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

From: Niel Henriksen <shireham.gmail.com>
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.
https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00275

There are a number of different implementations of APR out there ... this
is one I've contributed to:
https://github.com/slochower/pAPRika

Best,
--Niel


On Thu, Jul 9, 2020 at 12:40 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> 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
> https://ambermd.org/tutorials/advanced/tutorial29/index.html
> Thanks everyone
> Regards
>
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>
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Received on Thu Jul 09 2020 - 17:00:03 PDT