AMBER Archive (2009)

Subject: Re: [AMBER] thioglycoside

From: Lachele Foley (Lists) (lf.list_at_gmail.com)
Date: Mon Jan 26 2009 - 09:36:26 CST

The problem might be that you should use 0MA and not 1MA. The 0MA
(zero-M-A) residue does not contain O1, the anomeric oxygen. 1MA
does. If you want to link to a sulfur, and you use 1MA, then you are
linking an O1 to the sulfur, which might not be what you had in mind.
If you use 0MA, you link the sulfur to C1.

Does that help?

:-) Lachele

On Mon, Jan 26, 2009 at 9:46 AM, Alexander Schierholt
<aschierholt_at_oc.uni-kiel.de> wrote:
> Dear all,
>
> I want to make a cysteine which has an S-link to a mannose. If I take CYM,
> protect the N and C-function and then set the S-atom to tail and connect
> this to 1MA I can't save my top and crd. I also tried to make the molecule
> with antechamber but again, I couldn't save the top and crd files. Does
> anybody has an idea or experience with this problem?
>
> Thanks a lot
> Alexander Schierholt
>
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> 

-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA

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