AMBER Archive (2008)

Subject: AMBER: mm_pbsa positive ELE

From: Qi Yan (kid1412_at_uab.edu)
Date: Mon Mar 17 2008 - 13:20:21 CDT

Hi,all

I'm trying to calculate the binding affinity of a complex and its
mutants (I got three mutants. Each of them just change some residue
types which are in biding site). For these mutants, the results of
mm_pbsa seem reasonable, but, for the wild complex, the final ELE value
is positive (final ELE = com-rec-lig). Actually, these ELE values of
individual complex, receptor and ligand look normal. I don't know
whether the non-zero net charge can influence the results. I choose
"Dielectricity constant = 2.0" for all cases. Does anybody can point me
out?

Thanks in advance,

Qi Yan

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