[gmx-users] Re: Derive the heme charge

[Rui Zhang]

Dear Dr. Lemkul,

Thank you very much for your reply. Your reply is very helpful to me.The
reason for not using other better-defined method is that I did not know
much about such methods at the beginning. I took the computational work by
leaning myself (following manuals and references). I really appreciate your
valuable suggestion.

Best Regards,

Rui


On Sat, Feb 2, 2013 at 1:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/2/13 9:30 AM, Rui Zhang wrote:
>
>> 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.
>>
>
> The best answer to the original question is that there probably is no
> definitive answer.  There are a variety of ways in which people derive
> parameters for Gromos96 force fields, but most involve empirical fitting
> and transferability between equivalent groups.  Dealing with metals and
> such can be quite challenging.
>
> No one on this list is likely to give you a "peer review before peer
> review," if you will, based solely on incomplete information in an email,
> and it probably would have been better to ask questions before spending 2
> years working on this system - what if it turns out you were wrong all
> along?  Why not use a force field that has a better-defined method for
> deriving partial charges?
>
> In any case, Gromos96 53A6 does in fact have parameters for heme, though
> the charges are quite different from what you have derived.  That's not to
> say that your model isn't superior.  What you have to demonstrate is that
> your model provides some insight that can be compared to known experimental
> behavior. That's the task of any simulation model.
>
> -Justin
>
>
>  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
>>>
>>>
>>
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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Florida International University
Department of Chemistry & Biochemistry
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Dr. Xiaotang Wang Research Group
Miami, Florida  33199
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