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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
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 ++++++++++++++++++++++++++++++++++++++++++++++++++

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu