[AMBER] MMPBSA calculation

From: Mary Varughese <maryvj1985.gmail.com>
Date: Wed, 23 Oct 2013 04:27:59 +0530


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?
is MMPBSA a reasonable choice to calculate BE of the nucleic acid- ligand
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
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