Re: [AMBER] mm-pbsa & extra-point

From: Jason Swails <>
Date: Thu, 5 Mar 2015 20:36:04 -0500

On Thu, Mar 5, 2015 at 7:21 PM, Emilio Angelina <> wrote:

> Hi Jason
> So, if ​extra points do not work with the GB code how do you think i could
> compute the complex DeltaG considering the extra point. There is an easy to
> do that?

You can try deleting the extra point and transferring its charge back to
the heavy atom it was attached to. You could also try using LIE instead of
MM/PBSA (in sander, it's referred to as linear response theory, or LRT).
It should be documented in the manual.

I would recommend reading up on the literature regarding LIE if you are
unfamiliar with it.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 05 2015 - 18:00:02 PST
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