AMBER Archive (2006)

Subject: Re: AMBER: modeling of ligand concentrations

From: Sean Rathlef (sean_at_syncitium.net)
Date: Mon Oct 16 2006 - 17:48:16 CDT

David,

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
> On Mon, Oct 16, 2006, Sean Rathlef wrote:
>
>
> But the *free* energy estimates will know about standard states.
Basically
> the standard state of the the ligand (by default, 1M) is included in its
> translational entropy (ditto for the receptor and the complex). So, the
> mm-pbsa procedure would naturally account for ligand concentration.

Is it possible to adjust the default ligand standard state (1M) to a user
defined value (or range of values)?
...

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