Hi Citra!, as far as i understand theoretically, RMSD in MD simulation gives a notion about the stability of both protein and ligand. RMSD value

Hi Citra Hasanah ,

I agree with Prasenjit Bhowmik answer and just to add to that,

you may way to run MD simulation just for your protein to check its behaviour without any ligand.

From there you can check its RMSD and compare accordingly.

It is also helpful if you are able to find any research article reporting on the same protein.

Your protein conformation is affected by the ligand binding. Therefore, you cannot expect RMSD to be small. Rather, you have a 'simulation result' that the ligand binding affects the conformation of the protein !!

Hi I agree with all i.e. the 7EAU coordinates you took were without being in complex with the ligand accordingly 7EAU may structurally change that much, I would research 7EAU in complex in the PDB with other ligands (if available) and superimpose this with your complex and also re-simulate 🚀

Thank you everyone for answering my question and explaining it!

Dear Prasenjit Bhowmik, May I know how to check the binding site? What should I take attention for? I confuse because this protein is only have 50 residue so it probably only have 1 binding site.

Dear Nor Farrah Wahidah Ridzwan and Joel Subach, I also have already tried to run a simulation for my protein but with the original small molecules that already attached on the molecule from PDB bank (PDB ID:7EAU). But i have a lot of problem in doing the simulation (like the Cgenff server cannot recognize the ligand (?), and i also tried using CHARMM-GUI, and still get a very high RMSD, means that its still structurally change that much. So if i want to check the behaviour of this protein, i need to grep the small molecule from the protein first?

Dear Kolattukudy P. Santo , thank you for mentioned it! but what i confuse is i have simulate a docking simulation of this protein and ligand before, and all the docking result shows negative binding affinity so i assume the complex should be stable and not change that much.

Thank you once again!

Hi Citra thank you for your kind update:), maybe you can try to dock your ligand to your protein via Medusadock and the proceed to Gromacs Tutorial 5 Protein-Ligand Complex. My understanding is that 7EAU is without your ligand in complex and Medusadock seems to be an accurate simple easy tool (or try Flex-LZerD for ≥10.0 Å RMSD ) if you need help with Medusa or Gromacs Tutorial 5 ask me:). i.e. dock your ligand and then proceed to simulate the complex via Gromacs this should function since my understanding is that there are no other ligands in complex with 7EAU in the PDB accordingly discover this. And if you have used this methodology please explain to me more in detail about the Cgenff problem, thanks and Good Luck 🚀

Hi, Citra Hasanah ! I am happy if my answer has helped you.

And for your second question, one thing is not clear to me. I previously assumed you have performed docking before dynamic simulation, didn't you? If you have done it then i am assuming you have already checked where the ligand (PCA) is bound. So, just check that domain/pocket and read some relevant articles.

You can also check in NCBI (https://www.ncbi.nlm.nih.gov/protein/2127820562) and look at those important bonds in the structure. As i can see three disulfide bonds are present in the structure.

As mush as i understand If the ligands you used binds to the same spot as PCA, then there should not be any structural issues.

Hi, Prasenjit Bhowmik . Yes, i did docking simulation before, and i used binds to the same spot as PCA. Thank you, i will check it!

Hi, Joel Subach. Apperciated it thank you so much for your help!

So i tried to run MD simulation of 7EAU with its original ligand, which is PCA. I followed the GROMACS Tutorial 5: Protein Ligand Complex. When i uploaded my pca_fix.mol2 to CGenFF, they cannot generate the .str output and i got this error message:

readmol2 warning: non-unique atoms were renamed.

Now processing molecule PCA1 ...

attype warning: peroxide not explicitly supported

attype warning: oxygen double bound to unexpected element not explicitly supported

attype warning: peroxide not explicitly supported

attype warning: formaldehyde not supported;

skipped molecule.

Do you know how to solve this?

Anyway, may i know what is the differences between Medusadock and Autodock vina? I haven't tried using Medusadock before, will i get a different docking result? Thank you so much

Hi Citra your welcome and thank you for your kind update:).

1. For your exhibited errors via CGenFF try emailing both below:

[email protected] and [email protected] (Abhishek) at CGenFF.

Abhishek assisted me via my penalty issue, he will probably help you,

I have no idea how to resolve your errors.

2. MedusaDock I believe is similar, like all of these softwares, but much much easier to work through towards results, if you need hep with Medusa feel free to ask. (If you use both dockers please for enrichment let me know if your results differ, I am guessing they will be similar.)

I am similarly investigating an unknown ligand binding to a protein within PDB hence my suggested methodology i.e. dock it then Gromacs Tutorial 5 it then perform your mutational analysis and or Umbrella Sampling etc. (not sure what results your searching for).

Thanks:)

Joel 🚀