AMBER Archive (2008)

Subject: Re: AMBER: Ac-Co Parameters for Amber

From: suhaib sh (suhaib.shekfeh_at_gmail.com)
Date: Thu Oct 02 2008 - 04:34:08 CDT

>
> "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-Universität Halle-Wittenberg

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