It is known that MM-PBSA overestimates the electrostatic binding energy. For such reasons I don't really expect a rigorous behavior of the method in the case of metalloprotein bounded zinc ion, interacting with a charged amino acid side (inhibitor). In your opinion, should the zinc cluster parameters be included in the estimation of the binding energy, or should it be eliminated from the system as also its corresponded atoms?
In other words, what is the most important: capturing the electrostatic perturbation caused by the presence of zinc, or avoiding introducing errors coming from the poor estimation of ion-ion interaction type?
The question is best answered by what your final goal is. While MM/PBSA does sometime overestimate binding energy, qualitatively you will still be able to learn something if you do your calculations with and without Zn. There will be an error but the error should be be large enough to blur the broader qualitative picture. However the exact values should be taken with a pinch of salt. Also, do use non-linear PB, it is more expensive but performance is much better than linear PB.
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