AMBER Archive (2006)

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

From: lhsong (
Date: Tue Apr 25 2006 - 22:22:41 CDT

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


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