Dear Francois:
Thank you for you rapidly responce. If you have time I want to ask you a
question about the charge derivation. The chromophore was made from the
cyclization of THR-TYR-GLY
(
http://pps.cryst.bbk.ac.uk/PPS2/projects/jonda/chromoph.htm). It have the
side chains of the THR and GLY. During the charge derivation procedure could
be good idea to do intra-molecular charge constraint in this sidechains or
only on the N-H and C-O terminal atoms?
Best Regard,
Anthony Cruz
On Friday 11 January 2008 4:57 pm, FyD wrote:
> Quoting Anthony Cruz <acb15885.uprm.edu>:
> > I am working in a new projec and we plan to do some molecular dynamic
> > experiment to an engineered GFP molecule. I have been searching for the
> > parameters for the GFP chromophore without success. Can some one help me?
> > Any reference or parameters??
>
> Do you mean something like:
> http://pps.cryst.bbk.ac.uk/PPS2/projects/jonda/chromoph.htm
>
> If so, this is a pseudo amino-acid (AA):
> For deriving a FF library for a new central fragment (AA) see:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
> & more particularly:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
>
> It looks like there is a diazol group in that GFP chromophore. We
> developed a FF with a triazol derivative (similar group). You might
> look at the Scheme 3 in the following paper
> http://pubs.acs.org/cgi-bin/abstract.cgi/joceah/2007/72/i24/abs/jo071248a.h
>tml The FF is fully described in the paper. The corresponding project is
> also available in R.E.DD.B., but it is unfortunately not readable as
> protected.
>
> regards, Francois
>
>
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Received on Sun Jan 20 2008 - 06:07:05 PST
