AMBER Archive (2004)

Subject: Re: AMBER: MM binding energy with ANAL

From: David A. Case (case_at_scripps.edu)
Date: Tue Sep 14 2004 - 17:32:48 CDT

On Tue, Sep 14, 2004, Ben Cossins wrote:

> I have attempted to use ANAL to calculate the MM component of a binding
> energy. I analysed two groups in ANAL one being the receptor atoms and the
> other being the Ligand atoms. I took the computed Total INTER energy as the
> MM binding energy, which as seen in the ouput below was -112.88.
>
>
> GROUP INTRA INTER TOTAL
>
> 1 106.32 -112.88 -6.56
> 2 -2758.95 -112.88 -2871.83
>
>
> TOTAL -2652.63 -112.88 -2765.51
>
> This gives different figures from those given by using mm-pbsa and therefore
> sander to get figures for seperated Ligand , Receptor and Complex structures
> and finding the difference. The comparable figure from mm-pbsa was -124.20.

Does sander give numbers for the separated fragments that match the INTRA
numbers above? Is the TOTAL for the full system using sander equal to
-2765.51?

Generally, it would be helpful to try to see where (if ever) Anal and Sander
are giving equivalent energies, in order to try to narrow down the problem.

...dac

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