AMBER Archive (2007)

Subject: Re: AMBER: quasiharnomic analysis

From: David A. Case (case_at_scripps.edu)
Date: Mon Feb 12 2007 - 10:31:36 CST

On Sun, Feb 11, 2007, Hans Lee wrote:
>
> I am trying to estimate the entropy change upon the binding of a
> ligand to a receptor using quasiharmonic analysis implemented in
> ptraj. Now I only have the 10ns MD trajectories of receptor-ligand
> complex. My question is if I can get the entropy change only from
> the complex trajectories or I have to have the solvated receptor and
> solvated ligand trajectories as well? Thanks for your help in
> advance!

If you use the "one trajectory" approximation, you would split up the
complex trajectory into a ligand part and a protein part; then analyze
all three, and take the difference: complex - (protein + ligand).

...hope this helps...dac

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