Re: [AMBER] Non-integer pbsa surface charge?

From: David A Case <>
Date: Thu, 16 Sep 2021 08:18:51 -0400

On Thu, Sep 16, 2021, Matthew Guberman-Pfeffer wrote:
>I noticed that the surface charge I obtain with he pbsa module is, for
>example, 28.5572e. Is the deviation from 29e, which is what I expect
>an issue with numerical accuracy settings, or is there something more
>fundamental at work that I don’t know.
>The molecular system I gave to PBSA is just the protein (explicit water and
>ions stripped off) and has a net charge of -29e.

This is exactly what you should expect. For a finite exterior dielectric,
the induced surface charges do not fully screen the molecular charge.
The result is that a test charge outside the molecule would still feel a
(screened) electrostatic interaction with the molecule plus its surface

The amount by which the surface charge differ from the molecule charge is a
factor of (1 - 1/epsilon), where epsilon is the exterior dieletric. This
matches you result pretty closely.


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Received on Thu Sep 16 2021 - 05:30:02 PDT
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