Sir,
I performed MMPBSA calculation on a DNA-ligand system.
I got the values
PBTOT = -27.38
TSTOT = -23.54 (from nmode of mmpbsa )
delta G= -27.38 - (-23.54) = -3.84
Is this the correct way.
What do you think about the values i got?
I have read that for nucleic acids usually entropic contribution is
unfavorable and better to be ignored?
Have you heard something like that? Why is it like that?
Also
is MMPBSA a reasonable choice to calculate BE of the nucleic acid- ligand
systems?
Would you prefer DOCK or autodock or vina?
Thanking you
Mary Varughese
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Received on Tue Oct 22 2013 - 16:00:03 PDT
