AMBER Archive (2006)Subject: Re: AMBER: error propagation in MMPBSA binding free energy calculation
From: lhsong (lsong_at_mail.rockefeller.edu)
Date: Fri Apr 28 2006  17:37:42 CDT
Hi Juanyin,
Thank you. it is a typo with the formulation of standard error of the mean in my previous email. I wonder how the standard deviation was calculated for some addition terms such as Ggas=Gele+Gint+Gvdw using the error propagation rule? I checked with some results from MMPBSA, the SD values for Ggas, Gsol, Gtotal seem not calculated from the propagation rule. In addition, the SEtotal for the binding free energies Gtotal, which obtained from SQRT (SE*SEsubtotal + SE*SEentropy), usually up to ~10kcal/mol, is it sound?
Thanks for your help.
Lihong
 Original Message 
From: Jianyin Shao
To: amber_at_scripps.edu
Sent: Wednesday, April 26, 2006 9:43 PM
Subject: Re: AMBER: error propagation in MMPBSA binding free energy calculation
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.
Jianyin
On 4/25/06, lhsong <lsong_at_mail.rockefeller.edu> wrote:
Dear Amber user,
In the output of MMPBSA 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 100200 snapshots, I found the propagated standard errors of the binding free energies are usually up to 710 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 proteinprotein interaction (or a reason not to report)?
Thank you for your help
Lihong

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