[gmx-users] Derive the heme charge
rzhan001 at fiu.edu
Fri Feb 1 16:49:53 CET 2013
I want to derive the atomic partial charges for heme in chloroperoxidase,
since these parameters cannot be found in the GROMOS53a6 force field.
Chloroperoxidase is a cysteine-ligated heme protein (high spin) much like
P450. In my work, I want to study the interactions between the protein
residues of chloroperoxidase and its substrates. Thus, I used the QM
software ORCA to optimize the heme-thiolate structure (TPSS/def2-SPVD), and
then I used CHELPG method to derive the heme charges. Could anyone tell me
if the method I used is suitable for my purpose?
In addition, the charges I obtained for Fe (0.931877) and nitrogen
(-0.44572, -0.34427, -0.39467, and -0.39467) are largely consistent with
two reference. The reference are one in 1995 (Fe: 1.0, N: -0.4; Helms et
al. Thermodynamics of water mediating protein-ligand interactions in
cytochrome P450cam: a molecular dynamics study, Biophys. J. 69: 810-24) and
one in recent (Fe: 0.847, N: -0.37, -0.423, -0.504, and -0.528; Favia et
al. (2006) Three-dimensional model of the human aromatase enzyme and
density functional parameterization of the iron-containing protoporphyrin
IX for a molecular dynamics study of heme-cysteinato cytochromes, Proteins
62: 1073-84). I will greatly appreciate any comment and suggestions.
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