VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Fri Jun 15 2007 - 10:04:37 CDT

Francesco,

Now I see what you mean. Maybe the example is not very well chosen since
it is actually not simple. Indeed aspartate can be combined from glycine
and acetate. But where do the parameters for the peptide bond come from?
The peptide bond is infact parametrized using N-methylacetamide as model
compound. In the corresponding dipeptide CR and CL would be the
alpha-Carbons of the two aminoacids. So in order to get glycine with a
half peptide bond in both chain directions you have to meantally "wrap"
NMA. If you want to know the parameters of the N-terminal peptide bond
you look at CR fro the C-terminal bond you look at CL.

Is it more clear now?
Maybe I should change the example...

Jan

> perhaps we are looking at different places - or
> versions - of the "Paratool User's Guide". The one I
> have, illustrates graphic representations of, in the
> order, aspartate, acetate, and N-methylacetamide.
> Aspartate is made of glycine and acetate, if you look
> at the CA--CB bond.
>
> If you combine the residues of acetate (less H2) and
> N-methylacetamide (less HR3) - as you suggest above -
> one obviously does not come close to aspartate. I can
> only imagine that the the endeavor was not of getting
> aspartate that way. Than, which the goal was?
>
> Regards
> francesco
>
>
>
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-- 
---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany
+49 30 450-528-446
saam_at_charite.de