Dear AMBER users,
I'm using MMPBSA to calculate the binding free energy between a small DNA
molecule and an anti-DNA antibody. The numbers I got have a 2~3kcal/mol
difference for the perl and python version when I run PB. When I run GB,
the difference between perl version and python version is much smaller,
only about 0.3~0.5kcal/mol. Anyone knows the reason for this difference?
Which version is better for DNA-protein binding? Thanks a lot.
Yi An
Graduate student
Department of Chemistry
Texas A&M University
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Received on Tue Apr 12 2011 - 09:30:06 PDT
