Hello,
I didn't get a response to this question before, so here I go again: I have a protein that has a residue modeled as a 2-state rotamer in the crystal structure. The transition occurs in ms, so I cannot see it in the MD simulations. I'd like to calculate the free energy difference between both states, possibly using the perturbation method. But I am not sure how to do this, as examples are usually done for mutations and hydration. Has anyone an idea of how to do this? So far I have thought of changing the dihedral of the side chain in the top file (which goes from avge -90 to 90), but I am thinking that maybe there are other things that I need to account for. Any ideas …?
Thanks!!
Esther Caballero-Manrique
Graduate Teaching Fellow
Chemistry Department
1253 University of Oregon
Eugene, OR 97403-1253
(541) 346-2485
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