AMBER Archive (2004)

Subject: Re: AMBER: MM-PBSA:??Decomposition of receptor energies??

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Mon Feb 16 2004 - 04:09:07 CST

ML schrieb:
>
> Dear Holger and MM-PBSA people,
> I cannot get working the decomposition of energies in MM-PBSA with
> receptor only. The error message is : Param COMLIG does not exists
>
> How shall I treat the COMREC etc. parameters?

Getting a decomposition for a receptor alone doesn't work (mainly
because the intention was to decompose contributions to binding, and for
this you need a mapping from residues in the receptor/ligand to residues
in the complex, which would be difficult if not everything is specified
at once.)

So, for decomposing binding free energies, you need to specify
com/rec/lig at once. If you want to decompose the "conformational free
energy" of just the receptor, try to specify these snapshots as com,
rec, and lig. You should then get 3 times the same decomposition. (I
have never tried this way, though.) I admit, this is not elegant and
something needs to be done here.

Best regards

Holger

> Thank you for your help.
>
> Best regards,
>
> Martin Lepsik
>
> --
> -----------
> Martin Lepsik
> Dept. of Molecular Modeling
> Institute of Organic Chemistry & Biochemistry
> Czech Academy of Sciences
> phone: +420-220 183 540
> fax:+420-220 183 292
> e-mail:lepsik_at_uochb.cas.cz
>
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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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