Re: [AMBER] - Free energy calculations of protein molecule with two binding sites

From: David A Case <>
Date: Thu, 8 Jul 2021 16:31:47 -0400

On Thu, Jul 08, 2021, Patil Pranita Uttamrao wrote:
>I am planning to run an MMPB/GBSA analysis
>for an AMBER trajectory system. How to calculate overall binding free
>energy if our trajectory has a protein molecule with two binding partners
>simultaneously? I will kindly appreciate your suggestions.

You need to consider what sort of experiment you might make comparisons to.
Generally, if a protein has two ligands, you would need to estimate the free
energies of four states: no ligand, ligand A bound, ligand B bound, and both
ligands bound.


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Received on Thu Jul 08 2021 - 14:00:02 PDT
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