I performed a dynamic simulation of an aptamer-protein complex, Is it better to calculate RMSD value for the protein, the aptamer, or the complex?

16 February 2024 1 6K Report

I performed a dynamic simulation of an aptamer-protein complex using the Namd software, and I want to the calculate the RMSD value using vmd

Ayaz Anwar

All three, so you can compare the differences in complex RMSD are due to either protein only or aptamer only or both.

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