AMBER Archive (2004)

Subject: Re: AMBER: Output of sander

From: David A. Case (
Date: Wed Dec 22 2004 - 11:35:27 CST

On Wed, Dec 22, 2004, Harianto wrote:

> Could you explain me what 1-4VdW and 1-4EEL in the output files of sander?

"1-4" pairs are pairs of atoms that are connected by three covalent bonds.

> What command do you use to calculate parts of VdW (also Electrostatic)
> contributions (namely, protein-water only, water-water, etc.) ?

The anal program can be used to generate some of these these decompositions;
there is also a "DECOMP" section of mm-pbsa (see p. 221 of the Users' Manual).
But you may have to modify the code to get the averages you want.


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