Re: AMBER: MM binding energy with ANAL

From: David A. Case <>
Date: Tue, 14 Sep 2004 15:32:48 -0700

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.
> 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

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.


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Received on Tue Sep 14 2004 - 23:53:00 PDT
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