Dear Gabriela de Lima Menezes

your question is not clear......

You do not specify that the protein is complex or in the form ApoProtein........

And that you did not specify that you have modeled the mutated protein or downloaded from the RCSB....(These two modes give different results)

To compare the structure of the two proteins using the gromacs software, you must use the parameters included RMSD,RMSF,Hbond,Rg,Phi,Psi,angle, distance and ...in the general state.(in .xvg format)

But for further investigation, it is better to compare the region that makes the mutation in terms of the type of bond formed....

If you have questions, ask

Best wish

Milad Bagheri Dear, you can create separate rmsd.xvg files, and after comparing these ::: xmgrace rmsd.xvg rmsd1.xvg ::: commands in the same way, you can consider one or two :: color-wise, black color trajectory shows the first rmsd and red shows the second rmsd, maybe you have got my point. Thanks!!!

Mohd. Babu Khan thanks for your reply! yeah.. I know how to compare two RMSD graphics (angstroms vs time), my problem is about RMSD frame vs frame.. I’ve attached two PDF files.. they are RMSD matrix (frame vs frame). I would like to compare them. It seems mutant is more stable. Is this not a good approach to compare? Thank you!

Hey Milad Bagheri thanks for your reply!

I’ve attached two pdf files. They are RMSD matrix (frame vs frame). I’d like to “extract” some information about them. For me, it seems mutant is more stable. I’ve done many other analysis and I know mutant has greater instability. Is this not a good approach to compare? Do you know if I can set RMSD threshold (change color scale) so I could choose the same for both proteins? Thanks!

Gabriela de Lima Menezes, Madam, your analysis on Mutant shows greater instability depending on rmsd value. The value of rmsd relative to the Wild type is larger. Maybe I do not have much idea about it. Please review some books on this topic. Good luck. Thank you for your interest!!!

Dear Gabriela de Lima Menezes i should mention it will be better which insert RMSD values of both protein (WT and MT) in microsoft excel and make plot ..Like the attached image.....In this case, you can compare two proteins more easily..For me RMSD matrix is not suitable for compare two protein...

Then you have to interpret why the wild protein curve is more stable than the mutated protein curve....To do this, you need to consider two aspects

1-

In addition to analysis RMSD , use the van der waals and Coulombic force assays to show that wild protein is more structurally stable than the mutated protein.Of course, you have to pay attention to other structural points. This is just an example...For another example, consider the RMSF chart and examine the protein loops ...

2-

Usually in a protein, a number of amino acids are vital ...( You can check this through the protein PDB article ...)The presence of these amino acids is essential for protein function...There are also a number of amino acids that play the role of stability in the protein structure. For example, the presence of two aromatic amino acids against each other in core of protein ....(You should identify these important amino acids and important bonds and discuss about them) So I suggest that you check your protein WT in terms of physicochemical properties...(Adding details that are based on the knowledge base will increase the credibility of the project)

If you have questions, ask

Best wish

Milad

Hey, Milad Bagheri thank you so much!!! You're so kind!

Your answer was very helpful. Now, I agree with you.. Indeed, RMSD matrix for compare two proteins is not a good approach. It would be better If I could set up a max RMSD at the scale. As you can see, RMSD scale is different so it makes comparison complicated.. But this is GROMACS default.

Thank you again!

Best regards,

Gabriela

You cant compare two proteins stability based on RMSD. Sometimes the fluctuations or changes lead to better/higher activity of the protein.