Re: [AMBER] Positive value of electrostatic and negative value of EPB

From: David A Case <>
Date: Tue, 17 Aug 2021 07:42:45 -0400

On Mon, Aug 16, 2021, assawin daducale wrote:

>I've just calculate the mmpbsa decomposition of my
>complex. And I got the output file including electrostatic energy EPB
>etc. But I found there are something strange. For example,I found the
>electrostatic value of one of my complex is positive and negative value
>of EPB in the same complex as well. But when I view the interaction
>of ligand-receptor, I found that the ligand is placed in hydrophobic
>region. Shouldn`t it be the reason why electrostatic is positive value and
>EPS is negative? thanks

Energy differences are the only items that can generally be interpreted in
such a way. Individual electrostatic energies are are often dominated by
1-4 interactions that depend on the composition of the protein.

That said, the "vacuum" electrostatic energy is generally largely cancelled
by the Poisson-Boltzmann term, since interactions are being screened. So it
is to be expected that these two terms may have opposite signs.

...good luck...dac

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Received on Tue Aug 17 2021 - 05:00:02 PDT
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