AMBER Archive (2006)

Subject: Re: AMBER: Question about free energy with mm_pbsa

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 01 2006 - 00:32:54 CDT

On Thu, Aug 31, 2006, William Wei wrote:
>
> Question 1: While we use mm-pbsa for calculating the delta G, both GB and
> PB do not minimize the complex, receptor and ligand. The complex snapshots
> are at a relatively low energy conformations, but those snapshots of
> receptor and ligand are at a relatively high energy conformation because the
> induced fit. The delta E (orH) from this calculation may be lower than what
> they should be! Could anybody point me out if I am wrong.

This is a feature of using only one trajectory, and splitting apart into
ligand and receptor. If you want to estimate the induced fit energies, you
need to use the "three trjaectory" option. But note that this has rather more
severe requirements on convergence and sampling.

...dac

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