Hi, sorry but i dont think i understand your question/doubt...you mean why there is fluctuation in Ca? can you attach some rmsf-profile?

Usually the protein structure retrieved from PDB are not a complete one, this is especially true for the one determined with X-ray crystallography. Because the fluctuative nature (or highly disordered) of the N-terminal and C-terminal making it unable to be determined. You might want to check the PDB file you retrieved from PDB and open it with text editor and see the annotation part to ensure the number of amino acid inside the crystal structure.

Hope that help,

Radif

Dear Mr. Radifar

I have  checked pdb structure of protein before and after the simulation, there is no problem with them. In addition, as I mentioned before the other groups like atoms are correct. However I appreciate your advice.

Dear Diego

I'm using Gromacs software for protein in water simulation. RMSF calculation is necessary for the stability analysis. This program allow me to select a group for the calculation like backbones, atoms and etc . C-alpha has been explained as the best choice for investigation of residue fluctuation but this group content unexpectedly doesn't match the amino acid sequence of protein and I don't know why?

Ah right, I miss that one. Have you checked and count the C alpha atom in the PDB file? If it is possible could you upload the PDB file that is being used as input file for MD simulation?

Dear Muhammad

I counted CA elements which refers to c-alpha in pdb(input).  There was 667 c-alpha. So it means thatI have had misunderstanding about carbon alpha. It refers to both backbone and side chain atoms. Know I can find my amino acid sequence between them. That's enough for me but there is another question. How can I investigate Gly resides fluctuation while they are not considered in c-alpha group?

Thanks for your helpful advice

Ok, I get the point. First, in my opinion  the RMSD of Calpha not necessarily reflects the dynamic of side-chains, what you get is an estimation of backbone mobility, which usually is low if your protein is well behaved. It will consider all residues.

In the case you want to study study side-chains dynamic I prefer an mass-weighted RMSF calculation. In this case the gly residues, of course, has no mobility.

Interesting, it is a common sense that the number of CA should reflect the number of protein residue. May I know why did you suspect the glycine is the one not carrying the CA? Because I think it would be impossible that any residue didn't carry CA. Have you really done some manual inspection to the PDB file? And check if there really is any CA missing from any glycine residue.

And just to be sure, I would like to know, have you checked the number of the first residue? It is the 6th column, right after the chain column. Like in this picture:

I checked it again. I found some missing residue in pdb file! so that's my problem.

You were right all residues contain CA group although I didn't expect that because there is no chiral carbon in Gly!!!

Thanks for all help and support

You're welcome :)

I found it incredible that my first answer is downvoted by someone when it is actually the right answer LOL