[AMBER] Questions about the TI methods in binding free energy calculations.

From: <neildancer.sina.com>
Date: Mon, 02 Aug 2021 17:27:05 +0800

Dear, Amber community,
     I was confused by the thermodynamic intergration (TI) method for binding free energy calculation in this tutorial (http://ambermd.org/tutorials/advanced/tutorial9/#home). Does this method only use to compute the relative binding free energy? Because the final deltaG was from ΔGcomplex - ΔGligands. and the value was +2.2 kcal/mol. If this, how could I use some similar methods to calculate the absolutely binding free energy of protein-ligand complex? Another way, I still don't know how to choose the softe core atoms with a reasonable principle....... OKay, maybe I have a big mistake at the understanding of this tutorial. Please correct my understandings. Any suggestions are welcome.
Best regards,
Ning Wang <PhD>
National Laboratory of Biomacromolecules
Institute of Biophysics, Chinese Academy of Sciences

My reseached interests has foucsed on protein structure determinated by Cryo-EM, virtual screening of potential drugs, protein molecular dynamic simulation, and protein design via computational biology.

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Received on Mon Aug 02 2021 - 02:30:03 PDT
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