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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>
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Received on Tue Nov 03 2015 - 03:00:05 PST
