Dear AMBER users,
I calculated the binding energy using pbsa by setting RADIOPT=1 and NPOPT=2 in which the nonpolar contribution (Gnp) was evaluated by:
Gnp = Gdisp + CAVITY_SURFTEN*SASA + CAVITY_OFFET.
But in the x_statistics.out file, the sum between the polar contribution (PBCAL) and the nonpolar contribution (PBSUR) is not equal to total solvation energy (PBSOL).
Here is part of the output:
-------------
# DELTA
# -----------------------
# MEAN STD
# =======================
PBSUR -5.92 0.29
PBCAL 79.54 46.33
PBSOL 113.89 46.91
PBELE 66.83 20.17
PBTOT 60.82 19.42
-------
where PBSUR + PBCAL = -5.92 + 79.54 = 73.26 != PBSOL (113.89).
I am not sure whether I understand it correctly or not and request your comments.
Many thanks.
Jeffrey Yang
------
DICP, CAS
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Received on Thu Mar 18 2010 - 01:30:03 PDT
