AMBER Archive (2006)

Subject: Re: AMBER: about the decomposition energies using mm/pbsa

From: Holger Gohlke (
Date: Fri Apr 21 2006 - 02:25:44 CDT

Am Donnerstag, 20. April 2006 15:34 schrieb litong:
> Dear,
> We can decompose energies into residues contributions from groups in
> MM-PBSA . I wonder if the ligand must be peptide or protein because the
> software needs to know which atoms belong to backbone and which belong
> to sidechain? The protein-protein complex Ras-Raf is studied in the
> reference article from Holger Gohlke. Are there some examples about
> nonpeptide-protein complex?

No, there is no need that a ligand must be a peptide or protein. If it is, the
decomposition distinguishes between backbone and sidechain atoms, if not,
everything is considered to be part of a "sidechain".

Best regards


> Thanks in advance.
> Tong
> Disclaimer:

Dr. Holger Gohlke

J.W. Goethe-Universitaet Fachbereich Biowissenschaften Institut für Zellbiologie und Neurowissenschaft Max-von-Laue-Str. 9 60438 Frankfurt/Main Germany

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