Dear AMBER users,
I'm trying to estimate the free energy difference associated to the
formation of a duplex B-DNA from the two single strand
oligonucleotides within the mm-PBSA approach.
A quick search in the literature pointed out that such a method has
been extensively applied to dDNA-ligand system, but I could not find
any attempt to calculate the free energy associated to the formation
of the duplex from the two single strands sequence. So my first
question is: are there some severe limitations of these method just
considering one dna-strand like receptor and the other like ligand?
I'm also trying to do the same but in a system "duplex+drug". I
defined the ligand
as one single strand and the receptor like the other single
strand+drug. In the case i'm applying the three trajectory approach I
obtain a value of PBCAL with a huge variance from the trajectory of
the single-strand+drug. The mean value itself looks too high in
comparison to my expectation. This is not happening using the GB
approach or if I calculate the same quantities within the single
trajectory method.
Any suggestion on the origin of a highly variable PBCAL value?
thanks,
Barbara
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Received on Mon Jun 25 2012 - 07:30:01 PDT
