VdW parameters for Zn and Fe in metalloproteins

From: Erik Nordgren (nordgren_at_sas.upenn.edu)
Date: Fri Nov 12 2010 - 22:05:33 CST

Hi folks,

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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