On Tue, Oct 20, 2015 at 6:01 AM, MarcZhang <progress0935zhang.gmail.com>
wrote:
> Hi Jason
>
>
>
> Thanks a lot for your suggestions!
>
>
>
> I re-ran the calculation by adding inp=1, radiopt=0 into the PB section.
>
>
>
> The results showed that DELTA TOTAL (-90.8091) of the Differences (Complex
> -
> Receptor - Ligand) is much closer to the value (-86.3579) given in tutorial
> 3.1.
>
>
>
> However, TOTAL energy values of Complex, Receptor, and Ligand is still
> greatly deviated from the ones in the tutorial.
>
Define "greatly deviated". 10 kcal/mol? More? Less?
> Did I miss something in my calculations? What are the causes of this
> deviation?
>
I'm really not entirely sure. I suspect different default settings in the
PB solver, but it's been a very long time since I've generated the results
for that tutorial (I should probably update it). One thing to keep in mind
is that only energy differences matter in MM calculations, though, so the
fact that the results are much closer is encouraging.
Also, look at *where* the differences are. Is it all in the non-polar
solvation part? If so (and I suspect it is), then it's likely caused by
different surface tension defaults between the two versions, which
introduces bigger discrepancies in each system that tend to cancel to a
large degree when taking the difference.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 20 2015 - 07:00:07 PDT
