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

From: Matthew Guberman-Pfeffer <>
Date: Thu, 16 Sep 2021 14:56:13 -0400

Thanks, Dr. Case, for the explanation. I'm still a little confused on the
difference between an electrically neutral explicit solvent simulation and
the slightly charged implicit solvent result. Is the difference because
some charges in the explicit solvent are not confined to the surface of the


On Thu, Sep 16, 2021 at 8:19 AM David A Case <> wrote:

> *Message sent from a system outside of UConn.*
> 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
> charges.
> 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.
> ...dac
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Received on Thu Sep 16 2021 - 12:00:02 PDT
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