AMBER Archive (2005)

Subject: AMBER: MM-PBSA calculation

From: masi_at_nmr.mpibpc.mpg.de
Date: Tue May 31 2005 - 11:37:40 CDT

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 mm_pbsa.pl (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
 
 
 
 
 ---------------------------------------------------------------------------------------------------------
 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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