AMBER Archive (2004)

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

From: ML (lepsik_at_uochb.cas.cz)
Date: Mon Feb 16 2004 - 09:59:04 CST

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?

>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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