[AMBER] MMPBSA.py - dimer energy calculations

From: Julia Romanowska <jrom.icm.edu.pl>
Date: Fri, 11 Feb 2011 12:34:02 +0100 (CET)

I am trying to calculate binding energies between a protein and a drug. I
have one trajectory of the drug in water, one of the 'apo' enzyme and one
of the complex. There is a small problem, though because the enzyme is a
dimer, thus it has two drug molecules bound, while the trajectory of the
ligand itself has only one molecule.
Should the calculations be made as the two molecules in the complex were
one ligand, and then divide the result by two? Or should I try performing
two calculations: taking out from the complex only one ligand at a time?
I must note that the two drug molecules interact with themselves and with
both monomers of the dimer.

I would be grateful for any suggestions.


Julia Romanowska

PhD student, Biophysics,
Faculty of Physics
Interdisciplinary Centre for
Mathematical and Computational
Modelling (ICM),
University of Warsaw, Poland
tel.: +48 22-5540-832
fax.: +48 22-5540-801

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Received on Fri Feb 11 2011 - 04:00:03 PST
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