Thank you Jason for the advice
Emilio
> Date: Thu, 5 Mar 2015 20:36:04 -0500
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] mm-pbsa & extra-point
>
> On Thu, Mar 5, 2015 at 7:21 PM, Emilio Angelina <
> emilioluisangelina.hotmail.com> 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.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Mar 05 2015 - 20:00:02 PST
