Many thanks for information!
Actually I'm looking for the GFP (or any other fluorescent protein with the
same beta-barell topology) chromophore. I think some problems could arise
during the attachment of that residue to the rest of the protein's backbone
as it was when I've modeled it in Gromacs :). I'll try to look for that
residue on one of those databases.
James
2014-05-12 15:41 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Mon, 2014-05-12 at 11:05 +0400, James Starlight wrote:
> > Brent,
> > Many thanks for suggestions!
> > Also I wounder to know if some non-standard residues (for example hem)
> has
> > been already included in one of the existing amber's param sets ?
>
> You can see the different libraries that are provided in
> $AMBERHOME/dat/leap/lib.
>
> You may also be interested in 3rd-party parameter databases, such as the
> one maintained at http://www.pharmacy.manchester.ac.uk/bryce/amber/ and
> the R.E.D. Database (http://q4md-forcefieldtools.org/REDDB/index.php).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Tue May 13 2014 - 05:00:07 PDT
