From: Erik Nordgren (nordgren_at_sas.upenn.edu)
Date: Fri Nov 12 2010 - 22:05:33 CST
I'm wondering if anyone knows of a reference where I could obtain nonbonded
parameters (compatible with the CHARMM force field) appropriate for Zn(II)
in a Zn-porphyrin cofactor within a metalloprotein? I've spent a good
amount of time searching but haven't managed to find what I need... but
hopefully I've just been looking in the wrong places!
Now, the standard CHARMM22 protein parameters (e.g.,
"par_all27_prot_lipid.prm") do include these two lines:
ZN 0.000000 -0.250000 1.090000 ! ALLOW ION
! RHS March 18, 1990
FE 0.010000 0.000000 0.650000 ! ALLOW HEM
! Heme (6-liganded): Iron atom (KK 05/13/91)
.. but I'm pretty sure that Zn entry is specifically for an isolated Zn(+2)
ion, which would have rather different parametrization from that of a
covalently-coordinated Zn atom.
Also, while I'm at it, another question: does anyone know why the parameter
entry here for heme-iron is different from every other nonbonded term in the
FF, in the sense that the first number (supposedly ignored) is non-zero, and
the second number (epsilon, the potential well depth) is zero? Doesn't this
mean that Fe atoms using this parameter would not have any VdW interaction
with other atoms whatsoever?
-- C. Erik Nordgren, Ph.D. Chemistry Department University of Pennsylvania
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