Re: [AMBER] - Including ion type of interactions in free energy calculation

From: David A Case <>
Date: Wed, 26 May 2021 10:27:44 -0400

On Tue, May 25, 2021, Patil Pranita Uttamrao wrote:
> I am planning to run an MMPB/GBSA analysis for an
>AMBER-derived protein-DNA complex with a single trajectory protocol method.
>In my MD trajectories, I observed ion-mediated interaction between protein
>and DNA . How to include this ion type of interaction in free energy
>calculation. Is it a good idea to retain ions during the extract coordinate
>step or should I strip the ions?. I would kindly appreciate your

I don't know that there is any simple way to handle this situation in an
endpoint analysis. Two basic questions need to be answered:

1. Where is the ion when the protein and DNA are separated? You could make
a model where the ion sticks with (say) the DNA, and mediates an interaction
when the protein approaches. But since you haven't done any simulations of
the separated systems, this might or might not be a good assumption. You
could try two calculations, one with the ion removed, and a second with the
ion treated as a part of the DNA, and see how big the differences are.

2. What experiment would you try to compare to? You really have a system
with three components: protein, DNA and ion(s). Even defining an
equilibrium constant there is tricky. Experiments probably measure the
protein/DNA affinity as a function of ion concentration, treating the
equilibrium as a two-body problem. In principle, an MM-RISM analysis could
be used for the same purpose, but that is for sure and advanced topic.

...good luck....dac

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Received on Wed May 26 2021 - 07:30:02 PDT
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