Re: [AMBER] Entropy can be neglecected under which condition

From: Marc Zhang <marczhang_md.zoho.com>
Date: Tue, 3 Nov 2015 14:35:54 +0100

Dear Carlos

Thank you very much for your explanation.

I will look into some well-cited papers and check their approaches.

Cheers

-----Original Message-----
From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
Sent: 2015113 11:50
To: AMBER Mailing List
Subject: Re: [AMBER] Entropy can be neglecected under which condition

there really is no broad answer such as "yes entropy is not important for
this situation". neglecting entropy is always an approximation. yes, it is a
better approximation for relative affinities than it would be for absolute
affinities, but you still lose accuracy. whether it is ok to neglect entropy
for relative affinities depends on how similar the ligands are (congeneric
series is better, different scaffolds is worse), and how accurate you need
your results to be.

On Tue, Nov 3, 2015 at 4:05 AM, Marc Zhang <marczhang_md.zoho.com> wrote:

> Dear amber users group
>
>
>
> I would like to know the entropic term can be neglected under which
> conditions during MMPBSA calculation?
>
>
>
> Can I neglect the term when calculating the binding free energies of
> different ligands to the same protein?
>
>
>
> Thanks a lot for your help!
>
>
>
> Cheers
>
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Received on Tue Nov 03 2015 - 06:00:02 PST
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