Re: AMBER: Ac-Co Parameters for Amber

From: suhaib sh <suhaib.shekfeh.gmail.com>
Date: Thu, 2 Oct 2008 11:34:08 +0200

>
> "Which" Acetyl-coA do you wish ?
> If we consider http://en.wikipedia.org/wiki/Acetyl-CoA:
> * terminal -SH or -SAc ?

well .. the crystal structure I,m using right now has -SH terminal .. so I
will choose it


>
> * phosphate . position C3' of the base: charge value = -2 or -1 ?


in the pysiological conditions .. I think the Phosphate at position C3' has
a charge = -2

>
> * which base: A, C, G or U ?


I am confused here , as much as I know , ACCoA contains certainly Adenosine
tri-phosphate .. anyway in my case the Nucleobase is Adenine offcourse.

many thanks

>
>
> regards
>
>
>
>

-- 
Pharmacist. Suhaib Shekfeh
Medicinal Chemistry
Institute of Pharmacy
Martin-Luther-Universitšt Halle-Wittenberg
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Received on Fri Oct 03 2008 - 05:09:58 PDT
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