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

From: Matthew Guberman-Pfeffer <>
Date: Wed, 8 Sep 2021 13:59:34 -0400

Thank you so much, David, and Carlos, for your very helpful replies.
David, I really appreciated all the options you mentioned for me to explore.
The isurfchg keyword for PBSA seems to give me exactly what I wanted— an xyzq formatted file that I can use in a QM package to represent the solvent.
I’m trying to compare how explicit/implicit representations impact the energetics of cofactors.


> On Sep 6, 2021, at 8:52 AM, David A Case <> wrote:
> *Message sent from a system outside of UConn.*
> 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
> that.
> 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
> experiment.
> The afnmr package (;data=04%7C01%7C%7Cc8fe11d7f0334d8f9ec108d9713556dd%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637665296182054405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=rDOQir7%2B74kdy6FEHT2HyETV9J98zuIE9MpcAQEnswo%3D&amp;reserved=0) 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
> helps.
> ...good luck....dac
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Received on Wed Sep 08 2021 - 11:30:02 PDT
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