Re: [AMBER] Deprotonated Tyrosine

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Sun, 05 Feb 2012 09:04:46 +0100

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 - 00:30:02 PST
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