VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu Jun 14 2007 - 01:45:23 CDT

Jan:
Thanks, also for aceh.xbgf file attachment in another
email.

Yes, I made a bad cocktail charmm/amger-gaff. Sorry.
It is perhaps the aptitude of the organic chemist,
seeking to solve his problems without sticking to
specific tools, and jumping from one to another, and
back. Sometimes it turns out to be a devastating
aptitude.

As to the following item, which I only save from the
thread:

> > Incidentally, I got a bit confused by the second
> page
> > of your "Paratool User's Guide", i.e., the way you
> > decomposed aspartate. What I see is acetate and
> > glycine as components.
> >
> I do't see any glycine I see N-methylacetamide. If
> you chop away HR3 of
> N-methylacetamide and H2 of acetate and draw a bond
> between the two
> associated carbons you'll have fused backbone and
> side chain.
>

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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