Dear Florent, Albert and Thomas,
Yes and if this Tyr(-) residue is connected to a metal ion, the charge
derivation approach is different: the entire site (metal + all
ligands/residues) has to be considered and involved in the QM job. In
this case, the partial charge of the metal ion in the complex is far
lower than the expected integer value...
in this case, R.E.D. Server or R.E.D. Server Development can be used...
http://q4md-forcefieldtools.org/REDS/
http://q4md-forcefieldtools.org/REDS-Development/
regards, Francois
> Tyrosine can be deprotonated in the vicinity of a metallic cation.
> Moreover, in electronic transfer of photosynthetic reactions a
> specific tyrosine is deprotonated. See
> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026808
> for an example of such system.
> On Sun, 05 Feb 2012 09:16:17 +0100
> Albert <mailmd2011.gmail.com> wrote:
>> I am just curious about in which condition the Tyr would be
>> deprotanated? As far I know , from the aspect of pKa, it is very
>> difficult for Tyr to be deprotanted.....
>>
>>
>> On 02/05/2012 09:04 AM, FyD wrote:
>>> Dear Thomas,
>>>
>>>> I would like to simulate a heme binding protein. In this protein,
>>>> the
>>>> heme is coordinated by a his and a tyr. From experimental
>>>> investigations
>>>> it is clear that the tyr is deprotonated. But unfortunately, I
>>>> cannot
>>>> find any parameters for the deprotonated tyr. Has anybody out there
>>>> such
>>>> parameters and is willing to share them.
>>> You need a molecular fragment for this Tyr(-); three fragments can
>>> be
>>> built: N-terminal, C-terminal and central. This is likely you only
>>> need the central one; See:
>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10 using
>>> R.E.D.
>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15 using
>>> R.E.D.Server
>>>
>>> Now R.E.D. Server can generate the three fragments in a single step;
>>> See:
>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
>>> vs
>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
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Received on Sun Feb 05 2012 - 02:30:02 PST
