Re: [AMBER] - dimer energy calculations

From: <>
Date: Fri, 11 Feb 2011 11:15:34 -0800 (PST)

If ligands interact with each other then you need to run
simulations with two drugs and two simulations with single drug
located in different positions, and the case without
the drugs bound. I think you could even attempt to capture some
kind of cooperativity effect from that. And, of course, the simulations
scenario depends on what the question is.


> Hi,
> 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.
> Best,
> Julia Romanowska
> ======================
> PhD student, Biophysics,
> Faculty of Physics
> and
> Interdisciplinary Centre for
> Mathematical and Computational
> Modelling (ICM),
> University of Warsaw, Poland
> tel.: +48 22-5540-832
> fax.: +48 22-5540-801
> _______________________________________________
> AMBER mailing list

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Received on Fri Feb 11 2011 - 11:30:04 PST
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