AMBER Archive (2003)

Subject: Re: AMBER: How to estimate SD of the delta delta G between two mm_pbsa runs

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Thu Nov 06 2003 - 01:24:42 CST

Zheng Suxin schrieb:
>
> Dear amber,
> When I use MM_PBSA to calculate the delta G, the program would give a SD(standard deviatia) of the delta G.
> If I want to get two run's delta delta G, how to estimate the SD.

If you want to combine variances (s_u, s_v) of individual parameters (u,
v) to get the variance of the result (s_x) and if the fluctuations in
the observations of u and v are uncorrelated, the following holds:

For x = f(u,v), s_x^2 = s_u^2 * (dx/du)^2 + s_v^2 *(dx/dv)^2.

In the case of DDG = DG2 - DG1, you would get: s_DDG^2 = s_DG2^2 +
s_DG1^2 for the variance of DDG.

(See e.g. P.R. Bevington, Data Reduction and Error Analysis for the
Physical Sciences.)

> Can MM_PBSA calculates it automately?

No.

Best regards

Holger

> Thanks
> sxzheng
>
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Germany                         

Tel.:  (+49) 69-798-29503; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.rz.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++

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