It doesn't show the RMSD graphic with the protein-ligand

[Eliel83]

It doesn't show the RMSD graphic with the protein-ligand

[pablo-arantes]

Hi @Eliel83,

Sorry for my delay. You can try to use pytraj to perform RMSD of the ligand and plot with the protein RMSD with matplotlib.
You can use the same cell we are using in Making it Rain. Just need to include the ligand RMSD calculation and plot.
Here, you can find more information regarding how to calculate the RMSD with pytraj: https://amber-md.github.io/pytraj/latest/analysis.html#pytraj.rmsd

I hope it helps.

Best,

Pablo

[Eliel83]

Good night Thank you, I ran the complex but it doesn't show the graphic Thank you in advance El mar., 7 de noviembre de 2023 23:03, Pablo Ricardo Arantes < ***@***.***> escribió:

…

Hi @Eliel83 <https://github.com/Eliel83>, Sorry for my delay. You can try to use pytraj to perform RMSD of the ligand and plot with the protein RMSD with matplotlib. You can use the same cell we are using in Making it Rain. Just need to include the ligand RMSD calculation and plot. Here, you can find more information regarding how to calculate the RMSD with pytraj: https://amber-md.github.io/pytraj/latest/analysis.html#pytraj.rmsd I hope it helps. Best, Pablo — Reply to this email directly, view it on GitHub <#83 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BDNCCUMZR62H5LZXZMF3VB3YDMHC5AVCNFSM6AAAAAA6IFPKQKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBRGA4TANJRG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>