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I performed a molecular docking and when I tried to validate it, the RMSD values are over $3 \overset{\circ}{\mathrm{A}}$. I don't understand how I can fix it. Could someone help me? Thanks in advance.

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You cannot "fix" it.

As a RMSD value is considered good below $2 \overset{\circ}{\mathrm{A}}$, you can try one of this two methods to obtain better RMSD:

  • Repeat the docking calculation several times. In general, docking software start the search from a generated conformer population. If you run it several times, this initial population will be different, so, the starting point will be different producing different results.
  • Change your docking software. Some times the score function of the docking software was tailored from a family of protein. Using a protein from different family can return bad results.
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