AMBER Archive (2006)

Subject: Re: AMBER: modeling of ligand concentrations

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Oct 23 2006 - 17:38:22 CDT

the way I learned Pchem, the overall free energy is the
sum of the standard state contribution and the reaction
quotient contribution. Your description sounds like the
latter. Remember that deltaG^zero is the value with the
concentrations in the standard state and actual deltaG
depends on this as well as a concentration (activity) correction.
The fact that free energies are concentration dependent
doesn't require changing the standard state.

>
>
>David Case went over this previously. My big question for the day is, can
>we arbitrarily assign a concentration for A in the reaction E+A --> EA?
>(i.e., something other than 1M)? Can this be done in Amber? If it can,
>then we have an entire method that will compute enzyme kinetic constants
>using mm-pbsa with modifications of the solvent dielectric (there is more
>talk of this on the new bioblade site that I am hosting on yahoo).
>
>
>
>Can we set the "standard state" from 1M to something else? That is all I
>need to know for now.
>
>
>
>Thanks in advance,
>
>Sean
>
>
>
>
>

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