Hello. I am working on some free energy calculations for a protein-protein interaction. I decided to try and reproduce the delta G for the well-studied barnase-barstar interaction before I work with a novel system. I am running the FE calculations on the barnase-barstar complex, and the barnase protein by itself using the g53a6 ff, and explicit solvent. I was having an issue with the barnase protein unfolding in both of the simulations, so I turned on the couple-intramol setting, and reran the simulations. I am a bit unsure about what I need to do in order to complete the cycle. Is a vacuum simulation required here? If so, any guidance on the appropriate settings would be appreciated. Thanks.
Elio Cino
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