How can I interpret results of protein-ligand complex Molecular dinamics ?

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MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

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fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

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Waseem Ahmad Ansari

Andrés Reyes Chaparro

I saw your complex result of simulation it is very stable and RMSD of both protein and ligand less than 2A. You can evaluate your data by some articles.

Article A dynamic simulation study of FDA drug from zinc database ag...

https://www.nature.com/articles/s41598-020-74468-0

Conrad Veranso Simoben

Based on the figure above, the rmsd shows that your system/complex is stable.

However, if you should generate that figure with the first frame during/from MD and not the input coordinates, i think you will get an even better and more satisfying figure.