I wrote a rather lengthy expose on MM/PBSA and errors/fluctuations back in
February. In the interest if not repeating myself, I'll simply provide a
link to it:
http://archive.ambermd.org/201202/0317.html
HTH,
Jason
On Fri, Sep 14, 2012 at 4:28 AM, George Tzotzos <gtzotzos.me.com> wrote:
> For a large number of DELTA G binding (Complex - Receptor - Ligand) the
> standard deviation is > 2 when DELTA G is ~30kcal/mol
>
> Translating DELTA G to dissociation constant, a 2kcal/mol difference
> (either way) would mean dissociation constants differing by two orders of
> magnitude from the mean.
>
> To put it in a different way. If DELTA G binding for ligand 1 to receptor
> A is 30kcal/mol and DELTA G binding of ligand 2 to the same receptor is
> 28kcal/mol with a standard deviation of 2, can one infer that the receptor
> has higher binding affinity for ligand 1?
>
> Furthermore, if one factors in DELTA S with SD 2 (or more) interpretation
> of the results becomes much more tenuous.
>
> And last, but not least. I have obtained standard deviations varying
> between 2 and 5 for nmode DELTA S calculations involving different ligands
> with the same receptor but the same number of frame readings. Is this to be
> expected?
>
> Looking forward to receiving any comments on the above,
>
> Regards
>
> George
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 14 2012 - 05:00:03 PDT
