.
Hope it will help.
If you are doing MDS on a ligand-receptor complex, of which one complex is from wild-type and one from the mutant, this is normal. The RMSD tend to be higher in the wild type due to the stable binding of ligand, which might led to more conformational changes in the receptor. However, if the ligand has lower affinity to the mutant receptor, so it is expected it induce lower RMSD or conformational changes.
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