Re: [AMBER] attach pull release method exploration for free energy calculations

From: Niel Henriksen <>
Date: Thu, 9 Jul 2020 16:34:55 -0700

Hi Debarati,

APR can be used for protein/ligand systems, but if the binding site is
buried, it can be a problem. Alchemical methods are probably advisable in
those cases. Germano Heinzelmann successfully used it on a bromodomain.

There are a number of different implementations of APR out there ... this
is one I've contributed to:


On Thu, Jul 9, 2020 at 12:40 PM Debarati DasGupta <> wrote:

> Hi
> Is there anyone in the mailing list who has applied the APR method to
> calculate binding affinities for protein ligand systems.
> I had some doubts and it will be good if someone can chime in. My doubts
> are related to
> Thanks everyone
> Regards
> _______________________________________________
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Received on Thu Jul 09 2020 - 17:00:03 PDT
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