AMBER Archive (2004)

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

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Tue Feb 17 2004 - 01:24:25 CST

ML schrieb:
>
> Dear Holger,
> thank you for your answer. The thing is I want to get decomposed
> interaction energies from separate trajectories.
>
> >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.)
> >
> >
> First, I made decomposition on the individual trajectories. Do you think
> I can get mm_pbsa_statistics work with options 2 1 when I specify
> residues of the receptor and the ligand in the manner they are
> specified in the complex (com.all.out file)? Or do you suggest sthing
> else?

For getting the {com,rec,lig}.all.out files, you can run the
decomposition using the com, rec, lig snapshot files as if they were
from a single trajectory (i.e. prepare a mm_pbsa.in file like the one in
the Example section). The files just need to have the same prefix, i.e.
xxx_{com,rec,lig}.crd.### . You can then postprocess these files with
mm_pbsa_statistics using options 2 1, as you write.

Best regards

Holger

>
> >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.
> >
>
> This doesn't work because LSTART and RSTART overlap and NGR error comes
> out. My workaroud was to use molecule with water as com, molecule as rec
> and water as lig.
>
> >I admit, this is not elegant and
> >something needs to be done here.
> >
> >
> >
> I agree, it would be of much use.
>
> Best regards,
>
> Martin
>
> -----------
> 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
Juniorprofessur fuer Molekulare Bioinformatik

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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