Re: [AMBER] relative binding free energy calculation

From: David A. Case <case.biomaps.rutgers.edu>
Date: Sat, 15 Oct 2011 11:54:36 -0400

On Sat, Oct 15, 2011, leila karami wrote:
>
> I want to obtain relative binding free energy in formation of protein-dna
> complex using thermodynamic cycle.
>
> I will investigate effect of type of dna in complex formation. I mutated dna
> by change of 1 nucleic acid in dna.
> Is there a tutorial for my case.

Tutorials A6 and A9 are the most relevant. Be sure to start with something
small first to learn how the codes work, and to be sure that you understand the
outputs. Only then try the protein/DNA complex you mention above.

...good luck...dac


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Received on Sat Oct 15 2011 - 09:00:06 PDT
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