I would like to calculate the free energy using MMPBSA in different segments of the trajectory. These segments correspond, mostly, to the dominant conformers. Considering that these segments include several frames of other conformers, is it correct to perform an average or if a weighted average should be performed?
i would calculate the free energies with and without the minor conformer and compare the values.
Hello Luis,
This methodology is applicable for binding free energy calculations. In this case, I suggest you calculate the free energy using convergent points of the protein conformation. Use PCA analysis and RMSD plot (plateau region) to select the most stable intervals of the trajectory. I suggest you select at least three converging points to calculate the binding free energy (the mean and standard deviation). This methodology is applied in this article:
Best wishes,
10.1021/acsomega.9b03157
Martin Klvana and Kauê Santana thanks for your answers, I'll read the paper.
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