Dear AMBER developers
Bugfix.49 does not seem to solve all problems with highly fluctuating
reaction field energies:
We try to repeat the calculations of the binding affinity of biotin
analogs to avidin by MM/PBSA in Kuhn & Kollman, J. Med Chem 43 (2000) 3786.
If we follow their recipy to neutralise the complex, we get very high
STD in PBCAL for ligands with a negative charge (because the complex is
neutral and not scaled, whereas the receptor has a +1 charge and is
therefore scaled):
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -363.44 11.39
VDW -35.35 3.78
INT 0.00 0.00
GAS -398.80 9.81
PBSUR -4.05 0.05
PBCAL 127.52 102.26
PBSOL 123.48 102.27
PBELE -235.92 102.45
PBTOT -275.32 101.49
The problem disappears if we force
scalfact = ONE
in pb_force.f:
ELE -363.44 11.39
VDW -35.35 3.78
INT 0.00 0.00
GAS -398.80 9.81
PBSUR -4.05 0.05
PBCAL 127.65 6.97
PBSOL 123.61 6.99
PBELE -235.79 6.38
PBTOT -275.19 4.78
What is the use of this scaling?
What is the current recommendation about neutralising the protein or not?
Best Regards,
Ulf
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Received on Thu Sep 22 2005 - 11:53:00 PDT
