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I hope you are doing well. I would like to ask you something that might be obvious to you, because I am a beginner in this field. After MMPBSA calculations and extract the plot the energetic components (decomposition, DELTA). The simulated molecule (LIG) was in the plot. If is ok, can I put it in my paper? If not how can I create it? Please.
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I am not sure I follow your question... LIG is expected to be in the plot since it is located at the interface. If the value makes sense or no that's a different topic and will depend on the methodology you used and the physicochemical properties of your system