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i need to understand the options for least-square fit and rmsd calculation, what to choose for each one and when?
i run this code for rmsd
gmx rms -s md.tpr -f md_fit.xtc -o rmsd.xvg -tu ns
for example : if my question is to detect stability of protein-ligand interaction what to choose for isq fit and for rmsd calculation?
also can you please send me publication links about MD simulation for for several compounds against one protein?
i have 22 ligand and one protein
If you’re doing a Protein Ligand Complex MD simulation,
You need to select Protein for the least square fit.
and, for RMSD calculation, select Ligand.
This allows you to evaluate the ligand’s stability within the protein throughout the simulation process.
if Apo protein alone
In that scenario, you need to select backbone for both lsqfit and RMSD.
your another question several compounds against one protein
This seems interesting, but typically people do virtual screening to sort out the best fit against the protein.
then perform an MD simulation for that complex
You can also leverage the CHARMM GUI to do MD preparation for the protein-ligand complex.
For your protein-ligand complex, RMSD provides information about the ligand’s stability within the protein. RMSF represents the fluctuation of individual residues or atoms, and Rg represents the protein’s compactness.
looking into your RMSD. The first thing I wanted to point out is that your RMSD fluctuates too much and does not even fall within the permissible range, making it impossible to consider your ligand is stable.
[A deviation of ≤ 2 Å was considered stable (this value of rmsd is often used as a threshold defining success in prospective docking simulations).]
RMSF seems quite good, but again, it completely depends upon your research question and the region where the ligand is bound within the protein.
gmx rmsf -f md.xtc -s md.tpr -o rmsf.xvg -res
At the end, the -res flag provides information about each and every individual residue instead of atoms. This allows you to gain a more comprehensive understanding of the fluctuations in the residue.
Your protein ligand complex’s Rg (radius of gyration) value, which again defines the compactness of the protein, falls between 1.825 and 1.85. Therefore, one can understand whether the protein undergoes any structural changes upon ligand binding or not.
In your condition, the protein is compact, and there isn’t any significant structural change.
