[apbs-users] question about interaction energies

[Martin, E. W <Erik.Martin@STJUDE.ORG>]

I recently did a quick calculation following the binding energy example (and recent thread on this list).  Essentially all I did was subtract the protein alone and peptide alone from the complex.  What confused me is that this interaction "should" be purely electrostatic and involve no conformational change.   The result I got was a net positive energy (albeit relatively low ~3kJ/mol).  This confused me, by inspection, there is no reason this interaction should be repulsive (even if weakly).

I can only imagine that there is some significantly repulsive interaction I'm not noticing.  Is there someway for me to get the per residue interaction energies?  That is to say, have apbs output the energy per residue or atom without redoing this type of calculation and individually removing amino acids from the peptide…

Thanks a lot,
Erik

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