Dear Amber Community,
I would like to calculate unfolding enthalpy change (ΔHunf) for a protein of interest. I am trying to calculate unfolding free energies for a wt protein wrt some mutants. Specifically, I am trying to replicate the methodology described in the [paper](
https://doi.org/10.1021/acs.jcim.9b00430).In this paper, the authors calculate the unfolding enthalpy change as the difference between the absolute enthalpies of the unfolded ensemble (⟨Hu⟩) and the folded state (⟨Hf⟩). They derive these absolute enthalpies by averaging the enthalpies obtained from individual replicas of each state, with each replica's enthalpy being an average of 1000 frames extracted from 2 ns productive trajectories.
I am looking for help on how to perform similar calculations in Amber. Specifically, how do you calculate absolute enthalpy values from the MD trajectories for every frame?
Thank you in advance for your assistance.
Best regards,
Aravind Ravichandran,
Graduate Student,
National Center for Biological Science, India
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Received on Wed Jul 24 2024 - 00:30:02 PDT
