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.
.....dac
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Received on Wed Dec 22 2004 - 17:53:00 PST
