On Mon, Apr 10, 2017, Mary Varughese wrote:
>
> In this paper where binding free energies are calculated using MMPBSA
> method : "Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1
> RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of
> Efavirenz by Docking and MM-PBSA. *J. Am. Chem. Soc. **2001, **123, *5221-5230
> 5221" there is a statement "
>
> Considering the root-mean-square deviation of entropy is relatively small
> for different conformations, only 20 snapshots (every fifth snapshot of the
> 100 collected snapshots) were used to estimate the contribution of the
> entropies of association." What does it mean by root-mean-square deviation
> of entropy in this case?
This refers to the variation of entropy estimates among the 20 snapshots
analyzed. The quantity referred to is the root-mean-square deviation from
the average over the twenty snapshots.
Generally, for folded systems with small conformational changes, estimates
of the configurational entropy don't change very much from one snapshot to the
next, so it is often possible to evalute this number less often than is needed
for the molecular mechanics energies, which fluctuate more widely from one
configuration to the next.
...hope this helps...dac
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Received on Mon Apr 10 2017 - 05:30:04 PDT
