AMBER: MM-PBSA calculation

From: <>
Date: Tue, 31 May 2005 18:37:40 +0200 (MEST)

Hi amber community,
I want to calculate the binding free energy of a ligand to a protein. Is the following the right way to do this: First, run a MD of
the ligand bound to the protein (i.e. the complex) and then post-process the trajectory with the (in amber8)
script? Why is default "nmode=0" ? Doesn't one need to calculate the entropy with nmode to get a binding free energy at all?
I am a complete rookie on this subject, so any help is greatly appreciated!

Best wishes,

 Martin Sippel
 Max-Planck-Institut für biophysikalische Chemie
 Abt. NMR-basierte Strukturbiologie, Office 5
 Am Fassberg 11
 D-37077 Göttingen
 Tel.: +49 551 201 2215

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Received on Tue May 31 2005 - 17:53:00 PDT
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