AMBER Archive (2006)

Subject: Re: AMBER: error propagation in MM-PBSA binding free energy calculation

From: Jianyin Shao (
Date: Wed Apr 26 2006 - 19:13:48 CDT

I am pretty sure that the output STD means standard deviation because I just
read the code.
And I think the standard error of the mean should be STD/SQRT(N), not what
you stated.

Just my 2 cents.


On 4/25/06, lhsong <> wrote:
> Dear Amber user,
> In the output of MM-PBSA calculations, the STD should be the "standard
> deviation" or "standard error of the mean energies"? Since I found it is
> quite confusing in the error report of free energy components in the
> literation.
> As I understand, the STD is the standard deviation, and the standard error
> of the mean value (SE) reported in, for example, Dr. Gohlke's paper (
> J.Comput. Chem, 2004, 25,238) is obtained by SE=SQRT(STD/N), n is the
> number of snapshots. The errors propagated to the binding free
> energies should be: SE = SQRT (SE*SEcom + SE*SElig +SE*SErec).
> Apparently, the standard errors for the calculated binding free energies
> is highly related with the data set N. When using a typical data set of
> 100-200 snapshots, I found the propagated standard errors of the binding
> free energies are usually up to 7-10 kcal/mol, comparable to the calculated
> binding free energy itselt. Is it sound? Also I note that most of published
> binding free energy calculations did not report the error at all.
> Does someone give me a suggestion on the error calculation for the binding
> free energies of protein-protein interaction (or a reason not to report)?
> Thank you for your help
> Lihong

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