Re: [AMBER] How to print out implicit solvent charges?

From: David A Case <>
Date: Mon, 6 Sep 2021 08:52:51 -0400

On Mon, Sep 06, 2021, Matthew Guberman-Pfeffer wrote:

>Thanks for the quick reply. Isn’t the implicit solvent evaluated at
>specific points in space? I was thinking of the xyz associated with those
>grid or cavity points at which the implicit solvent is evaluated, and the
>charges at those points. Or, are the implicit solvent models different in
>implementation than the picture I have from apparent surface charge or
>polarizable continuum models in QM calculations?

The standard GB models in Amber don't lead themselves to being changed into a
point-charge distribution. The gbnsr6 model (see Chapter 5 in the Amber
2021 Reference Manual) can probably to made to do this, but I've never used

The pbsa (Poisson-Bolztmann) program has an "isurfchg" variable that will
generate apparent surface charges. This doesn't seem(?) to be in the
Reference manual, but you could try to set it to 1 in the &pb namelist and

The afnmr package ( has a similar
functionality: it prepares inputs for a variety of quantum chemistry
packages (Gaussian, ORCA, Jaguar, QChem, deMon,...) that will illustrate how
the surface charges are used, although it sounds like you probably already
know that. This uses the MEAD Poisson-Boltzmann package, which is included.

For RISM, you can get the solvent charges on the Cartesian grid, which could
be put into a quantum program. It would probably be better to first convert
these to apparent surface charges. Let me know if you want to go this way:
I have some old code (somewhere) that did this, and it might be worthwhile
to resurrect it.

Like Carlos, I'm not sure that this answers your question, but I hope it

...good luck....dac

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Received on Mon Sep 06 2021 - 06:00:03 PDT
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