Re: [AMBER] Deprotonated Tyrosine

From: Albert <mailmd2011.gmail.com>
Date: Sun, 05 Feb 2012 09:16:17 +0100

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
>
> regards, Francois
>
>
>
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Received on Sun Feb 05 2012 - 00:30:03 PST