Dear AMBER Users:
I obtained 75 snapshots from 750ps to 1500ps every 10ps. The MM-PBSA
results are shown below.
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -37.81 5.48
VDW -70.03 3.67
INT -0.00 0.00
GAS -107.85 5.00
PBSUR -6.54 0.27
PBCAL 76.48 19.28
PBSOL 69.94 19.30
PBELE 38.67 18.51
PBTOT -37.91 18.33
As can be seen, PBCAL is quite inaccurate when compared STD value of GAS
energy. I got a suggestion that the origin of grids need to be checked. If
the origin was defined at the center of mass or center of charge, then the
origins in the complex and free protein are not necessarily the same,
which will cause inappropriate solvation calculations.
If the origin was always defined at the position of the same atom of the
protein, which means the origins in both the complex and free protein
should be the same, then what other factors that could cause the
inappropriately numerical PB solvation? Any suggestions will be highly
appriecated!
Best Regards!
Liu
--
JunJun Liu
College of Chemistry
Central China Normal University
WuHan 430079
P.R. China
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Received on Sun Aug 14 2005 - 18:53:01 PDT
