[gmx-users] Re: Derive the heme charge

[Rui Zhang]

Dear all,
Could anyone help me on my previous questions? Please reply me... (I know
it might be a hard question, and I did all the works by learning myself.)
I was very frustrated that the professor who works as the
co-author didn't use GROMACS (and GROMOS53a6 force field), but he concerned
about whether the heme charge is defensible before the manuscript can be
submitted. It takes me two years to write this manuscript. I was about to
graduate in this spring but have no paper published yet. I hope you can
give me some clue so that I can get the manuscript at least submitted.
Best Regards,
Rui



On Fri, Feb 1, 2013 at 10:49 AM, Rui Zhang <rzhan001 at fiu.edu> wrote:

> Hello,
>
> 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.
>
> Best Regards,
>
> Rui
>



-- 
Florida International University
Department of Chemistry & Biochemistry
University Park Campus,
Dr. Xiaotang Wang Research Group
Miami, Florida  33199
rzhan001 at fiu.edu
(305)301-7879