Hi Colvin,
I was waiting for others comments. If you are planning to calculate the
absolute free energy relative to experimental data then you should have
entropy term (deltaG(free energy)= deltaH(enthalpy)-TdeltaS). However, if
you are planning to compare the relative binding free energy of two or more
similar complexes then you may omit entropy contributions.
Hope it will help.
Regards
Kshatresh
On Tue, Jan 22, 2013 at 1:50 PM, colvin <colvin4367.gmail.com> wrote:
> Dear all,
>
> I use mmpbsa.py to calculate the free energy binding using a set of
> 120 snapshots and the Delta total = -14.5391 (using GB, no entropy).
>
> Later on, i turn on entropy=1 on the same system, and the result
> showed that: Using Quasi-Harmonic entropy approximation: Delta G
> binding = 32.7203 (Delta S total = -47.2595).
>
> The Delta G binding changed from negative to positive value if the
> entropy is included. From the tutorial, I understand that the entropy
> contributions can be excluded and most of the papers also do not
> included the entropy contribution, but some did, and the results do
> not show such a huge difference like what i have here.
>
> I hope to get some explanations here and pls advise.
>
> Thanks and regards,
> Colvin
>
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Received on Tue Jan 22 2013 - 02:30:03 PST
