AMBER Archive (2006)

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

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Mon May 01 2006 - 12:17:04 CDT

Hi, Lihong,

I think the mmpbsa script calculates the standard deviation directly from
the variables, not through the error propagation rules. I guess some
errors will be cancelled out so the standard deviation would be smaller
than what you get from the error propagation rules. (maybe not?) I will just
use standard deviation from the output file, not the error propagation
rules. Hope someone else may help.

Jianyin

On 4/28/06, lhsong <lsong_at_mail.rockefeller.edu> wrote:
>
> 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 MM-PBSA, 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 <jyshao2004_at_gmail.com>
> *To:* amber_at_scripps.edu
> *Sent:* Wednesday, April 26, 2006 9:43 PM
> *Subject:* Re: AMBER: error propagation in MM-PBSA 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 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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